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Ophthalmological ciliopathies v1.4 KIAA0556 Catherine Snow Tag new-gene-name tag was added to gene: KIAA0556.
Rare multisystem ciliopathy disorders v1.124 KIAA0556 Catherine Snow Tag new-gene-name tag was added to gene: KIAA0556.
Cerebral vascular malformations v2.4 MRVI1 Catherine Snow Tag new-gene-name tag was added to gene: MRVI1.
Renal ciliopathies v1.15 KIAA0556 Catherine Snow commented on gene: KIAA0556
Neurological ciliopathies v1.7 KIAA0556 Catherine Snow commented on gene: KIAA0556
Ophthalmological ciliopathies v1.4 KIAA0556 Catherine Snow commented on gene: KIAA0556
Rare multisystem ciliopathy disorders v1.124 KIAA0556 Catherine Snow commented on gene: KIAA0556
Cerebral vascular malformations v2.4 MRVI1 Catherine Snow commented on gene: MRVI1
Intellectual disability v3.35 UGDH Konstantinos Varvagiannis gene: UGDH was added
gene: UGDH was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: UGDH was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: UGDH were set to 32001716
Phenotypes for gene: UGDH were set to Epileptic encephalopathy, early infantile, 84 - MIM #618792
Penetrance for gene: UGDH were set to Complete
Review for gene: UGDH was set to GREEN
Added comment: Hengel et al (2020 - PMID: 32001716) report on 36 individuals with biallelic UGDH pathogenic variants.

The phenotype corresponded overall to a developmental epileptic encephalopathy with hypotonia, feeding difficulties, severe global DD, moderate or commonly severe ID in all. Hypotonia and motor disorder (incl. spasticity, dystonia, ataxia, chorea, etc) often occurred prior to the onset of seizures. A single individual did not present seizures and 2 sibs had only seizures in the setting of fever.

Affected subjects were tested by exome sequencing and UGDH variants were the only/best candidates for the phenotype following also segregation studies. Many were compound heterozygous or homozygous (~6 families were consanguineous) for missense variants and few were compound heterozygous for missense and pLoF variants. There were no individuals with biallelic pLoF variants identified. Parental/sib studies were all compatible with AR inheritance mode.

UGDH encodes the enzyme UDP-glucose dehydrogenase which converts UDP-glucose to UDP-glucuronate, the latter being a critical component of the glycosaminoglycans, hyaluronan, chondroitin sulfate, and heparan sulfate [OMIM].

Patient fibroblast and biochemical assays suggested a LoF effect of variants leading to impairment of UGDH stability, oligomerization or enzymatic activity (decreased UGDH-catalyzed reduction of NAD+ to NADH / hyaluronic acid production which requires UDP-glucuronate).

Attempts to model the disorder using an already developped zebrafish model (for a hypomorphic LoF allele) were unsuccessful as fish did not exhibit seizures spontaneously or upon induction with PTZ.

Modelling of the disorder in vitro using patient-derived cerebral organoids demonstrated smaller organoids due to reduced number of proliferating neural progenitors.
Sources: Literature
Early onset or syndromic epilepsy v2.47 UGDH Konstantinos Varvagiannis gene: UGDH was added
gene: UGDH was added to Genetic epilepsy syndromes. Sources: Literature
Mode of inheritance for gene: UGDH was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: UGDH were set to 32001716
Phenotypes for gene: UGDH were set to Epileptic encephalopathy, early infantile, 84 - MIM #618792
Penetrance for gene: UGDH were set to Complete
Review for gene: UGDH was set to GREEN
Added comment: Hengel et al (2020 - PMID: 32001716) report on 36 individuals with biallelic UGDH pathogenic variants.

The phenotype corresponded overall to a developmental epileptic encephalopathy with hypotonia, feeding difficulties, severe global DD, moderate or commonly severe ID in all. Hypotonia and motor disorder (incl. spasticity, dystonia, ataxia, chorea, etc) often occurred prior to the onset of seizures. A single individual did not present seizures and 2 sibs had only seizures in the setting of fever.

Affected subjects were tested by exome sequencing and UGDH variants were the only/best candidates for the phenotype following also segregation studies. Many were compound heterozygous or homozygous (~6 families were consanguineous) for missense variants and few were compound heterozygous for missense and pLoF variants. There were no individuals with biallelic pLoF variants identified. Parental/sib studies were all compatible with AR inheritance mode.

UGDH encodes the enzyme UDP-glucose dehydrogenase which converts UDP-glucose to UDP-glucuronate, the latter being a critical component of the glycosaminoglycans, hyaluronan, chondroitin sulfate, and heparan sulfate [OMIM].

Patient fibroblast and biochemical assays suggested a LoF effect of variants leading to impairment of UGDH stability, oligomerization or enzymatic activity (decreased UGDH-catalyzed reduction of NAD+ to NADH / hyaluronic acid production which requires UDP-glucuronate).

Attempts to model the disorder using an already developped zebrafish model (for a hypomorphic LoF allele) were unsuccessful as fish did not exhibit seizures spontaneously or upon induction with PTZ.

Modelling of the disorder in vitro using patient-derived cerebral organoids demonstrated smaller organoids due to reduced number of proliferating neural progenitors.
Sources: Literature
Fetal hydrops v1.19 AHCY Rebecca Foulger Phenotypes for gene: AHCY were changed from Hypermethioninemia with deficiency of S-adenosylhomocysteine hydrolase, 613752; S-adenosylhomocysteine hydrolase deficiency; AHCY deficiency to non-immune hydrops; Hypermethioninemia with deficiency of S-adenosylhomocysteine hydrolase, 613752; S-adenosylhomocysteine hydrolase deficiency; AHCY deficiency
Early onset or syndromic epilepsy v2.47 YIF1B Konstantinos Varvagiannis gene: YIF1B was added
gene: YIF1B was added to Genetic epilepsy syndromes. Sources: Literature
Mode of inheritance for gene: YIF1B was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: YIF1B were set to 32006098
Phenotypes for gene: YIF1B were set to Central hypotonia; Failure to thrive; Microcephaly; Global developmental delay; Intellectual disability; Seizures; Spasticity; Abnormality of movement
Penetrance for gene: YIF1B were set to Complete
Review for gene: YIF1B was set to AMBER
Added comment: AlMuhaizea et al (2020 - PMID: 32006098) report on the phenotype of 6 individuals (from 5 families) with biallelic YIF1B truncating variants.

Affected subjects presented hypotonia, failure to thrive, microcephaly (5/6), severe global DD and ID (as evident from best motor/language milestones achieved - Table S1) as well as features suggestive of a motor disorder (dystonia/spasticity/dyskinesia). Seizures were reported in 2 unrelated individuals (2/6). MRI abnormalities were observed in some with thin CC being a feature in 3.

Variable initial investigations were performed including SNP CMA, MECP2, microcephaly / neurotransmitter disorders gene panel testing did not reveal P/LP variants.

YIF1B variants were identified in 3 families within ROH. Following exome sequencing, affected individuals were found to be homozygous for truncating variants (4/5 families being consanguineous). The following 3 variants were identified (NM_001039672.2) : c.186dupT or p.Ala64fs / c.360_361insACAT or p.Gly121fs / c.598G>T or p.Glu200*.

YIF1B encodes an intracellular transmembrane protein.

It has been previously demonstrated that - similarly to other proteins of the Yip family being implicated in intracellular traffic between the Golgi - Yif1B is involved in the anterograde traffic pathway. Yif1B KO mice demonstrate a disorganized Golgi architecture in pyramidal hippocampal neurons (Alterio et al 2015 - PMID: 26077767). The rat ortholog interacts with serotonin receptor 1 (5-HT1AR) with colocalization of Yif1BB and 5-HT1AR in intermediate compartment vesicles and involvement of the former in intracellular trafficing/modulation of 5-HT1AR transport to dendrites (PMID cited: 18685031).

Available mRNA and protein expression data (Protein Atlas) suggest that the gene is widely expressed in all tissues incl. neuronal cells. Immunochemistry data from the Human Brain Atlas also suggest that YIF1B is found in vesicles and localized to the Golgi apparatus. Immunohistochemistry in normal human brain tissue (cerebral cortex) demonstrated labeling of neuronal cells (Human Protein Atlas).

Functional/network analysis of genes co-regulated with YIF1B based on available RNAseq data, suggest enrichement in in genes important for nervous system development and function.

Please consider inclusion in other panels that may be relevant (e.g. microcephaly, etc).
Sources: Literature
Intellectual disability v3.35 YIF1B Konstantinos Varvagiannis gene: YIF1B was added
gene: YIF1B was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: YIF1B was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: YIF1B were set to 32006098
Phenotypes for gene: YIF1B were set to Central hypotonia; Failure to thrive; Microcephaly; Global developmental delay; Intellectual disability; Seizures; Spasticity; Abnormality of movement
Penetrance for gene: YIF1B were set to Complete
Review for gene: YIF1B was set to GREEN
Added comment: AlMuhaizea et al (2020 - PMID: 32006098) report on the phenotype of 6 individuals (from 5 families) with biallelic YIF1B truncating variants.

Affected subjects presented hypotonia, failure to thrive, microcephaly (5/6), severe global DD and ID (as evident from best motor/language milestones achieved - Table S1) as well as features suggestive of a motor disorder (dystonia/spasticity/dyskinesia). Seizures were reported in 2 unrelated individuals (2/6). MRI abnormalities were observed in some with thin CC being a feature in 3.

Variable initial investigations were performed including SNP CMA, MECP2, microcephaly / neurotransmitter disorders gene panel testing did not reveal P/LP variants.

YIF1B variants were identified in 3 families within ROH. Following exome sequencing, affected individuals were found to be homozygous for truncating variants (4/5 families being consanguineous). The following 3 variants were identified (NM_001039672.2) : c.186dupT or p.Ala64fs / c.360_361insACAT or p.Gly121fs / c.598G>T or p.Glu200*.

YIF1B encodes an intracellular transmembrane protein.

It has been previously demonstrated that - similarly to other proteins of the Yip family being implicated in intracellular traffic between the Golgi - Yif1B is involved in the anterograde traffic pathway. Yif1B KO mice demonstrate a disorganized Golgi architecture in pyramidal hippocampal neurons (Alterio et al 2015 - PMID: 26077767). The rat ortholog interacts with serotonin receptor 1 (5-HT1AR) with colocalization of Yif1BB and 5-HT1AR in intermediate compartment vesicles and involvement of the former in intracellular trafficing/modulation of 5-HT1AR transport to dendrites (PMID cited: 18685031).

Available mRNA and protein expression data (Protein Atlas) suggest that the gene is widely expressed in all tissues incl. neuronal cells. Immunochemistry data from the Human Brain Atlas also suggest that YIF1B is found in vesicles and localized to the Golgi apparatus. Immunohistochemistry in normal human brain tissue (cerebral cortex) demonstrated labeling of neuronal cells (Human Protein Atlas).

Functional/network analysis of genes co-regulated with YIF1B based on available RNAseq data, suggest enrichement in in genes important for nervous system development and function.

Please consider inclusion in other panels that may be relevant (e.g. microcephaly, etc).
Sources: Literature
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.4 ISCA-37420-Loss Catherine Snow Mode of inheritance for Region: ISCA-37420-Loss was changed from to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Early onset or syndromic epilepsy v2.47 SPTBN4 Konstantinos Varvagiannis gene: SPTBN4 was added
gene: SPTBN4 was added to Genetic epilepsy syndromes. Sources: Literature
Mode of inheritance for gene: SPTBN4 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SPTBN4 were set to 28540413; 28940097; 29861105; 31230720; 31857255
Phenotypes for gene: SPTBN4 were set to Neurodevelopmental disorder with hypotonia, neuropathy, and deafness MIM#617519
Penetrance for gene: SPTBN4 were set to Complete
Review for gene: SPTBN4 was set to GREEN
Added comment: Biallelic pathogenic SPTBN4 variants cause Neurodevelopmental disorder with hypotonia, neuropathy, and deafness (MIM #617519).

There are several reports on the phenotype of relevant affected individuals with severe/profound DD/ID in at least 9 individuals :

- Knierim et al (2017 - PMID: 28540413) [1 affected individual]
- Anazi et al (2017 - PMID: 28940097) [1]
- Wang et al (2018 - PMID: 29861105) [6]
- Pehlivan et al (2019 - PMID: 31230720) [1]

A recent article by Häusler et al (2019 - PMID: 31857255) describes the phenotype of 2 sibs, both presenting with motor and speech delay, although the older one had reportedly 'normal' cognitive performance allowing attendance of regular school at the age of 6 years.

Features include congenital hypotonia, severe DD and ID (in most as outlined above, ID was the primary indication for testing on several occasions), poor or absent reflexes and weakness secondary to axonal motor neuropathy, feeding and respiratory difficulties, hearing and visual impairment. Seizures have been reported in at least 4 unrelated individuals (3 by Wang et al / 1 by Pehlivan et al).

Variants in most cases were nonsense/frameshift although biallelic missense variants have also been reported. Sibs in the report by Häusler et al harbored a homozygous splicing variant.

SPTBN4 encodes a member of the beta-spectrin protein family that is expressed in the brain, peripheral nervous system, pancreas, and skeletal muscle.

βIV spectrin links ankyrinG and clustered ion channels (at axon initial segments and nodes of Ranvier) to the axonal cytoskeleton. Pathogenic variants are proposed to disrupt the cytoskeletal machinery controlling proper localization of ion channels and function of axonal domains where ion channels are normally clustered in high density. Among the evidence provided : nerve biopsies from an affected individual displayed reduced nodal Na+ channels and no nodal KCNQ2 K+ channels / Loss of AnkyrinG and βIV spectrin in animal model resulted in loss of KCNQ2- and KCNQ3- subunit containing K+ channels.

Apart from the ID / epilepsy panels please consider inclusion in other relevant ones.
Sources: Literature
Intellectual disability v3.35 SPTBN4 Konstantinos Varvagiannis gene: SPTBN4 was added
gene: SPTBN4 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: SPTBN4 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SPTBN4 were set to 28540413; 28940097; 29861105; 31230720; 31857255
Phenotypes for gene: SPTBN4 were set to Neurodevelopmental disorder with hypotonia, neuropathy, and deafness MIM#617519
Penetrance for gene: SPTBN4 were set to Complete
Review for gene: SPTBN4 was set to GREEN
Added comment: Biallelic pathogenic SPTBN4 variants cause Neurodevelopmental disorder with hypotonia, neuropathy, and deafness (MIM #617519).

There are several reports on the phenotype of relevant affected individuals with severe/profound DD/ID in at least 9 individuals :

- Knierim et al (2017 - PMID: 28540413) [1 affected individual]
- Anazi et al (2017 - PMID: 28940097) [1]
- Wang et al (2018 - PMID: 29861105) [6]
- Pehlivan et al (2019 - PMID: 31230720) [1]

A recent article by Häusler et al (2019 - PMID: 31857255) describes the phenotype of 2 sibs, both presenting with motor and speech delay, although the older one had reportedly 'normal' cognitive performance allowing attendance of regular school at the age of 6 years.

Features include congenital hypotonia, severe DD and ID (in most as outlined above, ID was the primary indication for testing on several occasions), poor or absent reflexes and weakness secondary to axonal motor neuropathy, feeding and respiratory difficulties, hearing and visual impairment. Seizures have been reported in at least 4 unrelated individuals (3 by Wang et al / 1 by Pehlivan et al).

Variants in most cases were nonsense/frameshift although biallelic missense variants have also been reported. Sibs in the report by Häusler et al harbored a homozygous splicing variant.

SPTBN4 encodes a member of the beta-spectrin protein family that is expressed in the brain, peripheral nervous system, pancreas, and skeletal muscle.

βIV spectrin links ankyrinG and clustered ion channels (at axon initial segments and nodes of Ranvier) to the axonal cytoskeleton. Pathogenic variants are proposed to disrupt the cytoskeletal machinery controlling proper localization of ion channels and function of axonal domains where ion channels are normally clustered in high density. Among the evidence provided : nerve biopsies from an affected individual displayed reduced nodal Na+ channels and no nodal KCNQ2 K+ channels / Loss of AnkyrinG and βIV spectrin in animal model resulted in loss of KCNQ2- and KCNQ3- subunit containing K+ channels.

Apart from the ID / epilepsy panels please consider inclusion in other relevant ones.
Sources: Literature
Intellectual disability v3.35 TNRC6B Konstantinos Varvagiannis reviewed gene: TNRC6B: Rating: GREEN; Mode of pathogenicity: None; Publications: 32152250, 28135719, 25363768, 27479843, 28959963, 25228304; Phenotypes: Global developmental delay, Intellectual disability, Autistic behavior; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Early onset or syndromic epilepsy v2.47 CDC42BPB Konstantinos Varvagiannis gene: CDC42BPB was added
gene: CDC42BPB was added to Genetic epilepsy syndromes. Sources: Literature
Mode of inheritance for gene: CDC42BPB was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: CDC42BPB were set to 32031333
Phenotypes for gene: CDC42BPB were set to Central hypotonia; Global developmental delay; Intellectual disability; Seizures; Autistic behavior; Behavioral abnormality
Penetrance for gene: CDC42BPB were set to unknown
Review for gene: CDC42BPB was set to AMBER
Added comment: Chilton et al (2020 - PMID: 32031333) report on 14 individuals with missense and loss-of-function CDC42BPB variants.

Features included hypotonia (8/11), DD (12/13 - the 14th was a fetus), ID (7/13), ASD (8/12), clinical seizures (in 3 - a 4th had abnormal EEG without seizures), behavioral abnormalities. Variable non-specific dysmorphic features were reported in some (sparse hair being the most frequent - 4/8). Additional features were observed in few (=<4) incl. cryptorchidism, ophthalmological issues, constipation, kidney abnormalities, micropenis, etc.

All individuals had non-diagnostic prior genetic testing (incl. CMA, FMR1, MECP2, Angelman/Prader-Willi methylation studies, autism gene panel - suggesting relevance to the current panel) or metabolic testing.

Variants were identified following clinical exome sequencing with Sanger confirmation. Most occurred as de novo events (11/14) while inheritance was not available for few (3/14). Missense variants did not display (particular) clustering.

Almost all variants were absent from gnomAD and were predicted to be deleterious in silico (among others almost all had CADD scores >25).

As the authors comment, CDC42BPB encodes myotonic dystrophy-related Cdc42-binding kinase β (MRCKβ) a serine/threonine protein kinase playing a role in regulation of cytoskeletal reorganization and cell migration in nonmuscle cells (through phosporylation of MLC2).

Previous studies have demonstrated that it is ubiquitously expressed with prenatal brain expression.

The gene appears to be intolerant to pLoF (pLI of 1) as well as to missense variants (Z-score of 3.66).

CDC42BPB is a downstream effector of CDC42. Mutations of the latter cause Takenouchi-Kosaki syndrome with DD/ID and some further overlapping features (with CDC42BPB-associated phenotypes).

Homozygous Cdc42bpb KO in mouse appears to be nonviable (MGI:2136459). Loss of gek in the eyes of Drosophila results in disrupted growth cone targeting to the lamina (gek is the fly CDC42BPB ortholog).
Sources: Literature
Intellectual disability v3.35 CDC42BPB Konstantinos Varvagiannis gene: CDC42BPB was added
gene: CDC42BPB was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: CDC42BPB was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: CDC42BPB were set to 32031333
Phenotypes for gene: CDC42BPB were set to Central hypotonia; Global developmental delay; Intellectual disability; Seizures; Autistic behavior; Behavioral abnormality
Penetrance for gene: CDC42BPB were set to unknown
Review for gene: CDC42BPB was set to GREEN
Added comment: Chilton et al (2020 - PMID: 32031333) report on 14 individuals with missense and loss-of-function CDC42BPB variants.

Features included hypotonia (8/11), DD (12/13 - the 14th was a fetus), ID (7/13), ASD (8/12), clinical seizures (in 3 - a 4th had abnormal EEG without seizures), behavioral abnormalities. Variable non-specific dysmorphic features were reported in some (sparse hair being the most frequent - 4/8). Additional features were observed in few (=<4) incl. cryptorchidism, ophthalmological issues, constipation, kidney abnormalities, micropenis, etc.

All individuals had non-diagnostic prior genetic testing (incl. CMA, FMR1, MECP2, Angelman/Prader-Willi methylation studies, autism gene panel - suggesting relevance to the current panel) or metabolic testing.

Variants were identified following clinical exome sequencing with Sanger confirmation. Most occurred as de novo events (11/14) while inheritance was not available for few (3/14). Missense variants did not display (particular) clustering.

Almost all variants were absent from gnomAD and were predicted to be deleterious in silico (among others almost all had CADD scores >25).

As the authors comment, CDC42BPB encodes myotonic dystrophy-related Cdc42-binding kinase β (MRCKβ) a serine/threonine protein kinase playing a role in regulation of cytoskeletal reorganization and cell migration in nonmuscle cells (through phosporylation of MLC2).

Previous studies have demonstrated that it is ubiquitously expressed with prenatal brain expression.

The gene appears to be intolerant to pLoF (pLI of 1) as well as to missense variants (Z-score of 3.66).

CDC42BPB is a downstream effector of CDC42. Mutations of the latter cause Takenouchi-Kosaki syndrome with DD/ID and some further overlapping features (with CDC42BPB-associated phenotypes).

Homozygous Cdc42bpb KO in mouse appears to be nonviable (MGI:2136459). Loss of gek in the eyes of Drosophila results in disrupted growth cone targeting to the lamina (gek is the fly CDC42BPB ortholog).

Please consider inclusion with amber / green rating in the ID panel (>=4 relevant individuals / variants) and other panels (e.g. for epilepsy, ASD).
Sources: Literature
COVID-19 research v0.201 IFNL3 Catherine Snow Classified gene: IFNL3 as Amber List (moderate evidence)
COVID-19 research v0.201 IFNL3 Catherine Snow Gene: ifnl3 has been classified as Amber List (Moderate Evidence).
COVID-19 research v0.200 IFNL3 Catherine Snow gene: IFNL3 was added
gene: IFNL3 was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: IFNL3 was set to Unknown
Review for gene: IFNL3 was set to AMBER
Added comment: IFNL3 was identified in preprint https://doi.org/10.1101/2020.04.26.20080408 "A gene locus that controls expression of ACE2 in virus infection" A GWAS for performed for ACE2 expression in HCV-infected liver tissue from 195 individuals. it was discovered that polymorphisms in the host IFNL region which control expression of IFNL3 and IFNL4 modulate ACE2 expression.
Sources: Literature
COVID-19 research v0.199 IFNL4 Catherine Snow changed review comment from: IFNL4 was identified in preprint "A gene locus that controls expression of ACE2 in virus infection"
A GWAS for performed for ACE2 expression in HCV-infected liver tissue from 195 individuals. it was discovered that polymorphisms in the host IFNL region which control expression of IFNL3 and IFNL4 modulate ACE2 expression.
PMID: 31776283 Investigates the IFNL4 gene - it acts in a counterintuitive manner, as patients with a nonfunctional IFNL4 gene exhibit increased clearance of hepatitis C virus (HCV) but also increased liver inflammation.
Sources: Literature; to: IFNL4 was identified in preprint https://doi.org/10.1101/2020.04.26.20080408 "A gene locus that controls expression of ACE2 in virus infection" A GWAS for performed for ACE2 expression in HCV-infected liver tissue from 195 individuals. it was discovered that polymorphisms in the host IFNL region which control expression of IFNL3 and IFNL4 modulate ACE2 expression.

PMID: 31776283 Investigates the IFNL4 gene - it acts in a counterintuitive manner, as patients with a nonfunctional IFNL4 gene exhibit increased clearance of hepatitis C virus (HCV) but also increased liver inflammation.
Sources: Literature
COVID-19 research v0.199 IFNL4 Catherine Snow gene: IFNL4 was added
gene: IFNL4 was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: IFNL4 was set to Unknown
Publications for gene: IFNL4 were set to 31776283
Review for gene: IFNL4 was set to AMBER
Added comment: IFNL4 was identified in preprint "A gene locus that controls expression of ACE2 in virus infection"
A GWAS for performed for ACE2 expression in HCV-infected liver tissue from 195 individuals. it was discovered that polymorphisms in the host IFNL region which control expression of IFNL3 and IFNL4 modulate ACE2 expression.
PMID: 31776283 Investigates the IFNL4 gene - it acts in a counterintuitive manner, as patients with a nonfunctional IFNL4 gene exhibit increased clearance of hepatitis C virus (HCV) but also increased liver inflammation.
Sources: Literature
Primary immunodeficiency or monogenic inflammatory bowel disease v2.159 FCHO1 Sarah Leigh Classified gene: FCHO1 as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.159 FCHO1 Sarah Leigh Added comment: Comment on list classification: Not associated with phenotype in OMIM or in Gen2Phen. At least 5 biallelic variants reported in at least 5 unrelated cases, together with supportive functional studies.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.159 FCHO1 Sarah Leigh Gene: fcho1 has been classified as Green List (High Evidence).
COVID-19 research v0.198 ITPKC Catherine Snow changed review comment from: Adding ITPKC as Kawasaki disease in children linked to coronavirus.

Onouchi et al (PMID:18084290) identified a functional SNP in intron 1 of ITPKC (rs28493229) that was significantly associated with risk of Kawasaki disease and the formation of coronary artery aneurysms in both Japanese and U.S. children. But Chi et al. (2010) did not find a statistically significant association between the ITPKC gene SNP rs28493229 and Kawasaki disease or coronary artery lesions in Taiwanese children.
Sources: Literature, Research; to: Adding ITPKC as a Kawasaki like disease in children linked to coronavirus.

Onouchi et al (PMID:18084290) identified a functional SNP in intron 1 of ITPKC (rs28493229) that was significantly associated with risk of Kawasaki disease and the formation of coronary artery aneurysms in both Japanese and U.S. children. But Chi et al. (2010) did not find a statistically significant association between the ITPKC gene SNP rs28493229 and Kawasaki disease or coronary artery lesions in Taiwanese children.
Sources: Literature, Research
COVID-19 research v0.198 ITPKC Catherine Snow changed review comment from: Adding ITPKC as Kawasaki disease in children linked to coronavirus as becoming more "common".

Onouchi et al (PMID:18084290) identified a functional SNP in intron 1 of ITPKC (rs28493229) that was significantly associated with risk of Kawasaki disease and the formation of coronary artery aneurysms in both Japanese and U.S. children. But Chi et al. (2010) did not find a statistically significant association between the ITPKC gene SNP rs28493229 and Kawasaki disease or coronary artery lesions in Taiwanese children.
Sources: Literature, Research; to: Adding ITPKC as Kawasaki disease in children linked to coronavirus.

Onouchi et al (PMID:18084290) identified a functional SNP in intron 1 of ITPKC (rs28493229) that was significantly associated with risk of Kawasaki disease and the formation of coronary artery aneurysms in both Japanese and U.S. children. But Chi et al. (2010) did not find a statistically significant association between the ITPKC gene SNP rs28493229 and Kawasaki disease or coronary artery lesions in Taiwanese children.
Sources: Literature, Research
COVID-19 research v0.198 ITPKC Catherine Snow changed review comment from: Onouchi et al (PMID:18084290) identified a functional SNP in intron 1 of ITPKC (rs28493229) that was significantly associated with risk of Kawasaki disease and the formation of coronary artery aneurysms in both Japanese and U.S. children. But Chi et al. (2010) did not find a statistically significant association between the ITPKC gene SNP rs28493229 and Kawasaki disease or coronary artery lesions in Taiwanese children.
Sources: Literature, Research; to: Adding ITPKC as Kawasaki disease in children linked to coronavirus as becoming more "common".

Onouchi et al (PMID:18084290) identified a functional SNP in intron 1 of ITPKC (rs28493229) that was significantly associated with risk of Kawasaki disease and the formation of coronary artery aneurysms in both Japanese and U.S. children. But Chi et al. (2010) did not find a statistically significant association between the ITPKC gene SNP rs28493229 and Kawasaki disease or coronary artery lesions in Taiwanese children.
Sources: Literature, Research
COVID-19 research v0.198 ITPKC Catherine Snow Classified gene: ITPKC as Amber List (moderate evidence)
COVID-19 research v0.198 ITPKC Catherine Snow Gene: itpkc has been classified as Amber List (Moderate Evidence).
COVID-19 research v0.198 ITPKC Catherine Snow Classified gene: ITPKC as Amber List (moderate evidence)
COVID-19 research v0.198 ITPKC Catherine Snow Gene: itpkc has been classified as Amber List (Moderate Evidence).
COVID-19 research v0.197 ITPKC Catherine Snow gene: ITPKC was added
gene: ITPKC was added to Viral susceptibility. Sources: Literature,Research
Mode of inheritance for gene: ITPKC was set to Unknown
Publications for gene: ITPKC were set to 18084290; 20045869
Phenotypes for gene: ITPKC were set to Kawasaki disease, susceptibility to, 611775
Review for gene: ITPKC was set to AMBER
Added comment: Onouchi et al (PMID:18084290) identified a functional SNP in intron 1 of ITPKC (rs28493229) that was significantly associated with risk of Kawasaki disease and the formation of coronary artery aneurysms in both Japanese and U.S. children. But Chi et al. (2010) did not find a statistically significant association between the ITPKC gene SNP rs28493229 and Kawasaki disease or coronary artery lesions in Taiwanese children.
Sources: Literature, Research
Primary immunodeficiency or monogenic inflammatory bowel disease v2.158 IL6ST Sarah Leigh Classified gene: IL6ST as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.158 IL6ST Sarah Leigh Added comment: Comment on list classification: Based on expert review and the reporting of additional variants.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.158 IL6ST Sarah Leigh Gene: il6st has been classified as Green List (High Evidence).
Fetal hydrops v1.18 AHCY Rebecca Foulger Classified gene: AHCY as Amber List (moderate evidence)
Fetal hydrops v1.18 AHCY Rebecca Foulger Added comment: Comment on list classification: Updated rating from Red to Amber based on additional 2018 paper highlighted by Zornitza Stark (PMID:30121674) which reports an infant with non-immune hydrops. This takes total number of families to two.
Fetal hydrops v1.18 AHCY Rebecca Foulger Gene: ahcy has been classified as Amber List (Moderate Evidence).
Fetal hydrops v1.17 AHCY Rebecca Foulger commented on gene: AHCY: PMID:30121674. Judkins et al., 2018 report an infant with a prenatal diagnosis of non-immune hydrops. The infant was born with phenotypes including hypotonia, poor respiratory effort, chylothorax, encephalopathy, coagulopathy, progressive hepatic failure, and refractory pulmonary hypertension. Life support was withdrawn at 7 days. Novel compound het variants in the AHCY were found. Full text not available.
Fetal hydrops v1.17 AHCY Rebecca Foulger Publications for gene: AHCY were set to 23137060; 20852937
Fetal anomalies v1.46 AHCY Rebecca Foulger Phenotypes for gene: AHCY were changed from S-adenosylhomocysteine hydrolase deficiency; Hypermethioninemia with deficiency of S-adenosylhomocysteine hydrolase, 613752 to Fetal hydrops; S-adenosylhomocysteine hydrolase deficiency; Hypermethioninemia with deficiency of S-adenosylhomocysteine hydrolase, 613752
Fetal anomalies v1.45 AHCY Rebecca Foulger Classified gene: AHCY as Amber List (moderate evidence)
Fetal anomalies v1.45 AHCY Rebecca Foulger Added comment: Comment on list classification: Added to panel and rated Amber by Zornitza Stark. Two unrelated families with hydrops reported (PMID:30121674, 20852937). Note that previous reports of AHCY deficiency do not include hydrops (e.g. PMID:15024124). Overall, phenotype is relevant to the panel but currently insufficient evidence for Green rating. Rated Amber awaiting further evidence.
Fetal anomalies v1.45 AHCY Rebecca Foulger Gene: ahcy has been classified as Amber List (Moderate Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.157 IL6ST Sarah Leigh Added comment: Comment on phenotypes: Eosinophilia;Eczema;Bacterial infections, boiles, eczema, pulmonary abscesses, pneumatoceles, bone fractures, scoliosis, retention of primary teeth, craniosynostosis;Abnormal acute-phase responses;Recurrent infections;Elevated IgE;Combined immunodeficiencies with associated or syndromic features
Primary immunodeficiency or monogenic inflammatory bowel disease v2.157 IL6ST Sarah Leigh Phenotypes for gene: IL6ST were changed from Eosinophilia; Eczema; Bacterial infections, boiles, eczema, pulmonary abscesses, pneumatoceles, bone fractures, scoliosis, retention of primary teeth, craniosynostosis; Abnormal acute-phase responses; Recurrent infections; Elevated IgE; Combined immunodeficiencies with associated or syndromic features to Hyper-IgE recurrent infection syndrome 4, autosomal recessive 618523; Stuve-Wiedemann-like syndrome: skeletal dysplasia, neonatal lung dysfunction, thrombocytopenia, dermatitis, defective acute-phase response.; Hyper-IgE syndrome, autosomal dominant
Fetal anomalies v1.44 AHCY Rebecca Foulger commented on gene: AHCY: PMID:20852937. Grubbs et al., 2010 report 2 sisters born with fetal hydrops and compound het for 2 variants in AHCY (p.Arg49Cys and p.Asp86Gly). Phenotypes included severe hypotonia/myopathy, feeding problems, and respiratory failure. The sisters died age 25 days and 122 days.
Fetal anomalies v1.44 AHCY Rebecca Foulger commented on gene: AHCY
COVID-19 research v0.196 IL6ST Sarah Leigh Publications for gene: IL6ST were set to 31235509; 32086639; 30309848; 28747427; 32048120
Primary immunodeficiency or monogenic inflammatory bowel disease v2.156 IL6ST Sarah Leigh Publications for gene: IL6ST were set to 31235509; 32086639; 30309848; 28747427; 32048120
Fetal anomalies v1.44 AHCY Rebecca Foulger Phenotypes for gene: AHCY were changed from S-adenosylhomocysteine hydrolase deficiency to S-adenosylhomocysteine hydrolase deficiency; Hypermethioninemia with deficiency of S-adenosylhomocysteine hydrolase, 613752
Retinal disorders v2.13 USP45 Ivone Leong Phenotypes for gene: USP45 were changed from Lebers congenital amaurosis; retinal dystrophy to Lebers congenital amaurosis; retinal dystrophy; ?Leber congenital amaurosis 19, 618513
Hypogonadotropic hypogonadism (GMS) v1.8 NDNF Ivone Leong Classified gene: NDNF as Green List (high evidence)
Hypogonadotropic hypogonadism (GMS) v1.8 NDNF Ivone Leong Added comment: Comment on list classification: Gene added by expert reviewer (Simon Thomas (Wessex)) with suggested Green rating.

The gene is associated with a relevent disease in OMIM and is probably associated with a relevent disease in Gene2Phentoype. There are 3 unrelated cases. Therefore, there is enough evidence to support this gene-disease phenotype.
Hypogonadotropic hypogonadism (GMS) v1.8 NDNF Ivone Leong Gene: ndnf has been classified as Green List (High Evidence).
Hypogonadotropic hypogonadism (GMS) v1.7 NDNF Ivone Leong Phenotypes for gene: NDNF were changed from Congenital hypogonadotropic hypogonadism (CHH) to Congenital hypogonadotropic hypogonadism (CHH); Hypogonadotropic hypogonadism 25 with anosmia, 618841
Hypogonadotropic hypogonadism (GMS) v1.6 NDNF Ivone Leong Publications for gene: NDNF were set to PMID: 31883645
Hypogonadotropic hypogonadism v1.28 KLB Ivone Leong Classified gene: KLB as Green List (high evidence)
Hypogonadotropic hypogonadism v1.28 KLB Ivone Leong Added comment: Comment on list classification: Promoted from Red to Green based on expert review (Rachel Jones (GSTT))
Hypogonadotropic hypogonadism v1.28 KLB Ivone Leong Gene: klb has been classified as Green List (High Evidence).
DDG2P v2.5 CDK8 Rebecca Foulger Phenotypes for gene: CDK8 were changed from SYNDROMIC INTELLECTUAL DISABILITY 612100 to SYNDROMIC INTELLECTUAL DISABILITY
Retinal disorders v2.12 DRAM2 Ivone Leong Classified gene: DRAM2 as Green List (high evidence)
Retinal disorders v2.12 DRAM2 Ivone Leong Added comment: Comment on list classification: Promoted from Amber to Green based on expert review.
Retinal disorders v2.12 DRAM2 Ivone Leong Gene: dram2 has been classified as Green List (High Evidence).
Retinal disorders v2.11 DRAM2 Ivone Leong Phenotypes for gene: DRAM2 were changed from to Cone-rod dystrophy 21, 616502; macular dystrophy; cone-dystrophy
Retinal disorders v2.10 DRAM2 Ivone Leong Publications for gene: DRAM2 were set to
Retinal disorders v2.9 DRAM2 Ivone Leong Mode of inheritance for gene: DRAM2 was changed from to BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.195 CD4 Ivone Leong Classified gene: CD4 as Amber List (moderate evidence)
COVID-19 research v0.195 CD4 Ivone Leong Added comment: Comment on list classification: Promoted from Red to Amber based on expert review.

"Single individual reported, functional data, emerging gene.
Zornitza Stark (Australian Genomics), 1 May 2020" - review copied from Primary immunodeficiency (Version 2.155).
COVID-19 research v0.195 CD4 Ivone Leong Gene: cd4 has been classified as Amber List (Moderate Evidence).
COVID-19 research v0.194 CD4 Ivone Leong Phenotypes for gene: CD4 were changed from Selective CD4 cell deficiency to Selective CD4 cell deficiency; OKT4 epitope deficiency, 613949; Absence of CD4+ T cells; exuberant, relapsing, treatment-refractory warts
COVID-19 research v0.193 CD4 Ivone Leong Publications for gene: CD4 were set to 25611551
COVID-19 research v0.192 CD4 Ivone Leong Mode of inheritance for gene: CD4 was changed from Unknown to BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.155 CD4 Ivone Leong Classified gene: CD4 as Amber List (moderate evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.155 CD4 Ivone Leong Added comment: Comment on list classification: Promoted from Red to Amber based on expert review.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.155 CD4 Ivone Leong Gene: cd4 has been classified as Amber List (Moderate Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.154 CD4 Ivone Leong Mode of inheritance for gene: CD4 was changed from to BIALLELIC, autosomal or pseudoautosomal
Fetal anomalies v1.43 SMG9 Rebecca Foulger Publications for gene: SMG9 were set to
Fetal anomalies v1.43 SMG9 Rebecca Foulger Phenotypes for gene: SMG9 were changed from SMG9 Multiple Congenital Anomaly Syndrome to SMG9 Multiple Congenital Anomaly Syndrome; Heart and brain malformation syndrome, 616920
Fetal anomalies v1.42 SMG9 Rebecca Foulger Classified gene: SMG9 as Green List (high evidence)
Fetal anomalies v1.42 SMG9 Rebecca Foulger Added comment: Comment on list classification: Rated probable in Gene2Phenotype for SMG9 Multiple Congenital Anomaly Syndrome based on 2 families in PMID:27018474. Additional family now reported in PMID:31390136. Fetally-relevant phenotype (anomalies detected in-utero) and sufficient cases to support causation. Therefore upgraded from Amber to Green.
Fetal anomalies v1.42 SMG9 Rebecca Foulger Gene: smg9 has been classified as Green List (High Evidence).
Fetal anomalies v1.41 SMG9 Rebecca Foulger commented on gene: SMG9: PMID:31390136. Lecoquierre et al., 2019 performed exome sequencing in a patient with syndromic DD and diverse malformations including cleft lip and palate, facial dysmorphia, brain abnormalities, herat defect, growth retardation and severe infections. She carried a homozygous SMG9 variant, p.(Gln393*). Her unaffected parents were both heterozygous. Phenotypes were first noted in-utero: polyhydamnios, lateral cleft lip and palate, and IUGR noted on ultrasound.
COVID-19 research v0.191 CDC42 Ivone Leong Classified gene: CDC42 as Green List (high evidence)
COVID-19 research v0.191 CDC42 Ivone Leong Gene: cdc42 has been classified as Green List (High Evidence).
COVID-19 research v0.190 CDC42 Ivone Leong gene: CDC42 was added
gene: CDC42 was added to Viral susceptibility. Sources: Expert Review
Mode of inheritance for gene: CDC42 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: CDC42 were set to 31601675; 32303876; 32231661; 31271789
Phenotypes for gene: CDC42 were set to Neonatal-onset cytopaenia with dyshaematopoiesis; autoinflammation; rash; HLH
Review for gene: CDC42 was set to GREEN
Added comment: "PMID 31601675: four unrelated individuals with superimposable features, including neonatal-onset cytopenia with dyshematopoiesis, autoinflammation, rash, and HLH. All shared the same de novo CDC42 variant (Chr1:22417990C>T, p.R186C). Another pair of sibs reported in PMID 32303876 with infantile myelofibrosis and myeloproliferation and same variant (parental mosaicism). Yet another individual in PMID 32231661 with different de novo variant, p.Cys81Tyr who in addition developed haematological malignancy and also had syndromic features, including ID. Note other missense variants in this gene cause Takenouchi-Kosaki syndrome, MIM# 616737 Sources: Literature
Zornitza Stark (Australian Genomics), 30 Apr 2020" - review copied from Primary immunodeficiency (Version 2.153)

"Comment on list classification: Gene added by Zornitza Stark (Australian Genomics) with a suggested Green rating based on evidence she has provided. As well as the listed cases there is another paper (PMID: 31271789) describing 4 unrelated cases with de novo variants in CDC42 (p.C188Y, p.R186C, p.*192C*24). The patients predominantly had systemic autoinflammatory disease and development of HLH. Therefore there is enough evidence to rate this gene as Green.
Ivone Leong (Genomics England Curator), 5 May 2020" - review copied from Primary immunodeficiency (Version 2.153)
Sources: Expert Review
Fetal anomalies v1.41 SMG9 Rebecca Foulger commented on gene: SMG9: PMID:27018474. Shaheen et al, 2016 report 2 consanguineous families with different homozygous LOF variants in SMG9 and and a similar set of congenital anomalies including craniofacial dysmorphism, and major brain and heart malformations.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.153 CDC42 Ivone Leong Classified gene: CDC42 as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.153 CDC42 Ivone Leong Added comment: Comment on list classification: Gene added by Zornitza Stark (Australian Genomics) with a suggested Green rating based on evidence she has provided.

As well as the listed cases there is another paper (PMID: 31271789) describing 4 unrelated cases with de novo variants in CDC42 (p.C188Y, p.R186C, p.*192C*24). The patients predominantly had systemic autoinflammatory disease and development of HLH.

Therefore there is enough evidence to rate this gene as Green.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.153 CDC42 Ivone Leong Gene: cdc42 has been classified as Green List (High Evidence).
Fetal anomalies v1.41 TUBA8 Rebecca Foulger Classified gene: TUBA8 as Amber List (moderate evidence)
Fetal anomalies v1.41 TUBA8 Rebecca Foulger Added comment: Comment on list classification: The reanalysis in PMID:28388629 casts doubt that TUBA8 is responsible for the morphological phenotypes initially reported in PMID:19896110. Only 2 families (of possible shared descent) were reported. Therefore insufficient evidence for Green rating. Downgraded from Green to Amber.
Fetal anomalies v1.41 TUBA8 Rebecca Foulger Gene: tuba8 has been classified as Amber List (Moderate Evidence).
Fetal anomalies v1.40 TUBA8 Rebecca Foulger commented on gene: TUBA8: In 4 affected members of 2 consanguineous Pakistani families with MIM:613180, Abdollahi et al. (2009, PMID:19896110) identified a homozygous 14-bp deletion 11 bp upstream of the exon 2 splice site junction in TUBA8. The families may have common ancestory. All obligate carriers were heterozygous. The patients had neonatal hypotonia, profound mental retardation, essentially no psychomotor development, optic nerve hypoplasia, and thickened cortex with polymicrogyria and absent corpus callosum. BUT due to lack of a mouse TUBA8 phenotype, the authors in PMID:28388629 (Diggle et al 2017) reanalysed their patients from PMID:19896110 and found an additional LOF variant in SNAP29 (p.Ser163Lysfs*6). The authors suggest that SNAP29 deficiency, rather than TUBA8 deficiency, may be responsible for the patient phenotypes.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.152 CDC42 Ivone Leong Publications for gene: CDC42 were set to 31601675; 32303876; 32231661
COVID-19 research v0.189 KARS Sarah Leigh commented on gene: KARS: New gene name for KARS is KARS1
COVID-19 research v0.189 KARS Sarah Leigh Tag new-gene-name tag was added to gene: KARS.
COVID-19 research v0.189 ZFHX3 Sarah Leigh reviewed gene: ZFHX3: Rating: RED; Mode of pathogenicity: ; Publications: 32348764; Phenotypes: Influenza A Virus-Specific Antibody Responses; Mode of inheritance:
COVID-19 research v0.189 WSCD1 Sarah Leigh reviewed gene: WSCD1: Rating: RED; Mode of pathogenicity: ; Publications: 32348764; Phenotypes: Influenza A Virus-Specific Antibody Responses; Mode of inheritance:
COVID-19 research v0.189 UNC5CL Sarah Leigh reviewed gene: UNC5CL: Rating: RED; Mode of pathogenicity: ; Publications: 32348764; Phenotypes: Influenza A Virus-Specific Antibody Responses; Mode of inheritance:
COVID-19 research v0.189 TAPT1 Sarah Leigh reviewed gene: TAPT1: Rating: RED; Mode of pathogenicity: ; Publications: 32348764; Phenotypes: Influenza A Virus-Specific Antibody Responses; Mode of inheritance:
COVID-19 research v0.189 SPNS3 Sarah Leigh reviewed gene: SPNS3: Rating: RED; Mode of pathogenicity: ; Publications: 32348764; Phenotypes: Influenza A Virus-Specific Antibody Responses; Mode of inheritance:
COVID-19 research v0.189 RPAIN Sarah Leigh reviewed gene: RPAIN: Rating: RED; Mode of pathogenicity: ; Publications: 32348764; Phenotypes: Influenza A Virus-Specific Antibody Responses; Mode of inheritance:
COVID-19 research v0.189 PROM1 Sarah Leigh reviewed gene: PROM1: Rating: RED; Mode of pathogenicity: ; Publications: 32348764; Phenotypes: Influenza A Virus-Specific Antibody Responses; Mode of inheritance:
COVID-19 research v0.189 PKD1L3 Sarah Leigh reviewed gene: PKD1L3: Rating: RED; Mode of pathogenicity: ; Publications: 32348764; Phenotypes: Influenza A Virus-Specific Antibody Responses; Mode of inheritance:
COVID-19 research v0.189 NUP88 Sarah Leigh reviewed gene: NUP88: Rating: RED; Mode of pathogenicity: ; Publications: 32348764; Phenotypes: Influenza A Virus-Specific Antibody Responses; Mode of inheritance:
COVID-19 research v0.189 MLKL Sarah Leigh reviewed gene: MLKL: Rating: RED; Mode of pathogenicity: ; Publications: 32348764; Phenotypes: Influenza A Virus-Specific Antibody Responses; Mode of inheritance:
COVID-19 research v0.189 MIS12 Sarah Leigh reviewed gene: MIS12: Rating: RED; Mode of pathogenicity: ; Publications: 32348764; Phenotypes: Influenza A Virus-Specific Antibody Responses; Mode of inheritance:
COVID-19 research v0.189 LDB2 Sarah Leigh reviewed gene: LDB2: Rating: RED; Mode of pathogenicity: ; Publications: 32348764; Phenotypes: Influenza A Virus-Specific Antibody Responses; Mode of inheritance:
COVID-19 research v0.189 KARS Sarah Leigh reviewed gene: KARS: Rating: RED; Mode of pathogenicity: ; Publications: 32348764; Phenotypes: Influenza A Virus-Specific Antibody Responses; Mode of inheritance:
COVID-19 research v0.189 HYDIN Sarah Leigh reviewed gene: HYDIN: Rating: RED; Mode of pathogenicity: ; Publications: 32348764; Phenotypes: Influenza A Virus-Specific Antibody Responses; Mode of inheritance:
COVID-19 research v0.189 CC2D2A Sarah Leigh reviewed gene: CC2D2A: Rating: RED; Mode of pathogenicity: ; Publications: 32348764; Phenotypes: Influenza A Virus-Specific Antibody Responses; Mode of inheritance:
COVID-19 research v0.189 BCAR1 Sarah Leigh reviewed gene: BCAR1: Rating: RED; Mode of pathogenicity: ; Publications: 32348764; Phenotypes: Influenza A Virus-Specific Antibody Responses; Mode of inheritance:
Fetal anomalies v1.40 TUBA8 Rebecca Foulger Phenotypes for gene: TUBA8 were changed from POLYMICROGYRIA WITH OPTIC NERVE HYPOPLASIA to POLYMICROGYRIA WITH OPTIC NERVE HYPOPLASIA; Cortical dysplasia, complex, with other brain malformations 8, 613180
Fetal anomalies v1.39 TUBA8 Rebecca Foulger Publications for gene: TUBA8 were set to
Fetal anomalies v1.38 TUBA8 Rebecca Foulger Tag for-review tag was added to gene: TUBA8.
Fetal anomalies v1.38 PAICS Rebecca Foulger Classified gene: PAICS as Amber List (moderate evidence)
Fetal anomalies v1.38 PAICS Rebecca Foulger Added comment: Comment on list classification: Added to the panel and rated Red by Zornitza. Phenotype is appropriate for the panel, but insufficient cases to support causation. Therefore rated Amber, awaiting further publications/clinical evidence. Not yet associated with a disorder in Gene2Phenotype.
Fetal anomalies v1.38 PAICS Rebecca Foulger Gene: paics has been classified as Amber List (Moderate Evidence).
Fetal anomalies v1.37 PAICS Rebecca Foulger Phenotypes for gene: PAICS were changed from Polyhydramnios; multiple congenital abnormalities to Polyhydramnios; multiple congenital abnormalities; early neonatal death
Fetal anomalies v1.36 PAICS Rebecca Foulger changed review comment from: PMID:31600779. Pelet et al. report an AR inborn error of de novo purine synthesis due to homozygous missense vairant in PAICS (c.158A>G; p.Lys53Arg) in 2 siblings from the Faroe islands. Catalytic activity of the mutant protein was approx 25% of wild type levels. The siblings had multiple malformations resulting in early neonatal death.; to: PMID:31600779. Pelet et al. report an AR inborn error of de novo purine synthesis due to homozygous missense variant in PAICS (c.158A>G; p.Lys53Arg) in 2 siblings from the Faroe islands. Catalytic activity of the mutant protein was approx 25% of wild type levels. The siblings had multiple malformations resulting in early neonatal death.
Fetal anomalies v1.36 PAICS Rebecca Foulger commented on gene: PAICS
Fetal anomalies v1.36 MSL3 Rebecca Foulger Phenotypes for gene: MSL3 were changed from MSL3 syndrome to MSL3 syndrome; Basilicata-Akhtar syndrome, 301032
Fetal anomalies v1.35 CNOT3 Rebecca Foulger Phenotypes for gene: CNOT3 were changed from CNOT3 syndrome; Intellectual developmental disorder with speech delay, 618672 autism, and dysmorphic facies to CNOT3 syndrome; Intellectual developmental disorder with speech delay, autism, and dysmorphic facies, 618672
Fetal anomalies v1.34 CNOT3 Rebecca Foulger Phenotypes for gene: CNOT3 were changed from CNOT3 syndrome to CNOT3 syndrome; Intellectual developmental disorder with speech delay, 618672 autism, and dysmorphic facies
COVID-19 research v0.187 ZFHX3 Sarah Leigh gene: ZFHX3 was added
gene: ZFHX3 was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: ZFHX3 was set to
COVID-19 research v0.187 WSCD1 Sarah Leigh gene: WSCD1 was added
gene: WSCD1 was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: WSCD1 was set to
COVID-19 research v0.187 UNC5CL Sarah Leigh gene: UNC5CL was added
gene: UNC5CL was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: UNC5CL was set to
COVID-19 research v0.187 TAPT1 Sarah Leigh gene: TAPT1 was added
gene: TAPT1 was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: TAPT1 was set to
COVID-19 research v0.187 SPNS3 Sarah Leigh gene: SPNS3 was added
gene: SPNS3 was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: SPNS3 was set to
COVID-19 research v0.187 RPAIN Sarah Leigh gene: RPAIN was added
gene: RPAIN was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: RPAIN was set to
COVID-19 research v0.187 PROM1 Sarah Leigh gene: PROM1 was added
gene: PROM1 was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: PROM1 was set to
COVID-19 research v0.187 PKD1L3 Sarah Leigh gene: PKD1L3 was added
gene: PKD1L3 was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: PKD1L3 was set to
COVID-19 research v0.187 NUP88 Sarah Leigh gene: NUP88 was added
gene: NUP88 was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: NUP88 was set to
COVID-19 research v0.187 MLKL Sarah Leigh gene: MLKL was added
gene: MLKL was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: MLKL was set to
COVID-19 research v0.187 MIS12 Sarah Leigh gene: MIS12 was added
gene: MIS12 was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: MIS12 was set to
COVID-19 research v0.187 LDB2 Sarah Leigh gene: LDB2 was added
gene: LDB2 was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: LDB2 was set to
COVID-19 research v0.187 KARS Sarah Leigh gene: KARS was added
gene: KARS was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: KARS was set to
COVID-19 research v0.187 HYDIN Sarah Leigh gene: HYDIN was added
gene: HYDIN was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: HYDIN was set to
COVID-19 research v0.187 CC2D2A Sarah Leigh gene: CC2D2A was added
gene: CC2D2A was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: CC2D2A was set to
COVID-19 research v0.187 BCAR1 Sarah Leigh gene: BCAR1 was added
gene: BCAR1 was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: BCAR1 was set to
Cardiac arrhythmias - additional genes v1.10 TANGO2 Sarah Leigh Classified gene: TANGO2 as Green List (high evidence)
Cardiac arrhythmias - additional genes v1.10 TANGO2 Sarah Leigh Gene: tango2 has been classified as Green List (High Evidence).
Cardiac arrhythmias - additional genes v1.9 TANGO2 Sarah Leigh gene: TANGO2 was added
gene: TANGO2 was added to Cardiac arrhythmias - additional genes. Sources: Expert Review
Mode of inheritance for gene: TANGO2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TANGO2 were set to 26805782; 30245509
Phenotypes for gene: TANGO2 were set to Metabolic encephalomyopathic crises, recurrent, with rhabdomyolysis, cardiac arrhythmias, and neurodegeneration 616878
Review for gene: TANGO2 was set to GREEN
Added comment: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene. At least 10 variants reported in at least 14 unrelated cases, with arrhythmias in 8 unrelated cases.

Gene suggested by Rowenna Roberts, Clinical Scientist.
Sources: Expert Review
Likely inborn error of metabolism v2.7 TANGO2 Sarah Leigh Publications for gene: TANGO2 were set to 26805782; 26805781; 30245509
Likely inborn error of metabolism v2.6 TANGO2 Sarah Leigh Publications for gene: TANGO2 were set to 26805782; 26805781; 30245509
Likely inborn error of metabolism v2.6 TANGO2 Sarah Leigh Publications for gene: TANGO2 were set to 26805782; 26805781
Undiagnosed metabolic disorders v1.414 TANGO2 Sarah Leigh Publications for gene: TANGO2 were set to
Rhabdomyolysis and metabolic muscle disorders v1.39 TANGO2 Sarah Leigh edited their review of gene: TANGO2: Added comment: Gene suggested by Rowenna Roberts, Clinical Scientist.; Changed phenotypes: Metabolic encephalomyopathic crises, recurrent, with rhabdomyolysis, cardiac arrhythmias, and neurodegeneration 616878
Ketotic hypoglycaemia v1.4 TANGO2 Sarah Leigh Classified gene: TANGO2 as Green List (high evidence)
Ketotic hypoglycaemia v1.4 TANGO2 Sarah Leigh Gene: tango2 has been classified as Green List (High Evidence).
Ketotic hypoglycaemia v1.3 TANGO2 Sarah Leigh gene: TANGO2 was added
gene: TANGO2 was added to Ketotic hypoglycaemia. Sources: Expert Review
Mode of inheritance for gene: TANGO2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TANGO2 were set to 26805782; 30245509
Phenotypes for gene: TANGO2 were set to Metabolic encephalomyopathic crises, recurrent, with rhabdomyolysis, cardiac arrhythmias, and neurodegeneration 616878
Review for gene: TANGO2 was set to GREEN
Added comment: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene. At least 10 variants reported in at least 14 unrelated cases.
Gene suggested by Rowenna Roberts, Clinical Scientist.
Sources: Expert Review
COVID-19 research v0.186 PIK3CG Ivone Leong Classified gene: PIK3CG as Green List (high evidence)
COVID-19 research v0.186 PIK3CG Ivone Leong Gene: pik3cg has been classified as Green List (High Evidence).
Rhabdomyolysis and metabolic muscle disorders v1.39 TANGO2 Sarah Leigh Classified gene: TANGO2 as Green List (high evidence)
Rhabdomyolysis and metabolic muscle disorders v1.39 TANGO2 Sarah Leigh Gene: tango2 has been classified as Green List (High Evidence).
COVID-19 research v0.185 PIK3CG Ivone Leong gene: PIK3CG was added
gene: PIK3CG was added to Viral susceptibility. Sources: Expert list
Mode of inheritance for gene: PIK3CG was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PIK3CG were set to 32001535; 31554793
Phenotypes for gene: PIK3CG were set to Immune dysregulation; HLH-like; childhood-onset antibody defects; cytopenias; T lymphocytic pneumonitis and colitis
Review for gene: PIK3CG was set to GREEN
Added comment: "Two individuals with complex immunological phenotypes reported and a mouse model. Sources: Literature
Zornitza Stark (Australian Genomics), 30 Apr 2020" - review copied from Primary immunodeficiency (Version 2.151).

"Comment on list classification: Gene added by Zornitza Stark (Australian Genomics) with recommended Green status based on provided evidence. There is enough evidence for this gene to be rated Green.
Ivone Leong (Genomics England Curator), 5 May 2020" - review copied from Primary immunodeficiency (Version 2.151).
Sources: Expert list
Rhabdomyolysis and metabolic muscle disorders v1.38 TANGO2 Sarah Leigh gene: TANGO2 was added
gene: TANGO2 was added to Rhabdomyolysis and metabolic muscle disorders. Sources: Expert Review
Mode of inheritance for gene: TANGO2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TANGO2 were set to 26805782; 30245509
Phenotypes for gene: TANGO2 were set to Metabolic encephalomyopathic crises, recurrent, with rhabdomyolysis, cardiac arrhythmias, and neurodegeneration 616878
Review for gene: TANGO2 was set to GREEN
Added comment: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene. At least 10 variants reported in at least 14 unrelated cases, in which rabdomyolysis was reported in 11 unrelated cases.
Sources: Expert Review
Primary immunodeficiency or monogenic inflammatory bowel disease v2.151 PIK3CG Ivone Leong Classified gene: PIK3CG as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.151 PIK3CG Ivone Leong Added comment: Comment on list classification: Gene added by Zornitza Stark (Australian Genomics) with recommended Green status based on provided evidence. There is enough evidence for this gene to be rated Green.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.151 PIK3CG Ivone Leong Gene: pik3cg has been classified as Green List (High Evidence).
COVID-19 research v0.184 RIPK1 Ivone Leong Added comment: Comment on mode of inheritance: "Please note recent report of mono-allelic variants in two families.
Zornitza Stark (Australian Genomics), 30 Apr 2020" - review copied from Primary immunodeficiency (Version 2.150).

"Comment on mode of inheritance: MOI updated from Biallelic to Both monoallelic and biallelic based on new evidence provided by Zornitza Stark (Australian Genomics). PMID: 31827280.
Ivone Leong (Genomics England Curator), 5 May 2020" - review copied from Primary immunodeficiency (Version 2.150).
COVID-19 research v0.184 RIPK1 Ivone Leong Mode of inheritance for gene: RIPK1 was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.150 RIPK1 Ivone Leong Publications for gene: RIPK1 were set to 30026316; 30591564; 31213653; 31827280
COVID-19 research v0.183 RIPK1 Ivone Leong Publications for gene: RIPK1 were set to 30026316
Primary immunodeficiency or monogenic inflammatory bowel disease v2.149 RIPK1 Ivone Leong Added comment: Comment on mode of inheritance: MOI updated from Biallelic to Both monoallelic and biallelic based on new evidence provided by Zornitza Stark (Australian Genomics). PMID: 31827280.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.149 RIPK1 Ivone Leong Mode of inheritance for gene: RIPK1 was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.148 RIPK1 Ivone Leong Publications for gene: RIPK1 were set to 30026316
COVID-19 research v0.182 ITPKB Ivone Leong Classified gene: ITPKB as Amber List (moderate evidence)
COVID-19 research v0.182 ITPKB Ivone Leong Gene: itpkb has been classified as Amber List (Moderate Evidence).
COVID-19 research v0.181 ITPKB Ivone Leong gene: ITPKB was added
gene: ITPKB was added to Viral susceptibility. Sources: Expert list
Mode of inheritance for gene: ITPKB was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ITPKB were set to 31987846; 14517551
Phenotypes for gene: ITPKB were set to Severe combined immunodeficiency, absent T cells, present B cells and NK cells
Review for gene: ITPKB was set to AMBER
Added comment: "Single individual with homozygous bi-allelic LoF variant reported. Sources: Literature
Zornitza Stark (Australian Genomics), 1 May 2020" - review copied from Primary immunodeficiency panel (v2.147).

"Comment on list classification: Gene added by Zornitza Stark (Australian Genomics) with a recommended Red gene rating based on evidence provided. PMID: 31987846 describes a patient born of consanguineous Egyptian parents. The patient failed to thrive and had persistent thrush shortly after birth, recurrent pneumonias beginning at age 2 months, and Klebsiella pneumoniae skin abscesses at age 6 and 10 months. She had severe SCID.

PMID: 14517551 is a itpkb-/- mouse. Knockout of the gene caused a severe T cell deficiency. Based on these 2 pieces of information the gene has been given an Amber gene rating.
Ivone Leong (Genomics England Curator), 5 May 2020" - review copied from Primary immunodeficiency panel (v2.147).
Sources: Expert list
COVID-19 research v0.180 SMARCD2 Sophie Hambleton reviewed gene: SMARCD2: Rating: GREEN; Mode of pathogenicity: None; Publications: 28369036; Phenotypes: neutropenia, specific granule deficiency, myelodysplasia, developmental delay, dysmorphic features; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.147 ITPKB Ivone Leong Classified gene: ITPKB as Amber List (moderate evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.147 ITPKB Ivone Leong Added comment: Comment on list classification: Gene added by Zornitza Stark (Australian Genomics) with a recommended Red gene rating based on evidence provided. PMID: 31987846 describes a patient born of consanguineous Egyptian parents. The patient failed to thrive and had persistent thrush shortly after birth, recurrent pneumonias beginning at age 2 months, and Klebsiella pneumoniae skin abscesses at age 6 and 10 months. She had severe SCID.

PMID: 14517551 is a itpkb-/- mouse. Knockout of the gene caused a severe T cell deficiency. Based on these 2 pieces of information the gene has been given an Amber gene rating.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.147 ITPKB Ivone Leong Gene: itpkb has been classified as Amber List (Moderate Evidence).
COVID-19 research v0.180 SLX4 Sophie Hambleton reviewed gene: SLX4: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.180 SLC7A7 Sophie Hambleton reviewed gene: SLC7A7: Rating: GREEN; Mode of pathogenicity: None; Publications: 10080182, 28057010, 21308987; Phenotypes: lysinuric protein intolerance, failure to thrive, hyperammonaemia, encephalopathy, developmental disability, nephropathy, lupus nephritis, haemophagocytic lymphophistiocytosis, pancreatitis, pulmonary alveolar proteinosis; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.180 SLC39A7 Sophie Hambleton reviewed gene: SLC39A7: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: agammaglobulinaemia, B cell deficiency; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.180 SH3KBP1 Sophie Hambleton reviewed gene: SH3KBP1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: hypogammaglobulinaemia; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females
Primary immunodeficiency or monogenic inflammatory bowel disease v2.146 ITPKB Ivone Leong Publications for gene: ITPKB were set to 31987846
COVID-19 research v0.180 SH3BP2 Sophie Hambleton reviewed gene: SH3BP2: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Primary immunodeficiency or monogenic inflammatory bowel disease v2.145 NOS2 Ivone Leong Classified gene: NOS2 as Red List (low evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.145 NOS2 Ivone Leong Added comment: Comment on list classification: Gene was added to panel by Zornitza Stark (Australian Genomics). The gene was given the suggested Red rating based on evidence provided by expert reviewer.

PMID: 31995689 describes a 51 year old man from Iran who had an acute cytomegalovirus (CMV) infection which progressed to CMV disease and later died from it. The researchers found a homozygous variant that causes a frameshift mutation in NOS2 that caused NOS2 deficiency, which might cause the patient to be more susceptible to lethal CMV infection. The patient was otherwise healthy until the CMV infection.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.145 NOS2 Ivone Leong Gene: nos2 has been classified as Red List (Low Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.144 NOS2 Ivone Leong Publications for gene: NOS2 were set to 12433515; 31995689
Primary immunodeficiency or monogenic inflammatory bowel disease v2.143 IFNG Ivone Leong Classified gene: IFNG as Red List (low evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.143 IFNG Ivone Leong Added comment: Comment on list classification: This gene has been given Red status based on expert review. PMID: 32163377 does have some functional data; however, it is cellular-based work.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.143 IFNG Ivone Leong Gene: ifng has been classified as Red List (Low Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.142 CD4 Ivone Leong Phenotypes for gene: CD4 were changed from Selective CD4 cell deficiency; OKT4 epitope deficiency, 613949 to Selective CD4 cell deficiency; OKT4 epitope deficiency, 613949; Absence of CD4+ T cells; exuberant, relapsing, treatment-refractory warts
Primary immunodeficiency or monogenic inflammatory bowel disease v2.141 CD4 Ivone Leong Publications for gene: CD4 were set to
Primary immunodeficiency or monogenic inflammatory bowel disease v2.140 CD4 Ivone Leong Phenotypes for gene: CD4 were changed from Selective CD4 cell deficiency to Selective CD4 cell deficiency; OKT4 epitope deficiency, 613949
Hyperthyroidism v2.6 TTR Ivone Leong Classified gene: TTR as Green List (high evidence)
Hyperthyroidism v2.6 TTR Ivone Leong Added comment: Comment on list classification: Based on expert review by David Halsall (Cambridge University Hospitals Trust), there is enough evidence to support a gene-disease association for TTR. Therefore this gene has been given Green status.
Hyperthyroidism v2.6 TTR Ivone Leong Gene: ttr has been classified as Green List (High Evidence).
Hyperthyroidism v2.5 TTR Ivone Leong Phenotypes for gene: TTR were changed from # 145680 HYPERTHYROXINEMIA, DYSTRANSTHYRETINEMIC; DTTRH to [Dystransthyretinemic hyperthyroxinemia], 145680; DTTRH
Hyperthyroidism v2.4 TTR Ivone Leong Publications for gene: TTR were set to PMID: 31590893; 26522458
COVID-19 research v0.180 IL6 Sarah Leigh Classified gene: IL6 as Amber List (moderate evidence)
COVID-19 research v0.180 IL6 Sarah Leigh Gene: il6 has been classified as Amber List (Moderate Evidence).
COVID-19 research v0.179 IL6 Sarah Leigh changed review comment from: Strong association was observed between an IL6promoter polymorphism (G-174C) and susceptibility to KS in HIV-infected men (P?=?.0035). Homozygotes for IL6 allele G, associated with increased IL6 production, were overrepresented among patients with KS (P?=?.0046), whereas allele C homozygotes were underrepresented (P?=?.0062)(PMID 11001912).; to: Strong association was observed between an IL6 promoter polymorphism (G-174C) and susceptibility to Kaposi Sarcoma (KS) in HIV-infected men (P?=?.0035). Homozygotes for IL6 allele G, associated with increased IL6 production, were over represented among patients with KS (P?=?.0046), whereas allele C homozygotes were under represented (P?=?.0062)(PMID 11001912).
COVID-19 research v0.179 ERCC4 Catherine Snow commented on gene: ERCC4
COVID-19 research v0.179 ABO Catherine Snow Phenotypes for gene: ABO were changed from to Virus susceptibility
COVID-19 research v0.178 ABO Catherine Snow Classified gene: ABO as Amber List (moderate evidence)
COVID-19 research v0.178 ABO Catherine Snow Added comment: Comment on list classification: Identified by expert review. Two preprints and publication relating to ABO and Sars-COV. https://doi.org/10.1101/2020.04.08.20058073 authors found that COVID-19 positive vs negative test results were increased in blood groups A and decreased in blood groups O, consistent with previous results from Wuhan and Shenzhen (https://doi.org/10.1101/2020.03.11.20031096)
COVID-19 research v0.178 ABO Catherine Snow Gene: abo has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.35 ADAM22 Rebecca Foulger Classified gene: ADAM22 as Amber List (moderate evidence)
Intellectual disability v3.35 ADAM22 Rebecca Foulger Added comment: Comment on list classification: Set rating as Amber: 2 unrelated families with ID as part of the phenotype (PMID:27066583 and 30237576).
Intellectual disability v3.35 ADAM22 Rebecca Foulger Gene: adam22 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.34 ADAM22 Rebecca Foulger commented on gene: ADAM22: PMID:27066583. Muona et al., 2016 report a Finnish proband-parent-trio with intractable seizures and ID. Compound het variants c.1202G>A, p.Cys401Tyr and c.2396delG, p.Ser799IlefsTer96 were found in ADAM22. Functional assays showed that mutant proteins failed to form the LGI1-ADAM22 ligand-receptor complex. The variants are unlikely to be full LOF.
Intellectual disability v3.34 ADAM22 Rebecca Foulger commented on gene: ADAM22: PMID:30237576 (Maddirevula et al., 2019) searched their database of clinical exomes for homozygous variants and report an 18 year old male with Arg860* variant and recurrent seizures (Supplementary Table). His development was normal until 5 months when he had a slower gain of milestones. He has ID with severely delayed speech. Family history revealed ID and epilepsy in his old brother and in wider family.
Intellectual disability v3.34 ADAM22 Rebecca Foulger gene: ADAM22 was added
gene: ADAM22 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: ADAM22 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ADAM22 were set to 27066583; 30237576
Added comment: Added ADAM22 to ID panel based on literature curation for Epilepsy phenotype. Patients in PMID:27066583 (Finnish trio with compound het ADAM22 variants in the proband) and PMID:30237576 (18 year old male with Arg860* variant) both report ID alongside epilepsy.
Sources: Literature
Early onset or syndromic epilepsy v2.47 ADAM22 Rebecca Foulger changed review comment from: Comment on list classification: 2 Families with prominent seizure phenotype and biallelic ADAM22 variants reported (PMIDs:30237576, 27066583). Plus mouse model of seizures. Not yet associated with a disorder in Gene2Phenotype. Amber is appropriate rating awaiting further cases.; to: Comment on list classification: Added to panel and rated Amber by Zornitza Stark. 2 families with prominent seizure phenotype and biallelic ADAM22 variants reported (PMIDs:30237576, 27066583). Plus mouse model of seizures. Not yet associated with a disorder in Gene2Phenotype. Amber is appropriate rating awaiting further cases.
Early onset or syndromic epilepsy v2.47 ADAM22 Rebecca Foulger Classified gene: ADAM22 as Amber List (moderate evidence)
Early onset or syndromic epilepsy v2.47 ADAM22 Rebecca Foulger Added comment: Comment on list classification: 2 Families with prominent seizure phenotype and biallelic ADAM22 variants reported (PMIDs:30237576, 27066583). Plus mouse model of seizures. Not yet associated with a disorder in Gene2Phenotype. Amber is appropriate rating awaiting further cases.
Early onset or syndromic epilepsy v2.47 ADAM22 Rebecca Foulger Gene: adam22 has been classified as Amber List (Moderate Evidence).
Early onset or syndromic epilepsy v2.46 ADAM22 Rebecca Foulger Publications for gene: ADAM22 were set to 27066583; 30237576
Early onset or syndromic epilepsy v2.45 ADAM22 Rebecca Foulger commented on gene: ADAM22: Mouse model: Adam22-/- mice develop lethal seizures during the first postnatal weeks (e.g. PMID:15876356).
Early onset or syndromic epilepsy v2.45 ADAM22 Rebecca Foulger Phenotypes for gene: ADAM22 were changed from Epileptic encephalopathy, early infantile, 61, 617933 to ?Epileptic encephalopathy, early infantile, 61, 617933
Early onset or syndromic epilepsy v2.44 ADAM22 Rebecca Foulger commented on gene: ADAM22: PMID:30237576 (Maddirevula et al., 2019) searched their database of clinical exomes for homozygous variants and report an 18 year old male with an Arg860* variant in ADAM22. Seizures started age 5 months with a focal seizure, and continued with generalized tonic clonic seizures and status epilepticus (Supplementary Table). His development was normal until 5 months when he had a slower gain of milestones. He has ID with severely delayed speech. Family history revealed ID and epilepsy in his old brother and in wider family.
Early onset or syndromic epilepsy v2.44 ADAM22 Rebecca Foulger commented on gene: ADAM22
Early onset or syndromic epilepsy v2.44 ADAM22 Rebecca Foulger Phenotypes for gene: ADAM22 were changed from Epileptic encephalopathy, early infantile, 61, MIM# 617933 to Epileptic encephalopathy, early infantile, 61, 617933
COVID-19 research v0.177 IFNG Sarah Leigh Phenotypes for gene: IFNG were changed from to {AIDS, rapid progression to} 609423
Fetal anomalies v1.33 FGF20 Rebecca Foulger Classified gene: FGF20 as Red List (low evidence)
Fetal anomalies v1.33 FGF20 Rebecca Foulger Added comment: Comment on list classification: Not yet associated with a disorder in Gene2Phenotype. One consanguineous family plus functional studies in mice showing a role in kidney development. Therefore kept rating as Red awaiting further evidence.
Fetal anomalies v1.33 FGF20 Rebecca Foulger Gene: fgf20 has been classified as Red List (Low Evidence).
Fetal anomalies v1.32 FGF20 Rebecca Foulger gene: FGF20 was added
gene: FGF20 was added to Fetal anomalies. Sources: Literature
Mode of inheritance for gene: FGF20 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: FGF20 were set to 22698282; 23112089
Phenotypes for gene: FGF20 were set to ?Renal hypodysplasia/aplasia 2, 615721
Added comment: Added to Fetal panel based on literature search. PMID:22698282. Barak et al., 2012 identify a homozygous frameshift truncating variant (c.337delG) in FGF20, which segregated with the disorder in a consanguineous familly. Pregnancies showed anhydramnios and the fetuses had bilateral renal agenesis. All pregnancies were terminated. Mouse model shows loss of Fgf20 resulted in kidney agenesis. Additional papers report functional experiments (in mice) that confirm role of FGF20 in kidney development (e.g. PMID:23112089).
Sources: Literature
CAKUT v1.83 FGF20 Rebecca Foulger Classified gene: FGF20 as Amber List (moderate evidence)
CAKUT v1.83 FGF20 Rebecca Foulger Added comment: Comment on list classification: Added to panel and rated Amber by Zornitza. One consanguineous family plus functional data from mice studies. Therefore updated rating to Amber.
CAKUT v1.83 FGF20 Rebecca Foulger Gene: fgf20 has been classified as Amber List (Moderate Evidence).
CAKUT v1.82 FGF20 Rebecca Foulger Publications for gene: FGF20 were set to 22698282
CAKUT v1.81 FGF20 Rebecca Foulger commented on gene: FGF20: Functional experiments (in mice) confirm role of FGF20 in kidney development (e.g. PMID:23112089).
CAKUT v1.81 FGF20 Rebecca Foulger Phenotypes for gene: FGF20 were changed from Renal hypodysplasia/aplasia 2, MIM#615721 to ?Renal hypodysplasia/aplasia 2, 615721
CAKUT v1.80 FGF20 Rebecca Foulger changed review comment from: PMID:22698282. Barak et al., 2012 identify a homozygous frameshift truncating variant (c.337delG) in FGF20, which segregated with the disorder in a consanguineous familly. Pregnancies showed anhydramnios and the fetuses had bilateral renal agenesis. All pregnancies were terminated. Mouse model shows loss of Fgf20 resulted in kidney agenesis.; to: PMID:22698282. Barak et al., 2012 identify a consanguineous family where multiple pregnancies showed anhydramnios and the fetuses had bilateral renal agenesis. DNA analysis from the initial fetus identified homozygous variants in four genes expressed during early kidney development. One of these mutations was a single base-pair deletion in exon 2 of FGF20 which segregated with the disorder within the family. All pregnancies were terminated. A mouse model shows loss of Fgf20 resulted in kidney agenesis.
COVID-19 research v0.176 TNF Sarah Leigh reviewed gene: TNF: Rating: RED; Mode of pathogenicity: ; Publications: 12915457; Phenotypes: ; Mode of inheritance:
COVID-19 research v0.176 TLR2 Sarah Leigh reviewed gene: TLR2: Rating: RED; Mode of pathogenicity: ; Publications: 17085599; Phenotypes: ; Mode of inheritance:
COVID-19 research v0.176 SERPINA1 Sarah Leigh reviewed gene: SERPINA1: Rating: RED; Mode of pathogenicity: ; Publications: 11527807; Phenotypes: ; Mode of inheritance:
COVID-19 research v0.176 SCN5A Sarah Leigh reviewed gene: SCN5A: Rating: RED; Mode of pathogenicity: ; Publications: 25368329; Phenotypes: ; Mode of inheritance:
COVID-19 research v0.176 RB1 Sarah Leigh reviewed gene: RB1: Rating: RED; Mode of pathogenicity: ; Publications: 2968522, 18467589; Phenotypes: ; Mode of inheritance:
COVID-19 research v0.176 PDCD1 Sarah Leigh reviewed gene: PDCD1: Rating: RED; Mode of pathogenicity: ; Publications: 16921384; Phenotypes: ; Mode of inheritance:
COVID-19 research v0.176 NUP214 Sarah Leigh reviewed gene: NUP214: Rating: RED; Mode of pathogenicity: ; Publications: 31178128; Phenotypes: {Encephalopathy, acute, infection-induced, susceptibility to, 9} 618426; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.176 MET Sarah Leigh reviewed gene: MET: Rating: RED; Mode of pathogenicity: ; Publications: 9927037; Phenotypes: Hepatocellular carcinoma, childhood type, somatic 114550; Mode of inheritance: Unknown
COVID-19 research v0.176 LDLR Sarah Leigh reviewed gene: LDLR: Rating: GREEN; Mode of pathogenicity: ; Publications: 10535997, 32268133, 31386864, 31358055; Phenotypes: Hypercholesterolemia, familial, 1 143890, LDL cholesterol level QTL2 143890; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
COVID-19 research v0.176 KRT18 Sarah Leigh reviewed gene: KRT18: Rating: RED; Mode of pathogenicity: ; Publications: 8770877; Phenotypes: {Cirrhosis, noncryptogenic, susceptibility to} 215600, Cirrhosis, cryptogenic 215600; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.176 IRGM Sarah Leigh reviewed gene: IRGM: Rating: RED; Mode of pathogenicity: ; Publications: 11457893; Phenotypes: murine cytomegalovirus infection; Mode of inheritance:
COVID-19 research v0.176 IL6 Sarah Leigh reviewed gene: IL6: Rating: GREEN; Mode of pathogenicity: ; Publications: 11001912; Phenotypes: {Kaposi sarcoma, susceptibility to} 148000; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
COVID-19 research v0.176 IL4R Sarah Leigh reviewed gene: IL4R: Rating: RED; Mode of pathogenicity: ; Publications: 16189667; Phenotypes: {AIDS, slow progression to} 609423; Mode of inheritance:
COVID-19 research v0.176 IFNG Sarah Leigh reviewed gene: IFNG: Rating: AMBER; Mode of pathogenicity: ; Publications: 12854077; Phenotypes: AIDS, rapid progression to} 609423; Mode of inheritance: Unknown
COVID-19 research v0.176 IFITM3 Sarah Leigh reviewed gene: IFITM3: Rating: GREEN; Mode of pathogenicity: ; Publications: 22446628, 18505827, 32348495; Phenotypes: {Influenza, severe, susceptibility to} 614680; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.176 ICAM1 Sarah Leigh reviewed gene: ICAM1: Rating: RED; Mode of pathogenicity: ; Publications: 2538243, 12853962; Phenotypes: ; Mode of inheritance:
COVID-19 research v0.176 HTR2A Sarah Leigh reviewed gene: HTR2A: Rating: RED; Mode of pathogenicity: ; Publications: 15550673; Phenotypes: ; Mode of inheritance:
COVID-19 research v0.176 HLA-DQB1 Sarah Leigh reviewed gene: HLA-DQB1: Rating: AMBER; Mode of pathogenicity: ; Publications: 23710940, 10609818, 12473762; Phenotypes: ; Mode of inheritance:
COVID-19 research v0.176 HLA-C Sarah Leigh reviewed gene: HLA-C: Rating: RED; Mode of pathogenicity: ; Publications: 19935663, 21051598; Phenotypes: {HIV-1 viremia, susceptibility to} 609423; Mode of inheritance: Unknown
COVID-19 research v0.176 HFE Sarah Leigh reviewed gene: HFE: Rating: RED; Mode of pathogenicity: ; Publications: 16043695; Phenotypes: Hemochromatosis 235200; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.176 HBB Sarah Leigh reviewed gene: HBB: Rating: RED; Mode of pathogenicity: ; Publications: 8168595, 2599880, 8602627; Phenotypes: ; Mode of inheritance: Unknown
COVID-19 research v0.176 DMD Sarah Leigh reviewed gene: DMD: Rating: RED; Mode of pathogenicity: ; Publications: 10753926, 12118246; Phenotypes: ; Mode of inheritance: X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)
COVID-19 research v0.176 CYP2B6 Sarah Leigh reviewed gene: CYP2B6: Rating: RED; Mode of pathogenicity: ; Publications: 15622315, 20860463, 15194512, 23418033; Phenotypes: {Efavirenz central nervous system toxicity, susceptibility to} 614546, Efavirenz, poor metabolism of 614546; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.176 CX3CR1 Sarah Leigh reviewed gene: CX3CR1: Rating: AMBER; Mode of pathogenicity: ; Publications: 14607932, 10731151; Phenotypes: {Rapid progression to AIDS from HIV1 infection} 609423; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.176 CR1 Sarah Leigh reviewed gene: CR1: Rating: RED; Mode of pathogenicity: ; Publications: 16517720; Phenotypes: acute myocarditis and pericardial fibrosis due to coxsackievirus B3; Mode of inheritance: Unknown
COVID-19 research v0.176 CPT2 Sarah Leigh reviewed gene: CPT2: Rating: AMBER; Mode of pathogenicity: ; Publications: 15811315, 18306170, 20934285, 21697855; Phenotypes: {Encephalopathy, acute, infection-induced, 4, susceptibility to} 614212; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.176 CD209 Sarah Leigh reviewed gene: CD209: Rating: RED; Mode of pathogenicity: ; Publications: 15564514, 15838506, 16379498; Phenotypes: {Dengue fever, protection against} 614371, {HIV type 1, susceptibility to} 609423, {Mycobacterium tuberculosis, susceptibility to} 607948; Mode of inheritance: Unknown
COVID-19 research v0.176 CCR5 Sarah Leigh reviewed gene: CCR5: Rating: RED; Mode of pathogenicity: ; Publications: 16418398, 16418398, 9132277; Phenotypes: ; Mode of inheritance: Unknown
COVID-19 research v0.176 CCND1 Sarah Leigh reviewed gene: CCND1: Rating: RED; Mode of pathogenicity: ; Publications: ; Phenotypes: {Colorectal cancer, susceptibility to} 114500, {von Hippel-Lindau syndrome, modifier of} 193300; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
COVID-19 research v0.176 CCL3L1 Sarah Leigh reviewed gene: CCL3L1: Rating: RED; Mode of pathogenicity: ; Publications: 15637236, 15637236, 19812560, 19812561, 19812562; Phenotypes: {HIV/AIDS, susceptibility to} 609423; Mode of inheritance: Unknown
CAKUT v1.80 FGF20 Rebecca Foulger commented on gene: FGF20
CAKUT v1.80 FAM58A Rebecca Foulger Classified gene: FAM58A as Green List (high evidence)
CAKUT v1.80 FAM58A Rebecca Foulger Added comment: Comment on list classification: FAM58A added to panel and rated Green by Zornitza Stark. Updated rating from Grey to Green following literature review: sufficient cases to support gene:disease association, and renal phenotypes are common.
CAKUT v1.80 FAM58A Rebecca Foulger Gene: fam58a has been classified as Green List (High Evidence).
CAKUT v1.79 FAM58A Rebecca Foulger Phenotypes for gene: FAM58A were changed from STAR syndrome, MIM# 300707 to STAR syndrome, 300707; Syndactyly, Telecanthus, Anogenital malformations and Renal malformations
CAKUT v1.78 FAM58A Rebecca Foulger Added comment: Comment on mode of inheritance: Set MOI to XLD to match literature (PMID:28225384, PMID:18297069).
CAKUT v1.78 FAM58A Rebecca Foulger Mode of inheritance for gene: FAM58A was changed from X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)
CAKUT v1.77 FAM58A Rebecca Foulger Mode of inheritance for gene: FAM58A was changed from Other to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)
CAKUT v1.76 FAM58A Rebecca Foulger commented on gene: FAM58A: PMID:28225384 (Lefroy et al., 2017) report a 19 year old woman with STAR syndrome; phenotypes include a small left kidney and impaired renal function. The patient had a Xq28 deletion which included the whole FAM58A gene. The mother was mosaic for the deletion, and had a milder phenotype with normal renal ultrasound and renal function.
CAKUT v1.76 FAM58A Rebecca Foulger commented on gene: FAM58A
Respiratory ciliopathies including non-CF bronchiectasis v1.7 GAS2L2 Eleanor Williams Classified gene: GAS2L2 as Green List (high evidence)
Respiratory ciliopathies including non-CF bronchiectasis v1.7 GAS2L2 Eleanor Williams Added comment: Comment on list classification: Upgrading from amber to green, based on Expert review on the Primary ciliary disorders panel (https://panelapp.genomicsengland.co.uk/panels/178/gene/GAS2L2/). 2 cases plus animal model.
Respiratory ciliopathies including non-CF bronchiectasis v1.7 GAS2L2 Eleanor Williams Gene: gas2l2 has been classified as Green List (High Evidence).
Primary ciliary disorders v1.24 GAS2L2 Eleanor Williams Classified gene: GAS2L2 as Green List (high evidence)
Primary ciliary disorders v1.24 GAS2L2 Eleanor Williams Added comment: Comment on list classification: Promoting to Green based on expert review. Gene has been updated with Ensembl gene identifiers.
Primary ciliary disorders v1.24 GAS2L2 Eleanor Williams Gene: gas2l2 has been classified as Green List (High Evidence).
Osteogenesis imperfecta v2.3 TAPT1 Zornitza Stark reviewed gene: TAPT1: Rating: AMBER; Mode of pathogenicity: None; Publications: 26365339; Phenotypes: Osteochondrodysplasia, complex lethal, Symoens-Barnes-Gistelinck type (MIM#616897); Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.175 IFITM3 Ivone Leong Mode of inheritance for gene: IFITM3 was changed from BIALLELIC, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.175 IFITM3 Ivone Leong Mode of inheritance for gene: IFITM3 was changed from to BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.174 IFITM3 Ivone Leong Phenotypes for gene: IFITM3 were changed from to {Influenza, severe, susceptibility to}, 614680
COVID-19 research v0.173 IFITM3 Ivone Leong Classified gene: IFITM3 as Green List (high evidence)
COVID-19 research v0.173 IFITM3 Ivone Leong Added comment: Comment on list classification: PMID: 32348495 reports that individuals who are homozygous for the C allele of rs12252 SNP in IFITM3 is associated with more severe disease in older patients. This SNP is common in Asian populations (MAF reported on dbSNP for East Asians: 0.57; Europeans: 0.0546). This study was condicted in China with 80 patients who were confirmed to be positive for COVID-19.

PMID: 23361009 found that homozygous C allele of rs12252 is in 69% of Chinese patients who were infected with severe pandemic influenza A H1N1/09 virus infection compared with 25% who had mild infection. The homozygous C allele for rs12252 is associated with a 6-fold greater risk for severe infection than CT and TT genotypes.

Based on these studies there is enough evidence to promote this gene to Green status.
COVID-19 research v0.173 IFITM3 Ivone Leong Gene: ifitm3 has been classified as Green List (High Evidence).
COVID-19 research v0.172 IFITM3 Ivone Leong Publications for gene: IFITM3 were set to
Pain syndromes v1.9 FLVCR1 Tomislav Kokotovic gene: FLVCR1 was added
gene: FLVCR1 was added to Pain syndromes. Sources: Literature
Mode of inheritance for gene: FLVCR1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: FLVCR1 were set to 27923065
Phenotypes for gene: FLVCR1 were set to insensitivity to pain; neurodevelopmental delay; joint hypermobility; scoliosis; dysautonomia
Penetrance for gene: FLVCR1 were set to unknown
Review for gene: FLVCR1 was set to AMBER
Added comment: Sources: Literature
Intellectual disability v3.33 VPS51 Zornitza Stark gene: VPS51 was added
gene: VPS51 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: VPS51 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: VPS51 were set to 30624672; 31207318
Phenotypes for gene: VPS51 were set to Pontocerebellar hypoplasia, type 13, MIM# 618606
Review for gene: VPS51 was set to AMBER
Added comment: Two families reported with bi-allelic variants in this gene and global developmental delay, impaired intellectual development with absent speech, microcephaly, and progressive atrophy of the cerebellar vermis and brainstem. Additional features, including seizures and visual impairment, are variable.
Sources: Literature
Laterality disorders and isomerism v1.5 MNS1 Zornitza Stark gene: MNS1 was added
gene: MNS1 was added to Laterality disorders and isomerism. Sources: Literature
Mode of inheritance for gene: MNS1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MNS1 were set to 31534215; 30148830
Phenotypes for gene: MNS1 were set to Heterotaxy; male infertility
Review for gene: MNS1 was set to GREEN
gene: MNS1 was marked as current diagnostic
Added comment: Eight families reported altogether. However, four are Amish and share same homozygous founder variant, and some of the other reported families are consanguineous and share another founder variant. A reported female with a third variant, also had a homozygous variant in DNAH5 with a blended phenotype postulated.
Sources: Literature
Differences in sex development v2.4 DHX37 Zornitza Stark gene: DHX37 was added
gene: DHX37 was added to Disorders of sex development. Sources: Literature
Mode of inheritance for gene: DHX37 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: DHX37 were set to 31337883; 31745530
Phenotypes for gene: DHX37 were set to 46,XY gonadal dysgenesis; testicular regression syndrome (TRS)
Review for gene: DHX37 was set to GREEN
gene: DHX37 was marked as current diagnostic
Added comment: Seventeen individuals reported in two studies.
Sources: Literature
Cholestasis v1.3 GALM Zornitza Stark gene: GALM was added
gene: GALM was added to Cholestasis. Sources: Literature
Mode of inheritance for gene: GALM was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: GALM were set to 30451973; 30910422
Phenotypes for gene: GALM were set to type IV galactosaemia
Review for gene: GALM was set to GREEN
Added comment: Homozygous and compound heterozygous variants (missense, nonsense and frameshift) found in 8 Japanese patients from unrelated families with unexplained galactosaemia. (No variants in GALT, GALK1, and GALE). In vitro expression analysis and enzyme activity assay of the patients’ peripheral blood mononuclear cells showed total lack of or compromised expression of GALM protein. One homozygote for one of these variants p.(Gly142Arg) in gnomAD (African population). (Wada, Y. et al 2019; PMID: 30451973)

Note only two individuals were reported as having transient cholestasis.
Sources: Literature
Adult solid tumours cancer susceptibility v2.3 DGCR8 Zornitza Stark gene: DGCR8 was added
gene: DGCR8 was added to Adult solid tumours cancer susceptibility. Sources: Literature
Mode of inheritance for gene: DGCR8 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: DGCR8 were set to 31805011
Phenotypes for gene: DGCR8 were set to Early-onset multinodular goiter and schwannomatosis
Review for gene: DGCR8 was set to RED
Added comment: A germline missense variant segregates in one family with autosomal dominant Mendelian tumour susceptibility syndrome: familial multinodular goitre (MNG) with schwannomatosis. The missense is also a recurrent somatic missense variant in Wilms tumour.
Sources: Literature
Monogenic hearing loss v2.8 FOXF2 Zornitza Stark gene: FOXF2 was added
gene: FOXF2 was added to Hearing loss. Sources: Literature
Mode of inheritance for gene: FOXF2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: FOXF2 were set to 30561639; 22022403
Phenotypes for gene: FOXF2 were set to profound sensorineural hearing loss (SNHL); cochlea malformations; incomplete partition type I anomaly of the cochlea
Review for gene: FOXF2 was set to AMBER
Added comment: Single family: variant has functional data to demonstrate effect on protein, plus mouse model supports gene-disease association.
Sources: Literature
Cholestasis v1.3 WDR83OS Zornitza Stark gene: WDR83OS was added
gene: WDR83OS was added to Cholestasis. Sources: Literature
Mode of inheritance for gene: WDR83OS was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: WDR83OS were set to 30250217
Phenotypes for gene: WDR83OS were set to Cholestasis
Review for gene: WDR83OS was set to RED
Added comment: One consanguineous family with 3 affected individuals found to carry a homozygous splice site variant in WDR83OS. The variant results in an aberrant truncated RNA transcript as demonstrated by RT-PCR.
Sources: Literature
Cholestasis v1.3 LSR Zornitza Stark gene: LSR was added
gene: LSR was added to Cholestasis. Sources: Literature
Mode of inheritance for gene: LSR was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: LSR were set to 32303357; 30250217
Phenotypes for gene: LSR were set to transient neonatal cholestasis; intellectual disability; short stature
Review for gene: LSR was set to AMBER
Added comment: Two families reported.
Sources: Literature
Cholestasis v1.3 USP53 Zornitza Stark reviewed gene: USP53: Rating: GREEN; Mode of pathogenicity: None; Publications: 30250217, 32124521; Phenotypes: Cholestasis, deafness; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
COVID-19 research v0.171 SEC61A1 Sophie Hambleton reviewed gene: SEC61A1: Rating: GREEN; Mode of pathogenicity: None; Publications: 28782633, 32325141; Phenotypes: Hypogammaglobulinaemia, recurrent infections, plasma cell deficiency, severe congenital neutropenia, tubulointerstitial and Glomerulocystic Kidney Disease with Anemia; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
COVID-19 research v0.171 RNU4ATAC Sophie Hambleton reviewed gene: RNU4ATAC: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.171 RFWD3 Sophie Hambleton reviewed gene: RFWD3: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.171 RELA Sophie Hambleton reviewed gene: RELA: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: chronic mucocutaneous ulceration, autoimmune lymphoporliferative syndrome; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
COVID-19 research v0.171 REL Sophie Hambleton reviewed gene: REL: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: combined immunodeficiency; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.171 RANBP2 Sophie Hambleton reviewed gene: RANBP2: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: necrotizing encephalopathy; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
COVID-19 research v0.171 PSMG2 Sophie Hambleton reviewed gene: PSMG2: Rating: GREEN; Mode of pathogenicity: None; Publications: 30664889; Phenotypes: CANDLE syndrome; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.171 RAD51C Sophie Hambleton reviewed gene: RAD51C: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.171 RAD51 Sophie Hambleton reviewed gene: RAD51: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.171 POLR3F Sophie Hambleton reviewed gene: POLR3F: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.171 POLR3C Sophie Hambleton reviewed gene: POLR3C: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.171 POLR3A Sophie Hambleton reviewed gene: POLR3A: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.171 POLD2 Sophie Hambleton reviewed gene: POLD2: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: combined immunodeficiency, neurodevelopmental delay; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.171 POLD1 Sophie Hambleton changed review comment from: IUIS gene. Biallelic missense variant p.R1060C, that impairs association between POLD1 and POLD2, was associated with combined immunodeficiency in 3 affected members of one kindred. Allelic AD disorders cause alternative phenotypes; to: IUIS gene. Biallelic missense variant p.R1060C, that impairs association between POLD1 and POLD2, was associated with combined immunodeficiency in 3 affected members of one kindred. An unrelated case of combined immunodeficiency reported elsewhere (PMID 31449058) had 3 rare missense variants. Allelic AD disorders cause alternative phenotypes
COVID-19 research v0.171 POLD1 Sophie Hambleton reviewed gene: POLD1: Rating: GREEN; Mode of pathogenicity: Other; Publications: ; Phenotypes: combined immunodeficiency, T-cell lymphopenia, recurrent infections, hypogammaglobulinaemia; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.171 PAX1 Sophie Hambleton reviewed gene: PAX1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: severe combined immunodeficiency, thymic aplasia, otofaciocervical syndrome; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.171 PALB2 Sophie Hambleton reviewed gene: PALB2: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.171 OAS1 Sophie Hambleton reviewed gene: OAS1: Rating: ; Mode of pathogenicity: None; Publications: ; Phenotypes: Infantile-Onset Pulmonary Alveolar Proteinosis, Hypogammaglobulinemia.; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
COVID-19 research v0.171 NOS2 Sophie Hambleton reviewed gene: NOS2: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.171 NFE2L2 Sophie Hambleton reviewed gene: NFE2L2: Rating: GREEN; Mode of pathogenicity: Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments; Publications: ; Phenotypes: growth retardation, developmental delay, leukodystrophy, recurrent infections, hypogammaglobulinaemia, hypohomocysteinaemia, increased G-6-P-dehydrogenase activity; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
COVID-19 research v0.171 MAD2L2 Sophie Hambleton reviewed gene: MAD2L2: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.171 IRF9 Sophie Hambleton reviewed gene: IRF9: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.171 IRF4 Sophie Hambleton reviewed gene: IRF4: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: Whipple's disease; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
COVID-19 research v0.171 IL6ST Sophie Hambleton reviewed gene: IL6ST: Rating: GREEN; Mode of pathogenicity: None; Publications: 31914175, 32207811; Phenotypes: recurrent infections, eczema, bronchiectasis, high IgE, eosinophilia, defective B cell memory, impaired acute-phase response, stuve-wiedemann syndrome, craniosynostosis; Mode of inheritance: BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
COVID-19 research v0.171 IL6R Sophie Hambleton reviewed gene: IL6R: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: Impaired humoral immunity, hyper-IgE, recurrent infections, eczema; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.171 IL2RB Sophie Hambleton reviewed gene: IL2RB: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: very early onset inflammatory bowel disease, CMV disease, dermatitis, immune dysregulation; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.171 IL12RB2 Sophie Hambleton changed review comment from: IUIS gene; to: IUIS gene for MSMD, incomplete penetrance
see PMID 30578351
COVID-19 research v0.171 IL23R Sophie Hambleton reviewed gene: IL23R: Rating: ; Mode of pathogenicity: None; Publications: 30578351; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.171 IL18BP Sophie Hambleton reviewed gene: IL18BP: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.171 IL12RB2 Sophie Hambleton reviewed gene: IL12RB2: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.171 IFNAR1 Sophie Hambleton reviewed gene: IFNAR1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: Viral susceptibility, disseminated MMR; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.171 HLA-DRB1 Sophie Hambleton reviewed gene: HLA-DRB1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: Other
Cholestasis v1.3 PPM1F Zornitza Stark gene: PPM1F was added
gene: PPM1F was added to Cholestasis. Sources: Literature
Mode of inheritance for gene: PPM1F was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PPM1F were set to 30250217; 30976738
Phenotypes for gene: PPM1F were set to sclerosing cholangitis; short stature; hypothyroidism; abnormal tongue pigmentation
Review for gene: PPM1F was set to RED
Added comment: One consanguineous family reported.
Sources: Literature
COVID-19 research v0.171 HLA-B Sophie Hambleton reviewed gene: HLA-B: Rating: GREEN; Mode of pathogenicity: Other; Publications: ; Phenotypes: ; Mode of inheritance: None
Cholestasis v1.3 KIF12 Zornitza Stark gene: KIF12 was added
gene: KIF12 was added to Cholestasis. Sources: Literature
Mode of inheritance for gene: KIF12 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: KIF12 were set to 30250217; 30976738
Phenotypes for gene: KIF12 were set to Cholestasis; High Gamma-Glutamyltransferase (GGT)
Review for gene: KIF12 was set to GREEN
gene: KIF12 was marked as current diagnostic
Added comment: Five unrelated consanguineous families, with four different homozygous variants identified, some truncating, others missense.
Sources: Literature
COVID-19 research v0.171 HAVCR2 Sophie Hambleton reviewed gene: HAVCR2: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: Panniculitis, T-cell lymphoma, haemophagocytic lymphohistiocytosis; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.33 LRRC32 Zornitza Stark gene: LRRC32 was added
gene: LRRC32 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: LRRC32 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: LRRC32 were set to 30976112
Phenotypes for gene: LRRC32 were set to Intellectual disability; cleft palate; proliferative retinopathy
Review for gene: LRRC32 was set to AMBER
Added comment: Three individuals from two consanguineous families segregated the same homozygous bi-allelic variant, c.1630C>T; p.(Arg544Ter), shared haplotype indicative of founder effect. Mouse model has cleft palate and neonatal death.
Sources: Literature
COVID-19 research v0.171 FERMT1 Sophie Hambleton reviewed gene: FERMT1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Limb disorders v2.5 IQCE Zornitza Stark edited their review of gene: IQCE: Set current diagnostic: yes
Limb disorders v2.5 IQCE Zornitza Stark reviewed gene: IQCE: Rating: GREEN; Mode of pathogenicity: None; Publications: 31549751, 28488682; Phenotypes: Postaxial polydactyly; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Mitochondrial disorders v2.5 CRAT Zornitza Stark reviewed gene: CRAT: Rating: AMBER; Mode of pathogenicity: None; Publications: 29395073, 31448845; Phenotypes: Neurodegeneration with brain iron accumulation 8, MIM# 617917, Leigh syndrome; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Ataxia and cerebellar anomalies - narrow panel v2.6 THG1L Zornitza Stark gene: THG1L was added
gene: THG1L was added to Ataxia and cerebellar anomalies - narrow panel. Sources: Literature
Mode of inheritance for gene: THG1L was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: THG1L were set to 27307223; 30214071; 31168944
Phenotypes for gene: THG1L were set to Cerebellar ataxia
Review for gene: THG1L was set to GREEN
Added comment: Four Ashkenazi Jewish families reported, with same homozygous variant, p.V55A in affected individuals. Another individual from different ethnicity also reported. A carrier rate of 0.8%, but no THG1L V55A homozygotes, was found in a cohort of 3,232 unrelated Ashkenazi Jewish individuals, and no homozygotes found in Exac or gnomAD.
Sources: Literature
Congenital disorders of glycosylation v2.6 GALNT2 Zornitza Stark gene: GALNT2 was added
gene: GALNT2 was added to Congenital disorders of glycosylation. Sources: Literature
Mode of inheritance for gene: GALNT2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: GALNT2 were set to 32293671
Phenotypes for gene: GALNT2 were set to Congenital disorder of glycosylation
Review for gene: GALNT2 was set to GREEN
gene: GALNT2 was marked as current diagnostic
Added comment: Seven individuals from four families reported with bi-allelic LOF variants and global developmental delay, intellectual disability with language deficit, autistic features, behavioural abnormalities, epilepsy, chronic insomnia, white matter changes on brain MRI, dysmorphic features, decreased stature, and decreased high density lipoprotein cholesterol levels. Rodent (mouse and rat) models of GALNT2-CDG recapitulated much of the human phenotype, including poor growth and neurodevelopmental abnormalities. Suggest adding to ID and epilepsy panels.
Sources: Literature
Severe microcephaly v2.6 C7orf43 Zornitza Stark gene: C7orf43 was added
gene: C7orf43 was added to Severe microcephaly. Sources: Literature
Mode of inheritance for gene: C7orf43 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: C7orf43 were set to 30715179
Phenotypes for gene: C7orf43 were set to Microcephaly 25, primary, autosomal recessive, MIM# 618351
Review for gene: C7orf43 was set to AMBER
Added comment: Single family reported: three affected siblings with homozygous truncating variant. Supportive zebrafish model. HGNC approved name: MAP11.
Sources: Literature
Retinal disorders v2.8 SLC6A6 Zornitza Stark gene: SLC6A6 was added
gene: SLC6A6 was added to Retinal disorders. Sources: Literature
Mode of inheritance for gene: SLC6A6 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SLC6A6 were set to 31345061; 31903486; 29886034
Phenotypes for gene: SLC6A6 were set to Early retinal degeneration; cardiomyopathy
Review for gene: SLC6A6 was set to AMBER
Added comment: Different homozygous missense variants in 2 unrelated consanguineous families with early retinal degeneration, some functional studies. Patients in one of the families also had cardiomyopathy. (PMIDs: 31345061, 31903486) One dilated cardiomyopathy patient with a homozygous deletion at a splice site (PMID: 29886034).
Sources: Literature
Familial non syndromic congenital heart disease v1.51 ADAMTS19 Zornitza Stark gene: ADAMTS19 was added
gene: ADAMTS19 was added to Familial non syndromic congenital heart disease. Sources: Literature
Mode of inheritance for gene: ADAMTS19 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ADAMTS19 were set to 31844321
Phenotypes for gene: ADAMTS19 were set to Non-syndromic heart valve disease
Review for gene: ADAMTS19 was set to AMBER
Added comment: PMID: 31844321; Wünnemann 2020: 4 affected in 2 unrelated consanguineous families with non-syndromic heart valve disease. 1 family with an intragenic (exon 1-8) deletion and 1 nonsense variant. Carriers unaffected. Homozygous knockout mice for Adamts19 show aortic valve dysfunction, recapitulating aspects of the human phenotype
Sources: Literature
Skeletal dysplasia v2.7 POLR1B Zornitza Stark gene: POLR1B was added
gene: POLR1B was added to Skeletal dysplasia. Sources: Literature
Mode of inheritance for gene: POLR1B was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: POLR1B were set to 31649276
Phenotypes for gene: POLR1B were set to Treacher-Collins syndrome type 4
Review for gene: POLR1B was set to GREEN
gene: POLR1B was marked as current diagnostic
Added comment: Five unrelated families and a zebrafish model, variant inherited in two of the families, once from affected parent and once from mosaic parent. Note four of the families had missense variants affecting same residue, p.Arg1003
Sources: Literature
Hereditary neuropathy or pain disorder v1.4 C1orf194 Zornitza Stark gene: C1orf194 was added
gene: C1orf194 was added to Hereditary neuropathy NOT PMP22 copy number. Sources: Literature
Mode of inheritance for gene: C1orf194 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: C1orf194 were set to 31199454
Phenotypes for gene: C1orf194 were set to Charcot-Marie-Tooth disease, intermediate or demyelinating
Review for gene: C1orf194 was set to AMBER
Added comment: Two unrelated families with missense variants, one with intermediate CMT, the other with demyelinating CMT. Different phenotypic manifestations may relate to different mechanism, but this remains to be fully elucidated. Supportive mouse model.
Sources: Literature
Skeletal dysplasia v2.7 UBA2 Zornitza Stark gene: UBA2 was added
gene: UBA2 was added to Skeletal dysplasia. Sources: Literature
Mode of inheritance for gene: UBA2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: UBA2 were set to 31332306; 31587267
Phenotypes for gene: UBA2 were set to Split-Hand/Foot Malformation; Aplasia Cutis Congenita; Ectrodactyly
Review for gene: UBA2 was set to AMBER
Added comment: PMID: 31332306 - a single individual with a de novo PTC and split hand/foot malformation (SHFM). Additional two multigenic CNVs including this gene in individuals with SHFM and ectrodactyly. Authors mention an additional de novo missense but the patient didnt have SHFM, argue low penetrance PMID: 31587267 - a mother and son with aplasia cutis congenita (ACC), with a heterozygous PTC. Son also has ectrodactyly. Authors note an additional de novo missense in a patient with ACC.
Sources: Literature
Optic neuropathy v2.3 MCAT Zornitza Stark gene: MCAT was added
gene: MCAT was added to Optic neuropathy. Sources: Literature
Mode of inheritance for gene: MCAT was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MCAT were set to 31915829
Phenotypes for gene: MCAT were set to progressive autosomal recessive optic neuropathy
Review for gene: MCAT was set to RED
Added comment: Single family reported.
Sources: Literature
Primary immunodeficiency or monogenic inflammatory bowel disease v2.139 CD4 Zornitza Stark changed review comment from: Single individual reported, functional data, emerging gene.; to: Single individual reported, functional data, emerging gene.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.139 CD4 Zornitza Stark reviewed gene: CD4: Rating: AMBER; Mode of pathogenicity: None; Publications: 31781092; Phenotypes: Absence of CD4+ T cells, exuberant, relapsing, treatment-refractory warts; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.139 IFNG Zornitza Stark gene: IFNG was added
gene: IFNG was added to Primary immunodeficiency. Sources: Literature
Mode of inheritance for gene: IFNG was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IFNG were set to 32163377
Phenotypes for gene: IFNG were set to Mendelian susceptibility to mycobacterial disease
Review for gene: IFNG was set to RED
Added comment: Two cousins with MSMD and homozygous intragenic deletion, some functional data.
Sources: Literature
Primary immunodeficiency or monogenic inflammatory bowel disease v2.139 NOS2 Zornitza Stark gene: NOS2 was added
gene: NOS2 was added to Primary immunodeficiency. Sources: Literature
Mode of inheritance for gene: NOS2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: NOS2 were set to 12433515; 31995689
Phenotypes for gene: NOS2 were set to {Malaria, resistance to} 611162; Disseminated CMV disease
Review for gene: NOS2 was set to RED
Added comment: Promoter polymorphisms linked to malarial resistance. Single individual reported with homozygous NOS2 LOF variant and disseminated, progressive CMV disease.
Sources: Literature
Primary immunodeficiency or monogenic inflammatory bowel disease v2.139 ITPKB Zornitza Stark gene: ITPKB was added
gene: ITPKB was added to Primary immunodeficiency. Sources: Literature
Mode of inheritance for gene: ITPKB was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ITPKB were set to 31987846
Phenotypes for gene: ITPKB were set to Severe combined immunodeficiency, absent T cells, present B cells and NK cells
Review for gene: ITPKB was set to RED
Added comment: Single individual with homozygous bi-allelic LoF variant reported.
Sources: Literature
Primary immunodeficiency or monogenic inflammatory bowel disease v2.139 CDC42 Zornitza Stark gene: CDC42 was added
gene: CDC42 was added to Primary immunodeficiency. Sources: Literature
Mode of inheritance for gene: CDC42 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: CDC42 were set to 31601675; 32303876; 32231661
Phenotypes for gene: CDC42 were set to Neonatal-onset cytopaenia with dyshaematopoiesis; autoinflammation; rash; HLH
Review for gene: CDC42 was set to GREEN
Added comment: PMID 31601675: four unrelated individuals with superimposable features, including neonatal-onset cytopenia with dyshematopoiesis, autoinflammation, rash, and HLH. All shared the same de novo CDC42 variant (Chr1:22417990C>T, p.R186C). Another pair of sibs reported in PMID 32303876 with infantile myelofibrosis and myeloproliferation and same variant (parental mosaicism). Yet another individual in PMID 32231661 with different de novo variant, p.Cys81Tyr who in addition developed haematological malignancy and also had syndromic features, including ID. Note other missense variants in this gene cause Takenouchi-Kosaki syndrome, MIM# 616737
Sources: Literature
Primary immunodeficiency or monogenic inflammatory bowel disease v2.139 RIPK1 Zornitza Stark edited their review of gene: RIPK1: Added comment: Please note recent report of mono-allelic variants in two families.; Changed publications: 30026316, 30591564, 31213653, 31827280; Changed phenotypes: Severe immunodeficiency, arthritis, and intestinal inflammation, Immunodeficiency 57, MIM#618108; Changed mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.139 PIK3CG Zornitza Stark gene: PIK3CG was added
gene: PIK3CG was added to Primary immunodeficiency. Sources: Literature
Mode of inheritance for gene: PIK3CG was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PIK3CG were set to 32001535; 31554793
Phenotypes for gene: PIK3CG were set to Immune dysregulation; HLH-like; childhood-onset antibody defects; cytopenias; T lymphocytic pneumonitis and colitis
Review for gene: PIK3CG was set to GREEN
Added comment: Two individuals with complex immunological phenotypes reported and a mouse model.
Sources: Literature
CAKUT v1.76 EXOC3L2 Rebecca Foulger Classified gene: EXOC3L2 as Amber List (moderate evidence)
CAKUT v1.76 EXOC3L2 Rebecca Foulger Gene: exoc3l2 has been classified as Amber List (Moderate Evidence).
CAKUT v1.75 EXOC3L2 Rebecca Foulger Classified gene: EXOC3L2 as No list
CAKUT v1.75 EXOC3L2 Rebecca Foulger Added comment: Comment on list classification: Gene was added to panel and rated Green by Chirag Patel. Updated rating from Grey to Amber. Most reported cases are from fetuses (e.g. PMID: 27894351) and therefore EXOC3L2 is more appropriate on Fetal panel.
CAKUT v1.75 EXOC3L2 Rebecca Foulger Gene: exoc3l2 has been removed from the panel.
CAKUT v1.74 EXOC3L2 Rebecca Foulger commented on gene: EXOC3L2: PMID: 27894351: Shaheen et al., 2016 examined 371 individuals from 265 families with ciliopathy phenotypes. They identified a LOF variant in EXOC3L2 and a lethal phenotype that resembles Meckel–Gruber syndrome (severe posterior fossa malformation with kidney enlargement) in one family.
CAKUT v1.74 EXOC3L2 Rebecca Foulger commented on gene: EXOC3L2: PMID: 28749478: Shamseldin et al., 2018 performed exome sequencing as part of molecular autopsy in a cohort of 44 families with at least one death or lethal fetal malformation. They report one fetus with a biallelic EXOC3L2 variant and a phenotype similar to Meckel-Gruber syndrome.
Fetal anomalies v1.31 EXOC3L2 Rebecca Foulger Classified gene: EXOC3L2 as Green List (high evidence)
Fetal anomalies v1.31 EXOC3L2 Rebecca Foulger Added comment: Comment on list classification: Updated rating from Red to Green: 3 unrelated fetal cases (PMIDs:27894351,28749478,30327448).
Fetal anomalies v1.31 EXOC3L2 Rebecca Foulger Gene: exoc3l2 has been classified as Green List (High Evidence).
Fetal anomalies v1.30 EXOC3L2 Rebecca Foulger changed review comment from: PMID: 27894351: Shaheen et al., 2016 examined 371 individuals from 265 families with ciliopathy phenotypes. They identified a LOF variant in EXOC3L2 and a lethal phenotype that resembles Meckel–Gruber syndrome (severe posterior fossa malformation with kidney enlargement) in one family.; to: PMID: 27894351: Shaheen et al., 2016 examined 371 individuals from 265 families with ciliopathy phenotypes. They identified a LOF variant in EXOC3L2 and a lethal phenotype that resembles Meckel–Gruber syndrome (severe posterior fossa malformation with kidney enlargement) in one family (reviewed briefly in PMID:28749478).
Fetal anomalies v1.30 EXOC3L2 Rebecca Foulger commented on gene: EXOC3L2: PMID: 27894351: Shaheen et al., 2016 examined 371 individuals from 265 families with ciliopathy phenotypes. They identified a LOF variant in EXOC3L2 and a lethal phenotype that resembles Meckel–Gruber syndrome (severe posterior fossa malformation with kidney enlargement) in one family.
Fetal anomalies v1.30 EXOC3L2 Rebecca Foulger Publications for gene: EXOC3L2 were set to 30327448; 28749478
Fetal anomalies v1.29 EXOC3L2 Rebecca Foulger Publications for gene: EXOC3L2 were set to 30327448
Fetal anomalies v1.28 EXOC3L2 Rebecca Foulger commented on gene: EXOC3L2: PMID: 28749478: Shamseldin et al., 2018 performed exome sequencing as part of molecular autopsy in a cohort of 44 families with at least one death or lethal fetal malformation. They report one fetus with a biallelic EXOC3L2 variant and a phenotype similar to Meckel-Gruber syndrome.
Fetal anomalies v1.28 EXOC3L2 Rebecca Foulger gene: EXOC3L2 was added
gene: EXOC3L2 was added to Fetal anomalies. Sources: Literature
Mode of inheritance for gene: EXOC3L2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: EXOC3L2 were set to 30327448
Phenotypes for gene: EXOC3L2 were set to Dandy-Walker malformation
Added comment: Added to panel based on PMID:30327448: Shalata et al., 2019 report 3 fetuses from a family with homozygous variants in EXOC3L2 (missense p.Leu41Gln) and severe forms of Dandy-Walker that were detectable by prenatal ultrasound.
Sources: Literature
CAKUT v1.74 EXOC3L2 Rebecca Foulger commented on gene: EXOC3L2
CAKUT v1.74 EXOC3L2 Rebecca Foulger Publications for gene: EXOC3L2 were set to PMID: 30327448, 28749478, 27894351
CAKUT v1.73 DHCR7 Rebecca Foulger changed review comment from: Comment on list classification: Added to panel and rated Green by Zornitza Stark. Updated rating from Grey to Amber. Renal phenotypes are only seen in approximately 25% of SLOS patients, and renal anomalies are more commonly detected prenatally than postnatally (PMID:23059950) so DHCR7 is more suited to the Fetal anomalies panel.; to: Comment on list classification: Added to panel and rated Green by Zornitza Stark. Updated rating from Grey to Amber. Renal phenotypes are only seen in approximately 25% of SLOS patients, and renal anomalies are more commonly detected prenatally than postnatally (PMID:23059950) so DHCR7 is more appropriate for the Fetal anomalies panel.
CAKUT v1.73 DHCR7 Rebecca Foulger changed review comment from: Comment on list classification: Added to panel and rated Green by Zornitza Stark. Updated rating from Grey to Amber. Renal phenotypes are only seen in approximately 25% of SLOS patients, and renal anomalies are more commonly detected prenatally than postnatally (PMID:23059950).; to: Comment on list classification: Added to panel and rated Green by Zornitza Stark. Updated rating from Grey to Amber. Renal phenotypes are only seen in approximately 25% of SLOS patients, and renal anomalies are more commonly detected prenatally than postnatally (PMID:23059950) so DHCR7 is more suited to the Fetal anomalies panel.
CAKUT v1.73 DHCR7 Rebecca Foulger Classified gene: DHCR7 as Amber List (moderate evidence)
CAKUT v1.73 DHCR7 Rebecca Foulger Gene: dhcr7 has been classified as Amber List (Moderate Evidence).
CAKUT v1.72 DHCR7 Rebecca Foulger Classified gene: DHCR7 as No list
CAKUT v1.72 DHCR7 Rebecca Foulger Added comment: Comment on list classification: Added to panel and rated Green by Zornitza Stark. Updated rating from Grey to Amber. Renal phenotypes are only seen in approximately 25% of SLOS patients, and renal anomalies are more commonly detected prenatally than postnatally (PMID:23059950).
CAKUT v1.72 DHCR7 Rebecca Foulger Gene: dhcr7 has been removed from the panel.
CAKUT v1.71 DHCR7 Rebecca Foulger commented on gene: DHCR7: PMID:9678700. Ryan et al., 1998 reviewed all known UK cases of SLOS. Half had been terminated or died in infancy. 14 (29%) had structural renal abnormalities.
CAKUT v1.71 DHCR7 Rebecca Foulger commented on gene: DHCR7: PMID:23059950. Nowaczyk and Irons, 2012 note that approximately 25% of affected individuals have renal anomalies (most common being renal hypoplasia or agenesis, renal cortical cysts, hydronephrosis and structural anomalies of the collecting system). They also note that renal anomalies are amongst the phenotypes seen more commonly prenatally than postnatally.
CAKUT v1.71 DHCR7 Rebecca Foulger commented on gene: DHCR7: PMID:10069707. Kratz and Kelley, 1999 report on prenatal diagnosis of SLOS. Fetal phenotypes included renal agenesis, renal pyelectasis, hydronephrosis (4 patients)
Fetal anomalies v1.27 DHCR7 Rebecca Foulger commented on gene: DHCR7: PMID:31840946 (Schoner et al., 2020) performed autopsies and DHCR7 gene analyses in 8 fetuses suspected of having SLOS. 5/9 fetuses presented with classic SLOS features including 4 with atrial/atrioventricular septal defects and renal anomalies, and one with additional bilateral renal agenesis and a Dandy-Walker cyst. Two fetuses were mildly affected and two fetuses showed additional holoprosencephaly. DHCR7 variants were confirmed in cases 1-5 and 7.
CAKUT v1.71 DHCR7 Rebecca Foulger Phenotypes for gene: DHCR7 were changed from Smith-Lemli-Opitz syndrome, MIM# 270400 to Smith-Lemli-Opitz syndrome, 270400; renal agenesis
CAKUT v1.70 DHCR7 Rebecca Foulger Publications for gene: DHCR7 were set to 3812577; 10069707; 23059950; 9678700
CAKUT v1.69 DHCR7 Rebecca Foulger commented on gene: DHCR7
Fetal anomalies v1.27 DHCR7 Rebecca Foulger Publications for gene: DHCR7 were set to
Early onset or syndromic epilepsy v2.43 CTU2 Rebecca Foulger Classified gene: CTU2 as Amber List (moderate evidence)
Early onset or syndromic epilepsy v2.43 CTU2 Rebecca Foulger Added comment: Comment on list classification: Added to panel as Amber: Sufficient cases of seizures but 1 patient shows febrile seizures, and phenotype is variable. Plus just one study so far. Therefore Amber is appropriate, awaiting further evidence.
Early onset or syndromic epilepsy v2.43 CTU2 Rebecca Foulger Gene: ctu2 has been classified as Amber List (Moderate Evidence).
Early onset or syndromic epilepsy v2.42 CTU2 Rebecca Foulger gene: CTU2 was added
gene: CTU2 was added to Genetic epilepsy syndromes. Sources: Literature
Mode of inheritance for gene: CTU2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CTU2 were set to 31301155
Phenotypes for gene: CTU2 were set to seizures; DREAM‐PL syndrome; Microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome, 618142
Added comment: Added to panel based on PMID:31301155 (Shaheen et al., 2019) who characterise the phenotype of 5 patients with DREAM-PL syndrome (Dysmorphic facies, renal agenesis, ambiguous genitalia, microcephaly, polydactyly, and lissencephaly) and summarise 4 Founder patients from previous studies (PMID:27480277, PMID:26633546). In total 6/10 patients had seizures including Generalized epilepsy, atypical absence seizures, complex febriles seizures and focal epilepsy.
Sources: Literature
Intellectual disability v3.33 CTU2 Rebecca Foulger Classified gene: CTU2 as Green List (high evidence)
Intellectual disability v3.33 CTU2 Rebecca Foulger Added comment: Comment on list classification: Gene was added to panel and rated Green by Zornitza Stark. Sufficient cases of global DD in PMID:31301155 in patients that survived infancy to support causation. Therefore updated rating from Grey to Green.
Intellectual disability v3.33 CTU2 Rebecca Foulger Gene: ctu2 has been classified as Green List (High Evidence).
Intellectual disability v3.32 CTU2 Rebecca Foulger commented on gene: CTU2
Intellectual disability v3.32 CTU2 Rebecca Foulger Phenotypes for gene: CTU2 were changed from Microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome, MIM#618142 to DREAM‐PL syndrome; Microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome, 618142
CAKUT v1.69 CTU2 Rebecca Foulger Classified gene: CTU2 as Green List (high evidence)
CAKUT v1.69 CTU2 Rebecca Foulger Added comment: Comment on list classification: Added to panel and rated Green by Zornitza Stark. The Saudi cases all share a founder variant (PMIDs:26633546, 27480277) but a more recent study by the same authors (PMID:31301155) identifies a further 4 patients with a renal phenotype as part of DREAM‐PL syndrome, and new homozygous CTU2 variants. Therefore relevant renal phenotype and sufficient unrelated cases to support association.
CAKUT v1.69 CTU2 Rebecca Foulger Gene: ctu2 has been classified as Green List (High Evidence).
CAKUT v1.68 CTU2 Rebecca Foulger Phenotypes for gene: CTU2 were changed from Microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome, MIM#618142 to DREAM‐PL syndrome; Microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome, 618142
CAKUT v1.67 CTU2 Rebecca Foulger commented on gene: CTU2: PMID:31301155 (Shaheen et al., 2019) show that biallelic CTU2 variants cause DREAM-PL syndrome (dysmorphic facies, renal agenesis, ambiguous genitalia, microcephaly, polydactyly, and lissencephaly) in a further 5 patients. 4/5 patients had a renal phenotype. These 5 patients had different variants to the previously described founder variant, including Ala403Cysfs*23, Leu63Pro, p.Ile505Argfs*41.
CAKUT v1.67 CTU2 Rebecca Foulger commented on gene: CTU2: PMID:27480277 (Shaheen et al., 2016) identified 2 male cousins from the United Arab Emirates with the same founder T247T variant. This founder variant has a frequency of 1/769 in Saudi Arabia.
CAKUT v1.67 CTU2 Rebecca Foulger commented on gene: CTU2
CAKUT v1.67 CHRNA3 Rebecca Foulger Classified gene: CHRNA3 as Green List (high evidence)
CAKUT v1.67 CHRNA3 Rebecca Foulger Gene: chrna3 has been classified as Green List (High Evidence).
CAKUT v1.66 CHRNA3 Rebecca Foulger Classified gene: CHRNA3 as No list
CAKUT v1.66 CHRNA3 Rebecca Foulger Added comment: Comment on list classification: Gene was added to panel and rated Green by Zornitza Stark. Sufficient cases (3 unrelated families) from one paper, plus functional studies to support causation and therefore increased rating to Green.
CAKUT v1.66 CHRNA3 Rebecca Foulger Gene: chrna3 has been removed from the panel.
CAKUT v1.65 CHRNA3 Rebecca Foulger commented on gene: CHRNA3
COVID-19 research v0.171 IRF7 Rebecca Foulger Publications for gene: IRF7 were set to 26761402; 9315633; 32086639; 25814066; 32048120; 26621750; 31154625
COVID-19 research v0.170 IRF7 Rebecca Foulger Publications for gene: IRF7 were set to 26761402; 9315633; 32086639; 25814066; 32048120; 26621750
CAKUT v1.65 CHD1L Rebecca Foulger Tag missense tag was added to gene: CHD1L.
CAKUT v1.65 CHD1L Rebecca Foulger Classified gene: CHD1L as Amber List (moderate evidence)
CAKUT v1.65 CHD1L Rebecca Foulger Added comment: Comment on list classification: Updated rating from Red to Amber. Although there are 8 families with CAKUT and CHD1L variants, all variants are missense, and there is limited family data available for the patients in PMID:22146311. Also in PMID:22146311, only 2/3 variants were absent from controls, Patient 2 variant was inherited from an asymptomatic mother, and the variant in Patient 3 is predicted benign.
CAKUT v1.65 CHD1L Rebecca Foulger Gene: chd1l has been classified as Amber List (Moderate Evidence).
CAKUT v1.64 CHD1L Rebecca Foulger commented on gene: CHD1L: PMID:32164334 show CNVs in genes including CHD1L in 6 CAKUT patients. One patient with bilateral renal cortical cysts and renal stones (ID 41) had a duplication of 1q21.1 encompassing CHD1L.
CAKUT v1.64 CHD1L Rebecca Foulger Publications for gene: CHD1L were set to 24429398; 22146311
CAKUT v1.63 CHD1L Rebecca Foulger changed review comment from: PMID:24429398 detected heterozygous variants in CHD1L in 5 families with CAKUT (p.P333R in 1 family, p.E400G in 1 family, p.I517M in 3 Indian families).; to: PMID:24429398 (2014) detected heterozygous variants in CHD1L in 5 families with CAKUT (p.P333R in 1 family, p.E400G in 1 family, p.I517M in 3 Indian families).
CAKUT v1.63 CHD1L Rebecca Foulger commented on gene: CHD1L: PMID:24429398 detected heterozygous variants in CHD1L in 5 families with CAKUT (p.P333R in 1 family, p.E400G in 1 family, p.I517M in 3 Indian families).
CAKUT v1.63 CHD1L Rebecca Foulger commented on gene: CHD1L
Primary immunodeficiency or monogenic inflammatory bowel disease v2.139 LIG1 Rebecca Foulger Classified gene: LIG1 as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.139 LIG1 Rebecca Foulger Added comment: Comment on list classification: Updated rating from Red to Green. Red review pre-dates paper PMID:30395541 which provides 5 patients (3 kindreds) for evidence of association with immunodeficiency. Although severity of phenotype is variable, just sufficient cases for inclusion.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.139 LIG1 Rebecca Foulger Gene: lig1 has been classified as Green List (High Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.138 LIG1 Rebecca Foulger commented on gene: LIG1
Primary immunodeficiency or monogenic inflammatory bowel disease v2.138 NLRP1 Rebecca Foulger commented on gene: NLRP1: PMID:27662089: Zhong et al., 2016 report germline GOF variants in NLRP1 which cause two overlapping skin disorders (MSPC and FKLC), linking NLRP1 to skin inflammatory syndromes.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.138 NLRP1 Rebecca Foulger commented on gene: NLRP1
Primary immunodeficiency or monogenic inflammatory bowel disease v2.138 OAS1 Rebecca Foulger Classified gene: OAS1 as Amber List (moderate evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.138 OAS1 Rebecca Foulger Added comment: Comment on list classification: Updated from Red to Amber, awaiting clinical review.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.138 OAS1 Rebecca Foulger Gene: oas1 has been classified as Amber List (Moderate Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.137 OAS1 Rebecca Foulger commented on gene: OAS1
COVID-19 research v0.169 PAX1 Rebecca Foulger Classified gene: PAX1 as Green List (high evidence)
COVID-19 research v0.169 PAX1 Rebecca Foulger Gene: pax1 has been classified as Green List (High Evidence).
COVID-19 research v0.168 PAX1 Rebecca Foulger gene: PAX1 was added
gene: PAX1 was added to Viral susceptibility. Sources: Other,Literature
Mode of inheritance for gene: PAX1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PAX1 were set to 28657137; 32111619
Phenotypes for gene: PAX1 were set to Otofaciocervical syndrome 2, 615560; Syndromic SCID
Added comment: Added PAX1 to Viral susceptibility panel as Green to match recent addition of PAX1 to Primary immunodeficiency panel (Version 2.137).
Sources: Other, Literature
Primary immunodeficiency or monogenic inflammatory bowel disease v2.137 PAX1 Rebecca Foulger Classified gene: PAX1 as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.137 PAX1 Rebecca Foulger Added comment: Comment on list classification: Added to panel and rated Green by Zornitza Stark. Updated rating from Grey to Green based on 2 papers (PMID:28657137 and PMID:32111619): 8 individuals from 4 unrelated families with SCID.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.137 PAX1 Rebecca Foulger Gene: pax1 has been classified as Green List (High Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.136 PAX1 Rebecca Foulger Phenotypes for gene: PAX1 were changed from Syndromic SCID; dysmorphism; ear abnormalities; otofaciocervical syndrome to Otofaciocervical syndrome 2, 615560; Syndromic SCID; dysmorphism; ear abnormalities; otofaciocervical syndrome
Primary immunodeficiency or monogenic inflammatory bowel disease v2.135 PAX1 Rebecca Foulger Publications for gene: PAX1 were set to 32111619
Primary immunodeficiency or monogenic inflammatory bowel disease v2.134 PAX1 Rebecca Foulger commented on gene: PAX1: PMID:28657137. Paganini et al., 2017 report a North African family with AR Otofaciocervical syndrome (OFCS). Two of the children died from severe combined immunodeficiency (SCID) and had nonsense homozygous variants in PAX1. Functional studies were not performed.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.134 PAX1 Rebecca Foulger commented on gene: PAX1
Primary immunodeficiency or monogenic inflammatory bowel disease v2.134 POLE Rebecca Foulger changed review comment from: PMID:23230001: 1 large consanguineous family with FILS syndrome (including immunodeficiency) and homozygous single bp substitution in POLE1.; to: PMID:23230001: 1 large consanguineous family with FILS syndrome (all but 2 patients suffered from immunodeficiency) and homozygous single bp substitution in POLE1.
Fetal anomalies v1.26 POLE Rebecca Foulger changed review comment from: Comment on list classification: Updated rating from Amber to Green: Multiple cases of IUGR from 2 papers (PMID:25948378 and PMID:30503519). Phenotype relevant to panel, and sufficient evidence to support causation.; to: Comment on list classification: Originally added to panel as Amber based on PMID:30503519. Updated rating from Amber to Green with curation of additional paper PMID:25948378 who report a separate individual with IUGR. Phenotype relevant to panel, and sufficient evidence to support causation.
Fetal anomalies v1.26 POLE Rebecca Foulger Deleted their comment
Fetal anomalies v1.26 POLE Rebecca Foulger Classified gene: POLE as Green List (high evidence)
Fetal anomalies v1.26 POLE Rebecca Foulger Gene: pole has been classified as Green List (High Evidence).
Fetal anomalies v1.25 POLE Rebecca Foulger Classified gene: POLE as Green List (high evidence)
Fetal anomalies v1.25 POLE Rebecca Foulger Gene: pole has been classified as Green List (High Evidence).
Fetal anomalies v1.24 POLE Rebecca Foulger Classified gene: POLE as Amber List (moderate evidence)
Fetal anomalies v1.24 POLE Rebecca Foulger Added comment: Comment on list classification: Updated rating from Amber to Green: Multiple cases of IUGR from 2 papers (PMID:25948378 and PMID:30503519). Phenotype relevant to panel, and sufficient evidence to support causation.
Fetal anomalies v1.24 POLE Rebecca Foulger Gene: pole has been classified as Amber List (Moderate Evidence).
Fetal anomalies v1.23 POLE Rebecca Foulger Publications for gene: POLE were set to 23230001
Fetal anomalies v1.22 POLE Rebecca Foulger commented on gene: POLE: PMID:25948378 (Thiffault et al., 2015) report a girl homozygous for a splice variant in POLE1 (c.4444 + 3A > G). Fetal anomalies on the ultrasound included intrauterine growth restriction, short long bones, suspected skull abnormalities nad oligohydamnios.
Fetal anomalies v1.22 POLE Rebecca Foulger Phenotypes for gene: POLE were changed from IUGR; severe growth failure of prenatal onset to IUGR; severe growth failure of prenatal onset; FILS syndrome, 615139; facial dysmorphism, immunodeficiency, livedo, and short stature (FILS)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.134 POLE Rebecca Foulger Classified gene: POLE as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.134 POLE Rebecca Foulger Added comment: Comment on list classification: Updated rating from Amber to Green following review by Zornitza Stark: >3 cases from 3 separate papers of individuals with biallelic POLE variants and a phenotype that includes immunodeficiency.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.134 POLE Rebecca Foulger Gene: pole has been classified as Green List (High Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.133 POLE Rebecca Foulger commented on gene: POLE: PMID:23230001: 1 large consanguineous family with FILS syndrome (including immunodeficiency) and homozygous single bp substitution in POLE1.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.133 POLE Rebecca Foulger commented on gene: POLE: PMID:25948378 (Thiffault et al., 2015) report a girl with immune deficiency amongst her phenotypes. She was homozygous for a splice variant in POLE1 (c.4444 + 3A > G).
Fetal anomalies v1.21 POLE Rebecca Foulger Classified gene: POLE as Amber List (moderate evidence)
Fetal anomalies v1.21 POLE Rebecca Foulger Added comment: Comment on list classification: Added as Amber awaiting Clinical Review.
Fetal anomalies v1.21 POLE Rebecca Foulger Gene: pole has been classified as Amber List (Moderate Evidence).
Fetal anomalies v1.20 POLE Rebecca Foulger gene: POLE was added
gene: POLE was added to Fetal anomalies. Sources: Literature
Mode of inheritance for gene: POLE was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: POLE were set to 23230001
Phenotypes for gene: POLE were set to IUGR; severe growth failure of prenatal onset
Added comment: Added to panel based on prenatal phenotype reported in PMID:30503519: (Logan et al., 2018) report biallelic variants in POLE in 15 indivs from 12 families (mix of countries). All subjects shared the same intronic variant (c.1686+32C>G) as part of a common haplotype, in combination with different loss-of-function variants in trans. Phenotypically, affected individuals all had IUGR and severe growth failure of prenatal onset.
Sources: Literature
COVID-19 research v0.167 TP53 Sarah Leigh reviewed gene: TP53: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Primary immunodeficiency or monogenic inflammatory bowel disease v2.133 POLE Rebecca Foulger commented on gene: POLE
COVID-19 research v0.167 TP53 Sarah Leigh Publications for gene: TP53 were set to 32086639; 32048120
COVID-19 research v0.166 CIB1 Sarah Leigh reviewed gene: CIB1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.166 CIB1 Sarah Leigh Phenotypes for gene: CIB1 were changed from Epidermodysplasia verruciformis; Defects in intrinsic and innate immunity; CIB1 deficiency to Epidermodysplasia verruciformis 3 618267; Defects in intrinsic and innate immunity; CIB1 deficiency
CAKUT v1.63 TFAP2A Catherine Snow Publications for gene: TFAP2A were set to 21204207; 31160420
CAKUT v1.62 TFAP2A Catherine Snow Publications for gene: TFAP2A were set to 21204207; 31160420
CAKUT v1.62 TFAP2A Catherine Snow Publications for gene: TFAP2A were set to
CAKUT v1.61 TFAP2A Catherine Snow Classified gene: TFAP2A as Green List (high evidence)
CAKUT v1.61 TFAP2A Catherine Snow Added comment: Comment on list classification: TFAP2A identified by expert review. Phenotype for the gene disease association is mainly branchial cleft sinus defects, ocular anomalies such as microphthalmia and lacrimal duct obstruction and a dysmorphic facial appearance including cleft or pseudocleft lip/palate. However PMID: 21204207 - Genotype-phenotype Analysis of the Branchio-Oculo-Facial Syndrome states that renal anomalies, including dysplasia, agenesis,multicystic kidneys, and vesicoureteral reflux was seen in 12/34; 35% who had variants mainly in exon 4 &5 of the TFAP2A gene. Functional evidence PMID: 31160420 demonstrates that TFAP2A is involved in kidney development
CAKUT v1.61 TFAP2A Catherine Snow Gene: tfap2a has been classified as Green List (High Evidence).
Early onset or syndromic epilepsy v2.41 CACNA1H Sarah Leigh Publications for gene: CACNA1H were set to 12891677; 32227660
CAKUT v1.60 ZIC3 Catherine Snow Publications for gene: ZIC3 were set to
CAKUT v1.59 ZIC3 Catherine Snow Classified gene: ZIC3 as Green List (high evidence)
CAKUT v1.59 ZIC3 Catherine Snow Added comment: Comment on list classification: ZIC3 identified by expert review for the CAKUT panel. ZIC3 is associated with VATER/VACTERL. Renal malformations is a phenotype of this disorder. Phenotypic spectrum of ZIC3 mutation carriers is quite variable, with incomplete penetrance in males however sufficient number of unrelated cases with renal malformations for this to be classed as Green.
CAKUT v1.59 ZIC3 Catherine Snow Gene: zic3 has been classified as Green List (High Evidence).
Fetal anomalies v1.19 MYL9 Rebecca Foulger Publications for gene: MYL9 were set to
Fetal anomalies v1.18 MYL9 Rebecca Foulger Classified gene: MYL9 as Red List (low evidence)
Fetal anomalies v1.18 MYL9 Rebecca Foulger Added comment: Comment on list classification: Kept rating as Red to match review by Rhiannon Mellis (GOSH).
Fetal anomalies v1.18 MYL9 Rebecca Foulger Gene: myl9 has been classified as Red List (Low Evidence).
Fetal anomalies v1.17 LMOD1 Rebecca Foulger Classified gene: LMOD1 as Red List (low evidence)
Fetal anomalies v1.17 LMOD1 Rebecca Foulger Added comment: Comment on list classification: Kept rating as Red to match review by Rhiannon Mellis (GOSH).
Fetal anomalies v1.17 LMOD1 Rebecca Foulger Gene: lmod1 has been classified as Red List (Low Evidence).
Fetal anomalies v1.16 MYH11 Rebecca Foulger Publications for gene: MYH11 were set to
Fetal anomalies v1.15 MYH11 Rebecca Foulger Classified gene: MYH11 as Green List (high evidence)
Fetal anomalies v1.15 MYH11 Rebecca Foulger Added comment: Comment on list classification: Updated rating from Red to Green to match review by Rhiannon Mellis (GOSH).
Fetal anomalies v1.15 MYH11 Rebecca Foulger Gene: myh11 has been classified as Green List (High Evidence).
Fetal anomalies v1.14 MYH11 Rebecca Foulger Added comment: Comment on mode of inheritance: Set mode of inheritance to BIALLELIC to match papers: compound het and homozygous MYH11 variants associated with MMIH.
Fetal anomalies v1.14 MYH11 Rebecca Foulger Mode of inheritance for gene: MYH11 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to BIALLELIC, autosomal or pseudoautosomal
Fetal anomalies v1.13 MYLK Rebecca Foulger Publications for gene: MYLK were set to
Fetal anomalies v1.12 MYLK Rebecca Foulger Phenotypes for gene: MYLK were changed from Megacystis Microcolon Intestinal Hypoperistalsis Syndrome to Megacystis Microcolon Intestinal Hypoperistalsis Syndrome; MMIH
Fetal anomalies v1.11 MYL9 Rhiannon Mellis reviewed gene: MYL9: Rating: RED; Mode of pathogenicity: ; Publications: 29453416; Phenotypes: Megacystis Microcolon Intestinal Hypoperistalsis Syndrome (MMIH); Mode of inheritance:
Fetal anomalies v1.11 LMOD1 Rhiannon Mellis reviewed gene: LMOD1: Rating: RED; Mode of pathogenicity: ; Publications: 28292896; Phenotypes: Megacystis Microcolon Intestinal Hypoperistalsis Syndrome (MMIH); Mode of inheritance:
Fetal anomalies v1.11 MYH11 Rhiannon Mellis reviewed gene: MYH11: Rating: GREEN; Mode of pathogenicity: ; Publications: 25407000, 29575632, 31427716; Phenotypes: Megacystis Microcolon Intestinal Hypoperistalsis Syndrome (MMIH); Mode of inheritance:
Fetal anomalies v1.11 MYLK Rhiannon Mellis reviewed gene: MYLK: Rating: AMBER; Mode of pathogenicity: ; Publications: 28602422; Phenotypes: Megacystis Microcolon Intestinal Hypoperistalsis Syndrome (MMIH); Mode of inheritance:
Fetal anomalies v1.10 MYL9 Rebecca Foulger gene: MYL9 was added
gene: MYL9 was added to Fetal anomalies. Sources: Expert list
Mode of inheritance for gene: MYL9 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: MYL9 were set to Megacystis Microcolon Intestinal Hypoperistalsis Syndrome (MMIH)
Added comment: Added to panel as suggested by Rhiannon Mellis (GOSH).
Sources: Expert list
Fetal anomalies v1.9 LMOD1 Rebecca Foulger gene: LMOD1 was added
gene: LMOD1 was added to Fetal anomalies. Sources: Expert list
Mode of inheritance for gene: LMOD1 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: LMOD1 were set to Megacystis Microcolon Intestinal Hypoperistalsis Syndrome (MMIH)
Added comment: Added to panel as suggested by Rhiannon Mellis (GOSH).
Sources: Expert list
Fetal anomalies v1.8 MYH11 Rebecca Foulger gene: MYH11 was added
gene: MYH11 was added to Fetal anomalies. Sources: Expert list
Mode of inheritance for gene: MYH11 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes for gene: MYH11 were set to Megacystis Microcolon Intestinal Hypoperistalsis Syndrome (MMIH)
Added comment: Added to panel as suggested by Rhiannon Mellis (GOSH).
Sources: Expert list
CAKUT v1.58 GREB1L John Sayer reviewed gene: GREB1L: Rating: GREEN; Mode of pathogenicity: None; Publications: 29220675, 29100091; Phenotypes: renal agenesis, uterus agenesis; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Primary immunodeficiency or monogenic inflammatory bowel disease v2.133 DNASE1L3 Catherine Snow Classified gene: DNASE1L3 as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.133 DNASE1L3 Catherine Snow Added comment: Comment on list classification: Identified by expert review as Green. PMID: 30008451 reports a SLE patient with (c.289_290delAC/p.Thr97Ilefs*2) in DNASE1L3 in 1 patient. This variant had previously been reported in PMID: 23666765 for Hypocomplementemic Urticarial Vasculitis (HUVs) - Systemic lupus erythematosus (SLE) develops in >50% of patients with HUVS
Primary immunodeficiency or monogenic inflammatory bowel disease v2.133 DNASE1L3 Catherine Snow Gene: dnase1l3 has been classified as Green List (High Evidence).
COVID-19 research v0.165 ACE2 Rebecca Foulger commented on gene: ACE2: Preprint https://www.biorxiv.org/content/10.1101/2020.04.22.056127v1 show that ACE2 levels in the respiratory tract did not increase in association with risk factors for severe COVID-19 (e.g. age and underlying chronic comorbidities).
COVID-19 research v0.165 TMPRSS2 Rebecca Foulger commented on gene: TMPRSS2: Preprint http://biorxiv.org/cgi/content/short/2020.04.23.057190 analysed coding region variants in TMPRSS2 and the eQTL variants which may affect gene experssion. They suggest that lung-specific eQTL variants may confer different susceptibility or response to SARS-CoV-2 infection from different populations. In particular, we found that the regulatory region variant rs35074065 is associated with high expression of TMPRSS2 (but lower expression of MX1).
COVID-19 research v0.165 ACE2 Rebecca Foulger commented on gene: ACE2: Preprint https://www.biorxiv.org/content/10.1101/2020.04.24.050534v1 conclude that higher expression of ACE2 facilitated by natural variations (with different frequencies in different populations) results in ACE2 homo-dimerization which is disadvantageous for TMPRSS2 mediated cleavage of ACE2. They propose that monomeric ACE2 has higher preferential binding with SARS-CoV-2 S-Protein.
COVID-19 research v0.165 STAT2 Rebecca Foulger commented on gene: STAT2
COVID-19 research v0.165 TMPRSS2 Rebecca Foulger commented on gene: TMPRSS2: Preprint https://www.biorxiv.org/content/10.1101/2020.04.24.056259v2 suggests that ACE2 and TMPRSS2 co-expression in the prostate may explain sex differences in the observed COVID-19 disaparities.
COVID-19 research v0.165 ACE2 Rebecca Foulger commented on gene: ACE2: Preprint https://www.biorxiv.org/content/10.1101/2020.04.24.056259v2 suggests that ACE2 and TMPRSS2 co-expression in the prostate may explain sex differences in the observed COVID-19 disaparities.
COVID-19 research v0.165 IL18BP Rebecca Foulger commented on gene: IL18BP
COVID-19 research v0.165 IL18BP Rebecca Foulger Publications for gene: IL18BP were set to 32086639; 32048120; PubMed: 31213488
Primary immunodeficiency or monogenic inflammatory bowel disease v2.132 DBR1 Catherine Snow Classified gene: DBR1 as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.132 DBR1 Catherine Snow Added comment: Comment on list classification: DBR1 identified by expert review. DBR1 variants identified in unrelated patients from different ethnicities, each had brainstem infection due to herpes simplex virus 1 (HSV1), influenza virus, or norovirus
Primary immunodeficiency or monogenic inflammatory bowel disease v2.132 DBR1 Catherine Snow Gene: dbr1 has been classified as Green List (High Evidence).
COVID-19 research v0.164 CCR5 Ivone Leong Phenotypes for gene: CCR5 were changed from to {West nile virus, susceptibility to}, 610379; {HIV infection, susceptibility/resistance to}
Primary immunodeficiency or monogenic inflammatory bowel disease v2.131 DEF6 Catherine Snow Classified gene: DEF6 as Amber List (moderate evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.131 DEF6 Catherine Snow Added comment: Comment on list classification: Comment on list classification: Promoted from Red to Amber based on expert review. Insufficient individuals for DEF6 to be rated as Green.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.131 DEF6 Catherine Snow Gene: def6 has been classified as Amber List (Moderate Evidence).
Cytopenia - NOT Fanconi anaemia v1.6 EFL1 Catherine Snow Publications for gene: EFL1 were set to 29970384, 28331068
Cytopenia - NOT Fanconi anaemia v1.5 EFL1 Catherine Snow Classified gene: EFL1 as Green List (high evidence)
Cytopenia - NOT Fanconi anaemia v1.5 EFL1 Catherine Snow Added comment: Comment on list classification: Upgrading to Green based on further individuals identified in publication PMID: 31151987
Cytopenia - NOT Fanconi anaemia v1.5 EFL1 Catherine Snow Gene: efl1 has been classified as Green List (High Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.130 EFL1 Catherine Snow Classified gene: EFL1 as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.130 EFL1 Catherine Snow Added comment: Comment on list classification: EFL1 identified by expert review. Promoting from Grey to Green, sufficient number of unrelated individuals with Shwachman-Diamond like syndrome.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.130 EFL1 Catherine Snow Gene: efl1 has been classified as Green List (High Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.129 ERBIN Catherine Snow Classified gene: ERBIN as Amber List (moderate evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.129 ERBIN Catherine Snow Added comment: Comment on list classification: Promoted from Red to Amber based on expert review. Only one family identified and functional studies so will remain Amber.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.129 ERBIN Catherine Snow Gene: erbin has been classified as Amber List (Moderate Evidence).
Malformations of cortical development v2.5 EMX2 Zornitza Stark changed review comment from: Please note publication disputing gene-disease association.; to: Please note publication disputing gene-disease association. Also note only pathogenic variants in ClinVar are from 1996, all the rest are VOUS/LB.
Malformations of cortical development v2.5 EMX2 Zornitza Stark reviewed gene: EMX2: Rating: AMBER; Mode of pathogenicity: None; Publications: 18409201; Phenotypes: Schizencephaly, 269160; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
COVID-19 research v0.163 FCHO1 Sophie Hambleton reviewed gene: FCHO1: Rating: GREEN; Mode of pathogenicity: None; Publications: 30822429, 32098969; Phenotypes: combined immunodeficiency; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.163 FANCM Sophie Hambleton reviewed gene: FANCM: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.163 FANCL Sophie Hambleton reviewed gene: FANCL: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.163 FANCI Sophie Hambleton reviewed gene: FANCI: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: Fanconi anaemia, bone marrow failure; Mode of inheritance: None
COVID-19 research v0.163 FANCG Sophie Hambleton reviewed gene: FANCG: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.163 FANCF Sophie Hambleton reviewed gene: FANCF: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: Fanconi anaemia, bone marrow failure; Mode of inheritance: None
COVID-19 research v0.163 FANCE Sophie Hambleton reviewed gene: FANCE: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.163 FANCD2 Sophie Hambleton reviewed gene: FANCD2: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.163 FANCC Sophie Hambleton reviewed gene: FANCC: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.163 FANCB Sophie Hambleton reviewed gene: FANCB: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: Fanconi anaemia, bone marrow failure; Mode of inheritance: X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)
COVID-19 research v0.163 FANCA Sophie Hambleton reviewed gene: FANCA: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: Fanconi anaemia, bone marrow failure; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.163 ERCC4 Sophie Hambleton reviewed gene: ERCC4: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: xeroderma pigmentosum, Fanconi anaemia; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.163 ERBIN Sophie Hambleton reviewed gene: ERBIN: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.163 TMPRSS2 Rebecca Foulger commented on gene: TMPRSS2: Preprint https://www.medrxiv.org/content/10.1101/2020.04.22.20074963v1 Lopera et al shows a LACK of association between genetic variants at ACE2 and TMPRSS2 and human quantitative phenotypes. The authors recognise that the SARS-CoV-2 virus uses ACE2 for cell invasion, and the serine protease TMPRSS2 for S protein priming and therefore they investigated whether genetic variation in these two genes modulates an individual's genetic predisposition to infection and virus clearance. They examined 178 quantitative phenotypes in relation to 1,273 genetic variants located in or near ACE2 and TMPRSS2: none reached the threshold for significance though these variants may play a role in diseases such as hypertension and chronic inflammation that are often observed in the more severe COVID-19 cases.
COVID-19 research v0.163 ACE2 Rebecca Foulger commented on gene: ACE2: Preprint https://www.medrxiv.org/content/10.1101/2020.04.22.20074963v1 Lopera et al shows a LACK of association between genetic variants at ACE2 and TMPRSS2 and human quantitative phenotypes. The authors recognise that the SARS-CoV-2 virus uses ACE2 for cell invasion, and the serine protease TMPRSS2 for S protein priming and therefore they investigated whether genetic variation in these two genes modulates an individual's genetic predisposition to infection and virus clearance. They examined 178 quantitative phenotypes in relation to 1,273 genetic variants located in or near ACE2 and TMPRSS2: none reached the threshold for significance though these variants may play a role in diseases such as hypertension and chronic inflammation that are often observed in the more severe COVID-19 cases.
Additional findings health related - CNV analysis adults v0.14 Eleanor Williams Panel name changed from Additional findings health related adult CNVs to Additional findings health related - CNV analysis adults
Additional findings health related - adults v0.18 Eleanor Williams Panel name changed from Additional findings health related adult to Additional findings health related -  adults
Additional findings health related - CNV analysis children v0.11 Eleanor Williams Panel name changed from Additional findings health related child CNVs to Additional findings health related - CNV analysis children
Additional findings health related - CNV analysis adult specific v0.16 Eleanor Williams Panel name changed from Additional findings health related adult additional CNVs to Additional findings health related - CNV analysis adult specific
COVID-19 research v0.163 EFL1 Sophie Hambleton reviewed gene: EFL1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.163 DEF6 Sophie Hambleton reviewed gene: DEF6: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: Immune dysregulation, combined immunodeficiency, autoimmunity, autoimmune enteropathy, dilated cardiomyopathy; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Additional findings health related - children v0.13 Eleanor Williams Panel name changed from Additional findings health related child to Additional findings health related - children
COVID-19 research v0.163 DBR1 Sophie Hambleton reviewed gene: DBR1: Rating: GREEN; Mode of pathogenicity: None; Publications: 29474921; Phenotypes: Susceptibility to viral encephalitis; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Additional findings health related - adult specific v0.15 Eleanor Williams Panel name changed from Additional findings health related adult additional genes to Additional findings health related - adult specific
COVID-19 research v0.163 BRIP1 Sophie Hambleton reviewed gene: BRIP1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.163 CIB1 Sophie Hambleton reviewed gene: CIB1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.163 C17orf62 Sophie Hambleton reviewed gene: C17orf62: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: chronic granulomatous disease; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.163 CCL2 Sophie Hambleton reviewed gene: CCL2: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: Unknown
COVID-19 research v0.163 ARHGEF1 Sophie Hambleton reviewed gene: ARHGEF1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.163 ALPI Sophie Hambleton reviewed gene: ALPI: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: inflammatory bowel disease; Mode of inheritance: None
COVID-19 research v0.163 ACE2 Sophie Hambleton reviewed gene: ACE2: Rating: AMBER; Mode of pathogenicity: Other; Publications: ; Phenotypes: ; Mode of inheritance: Unknown
COVID-19 research v0.163 CTSB Eleanor Williams changed review comment from: The Covid-19 cell atlas (https://www.covid19cellatlas.org/) lists this gene as a COVID-19/SARS-CoV-2 entry-associated gene.
I cannot find reference to the gene in the two publications listed though PMID: 32142651 and 32015507.
Sources: Other; to: The Covid-19 cell atlas (https://www.covid19cellatlas.org/) lists this gene as a COVID-19/SARS-CoV-2 entry-associated gene.
PMID: 32142651 - Hoffman et al 2020 - Cell journal - CatB/L involved in S protein priming.
COVID-19 research v0.163 CTSL Eleanor Williams changed review comment from: The Covid-19 cell atlas (https://www.covid19cellatlas.org/) lists this gene as a COVID-19/SARS-CoV-2 entry-associated gene.
I cannot find reference to the gene in the two publications listed though PMID: 32142651 and 32015507.
Sources: Other; to: The Covid-19 cell atlas (https://www.covid19cellatlas.org/) lists this gene as a COVID-19/SARS-CoV-2 entry-associated gene.
PMID: 32142651 - Hoffman et al 2020 - Cell journal - CatB/L involved in S protein priming.
COVID-19 research v0.163 CTSL Eleanor Williams gene: CTSL was added
gene: CTSL was added to Viral susceptibility. Sources: Other
Mode of inheritance for gene: CTSL was set to Unknown
Added comment: The Covid-19 cell atlas (https://www.covid19cellatlas.org/) lists this gene as a COVID-19/SARS-CoV-2 entry-associated gene.
I cannot find reference to the gene in the two publications listed though PMID: 32142651 and 32015507.
Sources: Other
COVID-19 research v0.162 CTSB Eleanor Williams gene: CTSB was added
gene: CTSB was added to Viral susceptibility. Sources: Other
Mode of inheritance for gene: CTSB was set to Unknown
Added comment: The Covid-19 cell atlas (https://www.covid19cellatlas.org/) lists this gene as a COVID-19/SARS-CoV-2 entry-associated gene.
I cannot find reference to the gene in the two publications listed though PMID: 32142651 and 32015507.
Sources: Other
COVID-19 research v0.161 ACE2 Eleanor Williams changed review comment from: PMID: 32015507 - Zhou et al 2020 - Nature article. Confirmed that 2019-nCoV uses the same cell entry receptor-angiotensin converting enzyme II (ACE2)-as SARS-CoV.; to: PMID: 32015507 - Zhou et al 2020 - Nature article. Confirmed that 2019-nCoV uses the same cell entry receptor-angiotensin converting enzyme II (ACE2)-as SARS-CoV.

PMID: 32142651 - Hoffman et al 2020 - demonstrate that SARS-CoV-2 uses the SARS-CoV receptor ACE2 for entry
COVID-19 research v0.161 ACE2 Eleanor Williams Publications for gene: ACE2 were set to 14647384; 15897467; 16007097; 32142651
COVID-19 research v0.160 ACE2 Eleanor Williams edited their review of gene: ACE2: Added comment: PMID: 32015507 - Zhou et al 2020 - Nature article. Confirmed that 2019-nCoV uses the same cell entry receptor-angiotensin converting enzyme II (ACE2)-as SARS-CoV.; Changed publications: 32015507
Intellectual disability v3.31 CDK19 Zornitza Stark reviewed gene: CDK19: Rating: GREEN; Mode of pathogenicity: None; Publications: 32330417; Phenotypes: Intellectual disability, epileptic encephalopathy; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
COVID-19 research v0.160 ABO Owen Siggs gene: ABO was added
gene: ABO was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: ABO was set to Other
Publications for gene: ABO were set to 15784866
Review for gene: ABO was set to AMBER
Added comment: Preliminary suggestion from preprints (https://www.medrxiv.org/content/10.1101/2020.03.11.20031096v2 & https://www.preprints.org/manuscript/202003.0356/v1) that ABO blood group may influence susceptibility to SARS-CoV-2 infection. Other preliminary evidence that ABO blood group may also influence susceptibility to SARS-CoV infection (PMID: 15784866). Both yet to be replicated, but suggest individuals of blood group O to be at lower risk of infection.
Sources: Literature
Fetal anomalies v1.7 PAICS Zornitza Stark gene: PAICS was added
gene: PAICS was added to Fetal anomalies. Sources: Literature
Mode of inheritance for gene: PAICS was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PAICS were set to 31600779
Phenotypes for gene: PAICS were set to Polyhydramnios; multiple congenital abnormalities
Review for gene: PAICS was set to RED
Added comment: Two sibs from single family reported with homozygous missense variant. Functional data to demonstrate effect on protein function.
Sources: Literature
COVID-19 research v0.160 TLR3 Abdelazeem Elhabyan edited their review of gene: TLR3: Added comment: I forgot to add severe influenza pneumonia in the associated phenotype in the previous comment; Changed phenotypes: Herpes simplex encephalitis predisposition , severe influenza Pneumonia ,HIV resistance to infection
COVID-19 research v0.160 TLR3 Abdelazeem Elhabyan changed review comment from: These studies demonstrate the deleterious effect of some TLR3 mutations and predisposition to Herpes simplex encephalitis in 4 separate studies on unrelated patients from different countries. TLR3 mutations in 3 children were associated with severe influenza pneumonitis. Finally, 2 other studies evaluate the protective effect of a common polymorphism of TLR3 against HIV infection in repetitively exposed individuals. Accordingly, we might find protective or deleterious effects in COVID19 patients due to different mutations of TLR3.

TLR3 is a receptor for dsRNA (intermediate in the replication of many viruses including HSV) which induces IFN response to prevent the cytopathic effects of different viruses. A heterozygous dominant-negative mutation of TLR3 was discovered in 2 unrelated children with HSE. TLR3 mutant fibroblasts from the 2 patients were infected by HSV-1 and vesicular stomatitis virus(VSV).IFNB and IFNL production were impaired in those cells, viral replication was higher and cell survival was lower in the 2 patients' cells when compared with the controls. Blood leukocyte response normally with to poly (I:C) which explains why the disease is not disseminated and also explains the redundant role of TLR3 in blood cells(13).
Similar findings were reported in a polish child in 2011, however, the patient here was compound heterozygous for a missense mutation leading to autosomal recessive inheritance of TLR3 deficiency(14).
Treatment with IFN alpha and beta canceled the effect of the dominant-negative mutation increasing the causality relationship between TLR3 mutants and viral immune response(13).
Relatives of the 2 patients with the same mutation did not show decreased interferon response nor they showed HSE as a complication of HSV which means that this mutation does not have full penetrance(13).

In another study, 110 patients with HSE were sequenced (exons of TLR3) to establish a new association of TLR3 mutations and HSE. The study reported 5 novel variants other than those previously described in the literature. 2 of them were not pathogenically demonstrated by in vitro studies while 3 of them were pathogenic with similar findings to those described above. Additionally, they found 3 patients with the same mutations previously described in the literature so the total of patients with deleterious TLR3 mutations would be 6 out of 110. 4 of those 6 patients(66%) with TLR6 mutations had a relapse In contrast to 12 out of 120(total cohort) (10%)(15).

In a recent study done on 16 patients with adult-onset HSE using whole-exome sequencing(WES), 1 patient was discovered to have TLR3 deficiency, while 8 other patients had mutations in other genes in the TLR3 pathway(2 patients with a mutation in IRF3, 2 patients with mutations in STAT1, 2 patients with mutations in TRIF, 1 patient with a mutation in TYK2,1 patients with a mutation in MAVS, and finally 1 patient with a mutation in TBK1)(16)

A common polymorphism in TLR3(rs3775291) was linked to increased resistance to HIV1 infection by the genotyping study of Spanish and Italian cohorts with a P value of .023 and .029 respectively. The study compared HIV exposed seronegative cohort(IV drug abuse and sexually active ) with controls. Repetitive HIV exposure in the cohort was evidenced by HCV seropositivity. In vitro infection of PBMCs with HIV showed increased resistance in cells carrying the allele and also TLR3 stimulation by TLR3 agonists showed an increased level of expression of CD69, IL-6, and CCL3(17).

A similar study was conducted on the Caucasian population showing the protective effect of the allele against HIV infection(18).

Autosomal recessive IRF7 and IRF9 deficiencies impair type I and III IFN immunity and underlie severe influenza pneumonitis. We report three unrelated children with influenza A virus (IAV) infection manifesting as acute respiratory distress syndrome (IAV-ARDS), heterozygous for rare TLR3 variants (P554S in two patients and P680L in the third) causing autosomal dominant (AD) TLR3 deficiency. AD TLR3 deficiency can underlie herpes simplex virus-1 (HSV-1) encephalitis (HSE) by impairing cortical neuron-intrinsic type I IFN immunity to HSV-1. TLR3-mutated leukocytes produce normal levels of IFNs in response to IAV. In contrast, TLR3-mutated fibroblasts produce lower levels of IFN-β and -λ, and display enhanced viral susceptibility, upon IAV infection. Moreover, the patients’ iPSC-derived pulmonary epithelial cells (PECs) are susceptible to IAV. Treatment with IFN-α2b or IFN-λ1 rescues this phenotype. AD TLR3 deficiency may thus underlie IAV-ARDS by impairing TLR3-dependent, type I, and/or III IFN–mediated, PEC-intrinsic immunity. Its clinical penetrance is incomplete for both IAV-ARDS and HSE, consistent with their typically sporadic nature(PMID: 31217193
)




13.Zhang SY, Jouanguy E, Ugolini S, et al. TLR3 deficiency in patients with herpes simplex encephalitis. Science. 2007;317(5844):1522–1527. doi:10.1126/science.1139522

14.Guo Y, Audry M, Ciancanelli M, et al. Herpes simplex virus encephalitis in a patient with complete TLR3 deficiency: TLR3 is otherwise redundant in protective immunity. J Exp Med. 2011;208(10):2083–2098. doi:10.1084/jem.20101568

15.Lim HK, Seppänen M, Hautala T, et al. TLR3 deficiency in herpes simplex encephalitis: high allelic heterogeneity and recurrence risk. Neurology. 2014;83(21):1888–1897. doi:10.1212/WNL.0000000000000999

16.Mørk N, Kofod-Olsen E, Sørensen KB, et al. Mutations in the TLR3 signaling pathway and beyond in adult patients with herpes simplex encephalitis. Genes Immun. 2015;16(8):552–566. doi:10.1038/gene.2015.46

17.Sironi M, Biasin M, Cagliani R, et al. A common polymorphism in TLR3 confers natural resistance to HIV-1 infection. J Immunol. 2012;188(2):818–823. doi:10.4049/jimmunol.1102179

18.Huik K, Avi R, Pauskar M, et al. Association between TLR3 rs3775291 and resistance to HIV among highly exposed Caucasian intravenous drug users. Infect Genet Evol. 2013;20:78–82. doi:10.1016/j.meegid.2013.08.008

19.Lim HK, Huang SXL, Chen J, et al. Severe influenza pneumonitis in children with inherited TLR3 deficiency. J Exp Med. 2019;216(9):2038–2056. doi:10.1084/jem.20181621; to: These studies demonstrate the deleterious effect of some TLR3 mutations and predisposition to Herpes simplex encephalitis in 4 separate studies on unrelated patients from different countries. TLR3 mutations in 3 children were associated with severe influenza pneumonitis. Finally, 2 other studies evaluate the protective effect of a common polymorphism of TLR3 against HIV infection in repetitively exposed individuals. Accordingly, we might find protective or deleterious effects in COVID19 patients due to different mutations of TLR3.

TLR3 is a receptor for dsRNA (intermediate in the replication of many viruses including HSV) which induces IFN response to prevent the cytopathic effects of different viruses. A heterozygous dominant-negative mutation of TLR3 was discovered in 2 unrelated children with HSE. TLR3 mutant fibroblasts from the 2 patients were infected by HSV-1 and vesicular stomatitis virus(VSV).IFNB and IFNL production were impaired in those cells, viral replication was higher and cell survival was lower in the 2 patients' cells when compared with the controls. Blood leukocyte response normally with to poly (I:C) which explains why the disease is not disseminated and also explains the redundant role of TLR3 in blood cells(13).
Similar findings were reported in a polish child in 2011, however, the patient here was compound heterozygous for a missense mutation leading to autosomal recessive inheritance of TLR3 deficiency(14).
Treatment with IFN alpha and beta canceled the effect of the dominant-negative mutation increasing the causality relationship between TLR3 mutants and viral immune response(13).
Relatives of the 2 patients with the same mutation did not show decreased interferon response nor they showed HSE as a complication of HSV which means that this mutation does not have full penetrance(13).

In another study, 110 patients with HSE were sequenced (exons of TLR3) to establish a new association of TLR3 mutations and HSE. The study reported 5 novel variants other than those previously described in the literature. 2 of them were not pathogenically demonstrated by in vitro studies while 3 of them were pathogenic with similar findings to those described above. Additionally, they found 3 patients with the same mutations previously described in the literature so the total of patients with deleterious TLR3 mutations would be 6 out of 110. 4 of those 6 patients(66%) with TLR6 mutations had a relapse In contrast to 12 out of 120(total cohort) (10%)(15).

In a recent study done on 16 patients with adult-onset HSE using whole-exome sequencing(WES), 1 patient was discovered to have TLR3 deficiency, while 8 other patients had mutations in other genes in the TLR3 pathway(2 patients with a mutation in IRF3, 2 patients with mutations in STAT1, 2 patients with mutations in TRIF, 1 patient with a mutation in TYK2,1 patients with a mutation in MAVS, and finally 1 patient with a mutation in TBK1)(16)

A common polymorphism in TLR3(rs3775291) was linked to increased resistance to HIV1 infection by the genotyping study of Spanish and Italian cohorts with a P value of .023 and .029 respectively. The study compared HIV exposed seronegative cohort(IV drug abuse and sexually active ) with controls. Repetitive HIV exposure in the cohort was evidenced by HCV seropositivity. In vitro infection of PBMCs with HIV showed increased resistance in cells carrying the allele and also TLR3 stimulation by TLR3 agonists showed an increased level of expression of CD69, IL-6, and CCL3(17).

A similar study was conducted on the Caucasian population showing the protective effect of the allele against HIV infection(18).

Autosomal recessive IRF7 and IRF9 deficiencies impair type I and III IFN immunity and underlie severe influenza pneumonitis. We report three unrelated children with influenza A virus (IAV) infection manifesting as acute respiratory distress syndrome (IAV-ARDS), heterozygous for rare TLR3 variants (P554S in two patients and P680L in the third) causing autosomal dominant (AD) TLR3 deficiency. AD TLR3 deficiency can underlie herpes simplex virus-1 (HSV-1) encephalitis (HSE) by impairing cortical neuron-intrinsic type I IFN immunity to HSV-1. TLR3-mutated leukocytes produce normal levels of IFNs in response to IAV. In contrast, TLR3-mutated fibroblasts produce lower levels of IFN-β and -λ, and display enhanced viral susceptibility, upon IAV infection. Moreover, the patients’ iPSC-derived pulmonary epithelial cells (PECs) are susceptible to IAV. Treatment with IFN-α2b or IFN-λ1 rescues this phenotype. AD TLR3 deficiency may thus underlie IAV-ARDS by impairing TLR3-dependent, type I, and/or III IFN–mediated, PEC-intrinsic immunity. Its clinical penetrance is incomplete for both IAV-ARDS and HSE, consistent with their typically sporadic nature(PMID: 31217193
)




13.Zhang SY, Jouanguy E, Ugolini S, et al. TLR3 deficiency in patients with herpes simplex encephalitis. Science. 2007;317(5844):1522–1527. doi:10.1126/science.1139522

14.Guo Y, Audry M, Ciancanelli M, et al. Herpes simplex virus encephalitis in a patient with complete TLR3 deficiency: TLR3 is otherwise redundant in protective immunity. J Exp Med. 2011;208(10):2083–2098. doi:10.1084/jem.20101568

15.Lim HK, Seppänen M, Hautala T, et al. TLR3 deficiency in herpes simplex encephalitis: high allelic heterogeneity and recurrence risk. Neurology. 2014;83(21):1888–1897. doi:10.1212/WNL.0000000000000999

16.Mørk N, Kofod-Olsen E, Sørensen KB, et al. Mutations in the TLR3 signaling pathway and beyond in adult patients with herpes simplex encephalitis. Genes Immun. 2015;16(8):552–566. doi:10.1038/gene.2015.46

17.Sironi M, Biasin M, Cagliani R, et al. A common polymorphism in TLR3 confers natural resistance to HIV-1 infection. J Immunol. 2012;188(2):818–823. doi:10.4049/jimmunol.1102179

18.Huik K, Avi R, Pauskar M, et al. Association between TLR3 rs3775291 and resistance to HIV among highly exposed Caucasian intravenous drug users. Infect Genet Evol. 2013;20:78–82. doi:10.1016/j.meegid.2013.08.008

19.Lim HK, Huang SXL, Chen J, et al. Severe influenza pneumonitis in children with inherited TLR3 deficiency. J Exp Med. 2019;216(9):2038–2056. doi:10.1084/jem.20181621
COVID-19 research v0.160 TLR3 Abdelazeem Elhabyan reviewed gene: TLR3: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: Herpes simplex encephalitis predisposition , HIV resistance to infection; Mode of inheritance: Other
COVID-19 research v0.160 UNC93B1 Abdelazeem Elhabyan reviewed gene: UNC93B1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: Other
COVID-19 research v0.160 PHB2 Rebecca Foulger gene: PHB2 was added
gene: PHB2 was added to Viral susceptibility. Sources: Other,Literature
Mode of inheritance for gene: PHB2 was set to Unknown
Added comment: Added to panel based on presence in UniProt COVID portal: https://covid-19.uniprot.org/uniprotkb/Q99623
Sources: Other, Literature
COVID-19 research v0.159 DDX1 Rebecca Foulger gene: DDX1 was added
gene: DDX1 was added to Viral susceptibility. Sources: Other,Literature
Mode of inheritance for gene: DDX1 was set to Unknown
Publications for gene: DDX1 were set to 20573827
Added comment: Added to panel based on presence in UniProt COVID portal: https://covid19.uniprot.org/uniprotkb/Q92499. The cellular RNA helicase DDX1 interacts with coronavirus nonstructural protein 14 and enhances viral replication (PMID:20573827).
Sources: Other, Literature
COVID-19 research v0.158 MPP5 Rebecca Foulger gene: MPP5 was added
gene: MPP5 was added to Viral susceptibility. Sources: Other,Literature
Mode of inheritance for gene: MPP5 was set to Unknown
Publications for gene: MPP5 were set to 20861307
Added comment: Added to panel based on presence in the UniProt COVID portal (https://covid-19.uniprot.org/uniprotkb/Q8N3R9). Acts as an interaction partner for human SARS coronavirus envelope protein E (MPP5 aka PALS1) (PMID:20861307).
Sources: Other, Literature
COVID-19 research v0.157 SMAD3 Rebecca Foulger gene: SMAD3 was added
gene: SMAD3 was added to Viral susceptibility. Sources: Other,Literature
Mode of inheritance for gene: SMAD3 was set to Unknown
Publications for gene: SMAD3 were set to 18055455
Added comment: Added to panel based on presence in the UniProt COVID portal: https://covid-19.uniprot.org/uniprotkb/P84022. SMAD3 interacts with SARS-associated coronavirus (SARS-CoV) nucleocapsid (N) protein (PMID:18055455).
Sources: Other, Literature
COVID-19 research v0.156 CCL11 Sarah Leigh Publications for gene: CCL11 were set to
COVID-19 research v0.155 CCL11 Sarah Leigh Classified gene: CCL11 as Red List (low evidence)
COVID-19 research v0.155 CCL11 Sarah Leigh Added comment: Comment on list classification: A cytokine (inflammatory biomarker), that is released in response to viral infections. Increased levels of CCL11 amongst other cytokines, is associated with immunity to West Nile virus (PMID 30915442). A haplotype that included c.-1385G>A was associated with resistance to HIV-1 infection (PMID 14571188).
COVID-19 research v0.155 CCL11 Sarah Leigh Gene: ccl11 has been classified as Red List (Low Evidence).
COVID-19 research v0.154 PHB Rebecca Foulger gene: PHB was added
gene: PHB was added to Viral susceptibility. Sources: Other
Mode of inheritance for gene: PHB was set to Unknown
Added comment: Added to panel based on presence in the UniProt COVID portal: https://covid-19.uniprot.org/uniprotkb/P35232.
Sources: Other
COVID-19 research v0.153 ITGAL Rebecca Foulger gene: ITGAL was added
gene: ITGAL was added to Viral susceptibility. Sources: Literature,Other
Mode of inheritance for gene: ITGAL was set to Unknown
Publications for gene: ITGAL were set to 18020948
Added comment: Added to panel based on presence in the UniProt COVID portal:
https://covid-19.uniprot.org/uniprotkb/P20701. Data in PMID:18020948 suggests ITGAL (LFA-1) to be an attachment factor or the receptor for SARS-CoV on human leukocytes. Kept rating as Red awaiting Expert Review.
Sources: Literature, Other
COVID-19 research v0.152 SGTA Rebecca Foulger Classified gene: SGTA as Red List (low evidence)
COVID-19 research v0.152 SGTA Rebecca Foulger Added comment: Comment on list classification: Kept rating as Red awaiting expert review. Role for protein in viral infection, but no population studies/SNP analyses yet.
COVID-19 research v0.152 SGTA Rebecca Foulger Gene: sgta has been classified as Red List (Low Evidence).
COVID-19 research v0.151 SGTA Rebecca Foulger gene: SGTA was added
gene: SGTA was added to Viral susceptibility. Sources: Other
Mode of inheritance for gene: SGTA was set to Unknown
Publications for gene: SGTA were set to 28356524; 24675744
Added comment: Added to panel based on presence in the UniProt COVID portal (https://covid-19.uniprot.org/uniprotkb/O43765). In case of infection by polyomavirus, involved in the virus endoplasmic reticulum membrane penetration and infection via protein interactions.
Sources: Other
COVID-19 research v0.150 ADAM17 Rebecca Foulger Publications for gene: ADAM17 were set to 22010916; 20603312; 25058236; 32086639; 11149563; 28930861; 32048120; 25171914
COVID-19 research v0.149 ACE2 Rebecca Foulger Classified gene: ACE2 as Green List (high evidence)
COVID-19 research v0.149 ACE2 Rebecca Foulger Added comment: Comment on list classification: Updated rating from Amber to Green. Multiple functional data demonstrates a role for ACE2 as a receptor for Coronaviruses. Plus a vast amount of preprint data that suggests SNPs in ACE2 should be explored for regional differences.
COVID-19 research v0.149 ACE2 Rebecca Foulger Gene: ace2 has been classified as Green List (High Evidence).
COVID-19 research v0.148 TMPRSS2 Rebecca Foulger Classified gene: TMPRSS2 as Green List (high evidence)
COVID-19 research v0.148 TMPRSS2 Rebecca Foulger Added comment: Comment on list classification: Updated rating from Amber to Green on this research panel: Known mechanisms for involvement in viral infection (including proteolytic cleavage of the viral receptor, ACE2) plus variants identified in preprints as candidates for COVID-19 severity.
COVID-19 research v0.148 TMPRSS2 Rebecca Foulger Gene: tmprss2 has been classified as Green List (High Evidence).
COVID-19 research v0.147 TMPRSS2 Rebecca Foulger commented on gene: TMPRSS2
COVID-19 research v0.147 TMPRSS2 Rebecca Foulger Publications for gene: TMPRSS2 were set to 31488196; 32142651; 24227843
COVID-19 research v0.146 TMPRSS2 Rebecca Foulger Publications for gene: TMPRSS2 were set to 31488196
COVID-19 research v0.145 ACE2 Rebecca Foulger commented on gene: ACE2: ACE2 gene present in the UniProt COVID portal (https://covid-19.uniprot.org/ 6-April-2020) which provides the latest available pre-release UniProtKB data for the SARS-CoV-2 coronavirus and other entries relating to the COVID-19 outbreak.
COVID-19 research v0.145 IL23A Rebecca Foulger commented on gene: IL23A
COVID-19 research v0.145 IL23A Rebecca Foulger Publications for gene: IL23A were set to
COVID-19 research v0.144 IL22 Rebecca Foulger Classified gene: IL22 as Red List (low evidence)
COVID-19 research v0.144 IL22 Rebecca Foulger Added comment: Comment on list classification: Kept rating as Red: mouse model in PMID:22952908 suggests IL22 deficiency promotes resistance. IL22 administration in PMID:25395539 report possible viral protection.
COVID-19 research v0.144 IL22 Rebecca Foulger Gene: il22 has been classified as Red List (Low Evidence).
COVID-19 research v0.143 IL22 Rebecca Foulger commented on gene: IL22: Mouse model in PMID:22952908: Il22(-/-) mice were more resistant to lethal West Nile virus (WNV) encephalitis.
Hereditary neuropathy or pain disorder v1.4 JAG1 Zornitza Stark gene: JAG1 was added
gene: JAG1 was added to Hereditary neuropathy NOT PMP22 copy number. Sources: Literature
Mode of inheritance for gene: JAG1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: JAG1 were set to 32065591; 25707699
Phenotypes for gene: JAG1 were set to Peripheral neuropathy
Mode of pathogenicity for gene: JAG1 was set to Other
Review for gene: JAG1 was set to GREEN
Added comment: Two unrelated families reported with CMT type 2. Affected individuals in both families exhibited severe vocal fold paresis, a rare feature of peripheral nerve disease that can be life-threatening. Studies of mutant protein posttranslational modification and localization indicated that the mutations (p.Ser577Arg, p.Ser650Pro) impair protein glycosylation and reduce JAG1 cell surface expression. Mice harboring heterozygous CMT2-associated mutations exhibited mild peripheral neuropathy, and homozygous expression resulted in embryonic lethality by midgestation. Pre-existing rat model.
Sources: Literature
COVID-19 research v0.141 FURIN Eleanor Williams gene: FURIN was added
gene: FURIN was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: FURIN was set to Unknown
Added comment: Preprint - https://doi.org/10.1101/2020.04.18.047951- Zhong et al
Found Furin is expressed in oral mucosal cells. A Furin cutting site has been identified in SARS-CoV-2 (https://doi.org/10.1101/2020.02.10.942185 - preprint)
Sources: Literature
COVID-19 research v0.140 ACE2 Eleanor Williams changed review comment from: Preprint - https://www.biorxiv.org/content/10.1101/2020.04.14.041434v1 - Li et al
Total death rate is higher in Spain compared to China, so looked differences between the Asian and Caucasian populations for ACE2 polymorphisms using gnomAD v2.1 exomes and compare the variability of hACE2 expression in peripheral blood among eight different populations. Four genetic variants reached statistical significance for differences in MAF between the two populations N720D, K26R, N638S, I468V. Found small differences in expression of hACE2 among various populations.

Preprint - https://www.biorxiv.org/content/10.1101/2020.04.05.026633v1 - Gibson et al
Analyse ACE2 variants in the gnomAD database and identify 15 missense variants likely to affect the affinity of the human ACE2 protein for the viral spike protein and estimated the change in binding energy of the 15 missense variants.

Preprint - https://www.biorxiv.org/content/10.1101/2020.04.07.024752v1 - Stawiski et al
Aassessed ACE2 protein-altering variations from a number of databases including the gnomAD, RotterdamStudy, ALSPAC, GenomeAsia100k, HGDP, TOMMO-3.5kjpnv2, IndiGen, and HGDP. Identified variants that are likely to either increase or decrease the binding affinity of ACE2 to the S-protein and thereby alter the ability of the
virus to infect the host cell.

Preprint - https://www.biorxiv.org/content/10.1101/2020.03.16.994236v1 Procko
Made a library of coding sequence of ACE2 containing all possible single amino acid substitutions at 117 sites spanning the interface with S and lining the substrate cavity. The ACE2 library was transiently expressed in human Expi293F cells and cells were then incubated in medium containing the receptor binding domain of SARS-CoV-2 fused C-terminallyto superfolder GFP. Sorted cells with high and low binding and the transcripts sequenced to identify the variants.

Preprint - https://www.medrxiv.org/content/10.1101/2020.04.03.20047977v1 - Renieri et al
Using the Network of Italian Genomes (NIG), they mined around 7000 exomes from 5 different Centers looking for ACE2 variants. Identified variants with a potential impact on protein stability. 3 missense changed identified that have never been reported in the Eastern Asia population, were predicted to interfere with protein cleavage and stabilization. Rare truncating variants that are likely to interfere with the internalization process and one missense variant, p.Trp69Cys, predicted to interfere with 2019-nCov spike protein binding were also observed.

Preprint - https://www.biorxiv.org/content/10.1101/2020.04.12.037580v1 - Asseleta et al
ACE2 SNP rs2285666 (also called G8790A), more common in Italians and Europeans that East Asians. This variant was extensively studied as a potential risk factor for hypertension, type 2 diabetes, and coronary artery disease hence possibly constituting a predisposing factor also for the comorbidities observed in COVID-19 patients.
; to: Preprint - https://www.biorxiv.org/content/10.1101/2020.04.14.041434v1 - Li et al
Total death rate is higher in Spain compared to China, so looked differences between the Asian and Caucasian populations for ACE2 polymorphisms using gnomAD v2.1 exomes and compare the variability of hACE2 expression in peripheral blood among eight different populations. Four genetic variants reached statistical significance for differences in MAF between the two populations N720D, K26R, N638S, I468V. Found small differences in expression of hACE2 among various populations.

Preprint - https://www.biorxiv.org/content/10.1101/2020.04.05.026633v1 - Gibson et al
Analyse ACE2 variants in the gnomAD database and identify 15 missense variants likely to affect the affinity of the human ACE2 protein for the viral spike protein and estimated the change in binding energy of the 15 missense variants.

Preprint - https://www.biorxiv.org/content/10.1101/2020.04.07.024752v1 - Stawiski et al
Aassessed ACE2 protein-altering variations from a number of databases including the gnomAD, RotterdamStudy, ALSPAC, GenomeAsia100k, HGDP, TOMMO-3.5kjpnv2, IndiGen, and HGDP. Identified variants that are likely to either increase or decrease the binding affinity of ACE2 to the S-protein and thereby alter the ability of the
virus to infect the host cell.

Preprint - https://www.biorxiv.org/content/10.1101/2020.03.16.994236v1 Procko
Made a library of coding sequence of ACE2 containing all possible single amino acid substitutions at 117 sites spanning the interface with S and lining the substrate cavity. The ACE2 library was transiently expressed in human Expi293F cells and cells were then incubated in medium containing the receptor binding domain of SARS-CoV-2 fused C-terminallyto superfolder GFP. Sorted cells with high and low binding and the transcripts sequenced to identify the variants.

Preprint - https://www.medrxiv.org/content/10.1101/2020.04.03.20047977v1 - Renieri et al
Using the Network of Italian Genomes (NIG), they mined around 7000 exomes from 5 different Centers looking for ACE2 variants. Identified variants with a potential impact on protein stability. 3 missense changed identified that have never been reported in the Eastern Asia population, were predicted to interfere with protein cleavage and stabilization. Rare truncating variants that are likely to interfere with the internalization process and one missense variant, p.Trp69Cys, predicted to interfere with 2019-nCov spike protein binding were also observed.

Preprint - https://www.biorxiv.org/content/10.1101/2020.04.12.037580v1 - Asselta et al
ACE2 SNP rs2285666 (also called G8790A), more common in Italians and Europeans that East Asians. This variant was extensively studied as a potential risk factor for hypertension, type 2 diabetes, and coronary artery disease hence possibly constituting a predisposing factor also for the comorbidities observed in COVID-19 patients.
COVID-19 research v0.140 ACE2 Eleanor Williams changed review comment from: Preprint - https://www.biorxiv.org/content/10.1101/2020.04.14.041434v1 - Li et al
Total death rate is higher in Spain compared to China, so looked differences between the Asian and Caucasian populations for ACE2 polymorphisms using gnomAD v2.1 exomes and compare the variability of hACE2 expression in peripheral blood among eight different populations. Four genetic variants reached statistical significance for differences in MAF between the two populations N720D, K26R, N638S, I468V. Found small differences in expression of hACE2 among various populations.

Preprint - https://www.biorxiv.org/content/10.1101/2020.04.05.026633v1 - Gibson et al
Analyse ACE2 variants in the gnomAD database and identify 15 missense variants likely to affect the affinity of the human ACE2 protein for the viral spike protein and estimated the change in binding energy of the 15 missense variants.

Preprint - https://www.biorxiv.org/content/10.1101/2020.04.07.024752v1 - Stawiski et al
Aassessed ACE2 protein-altering variations from a number of databases including the gnomAD, RotterdamStudy, ALSPAC, GenomeAsia100k, HGDP, TOMMO-3.5kjpnv2, IndiGen, and HGDP. Identified variants that are likely to either increase or decrease the binding affinity of ACE2 to the S-protein and thereby alter the ability of the
virus to infect the host cell.

Preprint - https://www.biorxiv.org/content/10.1101/2020.03.16.994236v1 Procko
Made a library of coding sequence of ACE2 containing all possible single amino acid substitutions at 117 sites spanning the interface with S and lining the substrate cavity. The ACE2 library was transiently expressed in human Expi293F cells and cells were then incubated in medium containing the receptor binding domain of SARS-CoV-2 fused C-terminallyto superfolder GFP. Sorted cells with high and low binding and the transcripts sequenced to identify the variants.

Preprint - https://www.medrxiv.org/content/10.1101/2020.04.03.20047977v1 - Renieri et al
Using the Network of Italian Genomes (NIG), they mined around 7000 exomes from 5 different Centers looking for ACE2 variants. Identified variants with a potential impact on protein stability. 3 missense changed identified that have never been reported in the Eastern Asia population, were predicted to interfere with protein cleavage and stabilization. Rare truncating variants that are likely to interfere with the internalization process and one missense variant, p.Trp69Cys, predicted to interfere with 2019-nCov spike protein binding were also observed.
; to: Preprint - https://www.biorxiv.org/content/10.1101/2020.04.14.041434v1 - Li et al
Total death rate is higher in Spain compared to China, so looked differences between the Asian and Caucasian populations for ACE2 polymorphisms using gnomAD v2.1 exomes and compare the variability of hACE2 expression in peripheral blood among eight different populations. Four genetic variants reached statistical significance for differences in MAF between the two populations N720D, K26R, N638S, I468V. Found small differences in expression of hACE2 among various populations.

Preprint - https://www.biorxiv.org/content/10.1101/2020.04.05.026633v1 - Gibson et al
Analyse ACE2 variants in the gnomAD database and identify 15 missense variants likely to affect the affinity of the human ACE2 protein for the viral spike protein and estimated the change in binding energy of the 15 missense variants.

Preprint - https://www.biorxiv.org/content/10.1101/2020.04.07.024752v1 - Stawiski et al
Aassessed ACE2 protein-altering variations from a number of databases including the gnomAD, RotterdamStudy, ALSPAC, GenomeAsia100k, HGDP, TOMMO-3.5kjpnv2, IndiGen, and HGDP. Identified variants that are likely to either increase or decrease the binding affinity of ACE2 to the S-protein and thereby alter the ability of the
virus to infect the host cell.

Preprint - https://www.biorxiv.org/content/10.1101/2020.03.16.994236v1 Procko
Made a library of coding sequence of ACE2 containing all possible single amino acid substitutions at 117 sites spanning the interface with S and lining the substrate cavity. The ACE2 library was transiently expressed in human Expi293F cells and cells were then incubated in medium containing the receptor binding domain of SARS-CoV-2 fused C-terminallyto superfolder GFP. Sorted cells with high and low binding and the transcripts sequenced to identify the variants.

Preprint - https://www.medrxiv.org/content/10.1101/2020.04.03.20047977v1 - Renieri et al
Using the Network of Italian Genomes (NIG), they mined around 7000 exomes from 5 different Centers looking for ACE2 variants. Identified variants with a potential impact on protein stability. 3 missense changed identified that have never been reported in the Eastern Asia population, were predicted to interfere with protein cleavage and stabilization. Rare truncating variants that are likely to interfere with the internalization process and one missense variant, p.Trp69Cys, predicted to interfere with 2019-nCov spike protein binding were also observed.

Preprint - https://www.biorxiv.org/content/10.1101/2020.04.12.037580v1 - Asseleta et al
ACE2 SNP rs2285666 (also called G8790A), more common in Italians and Europeans that East Asians. This variant was extensively studied as a potential risk factor for hypertension, type 2 diabetes, and coronary artery disease hence possibly constituting a predisposing factor also for the comorbidities observed in COVID-19 patients.
Monogenic hearing loss v2.8 ABCC1 Zornitza Stark gene: ABCC1 was added
gene: ABCC1 was added to Hearing loss. Sources: Literature
Mode of inheritance for gene: ABCC1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: ABCC1 were set to 31273342
Phenotypes for gene: ABCC1 were set to Nonsyndromic hearing loss
Review for gene: ABCC1 was set to AMBER
Added comment: Total of 3 variants reported in 3 families with post lingual ADSNHL, including 1 which segregates in a large family (10 affected)

The variant identified in the large multiplex family is present in gnomAD (10 hets), but onset noted to be in 2nd or 3rd decade of life. Functional studies performed. Other 2 variants reported absent in gnomAD. In light of gnomad frequency of one of the variants, suggest Amber rating.
Sources: Literature
COVID-19 research v0.140 DMBT1 Eleanor Williams gene: DMBT1 was added
gene: DMBT1 was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: DMBT1 was set to Unknown
Review for gene: DMBT1 was set to RED
Added comment: Preprint - https://www.biorxiv.org/content/10.1101/2020.04.16.045617v1 - Han et al
Found using single cell transcriptomics that DMBT1 (a viral binding scavenger) was highly expressed in alveolar type II cells relative to other lung epithelial subsets and its expression positively correlated with ACE2.
Sources: Literature
Intellectual disability v3.31 GNAI2 Zornitza Stark gene: GNAI2 was added
gene: GNAI2 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: GNAI2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: GNAI2 were set to 31036916; 27787898
Phenotypes for gene: GNAI2 were set to Syndromic intellectual disability
Review for gene: GNAI2 was set to AMBER
Added comment: Two individuals reported, some functional data.
Sources: Literature
Intellectual disability v3.31 FEM1B Zornitza Stark gene: FEM1B was added
gene: FEM1B was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: FEM1B was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: FEM1B were set to 31036916
Phenotypes for gene: FEM1B were set to Syndromic intellectual disability
Review for gene: FEM1B was set to AMBER
Added comment: PMID: 31036916 - a single individual with de novo variant reported in a neurodevelopmental disorder cohort. Authors note another de novo case with the exact same variant (p.Arg126Gln) from the DDD study, and a 3rd patient from GeneMatcher with the same de novo missense again. The variant is in a highly constrained region of the protein. Cannot be certain the DDD and GeneMatcher individuals are unrelated, therefore I have treated as two reports for now.
Sources: Literature
Intellectual disability v3.31 WIPI2 Zornitza Stark gene: WIPI2 was added
gene: WIPI2 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: WIPI2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: WIPI2 were set to 30968111
Phenotypes for gene: WIPI2 were set to Intellectual developmental disorder with short stature and variable skeletal anomalies 618453
Review for gene: WIPI2 was set to RED
Added comment: Four homozygous individuals from one consanguineous family with intellectual disability, short stature and variable skeletal anomalies. Functional studies in patient cells showed impaired protein function. One to watch.
Sources: Literature
Ataxia and cerebellar anomalies - narrow panel v2.6 SLC44A1 Zornitza Stark gene: SLC44A1 was added
gene: SLC44A1 was added to Ataxia and cerebellar anomalies - narrow panel. Sources: Literature
Mode of inheritance for gene: SLC44A1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SLC44A1 were set to 31855247
Phenotypes for gene: SLC44A1 were set to progressive ataxia; tremor; cognitive decline; dysphagia; optic atrophy; dysarthria
Review for gene: SLC44A1 was set to GREEN
Added comment: Childhood neurodegenerative condition. Four affected individuals from three families with homozygous frameshift variants reported. Functional evidence points to impaired choline transporter function yet unchanged membrane phosphatidylcholine content. Choline treatments may be beneficial. Suggest adding to optic neuropathy and possibly other panels, including severe paediatric disorders.
Sources: Literature
Intellectual disability v3.31 GSX2 Zornitza Stark gene: GSX2 was added
gene: GSX2 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: GSX2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: GSX2 were set to 31412107
Phenotypes for gene: GSX2 were set to Diencephalic-mesencephalic junction dysplasia syndrome 2 618646; Intellectual disability; Dystonia; Spastic tetra paresis
Review for gene: GSX2 was set to AMBER
Added comment: Two unrelated families, some functional data.
Sources: Literature
COVID-19 research v0.139 LY6E Eleanor Williams gene: LY6E was added
gene: LY6E was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: LY6E was set to Unknown
Review for gene: LY6E was set to RED
Added comment: Preprint - https://www.biorxiv.org/content/10.1101/2020.04.02.021469v1 - Zhao et al
Found that human cell line C3A was more susceptible to human coronavirus HCoV-OC43 infection than HepG2. Ectopic expression of LY6E in HEK 293 cells inhibited the entry of HCoV-OC43. Overexpression of LY6E in C3A and A549 cells efficiently inhibited the infection of HCoV-OC43 and knockdown of LY6E expression in HepG2 significantly increased its susceptibility to HCoV-OC43 infection. LY6E also restricted the entry mediated by the envelope spike proteins of other human coronaviruses, including the currently pandemic SARS-CoV-2.
Sources: Literature
COVID-19 research v0.138 ACE2 Eleanor Williams changed review comment from: Preprint - https://www.biorxiv.org/content/10.1101/2020.04.14.041434v1 - Li et al
Total death rate is higher in Spain compared to China, so looked differences between the Asian and Caucasian populations for ACE2 polymorphisms using gnomAD v2.1 exomes and compare the variability of hACE2 expression in peripheral blood among eight different populations. Four genetic variants reached statistical significance for differences in MAF between the two populations N720D, K26R, N638S, I468V. Found small differences in expression of hACE2 among various populations.

Preprint - https://www.biorxiv.org/content/10.1101/2020.04.05.026633v1 - Gibson et al
Analyse ACE2 variants in the gnomAD database and identify 15 missense variants likely to affect the affinity of the human ACE2 protein for the viral spike protein and estimated the change in binding energy of the 15 missense variants.

Preprint - https://www.biorxiv.org/content/10.1101/2020.04.07.024752v1 - Stawiski et al
Aassessed ACE2 protein-altering variations from a number of databases including the gnomAD, RotterdamStudy, ALSPAC, GenomeAsia100k, HGDP, TOMMO-3.5kjpnv2, IndiGen, and HGDP. Identified variants that are likely to either increase or decrease the binding affinity of ACE2 to the S-protein and thereby alter the ability of the
virus to infect the host cell.

Preprint - https://www.biorxiv.org/content/10.1101/2020.03.16.994236v1 Procko
Made a library of coding sequence of ACE2 containing all possible single amino acid substitutions at 117 sites spanning the interface with S and lining the substrate cavity. The ACE2 library was transiently expressed in human Expi293F cells and cells were then incubated in medium containing the receptor binding domain of SARS-CoV-2 fused C-terminallyto superfolder GFP. Sorted cells with high and low binding and the transcripts sequenced to identify the variants.; to: Preprint - https://www.biorxiv.org/content/10.1101/2020.04.14.041434v1 - Li et al
Total death rate is higher in Spain compared to China, so looked differences between the Asian and Caucasian populations for ACE2 polymorphisms using gnomAD v2.1 exomes and compare the variability of hACE2 expression in peripheral blood among eight different populations. Four genetic variants reached statistical significance for differences in MAF between the two populations N720D, K26R, N638S, I468V. Found small differences in expression of hACE2 among various populations.

Preprint - https://www.biorxiv.org/content/10.1101/2020.04.05.026633v1 - Gibson et al
Analyse ACE2 variants in the gnomAD database and identify 15 missense variants likely to affect the affinity of the human ACE2 protein for the viral spike protein and estimated the change in binding energy of the 15 missense variants.

Preprint - https://www.biorxiv.org/content/10.1101/2020.04.07.024752v1 - Stawiski et al
Aassessed ACE2 protein-altering variations from a number of databases including the gnomAD, RotterdamStudy, ALSPAC, GenomeAsia100k, HGDP, TOMMO-3.5kjpnv2, IndiGen, and HGDP. Identified variants that are likely to either increase or decrease the binding affinity of ACE2 to the S-protein and thereby alter the ability of the
virus to infect the host cell.

Preprint - https://www.biorxiv.org/content/10.1101/2020.03.16.994236v1 Procko
Made a library of coding sequence of ACE2 containing all possible single amino acid substitutions at 117 sites spanning the interface with S and lining the substrate cavity. The ACE2 library was transiently expressed in human Expi293F cells and cells were then incubated in medium containing the receptor binding domain of SARS-CoV-2 fused C-terminallyto superfolder GFP. Sorted cells with high and low binding and the transcripts sequenced to identify the variants.

Preprint - https://www.medrxiv.org/content/10.1101/2020.04.03.20047977v1 - Renieri et al
Using the Network of Italian Genomes (NIG), they mined around 7000 exomes from 5 different Centers looking for ACE2 variants. Identified variants with a potential impact on protein stability. 3 missense changed identified that have never been reported in the Eastern Asia population, were predicted to interfere with protein cleavage and stabilization. Rare truncating variants that are likely to interfere with the internalization process and one missense variant, p.Trp69Cys, predicted to interfere with 2019-nCov spike protein binding were also observed.
COVID-19 research v0.138 TRIB3 Eleanor Williams gene: TRIB3 was added
gene: TRIB3 was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: TRIB3 was set to Unknown
Publications for gene: TRIB3 were set to 27252525; https://www.biorxiv.org/content/10.1101/2020.04.07.030767v1
Added comment: Preprint - https://www.biorxiv.org/content/10.1101/2020.04.07.030767v1 - de Moraes et al
Analyzed Genotype-Tissue Expression (GTEx) data to test whether lung aging is associated with transcriptional changes in human protein-coding genes that potentially interact with these viruses. Identified TRIB3 expression was decreased in older males. Found TRIB3
expressed mainly in alveolar epithelial cells that express SARS-CoV-2 receptor ACE2.

PMID: 27252525 - Tran et al 2016- Silencing of TRIB3 resulted in increased RNA and protein levels of HCV, whereas overexpression of TRIB3 decreased Hepatitis C viral replication
Sources: Literature
Early onset or syndromic epilepsy v2.40 SAMD12 Zornitza Stark gene: SAMD12 was added
gene: SAMD12 was added to Genetic epilepsy syndromes. Sources: Literature
Mode of inheritance for gene: SAMD12 was set to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
Publications for gene: SAMD12 were set to 30194086; 29507423
Phenotypes for gene: SAMD12 were set to Epilepsy, familial adult myoclonic, 1, MIM# 601068
Mode of pathogenicity for gene: SAMD12 was set to Other
Review for gene: SAMD12 was set to GREEN
gene: SAMD12 was marked as current diagnostic
Added comment: Repeat expansions of intronic TTTCA and TTTTA motifs within SAMD12 have been identified in over 50 Japanese and Chinese families. Most families with affected individuals were heterozygous however 4 patients from 3 families had homozygous repeat expansions, which was associated with a more severe phenotype. Western blot analysis showed decreased levels of the protein in patient brains. Note these were identified on long-read sequencing and may not be detectable by all assays.
Sources: Literature
COVID-19 research v0.137 ACE2 Eleanor Williams changed review comment from: Preprint - https://www.biorxiv.org/content/10.1101/2020.04.14.041434v1 - Li et al
Total death rate is higher in Spain compared to China, so looked differences between the Asian and Caucasian populations for ACE2 polymorphisms using gnomAD v2.1 exomes and compare the variability of hACE2 expression in peripheral blood among eight different populations. Four genetic variants reached statistical significance for differences in MAF between the two populations N720D, K26R, N638S, I468V. Found small differences in expression of hACE2 among various populations.

Preprint - https://www.biorxiv.org/content/10.1101/2020.04.05.026633v1 - Gibson et al
Analyse ACE2 variants in the gnomAD database and identify 15 missense variants likely to affect the affinity of the human ACE2 protein for the viral spike protein and estimated the change in binding energy of the 15 missense variants.; to: Preprint - https://www.biorxiv.org/content/10.1101/2020.04.14.041434v1 - Li et al
Total death rate is higher in Spain compared to China, so looked differences between the Asian and Caucasian populations for ACE2 polymorphisms using gnomAD v2.1 exomes and compare the variability of hACE2 expression in peripheral blood among eight different populations. Four genetic variants reached statistical significance for differences in MAF between the two populations N720D, K26R, N638S, I468V. Found small differences in expression of hACE2 among various populations.

Preprint - https://www.biorxiv.org/content/10.1101/2020.04.05.026633v1 - Gibson et al
Analyse ACE2 variants in the gnomAD database and identify 15 missense variants likely to affect the affinity of the human ACE2 protein for the viral spike protein and estimated the change in binding energy of the 15 missense variants.

Preprint - https://www.biorxiv.org/content/10.1101/2020.04.07.024752v1 - Stawiski et al
Aassessed ACE2 protein-altering variations from a number of databases including the gnomAD, RotterdamStudy, ALSPAC, GenomeAsia100k, HGDP, TOMMO-3.5kjpnv2, IndiGen, and HGDP. Identified variants that are likely to either increase or decrease the binding affinity of ACE2 to the S-protein and thereby alter the ability of the
virus to infect the host cell.

Preprint - https://www.biorxiv.org/content/10.1101/2020.03.16.994236v1 Procko
Made a library of coding sequence of ACE2 containing all possible single amino acid substitutions at 117 sites spanning the interface with S and lining the substrate cavity. The ACE2 library was transiently expressed in human Expi293F cells and cells were then incubated in medium containing the receptor binding domain of SARS-CoV-2 fused C-terminallyto superfolder GFP. Sorted cells with high and low binding and the transcripts sequenced to identify the variants.
Intellectual disability v3.31 YARS Zornitza Stark gene: YARS was added
gene: YARS was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: YARS was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: YARS were set to 30304524; 29232904; 27633801
Phenotypes for gene: YARS were set to Intellectual disability; deafness; nystagmus; liver dysfunction
Review for gene: YARS was set to GREEN
gene: YARS was marked as current diagnostic
Added comment: Mono-allelic variants are associated with CMT. However, 10 individuals from three unrelated families reported with bi-allelic variants and a severe phenotype, comprising ID, nystagmus, deafness, liver dysfunction and a range of other features.
Sources: Literature
Skeletal dysplasia v2.7 PKDCC Zornitza Stark gene: PKDCC was added
gene: PKDCC was added to Skeletal dysplasia. Sources: Literature
Mode of inheritance for gene: PKDCC was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PKDCC were set to 30478137; 19097194
Phenotypes for gene: PKDCC were set to Rhizomelia; dysmorphism
Review for gene: PKDCC was set to AMBER
Added comment: Two unrelated consanguineous families reported with different homozygous variants
Pre-existing mouse model has similar phenotype
Sources: Literature
Primary ciliary disorders v1.22 SPEF2 Zornitza Stark gene: SPEF2 was added
gene: SPEF2 was added to Primary ciliary disorders. Sources: Literature
Mode of inheritance for gene: SPEF2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SPEF2 were set to 31151990; 31278745; 31048344; 31942643
Phenotypes for gene: SPEF2 were set to Spermatogenic failure 43, MIM#618751; Primary ciliary dyskinesia-like phenotype
Review for gene: SPEF2 was set to AMBER
Added comment: 4 families reported with bi-allelic variants and sperm morphological abnormalities plus recurrent sinopulmonary infections and bronchiectasis, consistent with a PCD-like phenotype. Morphological abnormalities of the respiratory cilia were not observed. Mouse model recapitulated the infertility phenotype but also had hydrocephalus and sinusitis, again arguing for broader impact on ciliary function. Note other reports of individuals with bi-allelic variants and no respiratory phenotype reported. Given respiratory phenotype is milder and currently it is unclear in what proportion of individuals it is present, Amber rating suggested.
Sources: Literature
Retinal disorders v2.8 USP45 Zornitza Stark gene: USP45 was added
gene: USP45 was added to Retinal disorders. Sources: Literature
Mode of inheritance for gene: USP45 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: USP45 were set to 30573563
Phenotypes for gene: USP45 were set to Lebers congenital amaurosis; retinal dystrophy
Review for gene: USP45 was set to GREEN
gene: USP45 was marked as current diagnostic
Added comment: 2 unrelated Chinese families reported with rare homozygous variants (one missense, one nonsense) and Leber congenital amaurosis. Animal knockout functional studies recapitulate retinal phenotype
Sources: Literature
Gastrointestinal neuromuscular disorders v1.12 MYH11 Zornitza Stark gene: MYH11 was added
gene: MYH11 was added to Gastrointestinal neuromuscular disorders. Sources: Expert list
Mode of inheritance for gene: MYH11 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: MYH11 were set to 31944481; 29575632
Phenotypes for gene: MYH11 were set to Megacystis microcolon intestinal hypoperistalsis syndrome, autosomal recessive; Dominant smooth muscle dysmotility syndrome
Review for gene: MYH11 was set to GREEN
gene: MYH11 was marked as current diagnostic
Added comment: Heterozygous dominant negative MYH11 pathogenic variants have been associated with thoracic aortic aneurysm and dissection while biallelic null alleles have been associated with megacystis microcolon intestinal hypoperistalsis syndrome. Recent report of two families with heterozygous protein‐elongating MYH11 variants affecting the SM2 isoforms of MYH11 as a cause for severe gastrointestinal dysmotility. The authors hypothesise that the mechanistic pathogenesis of this disease, dominant hypercontractile loss‐of‐function, is distinct from those implicated in other diseases involving MYH11 dysfunction.
Sources: Expert list
Intellectual disability v3.31 CACNB4 Zornitza Stark reviewed gene: CACNB4: Rating: AMBER; Mode of pathogenicity: None; Publications: 32176688; Phenotypes: Intellectual disability, epilepsy, movement disorder; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.137 ACE2 Eleanor Williams changed review comment from: Preprint - https://www.biorxiv.org/content/10.1101/2020.04.14.041434v1 - Li et al
Total death rate is higher in Spain compared to China, so looked differences between the Asian and Caucasian populations for ACE2 polymorphisms using gnomAD v2.1 exomes and compare the variability of hACE2 expression in peripheral blood among eight different populations. Four genetic variants reached statistical significance for differences in MAF between the two populations N720D, K26R, N638S, I468V. Found small differences in expression of hACE2 among various populations.; to: Preprint - https://www.biorxiv.org/content/10.1101/2020.04.14.041434v1 - Li et al
Total death rate is higher in Spain compared to China, so looked differences between the Asian and Caucasian populations for ACE2 polymorphisms using gnomAD v2.1 exomes and compare the variability of hACE2 expression in peripheral blood among eight different populations. Four genetic variants reached statistical significance for differences in MAF between the two populations N720D, K26R, N638S, I468V. Found small differences in expression of hACE2 among various populations.

Preprint - https://www.biorxiv.org/content/10.1101/2020.04.05.026633v1 - Gibson et al
Analyse ACE2 variants in the gnomAD database and identify 15 missense variants likely to affect the affinity of the human ACE2 protein for the viral spike protein and estimated the change in binding energy of the 15 missense variants.
COVID-19 research v0.137 ACE2 Eleanor Williams commented on gene: ACE2
Primary immunodeficiency or monogenic inflammatory bowel disease v2.128 ALPI Eleanor Williams Classified gene: ALPI as Amber List (moderate evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.128 ALPI Eleanor Williams Added comment: Comment on list classification: Changing rating from red to amber. 2 cases reported plus some functional data.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.128 ALPI Eleanor Williams Gene: alpi has been classified as Amber List (Moderate Evidence).
COVID-19 research v0.137 ALPI Eleanor Williams changed review comment from: Not associated with a phenotype in OMIM or Gene2Phenotype.

PMID: 29567797 - Parlato et al 2018- report ALPI mutations in two unrelated patients with severe intestinal inflammation and autoimmunity. WES was used. Patient 1 - non‐consanguineous parents. At 2 years old was diagnosed with coeliac disease from HLA-typing. At age 3 had recurrent abdominal pain, rectal bleeding and severe diarrhoea. Patient 2 - non‐consanguineous parents of Jewish Ashkenazi origin. Age 15 he was diagnosed with ileocolonic Crohn's disease. Compound heterozygous mutations in the ALPI gene were found in both patients. Three variants result in the substitution of residues highly conserved across species (A97T, A350V and A360) and one variant (Q439X) introducing a premature stop codon. Functional studies in HEK293T cells showed that all ALPI mutations were loss of function. ALPI expression was reduced in patients’ biopsies.; to: Not associated with a phenotype in OMIM or Gene2Phenotype.

PMID: 29567797 - Parlato et al 2018- report ALPI mutations in two unrelated patients with severe intestinal inflammation and autoimmunity. WES was used. Patient 1 - non‐consanguineous parents. At 2 years old was diagnosed with coeliac disease from HLA-typing. At age 3 had recurrent abdominal pain, rectal bleeding and severe diarrhoea. Patient 2 - non‐consanguineous parents of Jewish Ashkenazi origin. Age 15 he was diagnosed with ileocolonic Crohn's disease. Compound heterozygous mutations in the ALPI gene were found in both patients. Three variants result in the substitution of residues highly conserved across species (A97T, A350V and A360) and one variant (Q439X) introducing a premature stop codon. Functional studies in HEK293T cells showed that all ALPI mutations were loss of function. ALPI expression was reduced in patients’ biopsies.

Rated Amber by Zornitza Stark on the PID panel.
COVID-19 research v0.137 ALPI Eleanor Williams commented on gene: ALPI
Primary immunodeficiency or monogenic inflammatory bowel disease v2.127 ALPI Eleanor Williams changed review comment from: Not associated with a phenotype in OMIM or Gene2Phenotype.

PMID: 29567797 - report ALPI mutations in two unrelated patients with severe intestinal inflammation and autoimmunity. WES was used. Patient 1 - non‐consanguineous parents. At 2 years old was diagnosed with coeliac disease from HLA-typing. At age 3 had recurrent abdominal pain, rectal bleeding and severe diarrhoea. Patient 2 - non‐consanguineous parents of Jewish Ashkenazi origin. Age 15 he was diagnosed with ileocolonic Crohn's disease. Compound heterozygous mutations in the ALPI gene were found in both patients. Three variants result in the substitution of residues highly conserved across species (A97T, A350V and A360) and one variant (Q439X) introducing a premature stop codon. Functional studies in HEK293T cells showed that all ALPI mutations were loss of function. ALPI expression was reduced in patients’ biopsies.; to: Not associated with a phenotype in OMIM or Gene2Phenotype.

PMID: 29567797 - Parlato et al 2018- report ALPI mutations in two unrelated patients with severe intestinal inflammation and autoimmunity. WES was used. Patient 1 - non‐consanguineous parents. At 2 years old was diagnosed with coeliac disease from HLA-typing. At age 3 had recurrent abdominal pain, rectal bleeding and severe diarrhoea. Patient 2 - non‐consanguineous parents of Jewish Ashkenazi origin. Age 15 he was diagnosed with ileocolonic Crohn's disease. Compound heterozygous mutations in the ALPI gene were found in both patients. Three variants result in the substitution of residues highly conserved across species (A97T, A350V and A360) and one variant (Q439X) introducing a premature stop codon. Functional studies in HEK293T cells showed that all ALPI mutations were loss of function. ALPI expression was reduced in patients’ biopsies.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.127 ALPI Eleanor Williams commented on gene: ALPI
Primary immunodeficiency or monogenic inflammatory bowel disease v2.127 ADAM17 Eleanor Williams Classified gene: ADAM17 as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.127 ADAM17 Eleanor Williams Added comment: Comment on list classification: Changing rating from amber to green. 3 cases plus mouse model.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.127 ADAM17 Eleanor Williams Gene: adam17 has been classified as Green List (High Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.126 ADAM17 Eleanor Williams Phenotypes for gene: ADAM17 were changed from inflammatory skin; Inflammatory skin and bowel disease, neonatal, 1; Inflammatory skin and bowel disease, neonatal 1, 614328; ADAM17 deficiency; Autoinflammatory Disorders; IBD-1; Early onset diarrhea and skin lesions to inflammatory skin; Inflammatory skin and bowel disease, neonatal, 1; Inflammatory skin and bowel disease, neonatal 1, 614328; ADAM17 deficiency; Autoinflammatory Disorders; IBD-1; Early onset diarrhea and skin lesions; Recurrent infections
Primary immunodeficiency or monogenic inflammatory bowel disease v2.125 ADAM17 Eleanor Williams Publications for gene: ADAM17 were set to 22010916; 28930861; 20603312; 32048120; 25171914; 11149563; 25058236; 32086639
COVID-19 research v0.137 ADAM17 Eleanor Williams reviewed gene: ADAM17: Rating: ; Mode of pathogenicity: None; Publications: 22010916, 26683521, 25804906, 29560122; Phenotypes: ?Inflammatory skin and bowel disease, neonatal, 1 #614328; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.124 ADAM17 Eleanor Williams commented on gene: ADAM17
Primary immunodeficiency or monogenic inflammatory bowel disease v2.124 BCL11B Eleanor Williams changed review comment from: Associated with Immunodeficiency 49 #617237 (AD) in OMIM.

PMID: 29985992 - Lessel et al 2018 - identified de novo heterozygous germline mutations in BCL11B in nine unrelated patients, namely six frameshift, two nonsense and one missense mutation. A further patient inherited a heterozygous frameshift mutation, p.(Asp534Thrfs*29), transmitted from an affected mother with. All analysed individuals exhibited developmental delay and intellectual disability and a severe reduction of peripheral ILC2s and impaired T cell development, but no overt immune deficiency. Patient E:II-1 was the only patient with suspected immunodeficiency diagnosed upon newborn screening. Other de-novo variants were also detected in some patients.

PMID: 27959755 - Punwani et al 2016 - an infant with "leaky" SCID as well as craniofacial and dermal abnormalities and the absence of a corpus callosum. Exome sequencing revealed a heterozygous de novo missense mutation, p.N441K, in BCL11B. The mutant protein had dominant negative activity, which prevented the wild-type BCL11B to bind DNA, thereby arresting development of the T-cell lineage and disrupting hematopoietic stem-cell migration. bcl11ba-deficient zebrafish recapitulated the phenotype.; to: Associated with Immunodeficiency 49 #617237 (AD) in OMIM.

PMID: 29985992 - Lessel et al 2018 - identified de novo heterozygous germline mutations in BCL11B in nine unrelated patients, namely six frameshift, two nonsense and one missense mutation. A further patient inherited a heterozygous frameshift mutation, p.(Asp534Thrfs*29), transmitted from an affected mother with. All analysed individuals exhibited developmental delay and intellectual disability and a severe reduction of peripheral ILC2s and impaired T cell development, but no overt immune deficiency. Patient E:II-1, with a missense variant, was the only patient with suspected immunodeficiency diagnosed upon newborn screening. Other de-novo variants were also detected in some patients.

PMID: 27959755 - Punwani et al 2016 - an infant with "leaky" SCID as well as craniofacial and dermal abnormalities and the absence of a corpus callosum. Exome sequencing revealed a heterozygous de novo missense mutation, p.N441K, in BCL11B. The mutant protein had dominant negative activity, which prevented the wild-type BCL11B to bind DNA, thereby arresting development of the T-cell lineage and disrupting hematopoietic stem-cell migration. bcl11ba-deficient zebrafish recapitulated the phenotype.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.124 BCL11B Eleanor Williams commented on gene: BCL11B
Primary immunodeficiency or monogenic inflammatory bowel disease v2.124 BLOC1S6 Eleanor Williams changed review comment from: Provisionally associated with ?Hermansky-pudlak syndrome 9 #614171 (AR) in OMIM.
BLOC1S6 is also known as PLDN and HPS9.

PMID: 32245340 - Michaud et al 2020 - report 1 patient presenting with ocular features of albinism. Genetic analysis revealed two compound heterozygous variants in the BLOC1S6 gene. Extended hematological studies confirmed the platelet storage pool disease with absence of dense granules and abnormal platelet aggregation. (Abstract only accessed).

PMID: 22461475 - Badolato et al 2012 - report a northern Italian girl with oculocutaneous albinism, nystagmus, and normal neurologic development who presented with recurrent cutaneous infections but without hemorrhagic episodes. She had thrombocytopenia and leukopenia, with normal platelet aggregation. WES found a homozygous nonsense mutation, c.232C > T (p.Q78X) in PLDN (BLOC1S6). This variant was confirmed homozygous in the patient and heterozygous in her parents by Sanger sequencing, and was associated with absent PLDN protein expression

PMID: 26575419 - Yousaf et al 2016 - report a Pakistani family in which the proband had a nonsense mutation is the HPS9/PLDN gene (c.232C>T, p.Gln78*). The 4-year-old female patient reported here, had Oculocutaneous albinism, photophobia, nystagmus, prolonged bleeding and clotting times, which indicate platelet dysfunction.

PMID: 21665000 - Cullinane et al 2011 - RETRACTED PAPER - report 1 9-month old male patient of Indian ancestry with a homozygous c.232C>T; p.Gln78Och mutation and HPS-like phenotype. This paper has been retracted due to falsified and/or fabricated gel images which represent expression of PLDN in fibroblasts and melanocytes.

Summary: 3 reports + retracted paper. 2 out of the 3 patients had abnormal platelet aggregation.; to: Provisionally associated with ?Hermansky-pudlak syndrome 9 #614171 (AR) in OMIM.
BLOC1S6 is also known as PLDN and HPS9.

PMID: 32245340 - Michaud et al 2020 - report 1 patient presenting with ocular features of albinism. Genetic analysis revealed two compound heterozygous variants in the BLOC1S6 gene. Extended hematological studies confirmed the platelet storage pool disease with absence of dense granules and abnormal platelet aggregation. (Abstract only accessed).

PMID: 22461475 - Badolato et al 2012 - report a northern Italian girl with oculocutaneous albinism, nystagmus, and normal neurologic development who presented with recurrent cutaneous infections but without hemorrhagic episodes. She had thrombocytopenia and leukopenia, with normal platelet aggregation. WES found a homozygous nonsense mutation, c.232C > T (p.Q78X) in PLDN (BLOC1S6). This variant was confirmed homozygous in the patient and heterozygous in her parents by Sanger sequencing, and was associated with absent PLDN protein expression

PMID: 26575419 - Yousaf et al 2016 - report a Pakistani family in which the proband had a nonsense mutation is the HPS9/PLDN gene (c.232C>T, p.Gln78*). The 4-year-old female patient reported here, had Oculocutaneous albinism, photophobia, nystagmus, prolonged bleeding and clotting times, which indicate platelet dysfunction.

PMID: 21665000 - Cullinane et al 2011 - RETRACTED PAPER - report 1 9-month old male patient of Indian ancestry with a homozygous c.232C>T; p.Gln78Och mutation and HPS-like phenotype. This paper has been retracted due to falsified and/or fabricated gel images which represent expression of PLDN in fibroblasts and melanocytes.

Summary: 3 reports + retracted paper. 2 out of the 3 patients had abnormal platelet aggregation. The 3rd had thrombocytopenia and leukopenia, with normal platelet aggregation.
COVID-19 research v0.137 HLA-DRB1 Catherine Snow Classified gene: HLA-DRB1 as Green List (high evidence)
COVID-19 research v0.137 HLA-DRB1 Catherine Snow Added comment: Comment on list classification: Rating as Green due to expert review and publications associated with HLA-DRB1 and viral susceptibility
COVID-19 research v0.137 HLA-DRB1 Catherine Snow Gene: hla-drb1 has been classified as Green List (High Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.124 BLOC1S6 Eleanor Williams Publications for gene: BLOC1S6 were set to 22461475,20301464,26575419
COVID-19 research v0.136 FPR2 Catherine Snow Classified gene: FPR2 as Green List (high evidence)
COVID-19 research v0.136 FPR2 Catherine Snow Added comment: Comment on list classification: Upgrading to Green based on expert review
COVID-19 research v0.136 FPR2 Catherine Snow Gene: fpr2 has been classified as Green List (High Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.123 BLOC1S6 Eleanor Williams reviewed gene: BLOC1S6: Rating: ; Mode of pathogenicity: None; Publications: 32245340, 22461475, 26575419, 21665000; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.135 MPO Catherine Snow changed review comment from: Comment on list classification: Based on an external review detailing a number of publications where MPO is reviewed because of its association in the regulation of (neutrophil extracellular traps) NET formation upgrading from Amber to Green; to: Comment on list classification: Based on an external review detailing a number of publications where MPO is reviewed because of its association in the regulation of (neutrophil extracellular traps) NET formation upgrading from Amber to Green

Should also be noted that elevated levels of inflammatory mediators (including IL-6, IL-8, and MPO) in the airway of chronic/extended or recurrent RSV infection are associated with faster lung function decline in COPD patients. PMID: 32227102
COVID-19 research v0.135 MPO Catherine Snow Publications for gene: MPO were set to 9354683; 15108282; 9637725; 32082301; 27574522; 21703402; 29325098; 29769163; 24968347
COVID-19 research v0.134 MPO Catherine Snow Classified gene: MPO as Green List (high evidence)
COVID-19 research v0.134 MPO Catherine Snow Added comment: Comment on list classification: Based on an external review detailing a number of publications where MPO is reviewed because of its association in the regulation of (neutrophil extracellular traps) NET formation upgrading from Amber to Green
COVID-19 research v0.134 MPO Catherine Snow Gene: mpo has been classified as Green List (High Evidence).
COVID-19 research v0.133 MPO Catherine Snow Publications for gene: MPO were set to 9354683; 15108282; 9637725; 32082301; 27574522; 21703402; 29325098; 29769163; 24968347
COVID-19 research v0.132 MPO Catherine Snow Publications for gene: MPO were set to 9354683; 15108282; 9637725; 32082301
Primary immunodeficiency or monogenic inflammatory bowel disease v2.123 C17orf62 Eleanor Williams Classified gene: C17orf62 as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.123 C17orf62 Eleanor Williams Added comment: Comment on list classification: Changing rating from red to green. 6 Icelandic related cases with same variant, another variant identified in Saudia Arabian individual with related phenotype. Mouse model and functional studies support the role of this gene in Chronic granulomatous disease
Primary immunodeficiency or monogenic inflammatory bowel disease v2.123 C17orf62 Eleanor Williams Gene: c17orf62 has been classified as Green List (High Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.122 C17orf62 Eleanor Williams Phenotypes for gene: C17orf62 were changed from Autosomal recessive CGD EROS; Congenital defects of phagocyte number or function to Autosomal recessive CGD EROS; Congenital defects of phagocyte number or function; Chronic granulomatous disease
Primary immunodeficiency or monogenic inflammatory bowel disease v2.121 C17orf62 Eleanor Williams Publications for gene: C17orf62 were set to 30312704; 30361506; 32086639; 32048120
Primary immunodeficiency or monogenic inflammatory bowel disease v2.120 C17orf62 Eleanor Williams commented on gene: C17orf62
Primary immunodeficiency or monogenic inflammatory bowel disease v2.120 CIB1 Eleanor Williams Classified gene: CIB1 as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.120 CIB1 Eleanor Williams Added comment: Comment on list classification: Promoting this gene from Grey to Green. There are more than 3 cases with plausible disease causing variants.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.120 CIB1 Eleanor Williams Gene: cib1 has been classified as Green List (High Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.119 CIB1 Eleanor Williams reviewed gene: CIB1: Rating: ; Mode of pathogenicity: None; Publications: 30068544; Phenotypes: Epidermodysplasia verruciformis 3 #618267; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.119 IL18BP Ivone Leong Classified gene: IL18BP as Red List (low evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.119 IL18BP Ivone Leong Added comment: Comment on list classification: Gene given Red gene status based on expert review. This gene is also found in the IUIS 2019 paper (PMID: 31953710)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.119 IL18BP Ivone Leong Gene: il18bp has been classified as Red List (Low Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.118 IL18BP Ivone Leong Publications for gene: IL18BP were set to 31213488
Primary immunodeficiency or monogenic inflammatory bowel disease v2.117 IL12RB2 Ivone Leong Publications for gene: IL12RB2 were set to 30578351; 31953710
Primary immunodeficiency or monogenic inflammatory bowel disease v2.117 IL12RB2 Ivone Leong Publications for gene: IL12RB2 were set to 30578351
Primary immunodeficiency or monogenic inflammatory bowel disease v2.116 IL12RB2 Ivone Leong Classified gene: IL12RB2 as Red List (low evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.116 IL12RB2 Ivone Leong Added comment: Comment on list classification: Gene given Red gene status based on expert review. This gene is also found in the IUIS 2019 paper (PMID: 31953710)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.116 IL12RB2 Ivone Leong Gene: il12rb2 has been classified as Red List (Low Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.115 IL23R Ivone Leong Classified gene: IL23R as Red List (low evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.115 IL23R Ivone Leong Added comment: Comment on list classification: Gene given Red gene status based on expert review. This gene is also found in the IUIS 2019 paper (PMID: 31953710)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.115 IL23R Ivone Leong Gene: il23r has been classified as Red List (Low Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.114 IL23R Ivone Leong Publications for gene: IL23R were set to 30578351
Primary immunodeficiency or monogenic inflammatory bowel disease v2.113 POLR3F Ivone Leong Classified gene: POLR3F as Red List (low evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.113 POLR3F Ivone Leong Added comment: Comment on list classification: Gene given Red gene status based on expert review. This gene is also found in the IUIS 2019 paper (PMID: 31953710)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.113 POLR3F Ivone Leong Gene: polr3f has been classified as Red List (Low Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.112 POLR3F Ivone Leong Publications for gene: POLR3F were set to 30211253
Primary immunodeficiency or monogenic inflammatory bowel disease v2.111 IRF4 Ivone Leong Publications for gene: IRF4 were set to 29537367
Primary immunodeficiency or monogenic inflammatory bowel disease v2.110 IRF4 Ivone Leong Classified gene: IRF4 as Red List (low evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.110 IRF4 Ivone Leong Added comment: Comment on list classification: Gene given Red gene status based on expert review. This gene is also found in the IUIS 2019 paper (PMID: 31953710)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.110 IRF4 Ivone Leong Gene: irf4 has been classified as Red List (Low Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.109 CD247 Ivone Leong Publications for gene: CD247 were set to 16672702; 26690594; 17170122; 27555457; 25688246; https://doi.org/10.14785/lpsn-2014-0012
Primary immunodeficiency or monogenic inflammatory bowel disease v2.108 SLC7A7 Ivone Leong Classified gene: SLC7A7 as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.108 SLC7A7 Ivone Leong Added comment: Comment on list classification: Promoted from Red to Green. SLC7A7 causes lysinuric protein intolerance (LPI) and immunodeficiency is one of the phenotypes. There are >3 unrelated cases reported on OMIM.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.108 SLC7A7 Ivone Leong Gene: slc7a7 has been classified as Green List (High Evidence).
COVID-19 research v0.131 AKT1 Sarah Leigh Added comment: Comment on phenotypes: OMIM cites a general phenotypic description for Cowden syndrome 1 (158350) includes Immunodeficiency in some patients (PMID 26246517).
COVID-19 research v0.131 AKT1 Sarah Leigh Phenotypes for gene: AKT1 were changed from to Cowden syndrome 6 615109
COVID-19 research v0.130 AKT1 Sarah Leigh Publications for gene: AKT1 were set to 17931677
COVID-19 research v0.129 AKT1 Sarah Leigh Publications for gene: AKT1 were set to
COVID-19 research v0.128 AKT1 Sarah Leigh Classified gene: AKT1 as Red List (low evidence)
COVID-19 research v0.128 AKT1 Sarah Leigh Added comment: Comment on list classification: AKT1 gene product can inhibit apoptosis through phosphorylation,
and the inhibition of pro-apoptotic mediators to contribute to the maintenance of the virus latent state and may facilitate transformation of human lymphotropic virus type 1 infected cells (PMID 17931677).
COVID-19 research v0.128 AKT1 Sarah Leigh Gene: akt1 has been classified as Red List (Low Evidence).
Nephrocalcinosis or nephrolithiasis v2.13 VPS33B Rebecca Foulger Classified gene: VPS33B as Green List (high evidence)
Nephrocalcinosis or nephrolithiasis v2.13 VPS33B Rebecca Foulger Gene: vps33b has been classified as Green List (High Evidence).
Nephrocalcinosis or nephrolithiasis v2.12 VPS33B Rebecca Foulger gene: VPS33B was added
gene: VPS33B was added to Nephrocalcinosis or nephrolithiasis. Sources: Literature
Mode of inheritance for gene: VPS33B was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: VPS33B were set to 15052268; 22753090
Phenotypes for gene: VPS33B were set to Arthrogryposis, renal dysfunction, and cholestasis 1, 208085
Added comment: Added to panel as Green gene as advised by Helen Brittain, Genomics England Clinical Team. This rating should be reviewed by GLHs at the date of next GMS panel update. ARC phenotype (MIM:208085) is appropriate for the panel, and sufficient cases to support causation (see also the other ARC gene, VIPAS39).
Sources: Literature
Nephrocalcinosis or nephrolithiasis v2.11 VIPAS39 Rebecca Foulger Classified gene: VIPAS39 as Green List (high evidence)
Nephrocalcinosis or nephrolithiasis v2.11 VIPAS39 Rebecca Foulger Gene: vipas39 has been classified as Green List (High Evidence).
Nephrocalcinosis or nephrolithiasis v2.10 VIPAS39 Rebecca Foulger commented on gene: VIPAS39: PMID:20190753 (Cullinane et al., 2010) identify biallelic (homozygous or compound het) variants in 7 probands from consanguineous families with ARC (MIM:613404) from various ethnic backgrounds (Turkish, Croation, Israeli Arab, Italian). Variants include Q179X, T250ArgfsX279, R220X, Q291X, M1R. The paper does not further discuss the kidney phenotype.
Nephrocalcinosis or nephrolithiasis v2.10 VIPAS39 Rebecca Foulger gene: VIPAS39 was added
gene: VIPAS39 was added to Nephrocalcinosis or nephrolithiasis. Sources: Literature
Mode of inheritance for gene: VIPAS39 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: VIPAS39 were set to 20190753
Phenotypes for gene: VIPAS39 were set to Arthrogryposis, renal dysfunction, and cholestasis 2, 613404
Added comment: Added to panel as Green following advice from Helen Brittain, Genomics England Clinical Team. Nephrocalcinosis is a feature of the phenotype. Other syndromes are on this panel (Lesch-Nyhan and Lowe syndrome) as Green, and therefore rated Green to match. This rating should be reviewed by GLHs at the date of next GMS panel update.
Sources: Literature
Unexplained young onset end-stage renal disease v1.10 VIPAS39 Rebecca Foulger Phenotypes for gene: VIPAS39 were changed from Arthrogryposis, renal dysfunction, and cholestasis 2, 613404 to Arthrogryposis, renal dysfunction, and cholestasis 2, 613404
Unexplained young onset end-stage renal disease v1.9 VIPAS39 Rebecca Foulger changed review comment from: Comment on list classification: Updated rating from Red to Green following advice from Helen Brittain, Genomics England Clinical Team. PMID:20190753 (Cullinane et al., 2010) identify biallelic (homozygous or compound het) variants in 7 probands from consanguineous families with ARC (MIM:613404) from various ethnic backgrounds (Turkish, Croation, Israeli Arab, Italian). Variants include Q179X, T250ArgfsX279, R220X, Q291X, M1R. The paper does not further discuss the kidney phenotype but the other ARC syndrome gene, VPS33B, is already green on this panel.; to: Comment on list classification: Updated rating from Red to Green following advice from Helen Brittain, Genomics England Clinical Team. PMID:20190753 (Cullinane et al., 2010) identify biallelic (homozygous or compound het) variants in 7 probands from consanguineous families with ARC (MIM:613404) from various ethnic backgrounds (Turkish, Croation, Israeli Arab, Italian). Variants include Q179X, T250ArgfsX279, R220X, Q291X, M1R. The paper does not further discuss the kidney phenotype but the other ARC syndrome gene, VPS33B, is already green on this panel. This rating should be reviewed by GLHs at the date of next GMS panel update.
Unexplained young onset end-stage renal disease v1.9 VIPAS39 Rebecca Foulger Classified gene: VIPAS39 as Green List (high evidence)
Unexplained young onset end-stage renal disease v1.9 VIPAS39 Rebecca Foulger Added comment: Comment on list classification: Updated rating from Red to Green following advice from Helen Brittain, Genomics England Clinical Team. PMID:20190753 (Cullinane et al., 2010) identify biallelic (homozygous or compound het) variants in 7 probands from consanguineous families with ARC (MIM:613404) from various ethnic backgrounds (Turkish, Croation, Israeli Arab, Italian). Variants include Q179X, T250ArgfsX279, R220X, Q291X, M1R. The paper does not further discuss the kidney phenotype but the other ARC syndrome gene, VPS33B, is already green on this panel.
Unexplained young onset end-stage renal disease v1.9 VIPAS39 Rebecca Foulger Gene: vipas39 has been classified as Green List (High Evidence).
Unexplained young onset end-stage renal disease v1.8 VIPAS39 Rebecca Foulger Publications for gene: VIPAS39 were set to
Additional findings reproductive carrier status v0.4 Eleanor Williams Panel types changed to Additional Findings
Additional findings health related v0.110 Eleanor Williams Panel types changed to Additional Findings
Additional findings health related - CNV analysis adults v0.9 Eleanor Williams Panel types changed to Super Panel; Additional Findings
Additional findings health related - adults v0.9 Eleanor Williams Panel types changed to Super Panel; Additional Findings
Additional findings health related - CNV analysis adult specific v0.15 Eleanor Williams Panel types changed to Component Of Super Panel; Additional Findings
Additional findings health related - CNV analysis children v0.10 Eleanor Williams Panel types changed to Component Of Super Panel; Additional Findings
Additional findings health related - children v0.12 Eleanor Williams Panel types changed to Component Of Super Panel; Additional Findings
Additional findings health related - adult specific v0.14 Eleanor Williams Panel types changed to Component Of Super Panel; Additional Findings
CAKUT v1.58 BMP4 Rebecca Foulger commented on gene: BMP4: Kept rating as Amber following agreement from Helen Brittain, Genomics England Clinical Team: evidence is borderline and. further cases or supportive evidence is needed to be confident of a causal link. Rated Amber but can be re-assessed by GLH groups at a future date.
CAKUT v1.58 CENPF Rebecca Foulger commented on gene: CENPF: Kept rating as Amber following agreement from Helen Brittain, Genomics England Clinical Team: the evidence for a congenital renal anomaly is borderline, and in view of two families only, Amber is appropriate until further families are identified.
Limb disorders v2.5 CEP55 Rebecca Foulger Classified gene: CEP55 as Green List (high evidence)
Limb disorders v2.5 CEP55 Rebecca Foulger Added comment: Comment on list classification: Rated as Green after agreement with Eleanor Williams- relevant phenotype for panel, and sufficient cases to support association.
Limb disorders v2.5 CEP55 Rebecca Foulger Gene: cep55 has been classified as Green List (High Evidence).
Limb disorders v2.5 CEP55 Rebecca Foulger Classified gene: CEP55 as Green List (high evidence)
Limb disorders v2.5 CEP55 Rebecca Foulger Added comment: Comment on list classification: Rated as Green after agreement with Eleanor Williams- relevant phenotype for panel, and sufficient cases to support association.
Limb disorders v2.5 CEP55 Rebecca Foulger Gene: cep55 has been classified as Green List (High Evidence).
Renal ciliopathies v1.15 CEP55 Rebecca Foulger Classified gene: CEP55 as Amber List (moderate evidence)
Renal ciliopathies v1.15 CEP55 Rebecca Foulger Added comment: Comment on list classification: Rated as Amber on advice from Helen Brittain: all of the cases are prenatal / peri-natal lethal so better suited to Fetal panel.
Renal ciliopathies v1.15 CEP55 Rebecca Foulger Gene: cep55 has been classified as Amber List (Moderate Evidence).
Renal ciliopathies v1.14 CEP55 Rebecca Foulger Publications for gene: CEP55 were set to 28295209
Renal ciliopathies v1.13 CEP55 Rebecca Foulger gene: CEP55 was added
gene: CEP55 was added to Renal ciliopathies. Sources: Literature
Mode of inheritance for gene: CEP55 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CEP55 were set to 28295209
Phenotypes for gene: CEP55 were set to Meckel-like syndrome; autosomal recessive lethal ciliopathy; renal dysplasia
Review for gene: CEP55 was set to AMBER
Added comment: Added CEP55 to renal ciliopathy panel as Amber after agreement from Helen Brittain, Genomics England Clinical Team. PMID:28295209 (Bondeson et al) report a Swedish couple with 2 affected male fetuses homozygous for CEP55 p.Arg86*. Although the phenotype differed between fetuses, both exhibited kidney phenotypes (including renal dysplasia). Segregation analysis supported the gene:disease association, and haplotype analysis suggested a founder effect. The authors concluded the phenotype was consistent with an AR lethal ciliopathy. The lethal phenotype is similar to that reported in individuals in PMID:30622327 (Rawlins et al., 2019) and PMID:28264986 (Frosk et al, 2017).
Sources: Literature
Limb disorders v2.4 CEP55 Rebecca Foulger commented on gene: CEP55: PMID:32100459 (Barrie et al., 2020) describe 7 living indivduals (5 families) with biallelic CEP55 variants (compound het and homozygous splice site variant). The phenotype includes microcephaly, developmental delay and syndactyly. Patients 1,2,3,4 had bilateral toe syndactyly and 5th finger clinodactyly, Patient 5 had unilateral club foot. The three siblings (patients 5,6,7) all had small hands and feet.
Limb disorders v2.4 CEP55 Rebecca Foulger gene: CEP55 was added
gene: CEP55 was added to Limb disorders. Sources: Literature
Mode of inheritance for gene: CEP55 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CEP55 were set to 32100459
Phenotypes for gene: CEP55 were set to microcephaly, developmental delay and bilateral toe syndactyly
Added comment: Added to Limb disorders panel on advice from Helen Brittain, Genomics England Clinical Team. Phenotype of living individuals in PMID:32100459 (Barrie et al., 2020) includes syndactyly.
Sources: Literature
Additional findings health related - CNV analysis adult specific v0.14 Eleanor Williams Panel types changed to Component Of Super Panel
Additional findings health related - CNV analysis children v0.9 Eleanor Williams Panel types changed to Component Of Super Panel
Additional findings health related - children v0.11 Eleanor Williams Panel types changed to Component Of Super Panel
Additional findings health related - adult specific v0.12 Eleanor Williams Panel types changed to Component Of Super Panel
Intellectual disability v3.31 CEP55 Rebecca Foulger Classified gene: CEP55 as Green List (high evidence)
Intellectual disability v3.31 CEP55 Rebecca Foulger Added comment: Comment on list classification: Rated CEP55 as Green: >3 unrelated cases in PMID:32100459 with DD/ID (2 of which are severe).
Intellectual disability v3.31 CEP55 Rebecca Foulger Gene: cep55 has been classified as Green List (High Evidence).
Intellectual disability v3.30 CEP55 Rebecca Foulger changed review comment from: PMID:32100459 (Barrie et al., 2020) describe 7 living individuals (5 families) with biallelic variants (compound het and homozygous splice site variant) in CEP55. Global/severe DD was seen in patient 2, and the 3 siblings (patients 5,6,7). Mild/delayed motor/speech development was seen in unrelated patients 3 and 4.; to: PMID:32100459 (Barrie et al., 2020) describe 7 living individuals (5 families) with biallelic variants (compound het and homozygous splice site variant) in CEP55. Global/severe DD was seen in patient 2, and the 3 siblings (patients 5,6,7). Mild/delayed motor & speech development was seen in unrelated patients 3 and 4.
Intellectual disability v3.30 CEP55 Rebecca Foulger changed review comment from: PMID:32100459 (Barrie et al., 2020) describe 7 living individuals (5 families) with biallelic variants (compound het and homozygous splice site variant) in CEP55. Global/severe DD wax seen in patient 2, and the 3 siblings (patients 5,6,7). Mild/delayed motor/speech development was seen in unrelated patients 3 and 4.; to: PMID:32100459 (Barrie et al., 2020) describe 7 living individuals (5 families) with biallelic variants (compound het and homozygous splice site variant) in CEP55. Global/severe DD was seen in patient 2, and the 3 siblings (patients 5,6,7). Mild/delayed motor/speech development was seen in unrelated patients 3 and 4.
Intellectual disability v3.30 CEP55 Rebecca Foulger commented on gene: CEP55: PMID:32100459 (Barrie et al., 2020) describe 7 living individuals (5 families) with biallelic variants (compound het and homozygous splice site variant) in CEP55. Global/severe DD wax seen in patient 2, and the 3 siblings (patients 5,6,7). Mild/delayed motor/speech development was seen in unrelated patients 3 and 4.
Intellectual disability v3.30 CEP55 Rebecca Foulger gene: CEP55 was added
gene: CEP55 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: CEP55 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CEP55 were set to 32100459
Phenotypes for gene: CEP55 were set to microcephaly, delayed development, and bilateral toe syndactyly
Added comment: Added to ID panel on advice from Helen Brittain, Genomics England Clinical Team. Phenotype of living individuals in PMID:32100459 (Barrie et al., 2020) includes developmental delay.
Sources: Literature
Severe microcephaly v2.6 CEP55 Rebecca Foulger Classified gene: CEP55 as Green List (high evidence)
Severe microcephaly v2.6 CEP55 Rebecca Foulger Gene: cep55 has been classified as Green List (High Evidence).
Severe microcephaly v2.5 CEP55 Rebecca Foulger changed review comment from: PMID:32100459 (Barrie et al., 2020) describe 7 living indivduals (5 families) with biallelic CEP55 variants. Four unrelated individuals with microcephaly, speech delays, and bilateral toe syndactyly all have a common CEP55 variant c.70G>A p.(Glu24Lys) in trans with nonsense variants. Three siblings are homozygous for a consensus splice site variant near the end of the gene. These affected girls all have severely delayed development, microcephaly, and varying degrees of lissencephaly/pachygyria. The authors suggest that individuals compound het for missense + nonsense variants in CEP55 have a viable phenotype (compared to lethal MARCH phenotype).; to: PMID:32100459 (Barrie et al., 2020) describe 7 living indivduals (5 families) with biallelic CEP55 variants (compound het, or homozygous splice site variant). Three sisters (Patients 5,6,7) have severe microcephaly (-7.1 SD, -5.5, -5.5). An additional 3 unrelated patients (Patients 1,2,3) have microcephaly scores of -2 SD, -2.7 SD, and Patient 4 has borderline microcephaly. Severe microcephaly (NHS Test Directory) is defined as having an occipitofrontal circumference (OFC) beyond 3 standard deviations below the mean for age. There are 4 unrelated cases which meet this threshold (3 sisters) or are close to this threshold (3 unrelated patients) and therefore on balance have rated as Green awaiting further GLH review.
Early onset or syndromic epilepsy v2.40 CACNA1H Sarah Leigh Phenotypes for gene: CACNA1H were changed from to Hyperaldosteronism, familial, type IV 617027; {Epilepsy, childhood absence, susceptibility to, 6} 611942; {Epilepsy, idiopathic generalized, susceptibility to, 6} 611942
Early onset or syndromic epilepsy v2.39 CACNA1H Sarah Leigh Added comment: Comment on publications: PMID 32227660 presents further evidence refuting a monogenic contribution of this gene to epilepsy.
Early onset or syndromic epilepsy v2.39 CACNA1H Sarah Leigh Publications for gene: CACNA1H were set to 12891677
Severe microcephaly v2.5 CEP55 Rebecca Foulger commented on gene: CEP55: PMID:32100459 (Barrie et al., 2020) describe 7 living indivduals (5 families) with biallelic CEP55 variants. Four unrelated individuals with microcephaly, speech delays, and bilateral toe syndactyly all have a common CEP55 variant c.70G>A p.(Glu24Lys) in trans with nonsense variants. Three siblings are homozygous for a consensus splice site variant near the end of the gene. These affected girls all have severely delayed development, microcephaly, and varying degrees of lissencephaly/pachygyria. The authors suggest that individuals compound het for missense + nonsense variants in CEP55 have a viable phenotype (compared to lethal MARCH phenotype).
Severe microcephaly v2.5 CEP55 Rebecca Foulger gene: CEP55 was added
gene: CEP55 was added to Severe microcephaly. Sources: Literature
Mode of inheritance for gene: CEP55 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CEP55 were set to 32100459
Phenotypes for gene: CEP55 were set to microcephaly, speech delays, and bilateral toe syndactyly
Review for gene: CEP55 was set to GREEN
Added comment: Added to Microcephaly panel on advice from Helen Brittain, Genomics England Clinical Team. Phenotype of living individuals described in PMID:32100459 (Barrie et al., 2020) includes microcephaly.
Sources: Literature
Fetal anomalies v1.7 CEP55 Rebecca Foulger Classified gene: CEP55 as Green List (high evidence)
Fetal anomalies v1.7 CEP55 Rebecca Foulger Gene: cep55 has been classified as Green List (High Evidence).
Fetal anomalies v1.6 CEP55 Rebecca Foulger Classified gene: CEP55 as Red List (low evidence)
Fetal anomalies v1.6 CEP55 Rebecca Foulger Added comment: Comment on list classification: Added gene to panel as Green: MARCH phenotype is appropriate for fetal panel, and 3 unrelated fetal cases reported in literature. Not yet associated with a disorder in Gene2Phenotype.
Fetal anomalies v1.6 CEP55 Rebecca Foulger Gene: cep55 has been classified as Red List (Low Evidence).
Fetal anomalies v1.5 CEP55 Rebecca Foulger Publications for gene: CEP55 were set to 28264986; 28295209
Fetal anomalies v1.4 CEP55 Rebecca Foulger changed review comment from: PMID:30622327 (Rawlins et al., 2019) report a novel homozygous founder frameshift variant(p.Ile172Asnfs*17) in CEP55 in 2 siblings presenting with a lethal fetal disorder including cystic dysplastic kidneys. The variant is present at low frequency in the Amish community.; to: PMID:30622327 (Rawlins et al., 2019) report a novel homozygous founder frameshift variant (p.Ile172Asnfs*17) in CEP55 in 2 siblings presenting with a lethal fetal disorder including cystic dysplastic kidneys. The variant is present at low frequency in the Amish community.
Fetal anomalies v1.4 CEP55 Rebecca Foulger commented on gene: CEP55: PMID:30622327 (Rawlins et al., 2019) report a novel homozygous founder frameshift variant(p.Ile172Asnfs*17) in CEP55 in 2 siblings presenting with a lethal fetal disorder including cystic dysplastic kidneys. The variant is present at low frequency in the Amish community.
Fetal anomalies v1.4 CEP55 Rebecca Foulger commented on gene: CEP55: PMID:28295209. Bondeson et al report a Swedish couple with 2 affected male fetuses homozygous for CEP55 p.Arg86*. Although the phenotype differed between fetuses, both exhibited kidney phenotypes (including renal dysplaisa). Segregation analysis supported the gene:disease association, and Haplotype analysis suggested a founder effect.
Fetal anomalies v1.4 CEP55 Rebecca Foulger commented on gene: CEP55: PMID:28264986: Frosk et al, 2017 report a Dutch-German Mennonite family with 3 affected fetuses homozygous for CEP55 nonsense variant p.Ser425* presenting with MIM:236500 including renal dysplasia.
Fetal anomalies v1.4 CEP55 Rebecca Foulger gene: CEP55 was added
gene: CEP55 was added to Fetal anomalies. Sources: Other
Mode of inheritance for gene: CEP55 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CEP55 were set to 28264986; 28295209
Phenotypes for gene: CEP55 were set to Multinucleated neurons, anhydramnios, renal dysplasia, cerebellar hypoplasia, and hydranencephaly, 236500; lethal CEP55-related syndromes
Added comment: Added to Fetal anomalies panel on advice from Helen Brittain, Genomics England Clinical Team. MARCH phenotype is appropriate for this panel.
Sources: Other
COVID-19 research v0.127 NOS2 Ivone Leong Classified gene: NOS2 as Green List (high evidence)
COVID-19 research v0.127 NOS2 Ivone Leong Gene: nos2 has been classified as Green List (High Evidence).
COVID-19 research v0.126 NOS2 Ivone Leong gene: NOS2 was added
gene: NOS2 was added to Viral susceptibility. Sources: Expert list
Mode of inheritance for gene: NOS2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: NOS2 were set to 31995689; 11207313
Review for gene: NOS2 was set to GREEN
Added comment: NOS2 is part of the list of genes that confer susceptibility to viral infections on the COVID Human Genetic Effort website (https://www.covidhge.com/).

PMID: 31995689 describes a 51 year old man from Iran who had an acute cytomegalovirus (CMV) infection which progressed to CMV disease and later died from it. The researchers found a homozygous variant that causes a frameshift mutation in NOS2 that caused NOS2 deficiency, which might cause the patient to be more susceptible to lethal CMV infection. It is rare for CMV to cause fatality in healthy people; however, Nos2 knockout mice are susceptible to lethal infection with murine CMV (PMID: 11207313).

Based on the above evidence NOS2 has been given Green gene status.
Sources: Expert list
COVID-19 research v0.125 ACKR1 Sarah Leigh Classified gene: ACKR1 as Red List (low evidence)
COVID-19 research v0.125 ACKR1 Sarah Leigh Added comment: Comment on list classification: PMID 19180233 noted the clinical significance of the lower neutrophil counts in individuals homozygous for the Duffy-null variant in medical decision making, as white blood cell count is a marker of immunocompetence, infection, and inflammation, and they proposed the potential utility of rs2814778 genotyping. PMID 18621010, showed that rs2814778 -46CC was greater in HIV-positive patients, and -46CC individuals had a 50% higher risk of acquiring HIV, however, -46CC was associated with slower disease progression in terms of death or development of dementia. Survival appeared to be dependent on the level of WBC (PMID 19620399).
COVID-19 research v0.125 ACKR1 Sarah Leigh Gene: ackr1 has been classified as Red List (Low Evidence).
COVID-19 research v0.124 ACKR1 Sarah Leigh Publications for gene: ACKR1 were set to
COVID-19 research v0.123 ACKR1 Sarah Leigh Phenotypes for gene: ACKR1 were changed from to [Blood group, Duffy system] 110700
COVID-19 research v0.122 ACKR1 Sarah Leigh Mode of inheritance for gene: ACKR1 was changed from to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.121 TP53 Sarah Leigh Source OMIM was added to TP53.
COVID-19 research v0.121 TNF Sarah Leigh gene: TNF was added
gene: TNF was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: TNF was set to
COVID-19 research v0.121 TLR2 Sarah Leigh gene: TLR2 was added
gene: TLR2 was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: TLR2 was set to
COVID-19 research v0.121 SERPINA1 Sarah Leigh gene: SERPINA1 was added
gene: SERPINA1 was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: SERPINA1 was set to
COVID-19 research v0.121 SCN5A Sarah Leigh gene: SCN5A was added
gene: SCN5A was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: SCN5A was set to
COVID-19 research v0.121 RB1 Sarah Leigh gene: RB1 was added
gene: RB1 was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: RB1 was set to
COVID-19 research v0.121 PDCD1 Sarah Leigh gene: PDCD1 was added
gene: PDCD1 was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: PDCD1 was set to
COVID-19 research v0.121 NUP214 Sarah Leigh gene: NUP214 was added
gene: NUP214 was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: NUP214 was set to
COVID-19 research v0.121 MET Sarah Leigh gene: MET was added
gene: MET was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: MET was set to
COVID-19 research v0.121 LDLR Sarah Leigh gene: LDLR was added
gene: LDLR was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: LDLR was set to
COVID-19 research v0.121 KRT18 Sarah Leigh gene: KRT18 was added
gene: KRT18 was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: KRT18 was set to
COVID-19 research v0.121 IRGM Sarah Leigh gene: IRGM was added
gene: IRGM was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: IRGM was set to
COVID-19 research v0.121 IL6 Sarah Leigh gene: IL6 was added
gene: IL6 was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: IL6 was set to
COVID-19 research v0.121 IL4R Sarah Leigh gene: IL4R was added
gene: IL4R was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: IL4R was set to
COVID-19 research v0.121 IFNG Sarah Leigh gene: IFNG was added
gene: IFNG was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: IFNG was set to
COVID-19 research v0.121 IFITM3 Sarah Leigh gene: IFITM3 was added
gene: IFITM3 was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: IFITM3 was set to
COVID-19 research v0.121 ICAM1 Sarah Leigh gene: ICAM1 was added
gene: ICAM1 was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: ICAM1 was set to
COVID-19 research v0.121 HTR2A Sarah Leigh gene: HTR2A was added
gene: HTR2A was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: HTR2A was set to
COVID-19 research v0.121 HLA-DQB1 Sarah Leigh gene: HLA-DQB1 was added
gene: HLA-DQB1 was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: HLA-DQB1 was set to
COVID-19 research v0.121 HLA-C Sarah Leigh gene: HLA-C was added
gene: HLA-C was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: HLA-C was set to
COVID-19 research v0.121 HFE Sarah Leigh gene: HFE was added
gene: HFE was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: HFE was set to
COVID-19 research v0.121 HBB Sarah Leigh gene: HBB was added
gene: HBB was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: HBB was set to
COVID-19 research v0.121 DMD Sarah Leigh gene: DMD was added
gene: DMD was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: DMD was set to
COVID-19 research v0.121 CYP2B6 Sarah Leigh gene: CYP2B6 was added
gene: CYP2B6 was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: CYP2B6 was set to
COVID-19 research v0.121 CX3CR1 Sarah Leigh gene: CX3CR1 was added
gene: CX3CR1 was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: CX3CR1 was set to
COVID-19 research v0.121 CR1 Sarah Leigh gene: CR1 was added
gene: CR1 was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: CR1 was set to
COVID-19 research v0.121 CPT2 Sarah Leigh gene: CPT2 was added
gene: CPT2 was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: CPT2 was set to
COVID-19 research v0.121 CIB1 Sarah Leigh Source OMIM was added to CIB1.
COVID-19 research v0.121 CD209 Sarah Leigh gene: CD209 was added
gene: CD209 was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: CD209 was set to
COVID-19 research v0.121 CCR5 Sarah Leigh gene: CCR5 was added
gene: CCR5 was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: CCR5 was set to
COVID-19 research v0.121 CCND1 Sarah Leigh gene: CCND1 was added
gene: CCND1 was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: CCND1 was set to
COVID-19 research v0.121 CCL3L1 Sarah Leigh gene: CCL3L1 was added
gene: CCL3L1 was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: CCL3L1 was set to
COVID-19 research v0.121 CCL11 Sarah Leigh gene: CCL11 was added
gene: CCL11 was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: CCL11 was set to
COVID-19 research v0.121 AKT1 Sarah Leigh gene: AKT1 was added
gene: AKT1 was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: AKT1 was set to
COVID-19 research v0.121 ACKR1 Sarah Leigh gene: ACKR1 was added
gene: ACKR1 was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: ACKR1 was set to
Primary immunodeficiency or monogenic inflammatory bowel disease v2.107 RELA Ivone Leong Classified gene: RELA as Amber List (moderate evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.107 RELA Ivone Leong Added comment: Comment on list classification: Promoted from Red to Amber based on expert review. As there are only 2 cases and because the phenotype are slightly different, this gene will be rated Amber until more cases emerge.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.107 RELA Ivone Leong Gene: rela has been classified as Amber List (Moderate Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.106 RAC2 Ivone Leong Classified gene: RAC2 as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.106 RAC2 Ivone Leong Added comment: Comment on list classification: Promoted from Amber to Green based on expert review (Zornitza Stark) and evidence.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.106 RAC2 Ivone Leong Gene: rac2 has been classified as Green List (High Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.105 RAC2 Ivone Leong Publications for gene: RAC2 were set to 21167572; 30654050; 30723080; 31071452; 25512081; 10758162; 31382036; 10961859
Additional findings health related - CNV analysis adults v0.0 Eleanor Williams Added Panel Additional findings health related adult CNVs
Set child panels to: Additional findings health related adult additional CNVs; Additional findings health related child CNVs
Set panel types to: Super Panel
Additional findings health related - adults v0.0 Eleanor Williams Added Panel Additional findings health related adult
Set child panels to: Additional findings health related adult additional genes; Additional findings health related child
Set panel types to: Super Panel
Additional findings health related - CNV analysis children v0.7 Eleanor Williams Panel status changed from internal to public
Additional findings health related - children v0.9 Eleanor Williams Panel status changed from internal to public
Additional findings health related - adult specific v0.9 Eleanor Williams Panel status changed from internal to public
Additional findings health related - CNV analysis adult specific v0.10 Eleanor Williams Panel status changed from internal to public
Intellectual disability v3.29 RSRC1 Zornitza Stark edited their review of gene: RSRC1: Added comment: 17 additional individuals reported.; Changed rating: GREEN; Changed publications: 28640246, 29522154, 32227164; Changed phenotypes: Intellectual developmental disorder, autosomal recessive 70, MIM# 618402; Set current diagnostic: yes
Cerebellar hypoplasia v1.39 TSEN34 Zornitza Stark reviewed gene: TSEN34: Rating: RED; Mode of pathogenicity: None; Publications: 18711368; Phenotypes: Pontocerebellar hypoplasia type 2C 612390; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.120 HLA-B Rebecca Foulger changed review comment from: Comment on list classification: Updated rating from Red to Green. Although not all studies agree on the association of specific HLA-B alleles and SARS infection (e.g. PMIDs 12969506, 15243926), these studies do both report an association. PMID:18186801 do not report an association between tested HLA-B alleles and SARS development but on balance in-silico evidence also suggests that HLA-B alleles could play a role in modifying the response to the virus. Therefore Green rating is appropriate for this research panel.; to: Comment on list classification: Updated rating from Red to Green. Although not all studies agree on the association of specific HLA-B alleles and SARS infection (e.g. PMIDs 12969506, 15243926), these studies do both report an association. PMID:18186801 do not report an association between tested HLA-B alleles and SARS development, but on balance in-silico evidence also suggests that HLA-B alleles could play a role in modifying the response to the virus. Therefore Green rating is appropriate for this research panel.
COVID-19 research v0.120 HLA-B Rebecca Foulger Classified gene: HLA-B as Green List (high evidence)
COVID-19 research v0.120 HLA-B Rebecca Foulger Added comment: Comment on list classification: Updated rating from Red to Green. Although not all studies agree on the association of specific HLA-B alleles and SARS infection (e.g. PMIDs 12969506, 15243926), these studies do both report an association. PMID:18186801 do not report an association between tested HLA-B alleles and SARS development but on balance in-silico evidence also suggests that HLA-B alleles could play a role in modifying the response to the virus. Therefore Green rating is appropriate for this research panel.
COVID-19 research v0.120 HLA-B Rebecca Foulger Gene: hla-b has been classified as Green List (High Evidence).
Additional findings health related - CNV analysis children v0.6 VHL Eleanor Williams Transcript for gene VHL was changed from None to ENST00000256474.2; NM_000551.3
Additional findings health related - children v0.8 VHL Eleanor Williams Transcript for gene VHL was changed from None to ENST00000256474.2; NM_000551.3
Additional findings health related - children v0.7 RET Eleanor Williams Transcript for gene RET was changed from None to ENST00000355710.8; NM_020975.4
Additional findings health related - children v0.6 PCSK9 Eleanor Williams Transcript for gene PCSK9 was changed from None to ENST00000302118.5; NM_174936.3
Additional findings health related - adult specific v0.8 MUTYH Eleanor Williams Transcript for gene MUTYH was changed from None to ENST00000450313.5; NM_001128425.1
Tag adult-onset tag was added to MUTYH.
Additional findings health related - CNV analysis adult specific v0.9 MUTYH Eleanor Williams Transcript for gene MUTYH was changed from None to ENST00000450313.5; NM_001128425.1
Tag adult-onset tag was added to MUTYH.
COVID-19 research v0.119 HLA-B Rebecca Foulger commented on gene: HLA-B: PMID:15839463 (Umapathy et al., 2004). Full text is unavailable. Title: Absence of HLA B*46 in Indian population: could it be the cause for protection from SARS epidemic?
Additional findings health related - adult specific v0.7 MSH6 Eleanor Williams Transcript for gene MSH6 was changed from None to ENST00000234420.9; NM_000179.2
Tag adult-onset tag was added to MSH6.
Additional findings health related - CNV analysis adult specific v0.8 MSH6 Eleanor Williams Transcript for gene MSH6 was changed from None to ENST00000234420.9; NM_000179.2
Tag adult-onset tag was added to MSH6.
COVID-19 research v0.119 HLA-B Rebecca Foulger commented on gene: HLA-B: PMID:18540051 (Roder et al., 2008 examine the crystal structure of HLA-B*1501 in complex with a SARS coronavirus-derived nonapeptide (VQQESSFVM) (full text unavailable at time of curation).
Additional findings health related - adult specific v0.6 MSH2 Eleanor Williams Transcript for gene MSH2 was changed from None to ENST00000233146.6; NM_000251.2
Tag adult-onset tag was added to MSH2.
Additional findings health related - CNV analysis adult specific v0.7 MSH2 Eleanor Williams Transcript for gene MSH2 was changed from None to ENST00000233146.6; NM_000251.2
Tag adult-onset tag was added to MSH2.
COVID-19 research v0.119 HLA-B Rebecca Foulger commented on gene: HLA-B: PMID:32303592 (Nguyen et al., 2020) performed in-silico analysis of viral-binding affinity across HLA genotypes for SARS-CoV-2 peptides. Based on in-silico results, they suggest that individuals with HLA-B*46:01 may be vulnerable to COVID-19. Conversely, HLA-B*15:03 may enable greater immunity.
Additional findings health related - adult specific v0.5 MLH1 Eleanor Williams Transcript for gene MLH1 was changed from None to ENST00000231790.6; NM_000249.3
Tag adult-onset tag was added to MLH1.
Additional findings health related - CNV analysis adult specific v0.6 MLH1 Eleanor Williams Transcript for gene MLH1 was changed from None to ENST00000231790.6; NM_000249.3
Tag adult-onset tag was added to MLH1.
Additional findings health related - CNV analysis children v0.5 MEN1 Eleanor Williams Transcript for gene MEN1 was changed from None to ENST00000312049.10; NM_130799.2
Additional findings health related - children v0.5 MEN1 Eleanor Williams Transcript for gene MEN1 was changed from None to ENST00000312049.10; NM_130799.2
Additional findings health related - CNV analysis children v0.4 LDLR Eleanor Williams Transcript for gene LDLR was changed from None to ENST00000558518.5; NM_000527.4
Additional findings health related - children v0.4 LDLR Eleanor Williams Transcript for gene LDLR was changed from None to ENST00000558518.5; NM_000527.4
Additional findings health related - adult specific v0.4 BRCA2 Eleanor Williams Transcript for gene BRCA2 was changed from None to ENST00000544455.5; NM_000059.3
Tag adult-onset tag was added to BRCA2.
Additional findings health related - CNV analysis adult specific v0.5 BRCA2 Eleanor Williams Transcript for gene BRCA2 was changed from None to ENST00000544455.5; NM_000059.3
Tag adult-onset tag was added to BRCA2.
COVID-19 research v0.119 HLA-B Rebecca Foulger Publications for gene: HLA-B were set to 12969506; 15243926; 18186801
COVID-19 research v0.118 HLA-B Rebecca Foulger commented on gene: HLA-B
COVID-19 research v0.118 IL18 Rebecca Foulger changed review comment from: PMID:25395539 (Zhang et al 2014) report that IL-18 and IL-22 administration to mice offered protection against a broad range of RV inoculation, and may offer broad antibiral therapeutic potential.; to: PMID:25395539 (Zhang et al 2014) report that IL-18 and IL-22 administration to mice offered protection against a broad range of RV inoculation, and may offer broad antiviral therapeutic potential.
COVID-19 research v0.118 IL22 Rebecca Foulger changed review comment from: PMID:25395539 (Zhang et al 2014) report that IL-18 and IL-22 administration to mice offered protection against a broad range of RV inoculation, and may offer broad antibiral therapeutic potential.; to: PMID:25395539 (Zhang et al 2014) report that IL-18 and IL-22 administration to mice offered protection against a broad range of RV inoculation, and may offer broad antiviral therapeutic potential.
COVID-19 research v0.118 IL22 Rebecca Foulger Publications for gene: IL22 were set to 25395539
COVID-19 research v0.117 IL22 Rebecca Foulger Publications for gene: IL22 were set to
COVID-19 research v0.116 IL22 Rebecca Foulger commented on gene: IL22
COVID-19 research v0.116 IL18 Rebecca Foulger Classified gene: IL18 as Amber List (moderate evidence)
COVID-19 research v0.116 IL18 Rebecca Foulger Added comment: Comment on list classification: Updated rating from Red to Amber, based largely on PMID:31660404 who report identification of IL-18 polymorphisms that may confer a higher incidence of CMV infection (in kidney transplant patients). Additional expression assays studies in mice support a role for IL-18 in innate immunity viral response.
COVID-19 research v0.116 IL18 Rebecca Foulger Gene: il18 has been classified as Amber List (Moderate Evidence).
COVID-19 research v0.115 IL18 Rebecca Foulger commented on gene: IL18: PMID:31660404. Perez-Flores examines two SNPs in the promoter region of IL-18 gene (-607C/A (rs1946518) and -137G/C (rs187238) in 498 adult kidney transplant recipients. Results suggest that the rs1946518/rs187238 haplotype is associated with a higher incidence of post-prophylaxis cytomegalovirus (CMV) infection. Prior identification of these SNPs could help select alternative measures to prevent delayed-onset CMV infection in these patients.
COVID-19 research v0.115 IL18 Rebecca Foulger Publications for gene: IL18 were set to 15606801; 25395539
COVID-19 research v0.114 IL18 Rebecca Foulger Publications for gene: IL18 were set to 15606801
COVID-19 research v0.113 IL18 Rebecca Foulger commented on gene: IL18: PMID:25395539 (Zhang et al 2014) report that IL-18 and IL-22 administration to mice offered protection against a broad range of RV inoculation, and may offer broad antibiral therapeutic potential.
COVID-19 research v0.113 IL18 Rebecca Foulger changed review comment from: PMID:15606801 (Van Der Sluijs et al., 2005): IL18 is upregulated in after Influenza infection, and IL18 deficiency is associated with accelerated viral clearance.; to: PMID:15606801 (Van Der Sluijs et al., 2005): IL18 is upregulated in after Influenza infection, and IL18 deficiency is associated with accelerated viral clearance (mouse study).
COVID-19 research v0.113 IL18 Rebecca Foulger Publications for gene: IL18 were set to 15606801
COVID-19 research v0.112 IL18 Rebecca Foulger Publications for gene: IL18 were set to
COVID-19 research v0.111 IL18 Rebecca Foulger commented on gene: IL18
Additional findings health related - adult specific v0.3 BRCA1 Eleanor Williams Phenotypes for gene: BRCA1 were changed from Adult only; Breast and ovarian cancer predisposition; ENST00000357654.8 to Adult only; Breast and ovarian cancer predisposition
Transcript for gene BRCA1 was changed from None to ENST00000357654.8; NM_007294.3
Tag adult-onset tag was added to BRCA1.
Additional findings health related - CNV analysis adult specific v0.4 BRCA1 Eleanor Williams Phenotypes for gene: BRCA1 were changed from Adult only; ENST00000357654.8; Breast and ovarian cancer predisposition to Adult only; Breast and ovarian cancer predisposition
Transcript for gene BRCA1 was changed from None to ENST00000357654.8; NM_007294.3
Tag adult-onset tag was added to BRCA1.
Additional findings health related v0.109 BRCA1 Eleanor Williams Phenotypes for gene: BRCA1 were changed from ENST00000357654.8; Breast and ovarian cancer predisposition; Adult only to Breast and ovarian cancer predisposition; Adult only
Additional findings health related - children v0.3 APOB Eleanor Williams Transcript for gene APOB was changed from None to ENST00000233242.5; NM_000384.2
Additional findings health related - CNV analysis children v0.3 APC Eleanor Williams Transcript for gene APC was changed from None to ENST00000257430.9; NM_000038.5
Additional findings health related - children v0.2 APC Eleanor Williams Transcript for gene APC was changed from None to ENST00000257430.9; NM_000038.5
Additional findings health related - CNV analysis children v0.1 VHL Eleanor Williams gene: VHL was added
gene: VHL was added to Additional findings health related child CNVs. Sources: Expert Review Green,Other
Mode of inheritance for gene: VHL was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes for gene: VHL were set to Von Hippel Lindau Syndrome; Other cancer predisposition; Adult and child
Additional findings health related - CNV analysis children v0.1 MEN1 Eleanor Williams gene: MEN1 was added
gene: MEN1 was added to Additional findings health related child CNVs. Sources: Expert Review Green,Expert list
Mode of inheritance for gene: MEN1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes for gene: MEN1 were set to Myltiple endocrine Neoplasia Type 1; Other cancer predisposition; Adult and child
Additional findings health related - CNV analysis children v0.1 LDLR Eleanor Williams gene: LDLR was added
gene: LDLR was added to Additional findings health related child CNVs. Sources: Expert Review Green,Expert list
Mode of inheritance for gene: LDLR was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Phenotypes for gene: LDLR were set to Familial hypercholesterolaemia; Adult and child
Additional findings health related - CNV analysis children v0.1 APC Eleanor Williams gene: APC was added
gene: APC was added to Additional findings health related child CNVs. Sources: Expert Review Green,Expert list
Mode of inheritance for gene: APC was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes for gene: APC were set to Familial Adenomatous Polyposis; Adult and child; Bowel cancer predisposition
Additional findings health related - CNV analysis children v0.0 Eleanor Williams Added Panel Additional findings health related child CNVs
Additional findings health related - CNV analysis adult specific v0.2 MUTYH Eleanor Williams gene: MUTYH was added
gene: MUTYH was added to Additional findings health related adult additional CNVs. Sources: Expert Review Green,Other
Mode of inheritance for gene: MUTYH was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: MUTYH were set to Adult only; Bowel cancer predisposition; MYH-associated polyposis
Additional findings health related - CNV analysis adult specific v0.2 MSH6 Eleanor Williams gene: MSH6 was added
gene: MSH6 was added to Additional findings health related adult additional CNVs. Sources: Expert Review Green,Other
Mode of inheritance for gene: MSH6 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes for gene: MSH6 were set to Bowel cancer predisposition; Adult only; Hereditary non-polyposis colorectal cancer
Additional findings health related - CNV analysis adult specific v0.2 MSH2 Eleanor Williams gene: MSH2 was added
gene: MSH2 was added to Additional findings health related adult additional CNVs. Sources: Expert Review Green,Expert list
Mode of inheritance for gene: MSH2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes for gene: MSH2 were set to Bowel cancer predisposition; Adult only; Hereditary non-polyposis colorectal cancer
Additional findings health related - CNV analysis adult specific v0.2 MLH1 Eleanor Williams gene: MLH1 was added
gene: MLH1 was added to Additional findings health related adult additional CNVs. Sources: Expert Review Green,Expert list
Mode of inheritance for gene: MLH1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes for gene: MLH1 were set to Bowel cancer predisposition; Adult only; Hereditary non-polyposis colorectal cancer
Additional findings health related - CNV analysis adult specific v0.2 BRCA2 Eleanor Williams gene: BRCA2 was added
gene: BRCA2 was added to Additional findings health related adult additional CNVs. Sources: Expert Review Green,Expert list
Mode of inheritance for gene: BRCA2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes for gene: BRCA2 were set to Adult only; Breast and ovarian cancer predisposition
Additional findings health related - CNV analysis adult specific v0.2 BRCA1 Eleanor Williams gene: BRCA1 was added
gene: BRCA1 was added to Additional findings health related adult additional CNVs. Sources: Expert Review Green,Expert list
Mode of inheritance for gene: BRCA1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes for gene: BRCA1 were set to Adult only; ENST00000357654.8; Breast and ovarian cancer predisposition
Additional findings health related - CNV analysis adult specific v0.0 Eleanor Williams Added Panel Additional findings health related adult additional CNVs
COVID-19 research v0.111 TMPRSS2 Catherine Snow changed review comment from: PMID: 31488196 - Host susceptibility to severe influenza A virus infection, this paper reviews genes involved and identified TMPRSS2.

This gene has also been identified in this preprint - ACE2 and TMPRSS2 variants and expression as candidates to sex and country differences in COVID-19 severity in Italy https://doi.org/10.1101/2020.03.30.20047878
Sources: Literature; to: PMID: 31488196 - Host susceptibility to severe influenza A virus infection, this paper reviews genes involved and identified TMPRSS2. Papers identified include:
PMID: 25904605 which reported that higher TMPRSS2 expression variant, rs2070788 GG genotype, was associated with higher susceptibility to severe illness in patients with A(H1N1)pdm09 influenza.
PMID: 24600012 showed that TMPRSS2 is the key host protease that activates IAVs in vivo through proteolytic cleavage of their HA proteins
PMID: 24522916 looked at knockout mice that do not express TMPRSS2 that are resistant to pulmonary disease with lethal outcome when infected with influenza A viruses of subtypes H7N9 and H1N1, whereas they are not protected from lethal H3N2 virus infection

This gene has also been identified in this preprint - ACE2 and TMPRSS2 variants and expression as candidates to sex and country differences in COVID-19 severity in Italy https://doi.org/10.1101/2020.03.30.20047878
Sources: Literature
COVID-19 research v0.111 TMPRSS2 Catherine Snow Classified gene: TMPRSS2 as Amber List (moderate evidence)
COVID-19 research v0.111 TMPRSS2 Catherine Snow Gene: tmprss2 has been classified as Amber List (Moderate Evidence).
COVID-19 research v0.110 TMPRSS2 Catherine Snow gene: TMPRSS2 was added
gene: TMPRSS2 was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: TMPRSS2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: TMPRSS2 were set to 31488196
Review for gene: TMPRSS2 was set to AMBER
Added comment: PMID: 31488196 - Host susceptibility to severe influenza A virus infection, this paper reviews genes involved and identified TMPRSS2.

This gene has also been identified in this preprint - ACE2 and TMPRSS2 variants and expression as candidates to sex and country differences in COVID-19 severity in Italy https://doi.org/10.1101/2020.03.30.20047878
Sources: Literature
Additional findings health related - children v0.1 VHL Eleanor Williams gene: VHL was added
gene: VHL was added to Additional findings health related child. Sources: Expert Review Green,Other
Mode of inheritance for gene: VHL was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes for gene: VHL were set to Other cancer predisposition; Von Hippel Lindau Syndrome; Adult and child
Additional findings health related - children v0.1 RET Eleanor Williams gene: RET was added
gene: RET was added to Additional findings health related child. Sources: Expert Review Green,Other
Mode of inheritance for gene: RET was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes for gene: RET were set to Other cancer predisposition; Myltiple endocrine Neoplasia Type 2; Adult and child
Mode of pathogenicity for gene: RET was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
Additional findings health related - children v0.1 PCSK9 Eleanor Williams gene: PCSK9 was added
gene: PCSK9 was added to Additional findings health related child. Sources: Expert Review Green,Other
Mode of inheritance for gene: PCSK9 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes for gene: PCSK9 were set to Adult and child; Familial hypercholesterolaemia
Mode of pathogenicity for gene: PCSK9 was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
Additional findings health related - children v0.1 MEN1 Eleanor Williams gene: MEN1 was added
gene: MEN1 was added to Additional findings health related child. Sources: Expert list,Expert Review Green
Mode of inheritance for gene: MEN1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes for gene: MEN1 were set to Other cancer predisposition; Adult and child; Myltiple endocrine Neoplasia Type 1
Additional findings health related - children v0.1 LDLR Eleanor Williams gene: LDLR was added
gene: LDLR was added to Additional findings health related child. Sources: Expert list,Expert Review Green
Mode of inheritance for gene: LDLR was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Phenotypes for gene: LDLR were set to Adult and child; Familial hypercholesterolaemia
Additional findings health related - children v0.1 APOB Eleanor Williams gene: APOB was added
gene: APOB was added to Additional findings health related child. Sources: Expert Review Green,Other
Mode of inheritance for gene: APOB was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Phenotypes for gene: APOB were set to Adult and child; Familial hypercholesterolaemia
Mode of pathogenicity for gene: APOB was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
Additional findings health related - children v0.1 APC Eleanor Williams gene: APC was added
gene: APC was added to Additional findings health related child. Sources: Expert list,Expert Review Green
Mode of inheritance for gene: APC was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes for gene: APC were set to Familial Adenomatous Polyposis; Adult and child; Bowel cancer predisposition
Additional findings health related - children v0.0 Eleanor Williams Added Panel Additional findings health related child
Additional findings health related - adult specific v0.1 MUTYH Eleanor Williams gene: MUTYH was added
gene: MUTYH was added to Additional findings health related adult additional genes. Sources: Other,Expert Review Green
Mode of inheritance for gene: MUTYH was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: MUTYH were set to Bowel cancer predisposition; MYH-associated polyposis; Adult only
Additional findings health related - adult specific v0.1 MSH6 Eleanor Williams gene: MSH6 was added
gene: MSH6 was added to Additional findings health related adult additional genes. Sources: Other,Expert Review Green
Mode of inheritance for gene: MSH6 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes for gene: MSH6 were set to Bowel cancer predisposition; Hereditary non-polyposis colorectal cancer; Adult only
Additional findings health related - adult specific v0.1 MSH2 Eleanor Williams gene: MSH2 was added
gene: MSH2 was added to Additional findings health related adult additional genes. Sources: Expert list,Expert Review Green
Mode of inheritance for gene: MSH2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes for gene: MSH2 were set to Bowel cancer predisposition; Hereditary non-polyposis colorectal cancer; Adult only
Additional findings health related - adult specific v0.1 MLH1 Eleanor Williams gene: MLH1 was added
gene: MLH1 was added to Additional findings health related adult additional genes. Sources: Expert list,Expert Review Green
Mode of inheritance for gene: MLH1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes for gene: MLH1 were set to Bowel cancer predisposition; Hereditary non-polyposis colorectal cancer; Adult only
Additional findings health related - adult specific v0.1 BRCA2 Eleanor Williams gene: BRCA2 was added
gene: BRCA2 was added to Additional findings health related adult additional genes. Sources: Expert list,Expert Review Green
Mode of inheritance for gene: BRCA2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes for gene: BRCA2 were set to Adult only; Breast and ovarian cancer predisposition
Additional findings health related - adult specific v0.1 BRCA1 Eleanor Williams gene: BRCA1 was added
gene: BRCA1 was added to Additional findings health related adult additional genes. Sources: Expert list,Expert Review Green
Mode of inheritance for gene: BRCA1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes for gene: BRCA1 were set to Adult only; Breast and ovarian cancer predisposition; ENST00000357654.8
Additional findings health related - adult specific v0.0 Eleanor Williams Added Panel Additional findings health related adult additional genes
Primary ciliary disorders v1.22 TTC12 Zornitza Stark gene: TTC12 was added
gene: TTC12 was added to Primary ciliary disorders. Sources: Literature
Mode of inheritance for gene: TTC12 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TTC12 were set to 31978331
Phenotypes for gene: TTC12 were set to Ciliary dyskinesia
Review for gene: TTC12 was set to GREEN
gene: TTC12 was marked as current diagnostic
Added comment: Four unrelated families with LoF variants reported with a respiratory phenotype.
Sources: Literature
Intracerebral calcification disorders v1.18 JAM2 Zornitza Stark edited their review of gene: JAM2: Set current diagnostic: yes
Intracerebral calcification disorders v1.18 JAM2 Zornitza Stark gene: JAM2 was added
gene: JAM2 was added to Intracerebral calcification disorders. Sources: Literature
Mode of inheritance for gene: JAM2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: JAM2 were set to 31851307
Phenotypes for gene: JAM2 were set to Primary brain calcification
Review for gene: JAM2 was set to GREEN
Added comment: Three unrelated families with bi-allelic variants reported. The clinical phenotypes of the four patients included parkinsonism (3/4), dysarthria (3/4), seizures (1/4), and probable asymptomatic (1/4), with diverse onset ages.
Sources: Literature
Intellectual disability v3.29 EIF2AK2 Zornitza Stark gene: EIF2AK2 was added
gene: EIF2AK2 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: EIF2AK2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: EIF2AK2 were set to 32197074
Phenotypes for gene: EIF2AK2 were set to Intellectual disability; white matter abnormalities; ataxia; regression with febrile illness
Review for gene: EIF2AK2 was set to GREEN
gene: EIF2AK2 was marked as current diagnostic
Added comment: Eight individuals with de novo variants and complex neurodevelopmental phenotype.
Sources: Literature
Intellectual disability v3.29 EIF2AK1 Zornitza Stark gene: EIF2AK1 was added
gene: EIF2AK1 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: EIF2AK1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: EIF2AK1 were set to 32197074
Phenotypes for gene: EIF2AK1 were set to Intellectual disability; white matter abnormalities
Review for gene: EIF2AK1 was set to RED
Added comment: Single individual reported with de novo variant in this gene, one to watch.
Sources: Literature
Intellectual disability v3.29 NRROS Zornitza Stark gene: NRROS was added
gene: NRROS was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: NRROS was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: NRROS were set to 32100099; 32197075
Phenotypes for gene: NRROS were set to neurodegeneration; intracranial calcification; epilepsy
Review for gene: NRROS was set to GREEN
Added comment: Normal development or mild developmental delay until onset of regression around age of 1 concurrent with epilepsy
Biallelic LOF mutations with functional evidence of pathogenicity reported in 6 unrelated families. Suggest also add to Epilepsy panel, possibly others.
Sources: Literature
Early onset or syndromic epilepsy v2.38 SEMA6B Zornitza Stark gene: SEMA6B was added
gene: SEMA6B was added to Genetic epilepsy syndromes. Sources: Literature
Mode of inheritance for gene: SEMA6B was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: SEMA6B were set to 32169168
Phenotypes for gene: SEMA6B were set to Progressive myoclonic epilepsy
Review for gene: SEMA6B was set to GREEN
Added comment: Five individuals from unrelated families reported with de novo variants in the last exon, escaping NMD.
Sources: Literature
Intellectual disability v3.29 NOVA2 Zornitza Stark gene: NOVA2 was added
gene: NOVA2 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: NOVA2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: NOVA2 were set to 32197073
Phenotypes for gene: NOVA2 were set to Intellectual disability; autism; hypotonia; spasticity; ataxia
Review for gene: NOVA2 was set to GREEN
gene: NOVA2 was marked as current diagnostic
Added comment: Six individuals with de novo frameshift variants resulting in C-terminal extension suggesting partial LoF as mechanism.
Sources: Literature
Primary immunodeficiency or monogenic inflammatory bowel disease v2.104 POLD1 Ivone Leong Classified gene: POLD1 as Amber List (moderate evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.104 POLD1 Ivone Leong Added comment: Comment on list classification: Promoted from Red to Amber based on expert review and evidence.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.104 POLD1 Ivone Leong Gene: pold1 has been classified as Amber List (Moderate Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.103 HYOU1 Ivone Leong Phenotypes for gene: HYOU1 were changed from Hypoglycemia, inflammatory complications; Congenital defects of phagocyte number or function to Hypoglycemia, inflammatory complications; Congenital defects of phagocyte number or function; Immunodeficiency 59 and hypoglycemia, 233600
Primary immunodeficiency or monogenic inflammatory bowel disease v2.102 HYOU1 Ivone Leong Publications for gene: HYOU1 were set to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.101 MKL1 Ivone Leong Classified gene: MKL1 as Amber List (moderate evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.101 MKL1 Ivone Leong Added comment: Comment on list classification: Promoted from Red to Amber based on expert review and additional of second case.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.101 MKL1 Ivone Leong Gene: mkl1 has been classified as Amber List (Moderate Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.100 MKL1 Ivone Leong Publications for gene: MKL1 were set to 32048120; 26224645; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.99 POLD2 Ivone Leong Phenotypes for gene: POLD2 were changed from Polymerase d 2 deficiency; Recurrent respiratory tract infections, skin infections, warts and molluscum, short stature, intellectual disability; Immunodeficiencies affecting cellular and humoral immunity to Polymerase d 2 deficiency; Recurrent respiratory tract infections, skin infections, warts and molluscum, short stature, intellectual disability; Immunodeficiencies affecting cellular and humoral immunity; Low CD4 T cells; Low B cells, normal maturation
Primary immunodeficiency or monogenic inflammatory bowel disease v2.98 POLR3A Ivone Leong Classified gene: POLR3A as Amber List (moderate evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.98 POLR3A Ivone Leong Added comment: Comment on list classification: Amber rating given based on expert review.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.98 POLR3A Ivone Leong Gene: polr3a has been classified as Amber List (Moderate Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.97 POLR3C Ivone Leong Classified gene: POLR3C as Amber List (moderate evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.97 POLR3C Ivone Leong Added comment: Comment on list classification: Rating given based on expert review.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.97 POLR3C Ivone Leong Gene: polr3c has been classified as Amber List (Moderate Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.96 RNF31 Ivone Leong Classified gene: RNF31 as Amber List (moderate evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.96 RNF31 Ivone Leong Added comment: Comment on list classification: Promoted from Red to Amber based on expert review and evidence of a second case.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.96 RNF31 Ivone Leong Gene: rnf31 has been classified as Amber List (Moderate Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.95 RNF31 Ivone Leong Publications for gene: RNF31 were set to 32048120; 26008899; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.94 SEC61A1 Ivone Leong Publications for gene: SEC61A1 were set to 28782633; 32086639; 32048120
Primary immunodeficiency or monogenic inflammatory bowel disease v2.93 SH3BP2 Ivone Leong Publications for gene: SH3BP2 were set to 29669173; 22640988; 32048120; 28914985; 11381256; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.92 SH3KBP1 Ivone Leong Publications for gene: SH3KBP1 were set to 32086639; 32048120; 29636373
Primary immunodeficiency or monogenic inflammatory bowel disease v2.91 SLC39A7 Ivone Leong Classified gene: SLC39A7 as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.91 SLC39A7 Ivone Leong Added comment: Comment on list classification: Promoted from Red to Green based on expert reviews and evidence.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.91 SLC39A7 Ivone Leong Gene: slc39a7 has been classified as Green List (High Evidence).
COVID-19 research v0.109 PARP1 Sarah Leigh changed review comment from: PARP1 Enhances Influenza A Virus Propagation by Facilitating Degradation of Host Type I Interferon Receptor. Therefore, activiation of PARP1 could promote Influenza infection.
Sources: Literature; to: PARP1 Enhances Influenza A Virus Propagation by Facilitating Degradation of Host Type I Interferon Receptor. Therefore, activiation of PARP1 could promote Influenza infection, by interfering with the IFNAR1.
Sources: Literature
Primary immunodeficiency or monogenic inflammatory bowel disease v2.90 PARP1 Sarah Leigh gene: PARP1 was added
gene: PARP1 was added to Primary immunodeficiency. Sources: Literature
Mode of inheritance for gene: PARP1 was set to Unknown
Publications for gene: PARP1 were set to 31915279
Review for gene: PARP1 was set to RED
Added comment: PARP1 Enhances Influenza A Virus Propagation by Facilitating Degradation of Host Type I Interferon Receptor. Therefore, activiation of PARP1 could promote Influenza infection, by interfering with the IFNAR1.
Sources: Literature
COVID-19 research v0.109 PARP1 Sarah Leigh gene: PARP1 was added
gene: PARP1 was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: PARP1 was set to Unknown
Publications for gene: PARP1 were set to 31915279
Added comment: PARP1 Enhances Influenza A Virus Propagation by Facilitating Degradation of Host Type I Interferon Receptor. Therefore, activiation of PARP1 could promote Influenza infection.
Sources: Literature
Primary immunodeficiency or monogenic inflammatory bowel disease v2.89 RECQL4 Sarah Leigh Classified gene: RECQL4 as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.89 RECQL4 Sarah Leigh Gene: recql4 has been classified as Green List (High Evidence).
COVID-19 research v0.108 RECQL4 Sarah Leigh Classified gene: RECQL4 as Green List (high evidence)
COVID-19 research v0.108 RECQL4 Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene. At least 5 variants reported in 3 unrelated cases in which immunodeficiecy was a feature (PMID 16630167; 21143835; 26064716). In addition RECQL4 variants have been implicated in Acrodermatitis Enteropathica caused by SLC39A4 (p.Gly512Trp)(PMID 30174688)
COVID-19 research v0.108 RECQL4 Sarah Leigh Gene: recql4 has been classified as Green List (High Evidence).
COVID-19 research v0.107 RECQL4 Sarah Leigh Publications for gene: RECQL4 were set to 16630167
Primary immunodeficiency or monogenic inflammatory bowel disease v2.88 RECQL4 Sarah Leigh Publications for gene: RECQL4 were set to 16630167
Primary immunodeficiency or monogenic inflammatory bowel disease v2.87 RECQL4 Sarah Leigh Classified gene: RECQL4 as Amber List (moderate evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.87 RECQL4 Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene. At least 5 variants reported in 3 unrelated cases in which immunodeficiecy was a feature (PMID 16630167; 21143835; 26064716). In addition RECQL4 variants have been implicated in Acrodermatitis Enteropathica caused by SLC39A4 (p.Gly512Trp)(PMID 30174688)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.87 RECQL4 Sarah Leigh Gene: recql4 has been classified as Amber List (Moderate Evidence).
COVID-19 research v0.106 ELF4 Rebecca Foulger commented on gene: ELF4: Some evidence that ELF4 is involved in the anti-viral innate immune response, but no genetic data. Therefore keeping rating as Red.
COVID-19 research v0.106 ELF4 Rebecca Foulger changed review comment from: PMID:30089112 (Du et al., 2018) show that during the antiviral response, miR-221 was induced through ELF4 binding to its promoter.; to: PMID:30089112 (Du et al., 2018) show that during the antiviral response, miR-221 was induced through ELF4 binding to its promoter (mice cells, recombinant human ELF4).
COVID-19 research v0.106 ELF4 Rebecca Foulger commented on gene: ELF4: PMID:30089112 (Du et al., 2018) show that during the antiviral response, miR-221 was induced through ELF4 binding to its promoter.
COVID-19 research v0.106 ELF4 Rebecca Foulger commented on gene: ELF4
COVID-19 research v0.106 COLEC11 Rebecca Foulger commented on gene: COLEC11
COVID-19 research v0.106 CNBP Rebecca Foulger commented on gene: CNBP
Primary immunodeficiency or monogenic inflammatory bowel disease v2.86 IL18BP Zornitza Stark gene: IL18BP was added
gene: IL18BP was added to Primary immunodeficiency. Sources: Expert list
Mode of inheritance for gene: IL18BP was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IL18BP were set to 31213488
Phenotypes for gene: IL18BP were set to {?Hepatitis, fulminant viral, susceptibility to} 618549
Review for gene: IL18BP was set to RED
Added comment: Single individual reported with homozygous 40bp deletion in this gene and fulminant Hep A hepatitis.
Sources: Expert list
Primary immunodeficiency or monogenic inflammatory bowel disease v2.86 IRF4 Zornitza Stark gene: IRF4 was added
gene: IRF4 was added to Primary immunodeficiency. Sources: Expert list
Mode of inheritance for gene: IRF4 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: IRF4 were set to 29537367
Phenotypes for gene: IRF4 were set to Whipple's disease; [Skin/hair/eye pigmentation, variation in, 8] 611724
Review for gene: IRF4 was set to RED
Added comment: Single family reported with Whipple's disease and a rare missense in IRF4. Younger healthy carrier members of the family had the same variant as older affected individuals, leading the authors to speculate about age-dependent penetrance. GWAS indicates separate link with skin/hair/eye pigmentation.
Sources: Expert list
Primary immunodeficiency or monogenic inflammatory bowel disease v2.86 POLR3F Zornitza Stark gene: POLR3F was added
gene: POLR3F was added to Primary immunodeficiency. Sources: Expert list
Mode of inheritance for gene: POLR3F was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: POLR3F were set to 30211253
Phenotypes for gene: POLR3F were set to Severe VZV infection
Review for gene: POLR3F was set to RED
Added comment: Missense variant identified in a pair of monozygotic twins. Variant was paternally inherited.
Sources: Expert list
Primary immunodeficiency or monogenic inflammatory bowel disease v2.86 IL23R Zornitza Stark gene: IL23R was added
gene: IL23R was added to Primary immunodeficiency. Sources: Expert list
Mode of inheritance for gene: IL23R was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IL23R were set to 30578351
Phenotypes for gene: IL23R were set to Susceptibility to mycobacteria and Salmonella
Review for gene: IL23R was set to RED
Added comment: Single family reported.
Sources: Expert list
Primary immunodeficiency or monogenic inflammatory bowel disease v2.86 IL12RB2 Zornitza Stark gene: IL12RB2 was added
gene: IL12RB2 was added to Primary immunodeficiency. Sources: Expert list
Mode of inheritance for gene: IL12RB2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IL12RB2 were set to 30578351
Phenotypes for gene: IL12RB2 were set to Susceptibility to mycobacteria and Salmonella
Review for gene: IL12RB2 was set to RED
Added comment: Single individual reported, some functional data.
Sources: Expert list
Arthrogryposis v3.9 LMX1B Rebecca Foulger Publications for gene: LMX1B were set to 8403448; 19194568; 31369690; ISBN:9780199557509
Arthrogryposis v3.8 LMX1B Rebecca Foulger Publications for gene: LMX1B were set to 8403448
Arthrogryposis v3.7 LMX1B Rebecca Foulger Phenotypes for gene: LMX1B were changed from Nail-patella syndrome, 161200 to Nail-patella syndrome, 161200; Nail Patella syndrome; NPS
Arthrogryposis v3.6 LMX1B Rebecca Foulger Classified gene: LMX1B as Green List (high evidence)
Arthrogryposis v3.6 LMX1B Rebecca Foulger Added comment: Comment on list classification: Changed rating to Green with agreement from Zerin Hyder: overlap with Arthrogryposis phenotype and Nail patella syndrome.
Arthrogryposis v3.6 LMX1B Rebecca Foulger Gene: lmx1b has been classified as Green List (High Evidence).
Arthrogryposis v3.5 LMX1B Rebecca Foulger commented on gene: LMX1B: Dr Ataf Sabir notes (email, April 16 2020) that they had a 100K patient who presented with what looked like arthrogryposis, who had the Arthrogryposis panel with nil result, and on further investigation the patient had Nail Patella syndrome.
Arthrogryposis v3.5 LMX1B Ataf Sabir reviewed gene: LMX1B: Rating: ; Mode of pathogenicity: ; Publications: 19194568, 31369690, ISBN:9780199557509; Phenotypes: Nail Patella syndrome, NPS; Mode of inheritance:
Arthrogryposis v3.4 LMX1B Rebecca Foulger gene: LMX1B was added
gene: LMX1B was added to Arthrogryposis. Sources: Expert Review,Other
Mode of inheritance for gene: LMX1B was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: LMX1B were set to 8403448
Phenotypes for gene: LMX1B were set to Nail-patella syndrome, 161200
Added comment: Added LMX1B to the Arthrogryposis panel as requested by Dr Ataf Sabir.
Sources: Expert Review, Other
Optic neuropathy v2.3 UCHL1 Zornitza Stark gene: UCHL1 was added
gene: UCHL1 was added to Optic neuropathy. Sources: Expert list
Mode of inheritance for gene: UCHL1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: UCHL1 were set to 29735986; 23359680; 28007905
Phenotypes for gene: UCHL1 were set to Spastic paraplegia 79, autosomal recessive (MIM#615491)
Review for gene: UCHL1 was set to GREEN
Added comment: Three families reported, optic atrophy is a consistent feature and onset of OA preceded onset of other neurological features in at least some of the reported individuals.
Sources: Expert list
Optic neuropathy v2.3 NBAS Zornitza Stark gene: NBAS was added
gene: NBAS was added to Optic neuropathy. Sources: Expert list
Mode of inheritance for gene: NBAS was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: NBAS were set to 20577004; 26286438
Phenotypes for gene: NBAS were set to Short stature, optic nerve atrophy, and Pelger-Huet anomaly
Review for gene: NBAS was set to GREEN
Added comment: This gene causes two recessive phenotypes: OA is not a feature of the infantile liver failure syndrome. It is however a consistent feature of the second condition: Short stature, optic nerve atrophy, and Pelger-Huet anomaly, MIM# 614800, which has predominantly been described in the Yakult.

PMID: 20577004 - Study of 30 Yakut families found ALL had OA, 33/34 patients had the same homozygous missense, founder very likely

PMID: 26286438 - 1 patient chet for a PTC and missense and had OA. Second patient (also chet PTC/missense) had NO OA.

Remains to be seen whether OA is an association with specific variants in this gene, and what the underlying mechanism for this is.
Sources: Expert list
Optic neuropathy v2.3 MECR Zornitza Stark gene: MECR was added
gene: MECR was added to Optic neuropathy. Sources: Expert list
Mode of inheritance for gene: MECR was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MECR were set to 27817865; 31137067
Phenotypes for gene: MECR were set to Dystonia, childhood-onset, with optic atrophy and basal ganglia abnormalities
Review for gene: MECR was set to GREEN
gene: MECR was marked as current diagnostic
Added comment: At least 6 families reported, optic atrophy is a consistent feature.
Sources: Expert list
Optic neuropathy v2.3 FDXR Zornitza Stark gene: FDXR was added
gene: FDXR was added to Optic neuropathy. Sources: Expert list
Mode of inheritance for gene: FDXR was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: FDXR were set to 30250212; 28965846
Phenotypes for gene: FDXR were set to Auditory neuropathy and optic atrophy, MIM#617717
Review for gene: FDXR was set to GREEN
Added comment: Six unrelated families reported with bi-allelic variants in this gene, optic atrophy is a consistent feature.
Sources: Expert list
Optic neuropathy v2.3 ATAD3A Zornitza Stark reviewed gene: ATAD3A: Rating: GREEN; Mode of pathogenicity: None; Publications: 27640307, 28652416; Phenotypes: Harel-Yoon syndrome, MIM#617183; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Optic neuropathy v2.3 AP3B2 Zornitza Stark gene: AP3B2 was added
gene: AP3B2 was added to Optic neuropathy. Sources: Expert list
Mode of inheritance for gene: AP3B2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: AP3B2 were set to 27889060
Phenotypes for gene: AP3B2 were set to Early-onset epileptic encephalopathy with optic atrophy, MIM#617276
Review for gene: AP3B2 was set to GREEN
Added comment: Optic atrophy is a feature of this neurological disorder.
Sources: Expert list
Optic neuropathy v2.3 AFG3L2 Zornitza Stark reviewed gene: AFG3L2: Rating: GREEN; Mode of pathogenicity: None; Publications: 29181157, 26539208, 30252181, 30389403; Phenotypes: Spastic ataxia 5, autosomal recessive (MIM#614487), Spinocerebellar ataxia 28 (MIM#610246); Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted; Current diagnostic: yes
Primary immunodeficiency or monogenic inflammatory bowel disease v2.86 SMARCD2 Ivone Leong Phenotypes for gene: SMARCD2 were changed from Neutropenia, developmental aberrations, skeletal abnormalities, hematopoietic stem cells, myelodysplasia; Congenital defects of phagocyte number or function to Neutropenia, developmental aberrations, skeletal abnormalities, hematopoietic stem cells, myelodysplasia; Congenital defects of phagocyte number or function; Specific granule deficiency 2, 617475
Primary immunodeficiency or monogenic inflammatory bowel disease v2.85 SMARCD2 Ivone Leong Classified gene: SMARCD2 as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.85 SMARCD2 Ivone Leong Added comment: Comment on list classification: Promoted from Red to Green based on expert review.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.85 SMARCD2 Ivone Leong Gene: smarcd2 has been classified as Green List (High Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.84 SMARCD2 Ivone Leong Publications for gene: SMARCD2 were set to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.83 SRP54 Ivone Leong Classified gene: SRP54 as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.83 SRP54 Ivone Leong Added comment: Comment on list classification: Promoted Red to Green based on expert review and evidence.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.83 SRP54 Ivone Leong Gene: srp54 has been classified as Green List (High Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.82 SRP54 Ivone Leong Phenotypes for gene: SRP54 were changed from Congenital defects of phagocyte number or function; Schwachman Diamond features to Congenital defects of phagocyte number or function; Schwachman Diamond features; Neutropenia, severe congenital, 8, autosomal dominant, 618752
Primary immunodeficiency or monogenic inflammatory bowel disease v2.81 TFRC Ivone Leong Classified gene: TFRC as Amber List (moderate evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.81 TFRC Ivone Leong Added comment: Comment on list classification: Promoted from Red to Amber based on expert review and evidence.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.81 TFRC Ivone Leong Gene: tfrc has been classified as Amber List (Moderate Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.80 TFRC Ivone Leong Phenotypes for gene: TFRC were changed from Recurrent infections, neutropenia, thrombocytopenia; Recurrent infections, thrombocytopenia; Immunodeficiencies affecting cellular and humoral immunity to Recurrent infections, neutropenia, thrombocytopenia; Recurrent infections, thrombocytopenia; Immunodeficiencies affecting cellular and humoral immunity; Immunodeficiency 46, 616740; T cells: normal number, poor proliferation; B cells: normal number, low memory B cells; recurrent infections, neutorpaenia; thrombocytopaenia
Primary immunodeficiency or monogenic inflammatory bowel disease v2.79 TFRC Ivone Leong Publications for gene: TFRC were set to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.78 TGFB1 Ivone Leong Classified gene: TGFB1 as Amber List (moderate evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.78 TGFB1 Ivone Leong Added comment: Comment on list classification: Promoted from Red to Amber based on expert review and evidence.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.78 TGFB1 Ivone Leong Gene: tgfb1 has been classified as Amber List (Moderate Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.77 NFE2L2 Ivone Leong Classified gene: NFE2L2 as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.77 NFE2L2 Ivone Leong Added comment: Comment on list classification: Promoted from Red to Green based on exper review.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.77 NFE2L2 Ivone Leong Gene: nfe2l2 has been classified as Green List (High Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.76 NFE2L2 Ivone Leong Phenotypes for gene: NFE2L2 were changed from white matter cerebral lesions, increased level of homocysteine; Recurrent respiratory and skin infections, growth retardation, , developmental delay; Immunodeficiency, developmental delay, and hypohomocysteinemia, 617744; NFE2L2 GOF; increased expression of stress response genes; Combined immunodeficiencies with associated or syndromic features to white matter cerebral lesions, increased level of homocysteine; Recurrent respiratory and skin infections, growth retardation, , developmental delay; Immunodeficiency, developmental delay, and hypohomocysteinemia, 617744; NFE2L2 GOF; increased expression of stress response genes; Combined immunodeficiencies with associated or syndromic features; mmunodeficiency, developmental delay, and hypohomocysteinemia, 617744; Recurrent respiratory and skin infection; Growth retardation; Developmental delay, borderline ID; White matter cerebral lesions
Primary immunodeficiency or monogenic inflammatory bowel disease v2.75 TNFRSF9 Ivone Leong Classified gene: TNFRSF9 as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.75 TNFRSF9 Ivone Leong Added comment: Comment on list classification: Promoted from Red to Green based on expert review and evidence.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.75 TNFRSF9 Ivone Leong Gene: tnfrsf9 has been classified as Green List (High Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.74 TOP2B Ivone Leong Classified gene: TOP2B as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.74 TOP2B Ivone Leong Added comment: Comment on list classification: Promoted from Red to Green based on expert review and evidence.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.74 TOP2B Ivone Leong Gene: top2b has been classified as Green List (High Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.73 TRAF3IP2 Ivone Leong Classified gene: TRAF3IP2 as Amber List (moderate evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.73 TRAF3IP2 Ivone Leong Added comment: Comment on list classification: Promoted from Red to Amber based on expert review and evidence.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.73 TRAF3IP2 Ivone Leong Gene: traf3ip2 has been classified as Amber List (Moderate Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.72 TRIM22 Ivone Leong Classified gene: TRIM22 as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.72 TRIM22 Ivone Leong Added comment: Comment on list classification: Promoted from Red to Green based on expert review and evidence.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.72 TRIM22 Ivone Leong Gene: trim22 has been classified as Green List (High Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.71 TRIM22 Ivone Leong Phenotypes for gene: TRIM22 were changed from Autoinflammatory Disorders; Granulomatous colitis; Diseases of Immune Dysregulation; TRIM22 to Autoinflammatory Disorders; Granulomatous colitis; Diseases of Immune Dysregulation; TRIM22; Inflammatory bowel disease
Primary immunodeficiency or monogenic inflammatory bowel disease v2.70 USP18 Ivone Leong Classified gene: USP18 as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.70 USP18 Ivone Leong Added comment: Comment on list classification: Promoted from Amber to Green based on expert reviews.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.70 USP18 Ivone Leong Gene: usp18 has been classified as Green List (High Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.69 TRAF3IP2 Ivone Leong Publications for gene: TRAF3IP2 were set to 32048120; 24120361; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.68 USP18 Ivone Leong Publications for gene: USP18 were set to 32048120; 27325888; 31272490; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.67 WDR1 Ivone Leong Classified gene: WDR1 as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.67 WDR1 Ivone Leong Added comment: Comment on list classification: Promoted from Amber to Green based on expert review.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.67 WDR1 Ivone Leong Gene: wdr1 has been classified as Green List (High Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.66 WDR1 Ivone Leong Publications for gene: WDR1 were set to 32048120; 27557945; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.65 ZNF341 Ivone Leong Classified gene: ZNF341 as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.65 ZNF341 Ivone Leong Added comment: Comment on list classification: Promoted from Red to Green based on expert reviews.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.65 ZNF341 Ivone Leong Gene: znf341 has been classified as Green List (High Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.64 PIK3CD Ivone Leong Added comment: Comment on mode of inheritance: Updated MOI from Monoallelic to Both Monoallelic and biallelic based on expert review and evidence provided by Zornitza Stark (Australian Genomics).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.64 PIK3CD Ivone Leong Mode of inheritance for gene: PIK3CD was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.63 PIK3CD Ivone Leong Publications for gene: PIK3CD were set to 24165795; 24136356; 29226301
Primary immunodeficiency or monogenic inflammatory bowel disease v2.62 TCF3 Ivone Leong Added comment: Comment on mode of inheritance: Updated MOI from Monoallelic to Both Monoallelic and biallelic based on expert review and evidence provided by Zornitza Stark (Australian Genomics).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.62 TCF3 Ivone Leong Mode of inheritance for gene: TCF3 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.61 STAT5B Ivone Leong Publications for gene: STAT5B were set to 13679528; 16920911; 15827093; 16787985; 17030597; 17389811; 20538865; 26703237
Primary immunodeficiency or monogenic inflammatory bowel disease v2.60 STAT5B Ivone Leong Added comment: Comment on mode of inheritance: Changed MOI from Biallelic to Both Monoallelic and biallelic based on expert review and evidence provided by Zornitza Stark (Australian Genomics). It should be noted that the AD has a dominant-negative effect.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.60 STAT5B Ivone Leong Mode of inheritance for gene: STAT5B was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.59 TCF3 Ivone Leong Publications for gene: TCF3 were set to 24216514; 28532655; 29114388
Primary immunodeficiency or monogenic inflammatory bowel disease v2.58 BCL10 Ivone Leong Classified gene: BCL10 as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.58 BCL10 Ivone Leong Added comment: Comment on list classification: Based on recent expert reviews and evidence, it has been decided that there is now enough evidence to support a gene-disease association. Therefore, this gene has been promoted from Amber to Green.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.58 BCL10 Ivone Leong Gene: bcl10 has been classified as Green List (High Evidence).
COVID-19 research v0.106 POLR3F Ivone Leong Publications for gene: POLR3F were set to 30211253
COVID-19 research v0.105 POLR3C Ivone Leong Publications for gene: POLR3C were set to 28783042
COVID-19 research v0.104 POLR3A Ivone Leong Publications for gene: POLR3A were set to 29728610; 28783042
COVID-19 research v0.103 OAS1 Ivone Leong reviewed gene: OAS1: Rating: GREEN; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance:
COVID-19 research v0.103 IKZF1 Ivone Leong reviewed gene: IKZF1: Rating: GREEN; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance:
COVID-19 research v0.103 TMEM173 Ivone Leong reviewed gene: TMEM173: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.103 TCF3 Ivone Leong reviewed gene: TCF3: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.103 STXBP2 Ivone Leong reviewed gene: STXBP2: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.103 STAT5B Ivone Leong reviewed gene: STAT5B: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.103 RANBP2 Ivone Leong reviewed gene: RANBP2: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.103 PSMB8 Ivone Leong reviewed gene: PSMB8: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.103 PIK3CD Ivone Leong reviewed gene: PIK3CD: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.103 JAK1 Ivone Leong reviewed gene: JAK1: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.103 FOXN1 Ivone Leong reviewed gene: FOXN1: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.103 C3 Ivone Leong reviewed gene: C3: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.103 C1S Ivone Leong reviewed gene: C1S: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.103 C1R Ivone Leong reviewed gene: C1R: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.103 AICDA Ivone Leong reviewed gene: AICDA: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.103 TP53 Ivone Leong reviewed gene: TP53: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: Bone marrow failure syndrome 5, 618165; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
COVID-19 research v0.103 SRP72 Ivone Leong reviewed gene: SRP72: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: Bone marrow failure syndrome 1, 614675; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
COVID-19 research v0.103 RFWD3 Ivone Leong reviewed gene: RFWD3: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: ?Fanconi anemia, complementation group W, 617784; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.103 MAD2L2 Ivone Leong reviewed gene: MAD2L2: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: ?Fanconi anemia, complementation group V, 617243 ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.103 XRCC2 Ivone Leong reviewed gene: XRCC2: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: ?Fanconi anemia, complementation group U, 617247; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.103 UBE2T Ivone Leong reviewed gene: UBE2T: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: Fanconi anemia, complementation group T, 616435; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.103 RAD51 Ivone Leong reviewed gene: RAD51: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: ?Fanconi anemia, complementation group R, 617244; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.103 SLX4 Ivone Leong reviewed gene: SLX4: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: Fanconi anemia, complementation group P, 613951; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.103 RAD51C Ivone Leong reviewed gene: RAD51C: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: Fanconi anemia, complementation group O, 613390; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.103 PALB2 Ivone Leong reviewed gene: PALB2: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: Fanconi anemia, complementation group N, 610832; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.103 FANCL Ivone Leong reviewed gene: FANCL: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: Fanconi anemia, complementation group L, 614083; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.103 BRIP1 Ivone Leong reviewed gene: BRIP1: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: Fanconi anemia, complementation group J, 609054; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.103 FANCG Ivone Leong reviewed gene: FANCG: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: Fanconi anemia, complementation group G, 614082; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.103 FANCE Ivone Leong reviewed gene: FANCE: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: Fanconi anemia, complementation group E, 600901; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.103 FANCD2 Ivone Leong reviewed gene: FANCD2: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: Fanconi anemia, complementation group D2, 227646; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.103 FANCC Ivone Leong reviewed gene: FANCC: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: Fanconi anemia, complementation group C, 227645; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.103 FANCB Ivone Leong reviewed gene: FANCB: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: Fanconi anemia, complementation group B, 300514; Mode of inheritance: X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)
COVID-19 research v0.103 FANCA Ivone Leong reviewed gene: FANCA: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: Fanconi anemia, complementation group A, 227650 ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.103 IL18BP Ivone Leong reviewed gene: IL18BP: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: Defects in intrinsic and innate immunity, inborn errors of immunity related to leukocytes, IL-18BP deficiency; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
COVID-19 research v0.103 IRF4 Ivone Leong reviewed gene: IRF4: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: Defects in intrinsic and innate immunity, inborn errors of immunity related to leukocytes, IRF4 haploinsufficiency; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
COVID-19 research v0.103 POLR3F Ivone Leong reviewed gene: POLR3F: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: Defects in intrinsic and innate immunity, Predisposition to severe viral infection, RNA polymerase III deficiency; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
COVID-19 research v0.103 POLR3C Ivone Leong reviewed gene: POLR3C: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: Defects in intrinsic and innate immunity, Predisposition to severe viral infection, RNA polymerase III deficiency; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
COVID-19 research v0.103 POLR3A Ivone Leong reviewed gene: POLR3A: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: Defects in intrinsic and innate immunity, Predisposition to severe viral infection, RNA polymerase III deficiency; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
COVID-19 research v0.103 CIB1 Ivone Leong reviewed gene: CIB1: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: Defects in intrinsic and innate immunity, Epidermodysplasia verruciformis, CIB1 deficiency; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.103 IL23R Ivone Leong reviewed gene: IL23R: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: Defects in intrinsic and innate immunity, Mendelian susceptibility to mycobacterial disease, IL-23R deficiency; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.103 IL12RB2 Ivone Leong reviewed gene: IL12RB2: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: Defects in intrinsic and innate immunity, Mendelian susceptibility to mycobacterial disease, IL-12Rb2 deficiency; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.103 EFL1 Ivone Leong reviewed gene: EFL1: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: Congenital defects of phagocyte number or function, Congenital neutropenias, Shwachman-Diamond Syndrome, 617941; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.102 TMEM173 Ivone Leong Source IUIS Classification December 2032 was added to TMEM173.
Mode of inheritance for gene TMEM173 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.102 TCF3 Ivone Leong Source IUIS Classification December 2031 was added to TCF3.
Mode of inheritance for gene TCF3 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.102 STXBP2 Ivone Leong Source IUIS Classification December 2030 was added to STXBP2.
Mode of inheritance for gene STXBP2 was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.102 STAT5B Ivone Leong Source IUIS Classification December 2029 was added to STAT5B.
Mode of inheritance for gene STAT5B was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.102 RANBP2 Ivone Leong Source IUIS Classification December 2028 was added to RANBP2.
Mode of inheritance for gene RANBP2 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.102 PSMB8 Ivone Leong Source IUIS Classification December 2027 was added to PSMB8.
Mode of inheritance for gene PSMB8 was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.102 PIK3CD Ivone Leong Source IUIS Classification December 2026 was added to PIK3CD.
Mode of inheritance for gene PIK3CD was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.102 JAK1 Ivone Leong Source IUIS Classification December 2025 was added to JAK1.
Mode of inheritance for gene JAK1 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.102 FOXN1 Ivone Leong Source IUIS Classification December 2024 was added to FOXN1.
Mode of inheritance for gene FOXN1 was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.102 C3 Ivone Leong Source IUIS Classification December 2022 was added to C3.
Mode of inheritance for gene C3 was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.102 C1S Ivone Leong Source IUIS Classification December 2021 was added to C1S.
Mode of inheritance for gene C1S was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.102 C1R Ivone Leong Source IUIS Classification December 2020 was added to C1R.
Mode of inheritance for gene C1R was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.102 AICDA Ivone Leong Source IUIS Classification December 2019 was added to AICDA.
Mode of inheritance for gene AICDA was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.102 TP53 Ivone Leong gene: TP53 was added
gene: TP53 was added to Viral susceptibility. Sources: Expert Review Green,IUIS Classification December 2019
Mode of inheritance for gene: TP53 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: TP53 were set to 32086639; 32048120
Phenotypes for gene: TP53 were set to Bone marrow failure syndrome 5, 618165
COVID-19 research v0.102 SRP72 Ivone Leong gene: SRP72 was added
gene: SRP72 was added to Viral susceptibility. Sources: Expert Review Green,IUIS Classification December 2019
Mode of inheritance for gene: SRP72 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: SRP72 were set to 32086639; 32048120
Phenotypes for gene: SRP72 were set to Bone marrow failure syndrome 1, 614675
COVID-19 research v0.102 RFWD3 Ivone Leong gene: RFWD3 was added
gene: RFWD3 was added to Viral susceptibility. Sources: Expert Review Green,IUIS Classification December 2019
Mode of inheritance for gene: RFWD3 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RFWD3 were set to 32086639; 32048120
Phenotypes for gene: RFWD3 were set to ?Fanconi anemia, complementation group W, 617784
COVID-19 research v0.102 MAD2L2 Ivone Leong gene: MAD2L2 was added
gene: MAD2L2 was added to Viral susceptibility. Sources: Expert Review Green,IUIS Classification December 2019
Mode of inheritance for gene: MAD2L2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MAD2L2 were set to 32086639; 32048120
Phenotypes for gene: MAD2L2 were set to ?Fanconi anemia, complementation group V, 617243
COVID-19 research v0.102 XRCC2 Ivone Leong gene: XRCC2 was added
gene: XRCC2 was added to Viral susceptibility. Sources: Expert Review Green,IUIS Classification December 2019
Mode of inheritance for gene: XRCC2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: XRCC2 were set to 32086639; 32048120
Phenotypes for gene: XRCC2 were set to ?Fanconi anemia, complementation group U, 617247
COVID-19 research v0.102 UBE2T Ivone Leong gene: UBE2T was added
gene: UBE2T was added to Viral susceptibility. Sources: Expert Review Green,IUIS Classification December 2019
Mode of inheritance for gene: UBE2T was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: UBE2T were set to 32086639; 32048120
Phenotypes for gene: UBE2T were set to Fanconi anemia, complementation group T, 616435
COVID-19 research v0.102 RAD51 Ivone Leong gene: RAD51 was added
gene: RAD51 was added to Viral susceptibility. Sources: Expert Review Green,IUIS Classification December 2019
Mode of inheritance for gene: RAD51 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RAD51 were set to 32086639; 32048120
Phenotypes for gene: RAD51 were set to ?Fanconi anemia, complementation group R, 617244
COVID-19 research v0.102 SLX4 Ivone Leong gene: SLX4 was added
gene: SLX4 was added to Viral susceptibility. Sources: Expert Review Green,IUIS Classification December 2019
Mode of inheritance for gene: SLX4 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SLX4 were set to 32086639; 32048120
Phenotypes for gene: SLX4 were set to Fanconi anemia, complementation group P, 613951
COVID-19 research v0.102 RAD51C Ivone Leong gene: RAD51C was added
gene: RAD51C was added to Viral susceptibility. Sources: Expert Review Green,IUIS Classification December 2019
Mode of inheritance for gene: RAD51C was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RAD51C were set to 32086639; 32048120
Phenotypes for gene: RAD51C were set to Fanconi anemia, complementation group O, 613390
COVID-19 research v0.102 PALB2 Ivone Leong gene: PALB2 was added
gene: PALB2 was added to Viral susceptibility. Sources: Expert Review Green,IUIS Classification December 2019
Mode of inheritance for gene: PALB2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PALB2 were set to 32086639; 32048120
Phenotypes for gene: PALB2 were set to Fanconi anemia, complementation group N, 610832
COVID-19 research v0.102 FANCL Ivone Leong gene: FANCL was added
gene: FANCL was added to Viral susceptibility. Sources: Expert Review Green,IUIS Classification December 2019
Mode of inheritance for gene: FANCL was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: FANCL were set to 32086639; 32048120
Phenotypes for gene: FANCL were set to Fanconi anemia, complementation group L, 614083
COVID-19 research v0.102 BRIP1 Ivone Leong gene: BRIP1 was added
gene: BRIP1 was added to Viral susceptibility. Sources: Expert Review Green,IUIS Classification December 2019
Mode of inheritance for gene: BRIP1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: BRIP1 were set to 32086639; 32048120
Phenotypes for gene: BRIP1 were set to Fanconi anemia, complementation group J, 609054
COVID-19 research v0.102 FANCG Ivone Leong gene: FANCG was added
gene: FANCG was added to Viral susceptibility. Sources: Expert Review Green,IUIS Classification December 2019
Mode of inheritance for gene: FANCG was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: FANCG were set to 32086639; 32048120
Phenotypes for gene: FANCG were set to Fanconi anemia, complementation group G, 614082
COVID-19 research v0.102 FANCE Ivone Leong gene: FANCE was added
gene: FANCE was added to Viral susceptibility. Sources: Expert Review Green,IUIS Classification December 2019
Mode of inheritance for gene: FANCE was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: FANCE were set to 32086639; 32048120
Phenotypes for gene: FANCE were set to Fanconi anemia, complementation group E, 600901
COVID-19 research v0.102 FANCD2 Ivone Leong gene: FANCD2 was added
gene: FANCD2 was added to Viral susceptibility. Sources: Expert Review Green,IUIS Classification December 2019
Mode of inheritance for gene: FANCD2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: FANCD2 were set to 32086639; 32048120
Phenotypes for gene: FANCD2 were set to Fanconi anemia, complementation group D2, 227646
COVID-19 research v0.102 FANCC Ivone Leong gene: FANCC was added
gene: FANCC was added to Viral susceptibility. Sources: Expert Review Green,IUIS Classification December 2019
Mode of inheritance for gene: FANCC was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: FANCC were set to 32086639; 32048120
Phenotypes for gene: FANCC were set to Fanconi anemia, complementation group C, 227645
COVID-19 research v0.102 FANCB Ivone Leong gene: FANCB was added
gene: FANCB was added to Viral susceptibility. Sources: Expert Review Green,IUIS Classification December 2019
Mode of inheritance for gene: FANCB was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)
Publications for gene: FANCB were set to 32086639; 32048120
Phenotypes for gene: FANCB were set to Fanconi anemia, complementation group B, 300514
COVID-19 research v0.102 FANCA Ivone Leong gene: FANCA was added
gene: FANCA was added to Viral susceptibility. Sources: Expert Review Green,IUIS Classification December 2019
Mode of inheritance for gene: FANCA was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: FANCA were set to 32086639; 32048120
Phenotypes for gene: FANCA were set to Fanconi anemia, complementation group A, 227650
COVID-19 research v0.102 IL18BP Ivone Leong Source Expert Review Green was added to IL18BP.
Source IUIS Classification December 2019 was added to IL18BP.
Mode of inheritance for gene IL18BP was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Added phenotypes Defects in intrinsic and innate immunity; IL-18BP deficiency; inborn errors of immunity related to leukocytes for gene: IL18BP
Publications for gene IL18BP were updated from PubMed: 31213488 to 32086639; 32048120; PubMed: 31213488
Rating Changed from No List (delete) to Green List (high evidence)
COVID-19 research v0.102 IRF4 Ivone Leong gene: IRF4 was added
gene: IRF4 was added to Viral susceptibility. Sources: Expert Review Green,IUIS Classification December 2019
Mode of inheritance for gene: IRF4 was set to
Phenotypes for gene: IRF4 were set to Defects in intrinsic and innate immunity; IRF4 haploinsufficiency; inborn errors of immunity related to leukocytes
COVID-19 research v0.102 POLR3F Ivone Leong Source Expert Review Green was added to POLR3F.
Source IUIS Classification December 2019 was added to POLR3F.
Added phenotypes RNA polymerase III deficiency; Defects in intrinsic and innate immunity; Predisposition to severe viral infection for gene: POLR3F
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.102 POLR3C Ivone Leong Source Expert Review Green was added to POLR3C.
Source IUIS Classification December 2019 was added to POLR3C.
Added phenotypes RNA polymerase III deficiency; Defects in intrinsic and innate immunity; Predisposition to severe viral infection for gene: POLR3C
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.102 POLR3A Ivone Leong Source Expert Review Green was added to POLR3A.
Source IUIS Classification December 2019 was added to POLR3A.
Added phenotypes RNA polymerase III deficiency; Defects in intrinsic and innate immunity; Predisposition to severe viral infection for gene: POLR3A
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.102 CIB1 Ivone Leong gene: CIB1 was added
gene: CIB1 was added to Viral susceptibility. Sources: Expert Review Green,IUIS Classification December 2019
Mode of inheritance for gene: CIB1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CIB1 were set to 32086639; 32048120
Phenotypes for gene: CIB1 were set to Epidermodysplasia verruciformis; Defects in intrinsic and innate immunity; CIB1 deficiency
COVID-19 research v0.102 IL23R Ivone Leong gene: IL23R was added
gene: IL23R was added to Viral susceptibility. Sources: Expert Review Green,IUIS Classification December 2019
Mode of inheritance for gene: IL23R was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IL23R were set to 32086639; 32048120
Phenotypes for gene: IL23R were set to Defects in intrinsic and innate immunity; Mendelian susceptibility to mycobacterial disease; IL-23R deficiency
COVID-19 research v0.102 IL12RB2 Ivone Leong gene: IL12RB2 was added
gene: IL12RB2 was added to Viral susceptibility. Sources: Expert Review Green,IUIS Classification December 2019
Mode of inheritance for gene: IL12RB2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IL12RB2 were set to 32086639; 32048120
Phenotypes for gene: IL12RB2 were set to Defects in intrinsic and innate immunity; Mendelian susceptibility to mycobacterial disease; IL-12Rb2 deficiency
COVID-19 research v0.102 EFL1 Ivone Leong gene: EFL1 was added
gene: EFL1 was added to Viral susceptibility. Sources: Expert Review Green,IUIS Classification December 2019
Mode of inheritance for gene: EFL1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: EFL1 were set to 32086639; 32048120
Phenotypes for gene: EFL1 were set to Congenital neutropenias; Congenital defects of phagocyte number or function; Shwachman-Diamond Syndrome, 617941
COVID-19 research v0.101 ACE2 Rebecca Foulger commented on gene: ACE2: Added ACE2 to the panel as an Amber gene: many papers demonstrate that ACE2 acts as a cell receptor for Coronaviruses (e.g. PMIDs 32142651, 15897467, 14647384).
COVID-19 research v0.101 ACE2 Rebecca Foulger Classified gene: ACE2 as Amber List (moderate evidence)
COVID-19 research v0.101 ACE2 Rebecca Foulger Gene: ace2 has been classified as Amber List (Moderate Evidence).
COVID-19 research v0.100 ACE2 Rebecca Foulger gene: ACE2 was added
gene: ACE2 was added to Viral susceptibility. Sources: Other
Mode of inheritance for gene: ACE2 was set to Unknown
Publications for gene: ACE2 were set to 14647384; 15897467; 16007097; 32142651
Review for gene: ACE2 was set to AMBER
Added comment: Sources: Other
COVID-19 research v0.99 CD4 Rebecca Foulger Publications for gene: CD4 were set to
COVID-19 research v0.98 CD4 Rebecca Foulger commented on gene: CD4
COVID-19 research v0.98 CD14 Rebecca Foulger Classified gene: CD14 as Amber List (moderate evidence)
COVID-19 research v0.98 CD14 Rebecca Foulger Added comment: Comment on list classification: Updated rating from Red to Amber: at least 2 publications supporting a link between CD14 polymorphism and viral infection (SARs and RSV).
COVID-19 research v0.98 CD14 Rebecca Foulger Gene: cd14 has been classified as Amber List (Moderate Evidence).
COVID-19 research v0.97 CD14 Rebecca Foulger Publications for gene: CD14 were set to 17913858
COVID-19 research v0.96 CD14 Rebecca Foulger commented on gene: CD14
COVID-19 research v0.96 ITGAM Catherine Snow Publications for gene: ITGAM were set to
COVID-19 research v0.95 ITGAM Catherine Snow Mode of inheritance for gene: ITGAM was changed from Unknown to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
COVID-19 research v0.94 ITGAM Catherine Snow Classified gene: ITGAM as Amber List (moderate evidence)
COVID-19 research v0.94 ITGAM Catherine Snow Gene: itgam has been classified as Amber List (Moderate Evidence).
COVID-19 research v0.93 ITGAM Catherine Snow reviewed gene: ITGAM: Rating: AMBER; Mode of pathogenicity: None; Publications: 29712964, 32257537; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
COVID-19 research v0.93 RC3H1 Sarah Leigh Classified gene: RC3H1 as Amber List (moderate evidence)
COVID-19 research v0.93 RC3H1 Sarah Leigh Added comment: Comment on list classification: Not associated with phenotype in OMIM (lasted edited 01/27/2017) or in Gen2Phen. PMID 31636267 reports a biallelic nonsense variant (p.R688*), in a case with immune dysregulation syndrome
characterized by severe hyperinflammation in a consanguineous family. The association of this variant with the phenotype is supported by functional studies and mouse model (PMID 15917799).
COVID-19 research v0.93 RC3H1 Sarah Leigh Gene: rc3h1 has been classified as Amber List (Moderate Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.57 RC3H1 Sarah Leigh Classified gene: RC3H1 as Amber List (moderate evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.57 RC3H1 Sarah Leigh Added comment: Comment on list classification: Not associated with phenotype in OMIM (lasted edited 01/27/2017) or in Gen2Phen. PMID 31636267 reports a biallelic nonsense variant (p.R688*), in a case with immune dysregulation syndrome
characterized by severe hyperinflammation in a consanguineous family. The association of this variant with the phenotype is supported by functional studies and mouse model (PMID 15917799).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.57 RC3H1 Sarah Leigh Gene: rc3h1 has been classified as Amber List (Moderate Evidence).
COVID-19 research v0.92 RC3H1 Sarah Leigh Publications for gene: RC3H1 were set to PMID: 31636267
Primary immunodeficiency or monogenic inflammatory bowel disease v2.56 RC3H1 Sarah Leigh Publications for gene: RC3H1 were set to PMID: 31636267
COVID-19 research v0.91 CCL5 Rebecca Foulger Classified gene: CCL5 as Amber List (moderate evidence)
COVID-19 research v0.91 CCL5 Rebecca Foulger Added comment: Comment on list classification: Updated rating from Red to Amber: Some evidence that CCL5 (aka RANTES) polymorphisms may be associated with viral infections, including SARS.
COVID-19 research v0.91 CCL5 Rebecca Foulger Gene: ccl5 has been classified as Amber List (Moderate Evidence).
COVID-19 research v0.90 CCL5 Rebecca Foulger Publications for gene: CCL5 were set to 17540042; 22576913
COVID-19 research v0.89 CCL5 Rebecca Foulger commented on gene: CCL5: PMID:30175654 (El-Bendary et al., 2019) report rs3817655 polymorphism in CCL5 may be associated with spontaneous clearance of Hepatitis C virus (HCV).
COVID-19 research v0.89 CCL5 Rebecca Foulger commented on gene: CCL5: PMID:31874580 (Sheng et al. 2019) study suggests that the CCL5 rs2107538 polymorphism was correlated with TB (infectious disease caused by Mycobacterium tuberculosis) susceptibility in Caucasians. The rs2107538 polymorphism is suggested to affect CCL5 expression.
COVID-19 research v0.89 CCL5 Rebecca Foulger Publications for gene: CCL5 were set to 17540042
COVID-19 research v0.88 CCL5 Rebecca Foulger commented on gene: CCL5
COVID-19 research v0.88 CCL2 Rebecca Foulger Classified gene: CCL2 as Green List (high evidence)
COVID-19 research v0.88 CCL2 Rebecca Foulger Added comment: Comment on list classification: Updated rating of CCL2 from Red to Green. 3 publications supporting an association between CCL2 SNP(s) and viral infections including HIV, Japanese encephalitis and SARs. Additional evidence that CCL2 levels are raised after viral infection.
COVID-19 research v0.88 CCL2 Rebecca Foulger Gene: ccl2 has been classified as Green List (High Evidence).
COVID-19 research v0.87 CCL2 Rebecca Foulger Phenotypes for gene: CCL2 were changed from {HIV-1, resistance to}, 609423; Susceptibility to Severe Acute Respiratory Syndrome Coronavirus Infection; Susceptibility to SARS-CoV to {HIV-1, resistance to}, 609423; Susceptibility to Severe Acute Respiratory Syndrome Coronavirus Infection; Susceptibility to SARS-CoV; Susceptibility to viral Japanese encephalitis
COVID-19 research v0.86 CCL2 Rebecca Foulger Publications for gene: CCL2 were set to 25818534; 26687605; 16916890; 24788844; 27260136
COVID-19 research v0.85 CCL2 Rebecca Foulger commented on gene: CCL2: PMID:29057937 (Chowdhury and Khan, 2017) report that SNPs of CCL2 (rs1024611G) and its receptor CCR2 (rs1799864A) significantly associated with Japanese encephalitis (JE) which may serve as possible genetic predisposing factor. JE is one of the major viral encephalitis in Asia and parts of Western Pacific.
COVID-19 research v0.85 PSMB10 Sarah Leigh Classified gene: PSMB10 as Amber List (moderate evidence)
COVID-19 research v0.85 PSMB10 Sarah Leigh Added comment: Comment on list classification: Not associated with phenotype in OMIM (last edited on 06/25/2007) or in Gen2Phen. PMID 31783057 reports a case of Proteasome-associated autoinflammatory syndrome in an infant with a biallelic variant (c.41T>C, p.Phe14Ser), together with supporting functional studies.
COVID-19 research v0.85 PSMB10 Sarah Leigh Gene: psmb10 has been classified as Amber List (Moderate Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.55 PSMB10 Sarah Leigh Classified gene: PSMB10 as Amber List (moderate evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.55 PSMB10 Sarah Leigh Added comment: Comment on list classification: Not associated with phenotype in OMIM (last edited on 06/25/2007) or in Gen2Phen. PMID 31783057 reports a case of Proteasome-associated autoinflammatory syndrome in an infant with a biallelic variant (c.41T>C, p.Phe14Ser), together with supporting functional studies.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.55 PSMB10 Sarah Leigh Gene: psmb10 has been classified as Amber List (Moderate Evidence).
COVID-19 research v0.84 PSMB10 Sarah Leigh Phenotypes for gene: PSMB10 were changed from Proteasome-associated autoinflammatory syndrome to Proteasome-associated autoinflammatory syndrome (PRAAS)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.54 PSMB10 Sarah Leigh Phenotypes for gene: PSMB10 were changed from Proteasome-associated autoinflammatory syndrome to Proteasome-associated autoinflammatory syndrome (PRAAS)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.53 NFKBID Sarah Leigh Classified gene: NFKBID as Red List (low evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.53 NFKBID Sarah Leigh Added comment: Comment on list classification: Not associated with phenotype in OMIM or in Gen2Phen. The only variants are structural rearrangements that include NFKBID amongst other genes. PMID 26973645 reports "heterozygous mutation in the nfkbid gene encoding the atypical IκB protein IκBNS led to reduced steady state IgM and IgG3 antibody levels and impaired response to vaccination with TI-2 antigens in mice". Thus, variants in human NFKBID may also result in reduced levels of IgM and IgG3 and compromized vaccination responses.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.53 NFKBID Sarah Leigh Gene: nfkbid has been classified as Red List (Low Evidence).
COVID-19 research v0.83 NFKBID Sarah Leigh Classified gene: NFKBID as Red List (low evidence)
COVID-19 research v0.83 NFKBID Sarah Leigh Added comment: Comment on list classification: Not associated with phenotype in OMIM or in Gen2Phen. The only variants are structural rearrangements that include NFKBID amongst other genes. PMID 26973645 reports "heterozygous mutation in the nfkbid gene encoding the atypical IκB protein IκBNS led to reduced steady state IgM and IgG3 antibody levels and impaired response to vaccination with TI-2 antigens in mice". Thus, variants in human NFKBID may also result in reduced levels of IgM and IgG3 and compromized vaccination responses.
COVID-19 research v0.83 NFKBID Sarah Leigh Gene: nfkbid has been classified as Red List (Low Evidence).
COVID-19 research v0.82 NFKBID Sarah Leigh Publications for gene: NFKBID were set to
Primary immunodeficiency or monogenic inflammatory bowel disease v2.52 NFKBID Sarah Leigh Publications for gene: NFKBID were set to
Intellectual disability v3.29 GAD1 Sarah Leigh Phenotypes for gene: GAD1 were changed from ?Cerebral palsy, spastic quadriplegic, 1; Developmental and epileptic encephalopathies, cleft palate, joint contractures and/or omphalocele to ?Cerebral palsy, spastic quadriplegic, 1 603513; Developmental and epileptic encephalopathies, cleft palate, joint contractures and/or omphalocele
Early onset or syndromic epilepsy v2.38 GAD1 Sarah Leigh Phenotypes for gene: GAD1 were changed from Developmental and epileptic encephalopathies, cleft palate, joint contractures and/or omphalocele to ?Cerebral palsy, spastic quadriplegic, 1 603513; Developmental and epileptic encephalopathies, cleft palate, joint contractures and/or omphalocele
Early onset or syndromic epilepsy v2.37 GAD1 Sarah Leigh Publications for gene: GAD1 were set to https://doi-org.ezproxy.library.qmul.ac.uk/10.1093/brain/awaa085
Early onset or syndromic epilepsy v2.36 GAD1 Sarah Leigh Classified gene: GAD1 as Green List (high evidence)
Early onset or syndromic epilepsy v2.36 GAD1 Sarah Leigh Gene: gad1 has been classified as Green List (High Evidence).
COVID-19 research v0.81 SART3 Catherine Snow reviewed gene: SART3: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Intellectual disability v3.28 GAD1 Sarah Leigh Publications for gene: GAD1 were set to 26503795; 24896178; 26350204; https://doi-org.ezproxy.library.qmul.ac.uk/10.1093/brain/awaa085
Intellectual disability v3.27 GAD1 Sarah Leigh Added comment: Comment on publications: https://doi-org.ezproxy.library.qmul.ac.uk/10.1093/brain/awaa085 new publication, without a PMID
Intellectual disability v3.27 GAD1 Sarah Leigh Publications for gene: GAD1 were set to 26503795; 24896178; 26350204; https://doi-org.ezproxy.library.qmul.ac.uk/10.1093/brain/awaa085
Intellectual disability v3.27 GAD1 Sarah Leigh Added comment: Comment on publications: https://doi-org.ezproxy.library.qmul.ac.uk/10.1093/brain/awaa085 new publication, without a PMID
Intellectual disability v3.27 GAD1 Sarah Leigh Publications for gene: GAD1 were set to
Intellectual disability v3.26 GAD1 Sarah Leigh Phenotypes for gene: GAD1 were changed from ?Cerebral palsy, spastic quadriplegic, 1 to ?Cerebral palsy, spastic quadriplegic, 1; Developmental and epileptic encephalopathies, cleft palate, joint contractures and/or omphalocele
Intellectual disability v3.25 GAD1 Sarah Leigh Classified gene: GAD1 as Green List (high evidence)
Intellectual disability v3.25 GAD1 Sarah Leigh Added comment: Comment on list classification: Five biallelic loss of function variants reported in 11 cases in 6 unrelated families. All cases had epilepsy syndrome, 10 profound intellectual disabilty (1 case died at day 9 of life) and other nuerological and developement features. Supportive functional studies were also presented
Intellectual disability v3.25 GAD1 Sarah Leigh Gene: gad1 has been classified as Green List (High Evidence).
Early onset or syndromic epilepsy v2.35 GAD1 Sarah Leigh gene: GAD1 was added
gene: GAD1 was added to Genetic epilepsy syndromes. Sources: Literature
Mode of inheritance for gene: GAD1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: GAD1 were set to https://doi-org.ezproxy.library.qmul.ac.uk/10.1093/brain/awaa085
Phenotypes for gene: GAD1 were set to Developmental and epileptic encephalopathies, cleft palate, joint contractures and/or omphalocele
Review for gene: GAD1 was set to GREEN
Added comment: Five biallelic loss of function variants reported in 11 cases in 6 unrelated families. All cases had epilepsy syndrome, 10 profound intellectual disabilty (1 case died at day 9 of life) and other nuerological and developement features. Supportive functional studies were also presented.
Sources: Literature
Mitochondrial disorders v2.5 UQCRB Zornitza Stark reviewed gene: UQCRB: Rating: GREEN; Mode of pathogenicity: None; Publications: 23281071, 28275242; Phenotypes: Mitochondrial complex III deficiency, nuclear type 3, 615158; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
Mitochondrial disorders v2.5 SDHB Zornitza Stark reviewed gene: SDHB: Rating: GREEN; Mode of pathogenicity: None; Publications: 22972948, 26925370, 27604842; Phenotypes: Complex II deficiency, mitochondrial leucoencephalopathy; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
Intellectual disability v3.24 NUP188 Zornitza Stark reviewed gene: NUP188: Rating: GREEN; Mode of pathogenicity: None; Publications: 32021605, 28726809, 32275884; Phenotypes: microcephaly, ID, cataract, structural brain abnormalities, hypoventilation; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
Mitochondrial disorders v2.5 MRPS23 Zornitza Stark reviewed gene: MRPS23: Rating: GREEN; Mode of pathogenicity: None; Publications: 26741492, 17873122, 25663021, 28752220; Phenotypes: Hepatic disease, Combined respiratory chain complex deficiencies, Cardiomyopathy, Tubulopathy, Lactic acidosis, Structural brain abnormalities; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 STAT5B Zornitza Stark reviewed gene: STAT5B: Rating: GREEN; Mode of pathogenicity: None; Publications: 29844444; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 TCF3 Zornitza Stark reviewed gene: TCF3: Rating: GREEN; Mode of pathogenicity: None; Publications: 30063982; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 PIK3CD Zornitza Stark reviewed gene: PIK3CD: Rating: GREEN; Mode of pathogenicity: None; Publications: 31073077; Phenotypes: Severe bacterial infections, autoimmunity; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 REL Zornitza Stark reviewed gene: REL: Rating: RED; Mode of pathogenicity: None; Publications: 31103457; Phenotypes: Combined immunodeficiency, T cells: normal, decreased memory CD4, poor proliferation, B cells: low, mostly naive, few switched memory B cells, impaired proliferation, Recurrent infections with bacteria, mycobacteria, salmonella and opportunistic organisms, Defective innate immunity; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 ZNF341 Zornitza Stark reviewed gene: ZNF341: Rating: GREEN; Mode of pathogenicity: None; Publications: 29907691, 29907690; Phenotypes: Hyper-IgE recurrent infection syndrome 3, autosomal recessive, MIM# 618282, Mild facial dysmorphism, Early onset eczema, Recurrent bacterial skin infections, abscesses, Recurrent respiratory infections, lung abscesses and pneumothoraces, Hyperextensible joints, bone fractures, retention of primary teeth; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 WDR1 Zornitza Stark edited their review of gene: WDR1: Changed phenotypes: Autoinflammatory periodic fever, immunodeficiency, and thrombocytopenia, Neutropaenia, Poor wound healing, Severe stomatitis, Neutrophil nuclei herniate
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 WDR1 Zornitza Stark reviewed gene: WDR1: Rating: GREEN; Mode of pathogenicity: None; Publications: 27994071, 27557945, 29751004; Phenotypes: Autoinflammatory periodic fever, neutrophil dysfunction, immunodeficiency, and thrombocytopenia; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 USP18 Zornitza Stark reviewed gene: USP18: Rating: GREEN; Mode of pathogenicity: None; Publications: 31940699, 27325888; Phenotypes: Pseudo-TORCH syndrome 2, MIM# 617397; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 TRIM22 Zornitza Stark reviewed gene: TRIM22: Rating: GREEN; Mode of pathogenicity: None; Publications: 26836588; Phenotypes: Inflammatory bowel disease; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 TRAF3IP2 Zornitza Stark reviewed gene: TRAF3IP2: Rating: AMBER; Mode of pathogenicity: None; Publications: 24120361, 31292894, 20660351; Phenotypes: Candidiasis, familial, 8, MIM# 615527; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 TOP2B Zornitza Stark reviewed gene: TOP2B: Rating: GREEN; Mode of pathogenicity: None; Publications: 31409799; Phenotypes: Antibody deficiency, Recurrent infections, Facial dysmorphism, Limb anomalies; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 TNFRSF9 Zornitza Stark reviewed gene: TNFRSF9: Rating: GREEN; Mode of pathogenicity: None; Publications: 30872117, 31501153; Phenotypes: EBV lymphoproliferation, B-cell lymphoma, Chronic active EBV infection; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 TNFRSF13B Zornitza Stark changed review comment from: Agree this gene is difficult to categorise. We have decided to include the gene in our panels, but report only the specific variants for which there is published evidence, and to report them as contributory rather than solely causative.; to: 2018: Agree this gene is difficult to categorise. We have decided to include the gene in our panels, but report only the specific variants for which there is published evidence, and to report them as contributory rather than solely causative.

2020: Variants in this gene do not readily fit the monogenic rare disease paradigm, but nevertheless there is evidence they make a contribution to CVID pathogenesis. We have 'whitelisted' specific variants and are reporting them separately as susceptibility alleles. It is unlikely that further evidence will alter this interpretation, this is more of a question about reporting policy.
COVID-19 research v0.81 IL18BP Abdelazeem Elhabyan gene: IL18BP was added
gene: IL18BP was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: IL18BP was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: IL18BP were set to PubMed: 31213488
Mode of pathogenicity for gene: IL18BP was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
Added comment: Inherited IL-18BP deficiency in human fulminant viral hepatitis

Fulminant viral hepatitis (FVH) is a devastating and unexplained condition that strikes otherwise healthy individuals during primary infection with common liver-tropic viruses. We report a child who died of FVH upon infection with hepatitis A virus (HAV) at age 11 yr and who was homozygous for a private 40-nucleotide deletion in IL18BP, which encodes the IL-18 binding protein (IL-18BP). This mutation is loss-of-function, unlike the variants found in a homozygous state in public databases. We show that human IL-18 and IL-18BP are both secreted mostly by hepatocytes and macrophages in the liver. Moreover, in the absence of IL-18BP, excessive NK cell activation by IL-18 results in the uncontrolled killing of human hepatocytes in vitro. Inherited human IL-18BP deficiency thus underlies fulminant HAV hepatitis by unleashing IL-18. These findings provide proof-of-principle that FVH can be caused by single-gene inborn errors that selectively disrupt liver-specific immunity. They also show that human IL-18 is toxic to the liver and that IL-18BP is its antidote.
Sources: Literature
COVID-19 research v0.81 HLA-DRB1 Abdelazeem Elhabyan gene: HLA-DRB1 was added
gene: HLA-DRB1 was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: HLA-DRB1 was set to Unknown
Publications for gene: HLA-DRB1 were set to PMID: 19445991,26456283,19597844,10823757,
Penetrance for gene: HLA-DRB1 were set to unknown
Mode of pathogenicity for gene: HLA-DRB1 was set to Other
Review for gene: HLA-DRB1 was set to GREEN
Added comment: Association of human leukocyte antigen class II alleles with severe acute respiratory syndrome in the Vietnamese population PMID: 19445991,

HLA-DRB1*12 was more frequently shown in SARS patients than in controls (corrected p = 0.042). HLA-DRB1*1202, the predominant allele in the Vietnamese population showed the strongest association with SARS in a dominant model (corrected p = 0.0065 and 0.0052, depending on the controls to be compared). Our results and accumulated data on HLA in the Asian populations would help in the understanding of associations with emerging infectious diseases.

Amino Acid Variation in HLA Class II Proteins Is a Major Determinant of Humoral Response to Common Viruses PMID: 26456283
The magnitude of the human antibody response to viral antigens is highly variable. To explore the human genetic contribution to this variability, we performed genome-wide association studies of the immunoglobulin G response to 14 pathogenic viruses in 2,363 immunocompetent adults. Significant associations were observed in the major histocompatibility complex region on chromosome 6 for influenza A virus, Epstein-Barr virus, JC polyomavirus, and Merkel cell polyomavirus. Using local imputation and fine mapping, we identified specific amino acid residues in human leucocyte antigen (HLA) class II proteins as the most probable causal variants underlying these association signals. Common HLA-DRβ1 haplotypes showed virus-specific patterns of humoral-response regulation

Clear and Independent Associations of Several HLA-DRB1 Alleles With Differential Antibody Responses to Hepatitis B Vaccination in Youth
PMID: 19597844
To confirm and refine associations of human leukocyte antigen (HLA) genotypes with variable antibody (Ab) responses to hepatitis B vaccination, we have analyzed 255 HIV-1 seropositive (HIV(+)) youth and 80 HIV-1 seronegatives (HIV(-)) enrolled into prospective studies. In univariate analyses that focused on HLA-DRB1, -DQA1, and -DQB1 alleles and haplotypes, the DRB1*03 allele group and DRB1*0701 were negatively associated with the responder phenotype (serum Ab concentration > or = 10 mIU/mL) (P = 0.026 and 0.043, respectively). Collectively, DRB1*03 and DRB1*0701 were found in 42 (53.8%) out of 78 non-responders (serum Ab <10 mIU/mL), 65 (40.6%) out of 160 medium responders (serum Ab 10-1,000 mIU/mL), and 27 (27.8%) out of 97 high responders (serum Ab >1,000 mIU/mL) (P < 0.001 for trend). Meanwhile, DRB1*08 was positively associated with the responder phenotype (P = 0.010), mostly due to DRB1*0804 (P = 0.008).

Influence of HLA Supertypes on Susceptibility and Resistance to Human Immunodeficiency Virus Type 1 Infection
PMID: 10823757
To determine whether HLA polymorphism influences HIV-1 susceptibility, a longitudinal cohort of highly HIV-1-exposed female sex workers based in Nairobi, Kenya, was prospectively analyzed. Decreased HIV-1 infection risk was strongly associated with possession of a cluster of closely related HLA alleles (A2/6802 supertype; incidence rate ratio [IRR], 0.45; 95% confidence interval [CI], 0.27-0.72; P=.0003). The alleles in this supertype are known in some cases to present the same peptide epitopes for T cell recognition. In addition, resistance to HIV-1 infection was independently associated with HLA DRB1*01 (IRR, 0.22; 95% CI, 0.06-0.60; P=.0003), which suggests that anti-HIV-1 class II restricted CD4 effector mechanisms may play an important role in protecting against viral challenge
Sources: Literature
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 NFE2L2 Zornitza Stark reviewed gene: NFE2L2: Rating: GREEN; Mode of pathogenicity: None; Publications: 29018201; Phenotypes: Immunodeficiency, developmental delay, and hypohomocysteinemia, MIM# 617744, Recurrent respiratory and skin infection, Growth retardation, Developmental delay, borderline ID, White matter cerebral lesions; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 TGFB1 Zornitza Stark reviewed gene: TGFB1: Rating: AMBER; Mode of pathogenicity: None; Publications: 29483653; Phenotypes: Inflammatory bowel disease, immunodeficiency, and encephalopathy MIM# 618213; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 TFRC Zornitza Stark reviewed gene: TFRC: Rating: AMBER; Mode of pathogenicity: None; Publications: 26642240; Phenotypes: Immunodeficiency 46, MIM# 616740, T cells: normal number, poor proliferation, B cells: normal number, low memory B cells, recurrent infections, neutorpaenia, thrombocytopaenia; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 SRP54 Zornitza Stark reviewed gene: SRP54: Rating: GREEN; Mode of pathogenicity: None; Publications: 29914977, 28972538; Phenotypes: Neutropenia, severe congenital, 8, autosomal dominant, MIM# 618752; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted; Current diagnostic: yes
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 SPPL2A Zornitza Stark reviewed gene: SPPL2A: Rating: AMBER; Mode of pathogenicity: None; Publications: 30127434; Phenotypes: Susceptibility to mycobacteria and Salmonella; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 SMARCD2 Zornitza Stark reviewed gene: SMARCD2: Rating: GREEN; Mode of pathogenicity: None; Publications: 28369036, 28369034; Phenotypes: Specific granule deficiency 2, MIM# 617475, Neutropaenia, Neurodevelopmental abnormalities in some, Myelodysplasia; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 SLC7A7 Zornitza Stark reviewed gene: SLC7A7: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: Lysinuric protein intolerance, MIM# 222700, Hyper-inflammatory response of macrophages, Normal NK cell function, Lysinuric protein intolerance, Bleeding tendency, Alverolar proteinosis; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 SLC39A7 Zornitza Stark reviewed gene: SLC39A7: Rating: GREEN; Mode of pathogenicity: None; Publications: 30718914; Phenotypes: Antibody deficiency, early onset infections, blistering dermatosis, failure to thrive, thrombocytopaenia; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 SH3KBP1 Zornitza Stark reviewed gene: SH3KBP1: Rating: RED; Mode of pathogenicity: None; Publications: 29636373, 21708930; Phenotypes: Immunodeficiency 61, MIM# 300310; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 SH3BP2 Zornitza Stark reviewed gene: SH3BP2: Rating: RED; Mode of pathogenicity: None; Publications: 26152156, 25705883, 25470448, 25220465; Phenotypes: ; Mode of inheritance: None
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 SEC61A1 Zornitza Stark reviewed gene: SEC61A1: Rating: GREEN; Mode of pathogenicity: None; Publications: 27392076, 28782633; Phenotypes: Hyperuricemic nephropathy, familial juvenile, 4, MIM# 617056, Hypogammaglobulinaemia, Severe recurrent respiratory tract infections; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 RNF31 Zornitza Stark reviewed gene: RNF31: Rating: AMBER; Mode of pathogenicity: None; Publications: 26008899, 30936877; Phenotypes: Immune deficiency, Autoinflammation; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 RELA Zornitza Stark reviewed gene: RELA: Rating: AMBER; Mode of pathogenicity: None; Publications: 28600438, 29305315; Phenotypes: Mucocutaneous ulceration, chronic, MIM# 618287, Impaired NFkB activation, reduced production of inflammatory cytokines, autoimmune cytopaenias; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 RAC2 Zornitza Stark edited their review of gene: RAC2: Changed phenotypes: SCID, recurrent bacterial and viral infections, lymphoproliferation, neutropaenia, reticular dysgenesis, deafness, selective IgA deficiency, Reduced Ab responses following vaccination, Neutrophil immunodeficiency syndrome, MIM# 608203, Common variable immunodeficiency
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 RAC2 Zornitza Stark reviewed gene: RAC2: Rating: GREEN; Mode of pathogenicity: None; Publications: 32198141, 31919089, 31382036, 31071452, 30723080, 30654050, 25512081; Phenotypes: SCID, recurrent bacterial and viral infections, lymphoproliferation, neutropaenia, reticular dysgenesis, deafness, selective IgA deficiency, Reduced Ab responses following vaccination; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal; Current diagnostic: yes
Infantile enterocolitis & monogenic inflammatory bowel disease v1.16 PTEN Zornitza Stark changed review comment from: GI polyps and diverticula are a feature of Cowden syndrome. The link between variants in PTEN and monogenic IBD appears based largely on experimental/mouse model evidence. There is a series of 34 individuals with PTEN variants and a range of autoimmune phenotypes reported in 22266152, including colitis. Considering PTEN-related conditions are relatively common as are auto-immune disorders, I am not convinced this is enough for causality.; to: GI polyps and diverticula are a feature of Cowden syndrome. The link between variants in PTEN and monogenic IBD appears based largely on experimental/mouse model evidence. There is a series of 34 individuals with PTEN variants and a range of autoimmune phenotypes reported in 22266152, including colitis. Considering PTEN-related conditions are relatively common as are auto-immune disorders, I am not convinced this is enough for causality. I also note this gene is Amber on the PID panel.
Infantile enterocolitis & monogenic inflammatory bowel disease v1.16 PTEN Zornitza Stark reviewed gene: PTEN: Rating: AMBER; Mode of pathogenicity: None; Publications: 23962154, 24882466, 25352295, 22266152; Phenotypes: Colitis; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 PSMG2 Zornitza Stark reviewed gene: PSMG2: Rating: RED; Mode of pathogenicity: None; Publications: 30664889; Phenotypes: CANDLE syndrome, Chronic atypical neutrophilic dermatitis with lipodystrophy; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 POLR3C Zornitza Stark gene: POLR3C was added
gene: POLR3C was added to Primary immunodeficiency. Sources: Expert list
Mode of inheritance for gene: POLR3C was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: POLR3C were set to 28783042
Phenotypes for gene: POLR3C were set to Severe VZV infection
Review for gene: POLR3C was set to AMBER
Added comment: One individual with POLR3C variant and another individual with both POL3RA and POL3RC variants.
Sources: Expert list
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 POLR3A Zornitza Stark gene: POLR3A was added
gene: POLR3A was added to Primary immunodeficiency. Sources: Expert list
Mode of inheritance for gene: POLR3A was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: POLR3A were set to 28783042; 29728610
Phenotypes for gene: POLR3A were set to Severe VZV infection
Review for gene: POLR3A was set to AMBER
Added comment: Two individuals with mono allelic POLR3A variants and another individual with both POLR3A and a POLR3C variants reported.
Sources: Expert list
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 POLE Zornitza Stark reviewed gene: POLE: Rating: GREEN; Mode of pathogenicity: None; Publications: 30503519, 23230001, 25948378; Phenotypes: FILS syndrome, MIM# 615139, IMAGE-I syndrome, MIM# 618336; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 POLD2 Zornitza Stark reviewed gene: POLD2: Rating: RED; Mode of pathogenicity: None; Publications: 31449058; Phenotypes: Low CD4 T cells, Low B cells, normal maturation, recurrent respiratory tract infections, skin infections, warts and molluscum, short stature, intellectual disability; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 POLD1 Zornitza Stark reviewed gene: POLD1: Rating: AMBER; Mode of pathogenicity: None; Publications: 31629014, 31449058; Phenotypes: Low CD4 T cells, Low B cells, normal maturation, recurrent respiratory tract infections, skin infections, warts and molluscum, short stature, intellectual disability; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 PAX1 Zornitza Stark gene: PAX1 was added
gene: PAX1 was added to Primary immunodeficiency. Sources: Expert list
Mode of inheritance for gene: PAX1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PAX1 were set to 32111619
Phenotypes for gene: PAX1 were set to Syndromic SCID; dysmorphism; ear abnormalities; otofaciocervical syndrome
Review for gene: PAX1 was set to GREEN
gene: PAX1 was marked as current diagnostic
Added comment: 6 individuals from three unrelated families.
Sources: Expert list
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 OAS1 Zornitza Stark reviewed gene: OAS1: Rating: GREEN; Mode of pathogenicity: None; Publications: 29455859; Phenotypes: infantile-onset pulmonary alveolar proteinosis, hypogammaglobulinemia; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted; Current diagnostic: yes
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 NOP10 Zornitza Stark reviewed gene: NOP10: Rating: RED; Mode of pathogenicity: None; Publications: 17507419; Phenotypes: Dyskeratosis congenita, autosomal recessive 1, MIM#224230; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 NLRP1 Zornitza Stark reviewed gene: NLRP1: Rating: GREEN; Mode of pathogenicity: Other; Publications: 27965258, 31484767, 27662089; Phenotypes: Autoinflammation with arthritis and dyskeratosis, MIM# 617388, Palmoplantar carcinoma, multiple self-healing 615225, Recurrent respiratory papillomatosis; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal; Current diagnostic: yes
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 MYO5B Zornitza Stark reviewed gene: MYO5B: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Microvillus inclusion disease, MIM# 251850; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 MKL1 Zornitza Stark reviewed gene: MKL1: Rating: AMBER; Mode of pathogenicity: None; Publications: 32128589, 26224645; Phenotypes: Neutropaenia with combined immune deficiency; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 LIG1 Zornitza Stark reviewed gene: LIG1: Rating: GREEN; Mode of pathogenicity: None; Publications: 30395541; Phenotypes: Combined immunodeficiency, Lymphopaenia, Hypogammaglobulinaemia, Recurrent bacterial and viral infections, Growth retardation, Sun sensitivity, radiation sensitivity, Macrocytosis; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 PSMA3 Abdelazeem Elhabyan reviewed gene: PSMA3: Rating: AMBER; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 PSMA3 Abdelazeem Elhabyan Deleted their review
COVID-19 research v0.81 PSMB4 Abdelazeem Elhabyan reviewed gene: PSMB4: Rating: AMBER; Mode of pathogenicity: None; Publications: PMID: 26829627,; Phenotypes: ; Mode of inheritance: None
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 PSMA3 Abdelazeem Elhabyan reviewed gene: PSMA3: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.81 POLR3C Abdelazeem Elhabyan reviewed gene: POLR3C: Rating: RED; Mode of pathogenicity: None; Publications: 28783042; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.81 POLR3A Abdelazeem Elhabyan changed review comment from: This gene is responsible for A subunit of Polymerase which sense DNA in viral infection eg Varicella Zoster. SARS-CoV-2 is an RNA virus.

Inborn errors in RNA polymerase III underlie severe varicella zoster virus infections(PMID: 28783042)

We report 4 cases of acute severe VZV infection affecting the central nervous system or the lungs in unrelated, otherwise healthy children who are heterozygous for rare missense mutations in POLR3A (one patient), POLR3C (one patient), or both (two patients). POLR3A and POLR3C encode subunits of RNA polymerase III. Leukocytes from all 4 patients tested exhibited poor IFN induction in response to synthetic or VZV-derived DNA. Moreover, leukocytes from 3 of the patients displayed defective IFN production upon VZV infection and reduced control of VZV replication. These phenotypes were rescued by transduction with relevant WT alleles. This work demonstrates that monogenic or digenic POLR3A and POLR3C deficiencies confer increased susceptibility to severe VZV disease in otherwise healthy children, providing evidence for an essential role of a DNA sensor in human immunity
Different classes of PRRs are involved in recognition of virus infections, including membrane-associated TLRs; cytosolic retinoic acid–inducible gene 1–like (RIG-I–like) receptors, which sense RNA; and DNA sensors (24). Each of these classes of PRRs stimulates production of IFNs, which exhibit antiviral activity through their ability to induce IFN-stimulated genes (ISGs). With respect to DNA sensors, TLR9 detects unmethylated DNA, RNA polymerase III (POL III) recognizes AT-rich DNA, while gamma-interferon-inducible protein 16 (IFI16) and cyclic GMP-AMP synthase (cGAS) sense double-stranded DNA in a sequence-independent manner (25–29).




Mutations in RNA Polymerase III genes and defective DNA sensing in adults with varicella-zoster virus CNS infection
PMID: 29728610

Recently, deficiency in the cytosolic DNA sensor RNA Polymerase III was described in children with severe primary varicella-zoster virus (VZV) infection in the CNS and lungs. In the present study we examined adult patients with VZV CNS infection caused by viral reactivation. By whole exome sequencing we identified mutations in POL III genes in two of eight patients. These mutations were located in the coding regions of the subunits POLR3A and POLR3E. In functional assays, we found impaired expression of antiviral and inflammatory cytokines in response to the POL III agonist Poly(dA:dT) as well as increased viral replication in patient cells compared to controls. Altogether, this study provides significant extension on the current knowledge on susceptibility to VZV infection by demonstrating mutations in POL III genes associated with impaired immunological sensing of AT-rich DNA in adult patients with VZV CNS infection.; to: This gene is responsible for A subunit of Polymerase which senses DNA viruses especially AT-rich regions eg Varicella Zoster. SARS-CoV-2 is an RNA virus.

Inborn errors in RNA polymerase III underlie severe varicella zoster virus infections(PMID: 28783042)

We report 4 cases of acute severe VZV infection affecting the central nervous system or the lungs in unrelated, otherwise healthy children who are heterozygous for rare missense mutations in POLR3A (one patient), POLR3C (one patient), or both (two patients). POLR3A and POLR3C encode subunits of RNA polymerase III. Leukocytes from all 4 patients tested exhibited poor IFN induction in response to synthetic or VZV-derived DNA. Moreover, leukocytes from 3 of the patients displayed defective IFN production upon VZV infection and reduced control of VZV replication. These phenotypes were rescued by transduction with relevant WT alleles. This work demonstrates that monogenic or digenic POLR3A and POLR3C deficiencies confer increased susceptibility to severe VZV disease in otherwise healthy children, providing evidence for an essential role of a DNA sensor in human immunity
Different classes of PRRs are involved in recognition of virus infections, including membrane-associated TLRs; cytosolic retinoic acid–inducible gene 1–like (RIG-I–like) receptors, which sense RNA; and DNA sensors (24). Each of these classes of PRRs stimulates production of IFNs, which exhibit antiviral activity through their ability to induce IFN-stimulated genes (ISGs). With respect to DNA sensors, TLR9 detects unmethylated DNA, RNA polymerase III (POL III) recognizes AT-rich DNA, while gamma-interferon-inducible protein 16 (IFI16) and cyclic GMP-AMP synthase (cGAS) sense double-stranded DNA in a sequence-independent manner (25–29).




Mutations in RNA Polymerase III genes and defective DNA sensing in adults with varicella-zoster virus CNS infection
PMID: 29728610

Recently, deficiency in the cytosolic DNA sensor RNA Polymerase III was described in children with severe primary varicella-zoster virus (VZV) infection in the CNS and lungs. In the present study we examined adult patients with VZV CNS infection caused by viral reactivation. By whole exome sequencing we identified mutations in POL III genes in two of eight patients. These mutations were located in the coding regions of the subunits POLR3A and POLR3E. In functional assays, we found impaired expression of antiviral and inflammatory cytokines in response to the POL III agonist Poly(dA:dT) as well as increased viral replication in patient cells compared to controls. Altogether, this study provides significant extension on the current knowledge on susceptibility to VZV infection by demonstrating mutations in POL III genes associated with impaired immunological sensing of AT-rich DNA in adult patients with VZV CNS infection.
COVID-19 research v0.81 POLR3A Abdelazeem Elhabyan reviewed gene: POLR3A: Rating: RED; Mode of pathogenicity: None; Publications: PMID: 28783042,29728610; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.81 ACE Abdelazeem Elhabyan reviewed gene: ACE: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.81 NRAS Abdelazeem Elhabyan reviewed gene: NRAS: Rating: AMBER; Mode of pathogenicity: None; Publications: PMID: 21595878,12670913,; Phenotypes: ; Mode of inheritance: None
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 IRF9 Zornitza Stark reviewed gene: IRF9: Rating: AMBER; Mode of pathogenicity: None; Publications: 30826365, 30143481; Phenotypes: Immunodeficiency 65, susceptibility to viral infections 618648; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.81 MRE11 Abdelazeem Elhabyan reviewed gene: MRE11: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.81 MPO Abdelazeem Elhabyan reviewed gene: MPO: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID: 27574522,21703402,29325098,29769163,24968347; Phenotypes: ; Mode of inheritance: None
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 IL6ST Zornitza Stark reviewed gene: IL6ST: Rating: GREEN; Mode of pathogenicity: None; Publications: 32207811, 28747427, 30309848, 12370259, 16041381, 31914175; Phenotypes: Hyper-IgE recurrent infection syndrome 4, autosomal recessive, MIM# 618523, Stuve-Wiedemann-like syndrome: skeletal dysplasia, neonatal lung dysfunction, thrombocytopenia, dermatitis, defective acute-phase response., Hyper-IgE syndrome, autosomal dominant; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 IL6R Zornitza Stark reviewed gene: IL6R: Rating: AMBER; Mode of pathogenicity: None; Publications: 31235509; Phenotypes: Recurrent pyogenic infections, cold abscesses, High circulating IL-6 levels, High IgE; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 IL2RB Zornitza Stark reviewed gene: IL2RB: Rating: GREEN; Mode of pathogenicity: None; Publications: 31040184, 31040185; Phenotypes: Immunodeficiency 63 with lymphoproliferation and autoimmunity, MIM# 618495, Lymphoproliferation, lymphadenopathy, hepatosplenomegaly, autoimmune haemolytic anaemia, dermatitis, enteropathy, hypergammaglobulinaemia, recurrent viral (EBV, CMV) infections; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 IL17F Zornitza Stark reviewed gene: IL17F: Rating: RED; Mode of pathogenicity: None; Publications: 21350122; Phenotypes: Candidiasis, familial, 6, autosomal dominant, MIM# 613956; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 ICOSLG Zornitza Stark reviewed gene: ICOSLG: Rating: AMBER; Mode of pathogenicity: None; Publications: 31532372, 30498080; Phenotypes: Combined immunodeficiency, recurrent bacterial and viral infections, neutropaenia; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 HYOU1 Zornitza Stark reviewed gene: HYOU1: Rating: RED; Mode of pathogenicity: None; Publications: 27913302; Phenotypes: Immunodeficiency 59 and hypoglycemia, MIM# 233600; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 HAVCR2 Zornitza Stark reviewed gene: HAVCR2: Rating: GREEN; Mode of pathogenicity: None; Publications: 30374066, 30792187; Phenotypes: T-cell lymphoma, subcutaneous panniculitis-like, MIM# 618398; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.81 KRAS Abdelazeem Elhabyan reviewed gene: KRAS: Rating: AMBER; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.81 GUCY2C Abdelazeem Elhabyan reviewed gene: GUCY2C: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 FCHO1 Zornitza Stark reviewed gene: FCHO1: Rating: GREEN; Mode of pathogenicity: None; Publications: 32098969, 30822429; Phenotypes: Combined immunodeficiency, T cells: low, poor proliferation, B cells: normal number, Recurrent infections (viral, mycobacteria, bacterial, fungal), lymphoproliferation, Failure to thrive, Increased activation-induced T-cell death, Defective clathrin-mediated endocytosis; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.81 FPR2 Abdelazeem Elhabyan reviewed gene: FPR2: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID: 28928730, 27034344,29738458,31398292,29127186; Phenotypes: ; Mode of inheritance: None
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 ERBIN Zornitza Stark reviewed gene: ERBIN: Rating: AMBER; Mode of pathogenicity: None; Publications: 28126831; Phenotypes: Recurrent respiratory infections, Susceptibility to S.aureus, Eczema, Hyperextensible joints, Scoliosis, Arterial dilatation in some; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 EFL1 Zornitza Stark gene: EFL1 was added
gene: EFL1 was added to Primary immunodeficiency. Sources: Expert list
Mode of inheritance for gene: EFL1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: EFL1 were set to 28331068; 31151987
Phenotypes for gene: EFL1 were set to Shwachman-Diamond syndrome 2, MIM# 617941
Review for gene: EFL1 was set to GREEN
gene: EFL1 was marked as current diagnostic
Added comment: Six unrelated families reported, two had the same homozygous variant, one family single variant plus 'expression defect' identified. Neutropaenia is part of the phenotype, and other SDS genes are part of the PID panel.
Sources: Expert list
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 DNASE1L3 Zornitza Stark reviewed gene: DNASE1L3: Rating: GREEN; Mode of pathogenicity: None; Publications: 22019780, 30008451; Phenotypes: Systemic lupus erythematosus 16, MIM# 614420; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 DEF6 Zornitza Stark reviewed gene: DEF6: Rating: AMBER; Mode of pathogenicity: None; Publications: 31308374; Phenotypes: Systemic autoimmunity; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 DBR1 Zornitza Stark reviewed gene: DBR1: Rating: GREEN; Mode of pathogenicity: None; Publications: 29474921; Phenotypes: Viral infections of the brainstem; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 CSF2RB Zornitza Stark reviewed gene: CSF2RB: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.81 FPR2 Abdelazeem Elhabyan Deleted their review
COVID-19 research v0.81 FPR2 Abdelazeem Elhabyan commented on gene: FPR2
Infantile enterocolitis & monogenic inflammatory bowel disease v1.16 COL7A1 Zornitza Stark reviewed gene: COL7A1: Rating: RED; Mode of pathogenicity: None; Publications: 27537055, 25058236; Phenotypes: Epidermolysis bullosa dystrophica, AR, MIM# 226600; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 CIB1 Zornitza Stark gene: CIB1 was added
gene: CIB1 was added to Primary immunodeficiency. Sources: Expert list
Mode of inheritance for gene: CIB1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CIB1 were set to 30068544
Phenotypes for gene: CIB1 were set to Epidermodysplasia verruciformis 3 618267; HPV infections and cancer of the skin
Review for gene: CIB1 was set to GREEN
Added comment: Underlying defect of innate immunity, though phenotype is dermatological. 24 individuals from 6 families reported. Part of IUIS classification 2019.
Sources: Expert list
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 C17orf62 Zornitza Stark reviewed gene: C17orf62: Rating: GREEN; Mode of pathogenicity: None; Publications: 30361506, 30312704, 28351984; Phenotypes: Chronic granulomatous disease; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 BLOC1S6 Zornitza Stark edited their review of gene: BLOC1S6: Changed rating: AMBER
COVID-19 research v0.81 MRE11 Sarah Leigh Classified gene: MRE11 as Amber List (moderate evidence)
COVID-19 research v0.81 MRE11 Sarah Leigh Added comment: Comment on list classification: Immunodeficiency does not appear to be a feature of Ataxia-telangiectasia-like disorder 1 604391. However, as part of the MRE11-RAD50-NBS1 Complex it is part of the core conductor for the initial and sustained responses to DNA double-strand breaks, stalled replication forks, dysfunctional telomeres, and viral DNA infection (pmid 29709199). Hence, variants in MRE11, could reduce the response to viral DNA integration in host cells,allowing infections to be propogated.
COVID-19 research v0.81 MRE11 Sarah Leigh Gene: mre11 has been classified as Amber List (Moderate Evidence).
COVID-19 research v0.80 MRE11 Sarah Leigh Publications for gene: MRE11 were set to 8445618; 10612394; 15574463; 32212377
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 MRE11 Sarah Leigh Publications for gene: MRE11 were set to 8445618; 10612394; 15574463; 32212377
Primary immunodeficiency or monogenic inflammatory bowel disease v2.50 MRE11 Sarah Leigh changed review comment from: Comment on list classification: Immunodeficiency does not appear to be a feature of Ataxia-telangiectasia-like disorder 1 604391. However, as part of the MRE11-RAD50-NBS1 Complex it is part of the core conductor for the initial and sustained responses to DNA double-strand breaks, stalled replication forks, dysfunctional telomeres, and viral DNA infection. Hence, variants in MRE11, could reduce the response to viral DNA integration in host cells,allowing infections to be propogated. ; to: Comment on list classification: Immunodeficiency does not appear to be a feature of Ataxia-telangiectasia-like disorder 1 604391. However, as part of the MRE11-RAD50-NBS1 Complex it is part of the core conductor for the initial and sustained responses to DNA double-strand breaks, stalled replication forks, dysfunctional telomeres, and viral DNA infection (pmid 29709199). Hence, variants in MRE11, could reduce the response to viral DNA integration in host cells,allowing infections to be propogated.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.50 MRE11 Sarah Leigh changed review comment from: Comment on list classification: Immunodeficiency does not appear to be a feature of Ataxia-telangiectasia-like disorder 1 604391; to: Comment on list classification: Immunodeficiency does not appear to be a feature of Ataxia-telangiectasia-like disorder 1 604391. However, as part of the MRE11-RAD50-NBS1 Complex it is part of the core conductor for the initial and sustained responses to DNA double-strand breaks, stalled replication forks, dysfunctional telomeres, and viral DNA infection. Hence, variants in MRE11, could reduce the response to viral DNA integration in host cells,allowing infections to be propogated.
COVID-19 research v0.79 MRE11 Sarah Leigh Classified gene: MRE11 as Red List (low evidence)
COVID-19 research v0.79 MRE11 Sarah Leigh Added comment: Comment on list classification: Immunodeficiency does not appear to be a feature of Ataxia-telangiectasia-like disorder 1 604391
COVID-19 research v0.79 MRE11 Sarah Leigh Gene: mre11 has been classified as Red List (Low Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.50 MRE11 Sarah Leigh Classified gene: MRE11 as Red List (low evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.50 MRE11 Sarah Leigh Added comment: Comment on list classification: Immunodeficiency does not appear to be a feature of Ataxia-telangiectasia-like disorder 1 604391
Primary immunodeficiency or monogenic inflammatory bowel disease v2.50 MRE11 Sarah Leigh Gene: mre11 has been classified as Red List (Low Evidence).
COVID-19 research v0.78 MRE11 Sarah Leigh Publications for gene: MRE11 were set to 10612394; 8445618; 15574463
Primary immunodeficiency or monogenic inflammatory bowel disease v2.49 MRE11 Sarah Leigh Publications for gene: MRE11 were set to 8445618; 10612394; 15574463
Primary immunodeficiency or monogenic inflammatory bowel disease v2.48 MRE11 Sarah Leigh Publications for gene: MRE11 were set to 8445618; 10612394; 15574463
COVID-19 research v0.77 SNORA31 Catherine Snow Classified gene: SNORA31 as Green List (high evidence)
COVID-19 research v0.77 SNORA31 Catherine Snow Added comment: Comment on list classification: Rating Green following external review
COVID-19 research v0.77 SNORA31 Catherine Snow Gene: snora31 has been classified as Green List (High Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.47 SNORA31 Catherine Snow Classified gene: SNORA31 as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.47 SNORA31 Catherine Snow Added comment: Comment on list classification: Rating as Green following external review
Primary immunodeficiency or monogenic inflammatory bowel disease v2.47 SNORA31 Catherine Snow Gene: snora31 has been classified as Green List (High Evidence).
COVID-19 research v0.76 POLR3A Rebecca Foulger changed review comment from: Added POLR3A to panel based on presence on VCGS 'Susceptibility to Viral Infections' panel: https://panelapp.agha.umccr.org/panels/237/; to: Added POLR3A to panel based on presence on VCGS 'Susceptibility to Viral Infections' panel V0.22: https://panelapp.agha.umccr.org/panels/237/
COVID-19 research v0.76 POLR3C Rebecca Foulger changed review comment from: Added POLR3C to panel based on presence on VCGS 'Susceptibility to Viral Infections' panel: https://panelapp.agha.umccr.org/panels/237/; to: Added POLR3C to panel based on presence on VCGS 'Susceptibility to Viral Infections' panel V0.22: https://panelapp.agha.umccr.org/panels/237/
COVID-19 research v0.76 POLR3F Rebecca Foulger changed review comment from: Added POLR3F to panel based on presence on VCGS 'Susceptibility to Viral Infections' panel: https://panelapp.agha.umccr.org/panels/237/; to: Added POLR3F to panel based on presence on VCGS 'Susceptibility to Viral Infections' panel V0.22: https://panelapp.agha.umccr.org/panels/237/
COVID-19 research v0.76 POLR3F Rebecca Foulger commented on gene: POLR3F
COVID-19 research v0.76 POLR3C Rebecca Foulger commented on gene: POLR3C
COVID-19 research v0.76 POLR3A Rebecca Foulger commented on gene: POLR3A
COVID-19 research v0.76 POLR3F Rebecca Foulger gene: POLR3F was added
gene: POLR3F was added to Viral susceptibility. Sources: Expert Review Red,Victorian Clinical Genetics Services,Expert list
Mode of inheritance for gene: POLR3F was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: POLR3F were set to 30211253
Phenotypes for gene: POLR3F were set to Severe VZV infection
COVID-19 research v0.76 POLR3C Rebecca Foulger gene: POLR3C was added
gene: POLR3C was added to Viral susceptibility. Sources: Victorian Clinical Genetics Services,Expert list,Expert Review Amber
Mode of inheritance for gene: POLR3C was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: POLR3C were set to 28783042
Phenotypes for gene: POLR3C were set to Severe VZV infection
COVID-19 research v0.76 POLR3A Rebecca Foulger gene: POLR3A was added
gene: POLR3A was added to Viral susceptibility. Sources: Victorian Clinical Genetics Services,Expert list,Expert Review Amber
Mode of inheritance for gene: POLR3A was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: POLR3A were set to 29728610; 28783042
Phenotypes for gene: POLR3A were set to Severe VZV infection
COVID-19 research v0.75 DBR1 Abdelazeem Elhabyan changed review comment from: I found that it has been promoted from the Australling susceptibility to viral infections on this link
https://panelapp.agha.umccr.org/panels/237/gene/DBR1/
This is based on this notion :
Seven individuals from three unrelated families with viral brainstem encephalitis and bi-allelic hypomorphic variants.

When I reviewed the paper, I found a notion of influenza viral encephalitis among other viruses(eg HSV-1) and a suggestion that this predisposition to the disease is due to involvement of DBR1 in intrinsic resistance of brainstem cells to those viruses via the enzyme encoded by DBR1.; to: I found that it has been promoted from the Australling susceptibility to viral infections on this link
https://panelapp.agha.umccr.org/panels/237/gene/DBR1/

This is based on this notion in this paper :
https://pubmed.ncbi.nlm.nih.gov/29474921/
Seven individuals from three unrelated families with viral brainstem encephalitis and bi-allelic hypomorphic variants.

When I reviewed the paper, I found a notion of influenza viral encephalitis among other viruses(eg HSV-1) and a suggestion that this predisposition to the disease is due to the involvement of DBR1 in intrinsic resistance of brainstem cells to those viruses via the enzyme encoded by DBR1.
COVID-19 research v0.75 DBR1 Abdelazeem Elhabyan commented on gene: DBR1: I found that it has been promoted from the Australling susceptibility to viral infections on this link
https://panelapp.agha.umccr.org/panels/237/gene/DBR1/
This is based on this notion :
Seven individuals from three unrelated families with viral brainstem encephalitis and bi-allelic hypomorphic variants.

When I reviewed the paper, I found a notion of influenza viral encephalitis among other viruses(eg HSV-1) and a suggestion that this predisposition to the disease is due to involvement of DBR1 in intrinsic resistance of brainstem cells to those viruses via the enzyme encoded by DBR1.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.46 BLOC1S6 Zornitza Stark reviewed gene: BLOC1S6: Rating: RED; Mode of pathogenicity: None; Publications: 32245340; Phenotypes: Hermansky-Pudlak syndrome 9, MIM# 614171; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.46 BCL11B Zornitza Stark reviewed gene: BCL11B: Rating: GREEN; Mode of pathogenicity: None; Publications: 29985992, 27959755; Phenotypes: Immunodeficiency 49, MIM# 617237, Intellectual developmental disorder with dysmorphic facies, speech delay, and T-cell abnormalities, MIM# 618092; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Primary immunodeficiency or monogenic inflammatory bowel disease v2.46 BCL10 Zornitza Stark reviewed gene: BCL10: Rating: GREEN; Mode of pathogenicity: None; Publications: 25365219, 32008135, 11163238, 12910267; Phenotypes: Immunodeficiency 37, MIM# 616098; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.46 ARHGEF1 Zornitza Stark reviewed gene: ARHGEF1: Rating: RED; Mode of pathogenicity: None; Publications: 30521495; Phenotypes: Immunodeficiency 62, MIM#618459; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.46 ALPI Zornitza Stark reviewed gene: ALPI: Rating: AMBER; Mode of pathogenicity: None; Publications: 29567797; Phenotypes: Inflammatory bowel disease; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.46 ADAM17 Zornitza Stark reviewed gene: ADAM17: Rating: GREEN; Mode of pathogenicity: None; Publications: 22010916, 29560122, 26683521, 25804906; Phenotypes: Inflammatory skin and bowel disease, neonatal, 1, MIM# 614328, Recurrent infections; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.75 MRE11 Sarah Leigh Publications for gene: MRE11 were set to 10612394; 8445618
Primary immunodeficiency or monogenic inflammatory bowel disease v2.46 MRE11 Sarah Leigh Publications for gene: MRE11 were set to 8445618; 10612394
COVID-19 research v0.74 FPR3 Catherine Snow changed review comment from: Formyl peptide receptors (FPRs) are classical chemoattractant receptors and although recently identified as being expressed in a sepsis patient derived neutrophils (PMID: 31982133) there is not enough evidence to upgrade to Amber.; to: Formyl peptide receptors (FPRs) are classical chemoattractant receptors and although FPR3 was recently identified as being expressed in a sepsis patient derived neutrophils (PMID: 31982133) there is not enough evidence to upgrade to Amber.
COVID-19 research v0.74 FPR3 Catherine Snow reviewed gene: FPR3: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.74 FPR2 Catherine Snow changed review comment from: FPR2 is a seven transmembrane G protein-coupled receptor, which plays an important role in sensing of bacteria and modulation of immune responses

Mouse model PMID: 31908042 Fpr2/3 knockout (KO) mice and wild‐type (WT) controls were infected intranasally with S pneumoniae. AnxA1 and Fpr2/3 KO mice were highly susceptible to infection, displaying uncontrolled inflammation, increased bacterial dissemination, and pulmonary dysfunction compared to WT animals

PMID: 28928730 The review gives an overview on the pathogenesis of influenza with a focus on the role of FPR2 and discusses the advantages of using FPR2 antagonists to treat the flu. Preclinical studies have proven that FPR2 antagonists efficiently protect mice against IAV infections, by inhibiting viral replication and deleterious inflammation of the lungs; to: FPR2 is a seven transmembrane G protein-coupled receptor, which plays an important role in sensing of bacteria and modulation of immune responses

Mouse model PMID: 31908042 Fpr2/3 knockout (KO) mice and wild‐type (WT) controls were infected intranasally with S pneumoniae. AnxA1 and Fpr2/3 KO mice were highly susceptible to infection, displaying uncontrolled inflammation, increased bacterial dissemination, and pulmonary dysfunction compared to WT animals

PMID: 28928730 The review gives an overview on the pathogenesis of influenza with a focus on the role of FPR2 and discusses the advantages of using FPR2 antagonists to treat the flu. Preclinical studies have proven that FPR2 antagonists efficiently protect mice against IAV infections, by inhibiting viral replication and deleterious inflammation of the lungs
COVID-19 research v0.74 FPR2 Catherine Snow changed review comment from: FPR2 is a seven transmembrane G protein-coupled receptor, which plays an important role in sensing of bacteria and modulation of immune responses

Mouse model PMID: 31908042 Fpr2/3 knockout (KO) mice and wild‐type (WT) controls were infected intranasally with S pneumoniae. AnxA1 and Fpr2/3 KO mice were highly susceptible to infection, displaying uncontrolled inflammation, increased bacterial dissemination, and pulmonary dysfunction compared to WT animals

PMID: 28928730 The review gives an overview on the pathogenesis of influenza with a focus on the role of FPR2 and discusses the advantages of using FPR2 antagonists to treat the flu. Preclinical studies have proven that FPR2 antagonists efficiently protect mice against IAV infections, by inhibiting viral replication and deleterious inflammation of the lungs; to: FPR2 is a seven transmembrane G protein-coupled receptor, which plays an important role in sensing of bacteria and modulation of immune responses

Mouse model PMID: 31908042 Fpr2/3 knockout (KO) mice and wild‐type (WT) controls were infected intranasally with S pneumoniae. AnxA1 and Fpr2/3 KO mice were highly susceptible to infection, displaying uncontrolled inflammation, increased bacterial dissemination, and pulmonary dysfunction compared to WT animals

PMID: 28928730 The review gives an overview on the pathogenesis of influenza with a focus on the role of FPR2 and discusses the advantages of using FPR2 antagonists to treat the flu. Preclinical studies have proven that FPR2 antagonists efficiently protect mice against IAV infections, by inhibiting viral replication and deleterious inflammation of the lungs
COVID-19 research v0.74 FPR2 Catherine Snow Classified gene: FPR2 as Amber List (moderate evidence)
COVID-19 research v0.74 FPR2 Catherine Snow Gene: fpr2 has been classified as Amber List (Moderate Evidence).
COVID-19 research v0.73 FPR2 Catherine Snow reviewed gene: FPR2: Rating: AMBER; Mode of pathogenicity: None; Publications: 31908042, 28928730; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Primary immunodeficiency or monogenic inflammatory bowel disease v2.45 CD247 Sophie Hambleton edited their review of gene: CD247: Added comment: There are at least 2 separate published reports of SCID caused by biallelic mutations in this gene, in keeping with understanding of its role in T cell biology.; Changed rating: GREEN; Changed publications: 16672702, 17170122; Changed phenotypes: T-B+ SCID
Primary immunodeficiency or monogenic inflammatory bowel disease v2.45 BCL10 Sophie Hambleton edited their review of gene: BCL10: Added comment: Additional case report describes recurrent infections with same cellular and immunological phenotypes in a child with homozygous null mutation, hence upgrade from amber to green gene status; Changed rating: GREEN; Changed publications: 25365219, 32008135
COVID-19 research v0.73 FCGRT Catherine Snow Classified gene: FCGRT as Red List (low evidence)
COVID-19 research v0.73 FCGRT Catherine Snow Added comment: Comment on list classification: No association found.
COVID-19 research v0.73 FCGRT Catherine Snow Gene: fcgrt has been classified as Red List (Low Evidence).
COVID-19 research v0.72 FCGR3B Catherine Snow Classified gene: FCGR3B as Red List (low evidence)
COVID-19 research v0.72 FCGR3B Catherine Snow Added comment: Comment on list classification: Comment on list classification: No link to viral susceptibility some evidence of FCGR3B that variants give rise to susceptibility to develop auto-immune diseases including SLE (PMID: 26683154).
COVID-19 research v0.72 FCGR3B Catherine Snow Gene: fcgr3b has been classified as Red List (Low Evidence).
COVID-19 research v0.71 FCGR2B Catherine Snow changed review comment from: Comment on list classification: No link to viral susceptibility some evidence of FCGR2B some evidence that variants give rise to susceptibility to develop auto-immune diseases (PMID: 26683154); to: Comment on list classification: No link to viral susceptibility some evidence of FCGR2B that variants give rise to susceptibility to develop auto-immune diseases (PMID: 26683154)
COVID-19 research v0.71 FCGR2B Catherine Snow changed review comment from: Comment on list classification: No link to viral susceptibility some evidence of FCGR2B some evidence that variants give rise to susceptibility to develop auto-immune diseases; to: Comment on list classification: No link to viral susceptibility some evidence of FCGR2B some evidence that variants give rise to susceptibility to develop auto-immune diseases (PMID: 26683154)
COVID-19 research v0.71 FCGR2B Catherine Snow Classified gene: FCGR2B as Red List (low evidence)
COVID-19 research v0.71 FCGR2B Catherine Snow Added comment: Comment on list classification: No link to viral susceptibility some evidence of FCGR2B some evidence that variants give rise to susceptibility to develop auto-immune diseases
COVID-19 research v0.71 FCGR2B Catherine Snow Gene: fcgr2b has been classified as Red List (Low Evidence).
COVID-19 research v0.70 FCGR2A Catherine Snow Publications for gene: FCGR2A were set to 16185324
COVID-19 research v0.69 FCGR2A Catherine Snow Mode of inheritance for gene: FCGR2A was changed from Unknown to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
COVID-19 research v0.68 FCGR2A Catherine Snow Classified gene: FCGR2A as Green List (high evidence)
COVID-19 research v0.68 FCGR2A Catherine Snow Gene: fcgr2a has been classified as Green List (High Evidence).
COVID-19 research v0.67 FCGR2A Catherine Snow Tag watchlist tag was added to gene: FCGR2A.
Tag polygenic tag was added to gene: FCGR2A.
COVID-19 research v0.67 FCGR2A Catherine Snow reviewed gene: FCGR2A: Rating: GREEN; Mode of pathogenicity: None; Publications: 19494086, 12752683, 16185324; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.67 NRAS Ellen McDonagh Mode of inheritance for gene: NRAS was changed from Unknown to Other
Primary immunodeficiency or monogenic inflammatory bowel disease v2.45 IL6 Ellen McDonagh gene: IL6 was added
gene: IL6 was added to Primary immunodeficiency. Sources: Literature
Mode of inheritance for gene: IL6 was set to Unknown
Publications for gene: IL6 were set to medRxiv 2020.04.01.20047381; doi: https://doi.org/10.1101/2020.04.01.20047381
Phenotypes for gene: IL6 were set to Potential marker for respiratory failure when infected with COVID-19
Review for gene: IL6 was set to RED
Added comment: Not yet peer-reviewed study available in medRxiv: https://www.medrxiv.org/content/10.1101/2020.04.01.20047381v1
reports an association between elevated interleukin-6 (IL-6) in COVID-19 infected patients with the need for mechanical ventilation (p=1.2.10-5). The maximal IL-6 level (cutoff 80 pg/ml) for each patient during disease predicted respiratory failure with high accuracy (p=1.7.10-8, AUC=0.98). The risk of respiratory failure for patients with IL-6 levels of ≥ 80 pg/ml was 22 times higher compared to patients with lower IL-6 levels.
Sources: Literature
Primary immunodeficiency or monogenic inflammatory bowel disease v2.44 IL6R Ellen McDonagh reviewed gene: IL6R: Rating: ; Mode of pathogenicity: None; Publications: medRxiv 2020.04.01.20047381, doi: https://doi.org/10.1101/2020.04.01.20047381; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.66 IL17A Ivone Leong Classified gene: IL17A as Green List (high evidence)
COVID-19 research v0.66 IL17A Ivone Leong Added comment: Comment on list classification: Promoted from Amber to Green as there is enough evidence in the literature to support this.
COVID-19 research v0.66 IL17A Ivone Leong Gene: il17a has been classified as Green List (High Evidence).
COVID-19 research v0.65 IRF2BP2 Eleanor Williams Phenotypes for gene: IRF2BP2 were changed from Recurrent infections, possible autoimmunity and inflammatory disease; Predominantly Antibody Deficiencies; CVID to Recurrent infections, possible autoimmunity and inflammatory disease; Predominantly Antibody Deficiencies; CVID; Immunodeficiency, common variable, 14, MIM# 617765
COVID-19 research v0.64 IRF2BP2 Eleanor Williams Publications for gene: IRF2BP2 were set to 27016798; 32086639; 32048120
COVID-19 research v0.62 IRF2BP2 Eleanor Williams commented on gene: IRF2BP2
COVID-19 research v0.62 DBR1 Louise Daugherty Deleted their review
COVID-19 research v0.62 DBR1 Louise Daugherty Deleted their comment
COVID-19 research v0.62 FCGR1A Catherine Snow Classified gene: FCGR1A as Red List (low evidence)
COVID-19 research v0.62 FCGR1A Catherine Snow Added comment: Comment on list classification: FCGR1 is on the Immunoplex Panel offered by the University of Washington Department of Laboratory Medicine however there is currently no link to alleles and disease (PMID: 31057544)
COVID-19 research v0.62 FCGR1A Catherine Snow Gene: fcgr1a has been classified as Red List (Low Evidence).
COVID-19 research v0.61 ADAM17 Abdelazeem Elhabyan reviewed gene: ADAM17: Rating: AMBER; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.61 ADAM17 Abdelazeem Elhabyan Deleted their review
COVID-19 research v0.61 ADAM17 Abdelazeem Elhabyan reviewed gene: ADAM17: Rating: AMBER; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.61 ACTB Abdelazeem Elhabyan reviewed gene: ACTB: Rating: AMBER; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Primary immunodeficiency or monogenic inflammatory bowel disease v2.44 MPO Sarah Leigh Classified gene: MPO as Amber List (moderate evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.44 MPO Sarah Leigh Added comment: Comment on list classification: Comment on list classification: PMID 3208230 outlines the role of neutrophil extracellular traps (NETs) in the control of some pathogens including viruses, by virus capture and neutralization. In vivo treatment of the mice with DNase resulted in the enhanced susceptibility of IFNAR-/- mice to the CHIKV virus. Furthermore, the levels of MPO-DNA complex in acutely CHIKV-infected patients, were correlated with the levels of NETs and the viral load in the blood, suggesting that NETs are also released in natural human infection cases. Therefore, variants that result in myeloperoxidase deficiency, may well contribute to an increased susceptiblity to viral infection. At least 9 variants have been reported in Myeloperoxidase deficiency 254600 and these could well be contributing to increased viral susceptibily.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.44 MPO Sarah Leigh Gene: mpo has been classified as Amber List (Moderate Evidence).
Skeletal dysplasia v2.7 NXN Ellen McDonagh Classified gene: NXN as Green List (high evidence)
Skeletal dysplasia v2.7 NXN Ellen McDonagh Added comment: Comment on list classification: Promoted to Green after expert review from Sian Ellard (by email).
Skeletal dysplasia v2.7 NXN Ellen McDonagh Gene: nxn has been classified as Green List (High Evidence).
COVID-19 research v0.60 DBR1 Louise Daugherty changed review comment from: PanelApp curators : you might need to re-review all the Green genes on this panel that were previously rated as Red on the PID panel, there may have been an error with the automatic upload changing Red Genes to Expert Review Green (https://panelapp.genomicsengland.co.uk/panels/398/gene/DBR1/), other examples are POLE2, BRCA1, BRCA2, ERCC4 etc unless there is evidence missed from the upload?; to: PanelApp curators : you might need to re-review all the Green genes on this panel that were previously rated as Red on the PID panel, there may have been an error with the automatic upload changing Red Genes to Expert Review Green (https://panelapp.genomicsengland.co.uk/panels/398/gene/DBR1/), other examples are IFNAR2, POLE2, BRCA1, BRCA2, ERCC4 etc unless there is evidence missed from the upload?
COVID-19 research v0.60 DBR1 Louise Daugherty changed review comment from: PanelApp curators : you might need to all the Green genes on this panel that were previously rated as Red on the PID panel, there may have been an error with the automatic upload changing Red Genes to Expert Review Green (https://panelapp.genomicsengland.co.uk/panels/398/gene/DBR1/), other examples are POLE2, BRCA1, BRCA2, ERCC4 etc unless there is evidence missed from the upload?; to: PanelApp curators : you might need to re-review all the Green genes on this panel that were previously rated as Red on the PID panel, there may have been an error with the automatic upload changing Red Genes to Expert Review Green (https://panelapp.genomicsengland.co.uk/panels/398/gene/DBR1/), other examples are POLE2, BRCA1, BRCA2, ERCC4 etc unless there is evidence missed from the upload?
COVID-19 research v0.60 DBR1 Louise Daugherty changed review comment from: PanelApp curators : you might need to all the Green genes on this panel that were previously rated as Red on the PID panel, there may have been an error with the automatic upload changing Red Genes to Expert Review Green (https://panelapp.genomicsengland.co.uk/panels/398/gene/DBR1/), other examples are POLE2, BRCA1, BRCA2, ERCC4 etc unless there as evidence missed from the upload?; to: PanelApp curators : you might need to all the Green genes on this panel that were previously rated as Red on the PID panel, there may have been an error with the automatic upload changing Red Genes to Expert Review Green (https://panelapp.genomicsengland.co.uk/panels/398/gene/DBR1/), other examples are POLE2, BRCA1, BRCA2, ERCC4 etc unless there is evidence missed from the upload?
COVID-19 research v0.60 DBR1 Louise Daugherty reviewed gene: DBR1: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.60 MPO Sarah Leigh Classified gene: MPO as Amber List (moderate evidence)
COVID-19 research v0.60 MPO Sarah Leigh Added comment: Comment on list classification: PMID 3208230 outlines the role of neutrophil extracellular traps (NETs) in the control of some pathogens including viruses, by virus capture and neutralization. In vivo treatment of the mice with DNase resulted in the enhanced susceptibility of IFNAR-/- mice to the CHIKV virus. Furthermore, the levels of MPO-DNA complex in acutely CHIKV-infected patients, were correlated with the levels of NETs and the viral load in the blood, suggesting that NETs are also released in natural human infection cases. Therefore, variants that result in myeloperoxidase deficiency, may well contribute to an increased susceptiblity to viral infection.
At least 9 variants have been reported in Myeloperoxidase deficiency 254600 and these could well be contributing to increased viral susceptibily.
COVID-19 research v0.60 MPO Sarah Leigh Gene: mpo has been classified as Amber List (Moderate Evidence).
Confirmed Fanconi anaemia or Bloom syndrome v1.5 XRCC2 Tom Cullup reviewed gene: XRCC2: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID: 22232082, 27208205; Phenotypes: Fanconi anaemia complementation group U; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Familial pulmonary fibrosis v1.9 SFTPB Helen Savage reviewed gene: SFTPB: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID: 8163685, 15331184; Phenotypes: Surfactant metabolism dysfunction, pulmonary, 1, 265120; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.59 C17orf62 Abdelazeem Elhabyan Deleted their review
COVID-19 research v0.59 C17orf62 Abdelazeem Elhabyan reviewed gene: C17orf62: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.59 DBR1 Abdelazeem Elhabyan reviewed gene: DBR1: Rating: AMBER; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.59 IL17A Abdelazeem Elhabyan commented on gene: IL17A: I agree that the level should be reviewed for being increased to Green especially the association of SNPs with H1N1 (influenza A) and influenza B.


Association with CNVs with pathology has been confirmed but the disease state was not revealed in any of the patients
https://www.ncbi.nlm.nih.gov/clinvar?LinkName=gene_clinvar&from_uid=3605
COVID-19 research v0.59 IL17A Abdelazeem Elhabyan edited their review of gene: IL17A: Changed rating: GREEN
COVID-19 research v0.59 IL17A Abdelazeem Elhabyan Deleted their comment
COVID-19 research v0.59 IL17A Abdelazeem Elhabyan changed review comment from: I agree that the level should be reviewed for being increased to Green especially the association of SNPs with H1N1 (influenza A) and influenza B.


Association with CNVs with pathology has been confirmed but the disease state was not revealed in any of the patients
https://www.ncbi.nlm.nih.gov/clinvar?LinkName=gene_clinvar&from_uid=3605; to: I agree that the level should be reviewed for being increased to Green especially the association of SNPs with H1N1 (influenza A) and influenza B.


Association with CNVs with pathology has been confirmed but the disease state was not revealed in any of the patients
https://www.ncbi.nlm.nih.gov/clinvar?LinkName=gene_clinvar&from_uid=3605
COVID-19 research v0.59 IL17A Abdelazeem Elhabyan commented on gene: IL17A
COVID-19 research v0.59 IRF9 Abdelazeem Elhabyan commented on gene: IRF9
COVID-19 research v0.59 ACP5 Abdelazeem Elhabyan reviewed gene: ACP5: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Skeletal dysplasia v2.6 NXN Ellen McDonagh Deleted their comment
Skeletal dysplasia v2.6 NXN Ellen McDonagh Deleted their comment
Skeletal dysplasia v2.6 NXN Ellen McDonagh Deleted their comment
Skeletal dysplasia v2.6 NXN Ellen McDonagh Classified gene: NXN as Amber List (moderate evidence)
Skeletal dysplasia v2.6 NXN Ellen McDonagh Added comment: Comment on list classification: Two family reports and mouse model...should this be promoted to Green?
Skeletal dysplasia v2.6 NXN Ellen McDonagh Gene: nxn has been classified as Amber List (Moderate Evidence).
Skeletal dysplasia v2.6 NXN Ellen McDonagh Classified gene: NXN as Amber List (moderate evidence)
Skeletal dysplasia v2.6 NXN Ellen McDonagh Added comment: Comment on list classification: Two family reports and mouse model...should this be promoted to Green?
Skeletal dysplasia v2.6 NXN Ellen McDonagh Gene: nxn has been classified as Amber List (Moderate Evidence).
Skeletal dysplasia v2.5 NXN Ellen McDonagh Classified gene: NXN as Amber List (moderate evidence)
Skeletal dysplasia v2.5 NXN Ellen McDonagh Added comment: Comment on list classification: Two family reports and mouse model...should this be promoted to Green?
Skeletal dysplasia v2.5 NXN Ellen McDonagh Gene: nxn has been classified as Amber List (Moderate Evidence).
Skeletal dysplasia v2.5 NXN Ellen McDonagh Classified gene: NXN as Amber List (moderate evidence)
Skeletal dysplasia v2.5 NXN Ellen McDonagh Added comment: Comment on list classification: Two family reports and mouse model...should this be promoted to Green?
Skeletal dysplasia v2.5 NXN Ellen McDonagh Gene: nxn has been classified as Amber List (Moderate Evidence).
Skeletal dysplasia v2.4 NXN Ellen McDonagh changed review comment from: Gene suggested by Sian Ellard (Royal Devon & Exeter NHS Foundation Trust, South West Genomic Laboratory Hub) to be added to this panel. PMID: 29276006 reports three individuals from two families with biallelic vairants in this gene that co-segregate with the disease. All three patients have typical facial characteristics of Robinow syndrome, mesomelia, brachydactyly, and broad thumbs/toes NXN knockout mice have craniofacial defects which is hypothesized to be caused by abnormal Wnt/Beta-catenin signalling.
Sources: Literature, Expert Review; to: Gene suggested by Sian Ellard (Royal Devon & Exeter NHS Foundation Trust, South West Genomic Laboratory Hub) to be added to this panel. PMID: 29276006 reports three individuals from two families with biallelic vairants in this gene that co-segregate with the disease. All three patients have typical facial characteristics of Robinow syndrome, mesomelia, brachydactyly, and broad thumbs/toes. NXN knockout mice have craniofacial defects which is hypothesized to be caused by abnormal Wnt/Beta-catenin signalling.
Skeletal dysplasia v2.4 NXN Ellen McDonagh gene: NXN was added
gene: NXN was added to Skeletal dysplasia. Sources: Literature,Expert Review
Mode of inheritance for gene: NXN was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: NXN were set to 29276006
Phenotypes for gene: NXN were set to Robinow syndrome, autosomal recessive 2 618529
Review for gene: NXN was set to AMBER
Added comment: Gene suggested by Sian Ellard (Royal Devon & Exeter NHS Foundation Trust, South West Genomic Laboratory Hub) to be added to this panel. PMID: 29276006 reports three individuals from two families with biallelic vairants in this gene that co-segregate with the disease. All three patients have typical facial characteristics of Robinow syndrome, mesomelia, brachydactyly, and broad thumbs/toes NXN knockout mice have craniofacial defects which is hypothesized to be caused by abnormal Wnt/Beta-catenin signalling.
Sources: Literature, Expert Review
COVID-19 research v0.59 IGHG2 Ivone Leong reviewed gene: IGHG2: Rating: ; Mode of pathogenicity: None; Publications: 16092453; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.59 HLA-B Ivone Leong Publications for gene: HLA-B were set to 12969506
COVID-19 research v0.58 IL17A Ivone Leong Classified gene: IL17A as Amber List (moderate evidence)
COVID-19 research v0.58 IL17A Ivone Leong Added comment: Comment on list classification: Promoted from Red to Amber. There appears to be enough evidence for this gene to be promoted Green; however, will wait for expert review before promoting to Green.
COVID-19 research v0.58 IL17A Ivone Leong Gene: il17a has been classified as Amber List (Moderate Evidence).
COVID-19 research v0.57 IL17A Ivone Leong Phenotypes for gene: IL17A were changed from Arthritis; Immunodeficiency 5 to Arthritis; Immunodeficiency 5; Susceptibility to influenza
COVID-19 research v0.56 IL17A Ivone Leong Mode of inheritance for gene: IL17A was changed from Unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.55 IL17A Ivone Leong Publications for gene: IL17A were set to
COVID-19 research v0.54 IL17A Ivone Leong reviewed gene: IL17A: Rating: ; Mode of pathogenicity: None; Publications: 28860146, 31196204, 27890033, 21703407, 27155288, 29530464; Phenotypes: ; Mode of inheritance: Unknown
COVID-19 research v0.54 GAD1 Catherine Snow Classified gene: GAD1 as Red List (low evidence)
COVID-19 research v0.54 GAD1 Catherine Snow Added comment: Comment on list classification: GAD1 has no relationship to virus susceptibility.
COVID-19 research v0.54 GAD1 Catherine Snow Gene: gad1 has been classified as Red List (Low Evidence).
COVID-19 research v0.53 EPCAM Catherine Snow Classified gene: EPCAM as Red List (low evidence)
COVID-19 research v0.53 EPCAM Catherine Snow Added comment: Comment on list classification: No gene disease association.
COVID-19 research v0.53 EPCAM Catherine Snow Gene: epcam has been classified as Red List (Low Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.43 MPO Sarah Leigh Publications for gene: MPO were set to 15108282; 9354683; 9637725
COVID-19 research v0.52 IFNAR1 Sarah Leigh Classified gene: IFNAR1 as Green List (high evidence)
COVID-19 research v0.52 IFNAR1 Sarah Leigh Added comment: Comment on list classification: Not associated with phenotype in OMIM or in Gen2Phen. However, the publications listed below give evidence that the three LOF variants in two unrelated cases are associated with an adverse reaction to attenuated virus vaccines, which are rescued by wt IFNAR1 protein in vitro.
COVID-19 research v0.52 IFNAR1 Sarah Leigh Gene: ifnar1 has been classified as Green List (High Evidence).
COVID-19 research v0.51 IFNAR1 Sarah Leigh Added comment: Comment on publications: PMID 31270247: reports three variants in two cases of healthy children with adverse reactions to live attuated virus vaccines. Each had biallelic loss-of-function IFNAR1 variations and the effects of these was demonstrated by the patient-derived fibroblasts being susceptible to viruses. This effect was recused by the WT IFNAR1.
PMID 26676772: reports the tageted degradation of IFNAR1 protein by
Influenza A virus (IAV), allowing the virus to escape the powerful innate immune system. Thus the loss of function of IFNAR1 would increase the susceptability to viral infection.
PMID 20020050: reports the tageted degradation of IFNAR1 protein by Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV). Confocal microscopic analysis showed increased translocation of IFNAR1 into the lysosomal compartment and flow cytometry showed reduced levels of IFNAR1 in 3a-expressing cells.
COVID-19 research v0.51 IFNAR1 Sarah Leigh Publications for gene: IFNAR1 were set to 31270247; 26676772; 20020050
Primary immunodeficiency or monogenic inflammatory bowel disease v2.42 IFNAR1 Sarah Leigh Classified gene: IFNAR1 as Amber List (moderate evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.42 IFNAR1 Sarah Leigh Added comment: Comment on list classification: Not associated with phenotype in OMIM or in Gen2Phen. However, the publications listed below give evidence that the three LOF variants in two unrelated cases are associated with an adverse reaction to attenuated virus vaccines, which are rescued by wt IFNAR1 protein in vitro.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.42 IFNAR1 Sarah Leigh Gene: ifnar1 has been classified as Amber List (Moderate Evidence).
COVID-19 research v0.50 UNC119 Eleanor Williams commented on gene: UNC119: Checked OMIM and literature (through PubMed) for updates in April 2020 - no new cases reported. Keep red.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.41 IFNAR1 Sarah Leigh Added comment: Comment on publications: PMID 31270247: reports two cases of healthy children with adverse reactions to live attuated virus vaccines. Each had biallelic loss-of-function IFNAR1 variations and the effects of these was demonstrated by the patient-derived fibroblasts being susceptible to viruses. This effect was recused by the WT IFNAR1.
PMID 26676772: reports the tageted degradation of IFNAR1 protein by
Influenza A virus (IAV), allowing the virus to escape the powerful innate immune system. Thus the loss of function of IFNAR1 would increase the susceptability to viral infection.
PMID 20020050: reports the tageted degradation of IFNAR1 protein by Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV). Confocal microscopic analysis showed increased translocation of IFNAR1 into the lysosomal compartment and flow cytometry showed reduced levels of IFNAR1 in 3a-expressing cells.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.41 IFNAR1 Sarah Leigh Publications for gene: IFNAR1 were set to 31270247; 26676772; 20020050
COVID-19 research v0.50 STAT5A Eleanor Williams Publications for gene: STAT5A were set to 16418296
COVID-19 research v0.49 STAT5A Eleanor Williams edited their review of gene: STAT5A: Added comment: April 2020
- no association with any human disease phenotype in OMIM (page last updated Feb 2020).
- no associations in Gene2Phenotype.
- PubMed search - no publications describing reports of variants in STAT5 and PID/viral susceptibility but :

PMID: 26541527- Leahy et al 2016 - mention that STAT5 mRNA (which is in the IL-15 pathway) is differentially expressed in children with severe bronchiolitis compared with those with moderate severity bronchiolitis.
PMID: 23593005- Hong et al 2013 - in human papillomavirus (HPV) infections STAT-5 is activated as part of the process to regulate genome amplification in suprabasal cells.
PMID: 22520852 - Li et al - show in mouse studies that tetramerization of STAT5 is critical for cytokine responses and normal immune function; Changed publications: 16418296, 26541527, 23593005, 22520852
COVID-19 research v0.49 IRF9 Catherine Snow Classified gene: IRF9 as Green List (high evidence)
COVID-19 research v0.49 IRF9 Catherine Snow Added comment: Comment on list classification: Rating Green on this panel following feedback with Genomics England clinical team, as this is a research panel and IRF9 has two unrelated cases and an animal model.
COVID-19 research v0.49 IRF9 Catherine Snow Gene: irf9 has been classified as Green List (High Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.40 IFNAR1 Sarah Leigh gene: IFNAR1 was added
gene: IFNAR1 was added to Primary immunodeficiency. Sources: Expert Review,Literature
Mode of inheritance for gene: IFNAR1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IFNAR1 were set to 31270247; 26676772; 20020050
Phenotypes for gene: IFNAR1 were set to IFNAR1 associated adverse reactions to certain live attenuated viral vaccines
Review for gene: IFNAR1 was set to AMBER
Added comment: Hypothesis from Abdelazeem Elhabyan (Tanta University Hospitals): this gene is involved in the interferon-mediated immune response to viruses of those is SARS Coronavirus (2003) which down-regulates the IFNAR1 receptors through its 3a protein. Additionally, Influenzavirus A suppress immune response by downregulation of this gene. It has been also linked to adverse reactions to measles and yellow fever vaccines in healthy individuals.
Sources: Expert Review, Literature
COVID-19 research v0.48 HLA-B Ivone Leong reviewed gene: HLA-B: Rating: ; Mode of pathogenicity: None; Publications: 15243926, 18186801; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.48 CCL2 Rebecca Foulger Publications for gene: CCL2 were set to 25818534; 26687605; 16916890; 24788844
COVID-19 research v0.47 CCL2 Rebecca Foulger commented on gene: CCL2: PMID:27260136 (Kim et al., 2016) report that CCL2 ablation highly increased susceptibility to Japanese encephalitis, indicating that CCL2 plays an essential role in conferring protection against JE caused by JE virus (JEV) infection. They also note a surprising opposite effect for ablation of the CCR2 (the corresponding receptor).
COVID-19 research v0.47 CCL2 Rebecca Foulger Publications for gene: CCL2 were set to 25818534; 26687605; 16916890
COVID-19 research v0.46 CCL2 Rebecca Foulger commented on gene: CCL2: PMID:24788844 (Han et al., 2014) studied 36 Chines patients and report that the CCL2-2510G allele is associated with susceptibility to EV71 encephalitis in Chinese patients.
COVID-19 research v0.46 CCL2 Rebecca Foulger Phenotypes for gene: CCL2 were changed from Susceptibility to Severe Acute Respiratory Syndrome Coronavirus Infection; Susceptibility to SARS-CoV to {HIV-1, resistance to}, 609423; Susceptibility to Severe Acute Respiratory Syndrome Coronavirus Infection; Susceptibility to SARS-CoV
COVID-19 research v0.45 CCL2 Rebecca Foulger commented on gene: CCL2: PMID:16916890 (Ansari et al.) report increased CCL2 levels in HIV-1 patients, and suggest inhibition of CCL2 production could provide a therapeutic intervention in HIV infection.
COVID-19 research v0.45 CCL2 Rebecca Foulger Publications for gene: CCL2 were set to 25818534
COVID-19 research v0.44 CCL2 Rebecca Foulger commented on gene: CCL2
COVID-19 research v0.44 IRF2BP2 Zornitza Stark reviewed gene: IRF2BP2: Rating: RED; Mode of pathogenicity: None; Publications: 27016798; Phenotypes: Immunodeficiency, common variable, 14, MIM# 617765; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
COVID-19 research v0.44 MPO Sarah Leigh Publications for gene: MPO were set to 9354683; 15108282; 9637725
COVID-19 research v0.43 ACE Rebecca Foulger Marked gene: ACE as ready
COVID-19 research v0.43 ACE Rebecca Foulger Gene: ace has been classified as Red List (Low Evidence).
COVID-19 research v0.43 KRAS Rebecca Foulger Added comment: Comment on mode of inheritance: Autosomal (AD) inheritance listed in OMIM for MIM:614470.
COVID-19 research v0.43 KRAS Rebecca Foulger Mode of inheritance for gene: KRAS was changed from Unknown to Unknown
COVID-19 research v0.42 KRAS Rebecca Foulger commented on gene: KRAS
COVID-19 research v0.42 KRAS Rebecca Foulger Phenotypes for gene: KRAS were changed from RAS associated lymphoproliferative disease, 614470; RALD to RALD; RAS-associated autoimmune leukoproliferative disorder, 614470
COVID-19 research v0.41 IRF8 Ellen McDonagh Classified gene: IRF8 as Green List (high evidence)
COVID-19 research v0.41 IRF8 Ellen McDonagh Gene: irf8 has been classified as Green List (High Evidence).
COVID-19 research v0.40 KDM6A Ellen McDonagh Source Expert Review Green was added to KDM6A.
Added phenotypes Combined immunodeficiencies with associated or syndromic features; Kabuki Syndrome 2 due to KDM6A deficiency; Typical facial abnormalities, cleft or high arched palate, skeletal abnormalities, short stature, intellectual disability, congenital heart defects, recurrent infections (otitis media, pneumonia) in 50% of patients. Autoimmunity may be present for gene: KDM6A
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 SH3KBP1 Ellen McDonagh Source Expert Review Green was added to SH3KBP1.
Added phenotypes Predominantly Antibody Deficiencies; Severe bacterial infections; SH3KBP1 (CIN85) deficiency; Immunodeficiency 61, 300310 for gene: SH3KBP1
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 IRAK1 Ellen McDonagh Source Expert Review Green was added to IRAK1.
Added phenotypes Bacterial infections, X-linked MECP2 deficiency-related syndrome due to a large de novo Xq28 chromosomal deletion encompassing both MECP2 and IRAK1; Defects in Intrinsic and Innate Immunity for gene: IRAK1
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 TRAF3 Ellen McDonagh Added phenotypes Herpetic encephalitis (HSE); Herpes simplex virus 1 encephalitis; Defects in Intrinsic and Innate Immunity; Defects in intrinsic and innate immunity; {?Encephalopathy, acute, infection-induced (herpes-specific), susceptibility to, 5},614849; Herpes simplex encephalitis, susceptibility to, 3 for gene: TRAF3
COVID-19 research v0.40 TOP2B Ellen McDonagh Source Expert Review Green was added to TOP2B.
Added phenotypes Recurrent infections, facial dysmorphism, limb anomalies; Hoffman syndrome/TOP2B deficiency; Predominantly Antibody Deficiencies for gene: TOP2B
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 TNFSF12 Ellen McDonagh Source Expert Review Green was added to TNFSF12.
Added phenotypes Immunodeficiency, common variable with lack of anti-pneumococcal antibody; Common variable immunodeficiency disorders (CVID); Predominantly Antibody Deficiencies; Pneumonia, bacterial infections, warts, thrombocytopenia. neutropenia; Pneumonia, bacterial infections, warts, thrombocytopenia for gene: TNFSF12
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 THBD Ellen McDonagh Source Expert Review Green was added to THBD.
Added phenotypes Complement Deficiencies; Thrombomodulin deficiency; Hemolytic uremic syndrome, atypical, susceptibility to, 6; Atypical hemolytic-uremic syndrome for gene: THBD
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 TGFBR2 Ellen McDonagh Source Expert Review Green was added to TGFBR2.
Added phenotypes Recurrent respiratory infections, eczema, food allergies, hyperextensible joints, scoliosis, retention of primary teeths, aortic anuerysms; Combined immunodeficiencies with associated or syndromic features; ALPS-FAS for gene: TGFBR2
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 TGFBR1 Ellen McDonagh Source Expert Review Green was added to TGFBR1.
Added phenotypes Loeys-Dietz syndrome 1, 609192; Loeys Dietz syndrome due to TGFBR1 deficiency; Combined immunodeficiencies with associated or syndromic features; Recurrent respiratory infectons, eczema, food allergies, hyperextensible joints, scoliosis, retention of primary teeths, aortic anuerysms for gene: TGFBR1
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 SRP54 Ellen McDonagh Source Expert Review Green was added to SRP54.
Added phenotypes Schwachman Diamond features; Congenital defects of phagocyte number or function for gene: SRP54
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 SH3BP2 Ellen McDonagh Source Expert Review Green was added to SH3BP2.
Added phenotypes Other autoinflammatory diseases with known genetic defect; Autoinflammatory Disorders; Cherubism 118400; Bone degeneration in jaws for gene: SH3BP2
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 SEMA3E Ellen McDonagh Source Expert Review Green was added to SEMA3E.
Added phenotypes CHARGE syndrome; immune-mediated cerebellar ataxia; Coloboma, heart anomaly, choanal atresia, intellectual retardation, genital and ear anomalies, CNS malformation, some are SCID-like and have low TRECs; Charge syndrome 214800; Combined immunodeficiencies with associated or syndromic features for gene: SEMA3E
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 SEC61A1 Ellen McDonagh Source Expert Review Green was added to SEC61A1.
Added phenotypes Severe recurrent respiratory tract infections; Predominantly Antibody Deficiencies; Hyperuricemic nephropathy, familial juvenile, 4, 617056; SEC61A1 deficiency for gene: SEC61A1
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 RELA Ellen McDonagh Source Expert Review Green was added to RELA.
Added phenotypes RelA haplosufficiency; Mucosal ulceration, impaired NFkB activation; Mucocutaneous ulceration, chronic, 618287; Immunodeficiencies affecting cellular and humoral immunity for gene: RELA
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 RANBP2 Ellen McDonagh Source Expert Review Green was added to RANBP2.
Added phenotypes Fever induces acute encephalopathy; Defects in intrinsic and innate immunity; Defects in Intrinsic and Innate Immunity for gene: RANBP2
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 PSEN1 Ellen McDonagh Source Expert Review Green was added to PSEN1.
Added phenotypes Hidradenitis suppurative with cutaneous hyperpigmentation; Acne inversa, familial, 3 613737; Defects in Intrinsic and Innate Immunity for gene: PSEN1
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 OAS1 Ellen McDonagh Source Expert Review Green was added to OAS1.
Added phenotypes OAS1 GOF; Autoinflammatory Disorders; Pulmonary alveolar proteinosis, skin rash for gene: OAS1
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 NFE2L2 Ellen McDonagh Source Expert Review Green was added to NFE2L2.
Added phenotypes Recurrent respiratory and skin infections, growth retardation, , developmental delay; increased expression of stress response genes; Immunodeficiency, developmental delay, and hypohomocysteinemia, 617744; white matter cerebral lesions, increased level of homocysteine; Combined immunodeficiencies with associated or syndromic features; NFE2L2 GOF for gene: NFE2L2
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 NFAT5 Ellen McDonagh Source Expert Review Green was added to NFAT5.
Added phenotypes NFAT5 haploinsufficieny; IBD, recurrent sinopulmonary infections; Diseases of Immune Dysregulation for gene: NFAT5
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 KMT2D Ellen McDonagh Source Expert Review Green was added to KMT2D.
Added phenotypes Kabuki syndrome 1, 147920; Combined immunodeficiencies with associated or syndromic features; Typical facial abnormalities, cleft or high arched palate, skeletal abnormalities, short stature, intellectual disability, congenital heart defects, recurrent infections (otitis media, pneumonia) in 50% of patients. Autoimmunity may be present for gene: KMT2D
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 KMT2A Ellen McDonagh Source Expert Review Green was added to KMT2A.
Added phenotypes Wiedemann-Steiner syndrome with Congenital immunodeficiency; Combined immunodeficiencies with associated or syndromic features; Unclassified antibody deficiency; Respiratory infections, short stature, hypertelorism, hairy elbows, developmental delay, intellectual disability for gene: KMT2A
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 JAK1 Ellen McDonagh Source Expert Review Green was added to JAK1.
Added phenotypes Hypereosinophilic syndrome; HSM, eosinophilia, eosinophilic enteritis, thyroid disease, poor growth, viral infections; Diseases of Immune Dysregulation; Susceptibility to mycobacteria and viruses, urothelial carcinoma; Defects in Intrinsic and Innate Immunity; HSM, eosinophilic enteritis, thyroid disease, poor growth, viral infections for gene: JAK1
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 IRF2BP2 Ellen McDonagh Source Expert Review Green was added to IRF2BP2.
Added phenotypes Recurrent infections, possible autoimmunity and inflammatory disease; Predominantly Antibody Deficiencies; CVID for gene: IRF2BP2
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 ERBIN Ellen McDonagh Source Expert Review Green was added to ERBIN.
Added phenotypes ERBIN deficiency; Combined immunodeficiencies with associated or syndromic features; Recurrent respiratory infections, susceptibility to S. aureus, eczema, hyperextensible joints, scoliosis, arterial dilatation in some for gene: ERBIN
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 BCL11B Ellen McDonagh Source Expert Review Green was added to BCL11B.
Added phenotypes Combined immunodeficiencies with associated or syndromic features; leaky SCID; ?Immunodeficiency 49, 617237; Immunodeficiencies affecting cellular and humoral immunity; Congenital abnormalities, neonatal teeth, dysmorphic facies, absent corpus callosum, neurocognitive deficits for gene: BCL11B
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 APOL1 Ellen McDonagh Source Expert Review Green was added to APOL1.
Added phenotypes Defects in Intrinsic and Innate Immunity; Trypanosomiasis, susceptibility to; Trypanosomias; Trypanosomiasis for gene: APOL1
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 ACTB Ellen McDonagh Source Expert Review Green was added to ACTB.
Added phenotypes Congenital defects of phagocyte number or function; neutrophil dysfunction; Mental retardation, short stature; Actin beta deficiency (ACTB); Phagocytic disorder; Poor neutrophil chemotaxis, oxidative burst and actin remodeling. Thrombocytopenia; Baraitser-Winter syndrome 1, 243310 for gene: ACTB
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 TNFRSF13B Ellen McDonagh Source Expert Review Green was added to TNFRSF13B.
Added phenotypes IgA with IgG subclass deficiency; Immunodeficiency, common variable, 2; Immunodeficiency, common variable, 2, 240500; Variable clinical expression; Isolated IgG subclass deficiency; IGAD; Selective IgA deficiency; Common variable immunodeficiency disorders (CVID); Predominantly Antibody Deficiencies; Immunoglobulin A deficiency 2, 609529; CVID for gene: TNFRSF13B
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 CFHR2 Ellen McDonagh Source Expert Review Green was added to CFHR2.
Added phenotypes Complement Deficiencies; Age related macular degeneration; Atypical hemolytic uremic syndrome susceptibility; Older onset atypical hemolytic-uremic syndrome, disseminated neisserial infections for gene: CFHR2
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 ZNF341 Ellen McDonagh Source Expert Review Green was added to ZNF341.
Added phenotypes Hyper-IgE syndrome; Combined immunodeficiencies with associated or syndromic features; Bacterial infections, mild facial dysmorphism, pneumatoceles, hyperextensible joints, bone fractures, retention of primary teeth for gene: ZNF341
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 WRAP53 Ellen McDonagh Source Expert Review Green was added to WRAP53.
Added phenotypes Bone marrow failure; Bone marrow failure, pulmonary and hepatic fibrosis, nail dystrophy, leukoplakia, reticulate skin pigmentation; Combined immunodeficiencies with associated or syndromic features; Intrauterine growth retardation, microcephaly, nail dystrophy, sparse scalp hair and eyelashes, hyperpigmentation of skin, palmar hyperkeratosis, premalignant oral leukoplakia, pancytopenia, myelodysplasia, +/- recurrent infections. A severe phenotype with developmental delay and cerebellar hypoplasia known as Hoyeraal-Hreidarsson Syndrome (HHS) may occur in some DKC patients; microcephaly, neurodevelopmental delay for gene: WRAP53
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 TRIM22 Ellen McDonagh Source Expert Review Green was added to TRIM22.
Added phenotypes TRIM22; Granulomatous colitis; Autoinflammatory Disorders; Diseases of Immune Dysregulation for gene: TRIM22
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 TRAF3IP2 Ellen McDonagh Source Expert Review Green was added to TRAF3IP2.
Added phenotypes Defects in Intrinsic and Innate Immunity; Chronic mucocutaneous candidiasis (CMC); Defects in intrinsic and innate immunity; Candidiasis, familial, 8 615527; CMC, blepharitis, folliculitis and macroglossia for gene: TRAF3IP2
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 TNFSF11 Ellen McDonagh Source Expert Review Green was added to TNFSF11.
Added phenotypes Osteopetrosis with severe growth retardation; Defects in intrinsic and innate immunity; Defects in Intrinsic and Innate Immunity for gene: TNFSF11
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 TNFRSF9 Ellen McDonagh Source Expert Review Green was added to TNFRSF9.
Added phenotypes EBV lymphoproliferation, B-cell lymphoma; CD137 deficiency (41BB) for gene: TNFRSF9
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 TNFRSF4 Ellen McDonagh Source Expert Review Green was added to TNFRSF4.
Added phenotypes Kaposi's Sarcoma, impaired immunity to HHV8, OX40 deficiency; Immunodeficiencies affecting cellular and humoral immunity; Impaired immunity to HHV8, Kaposis sarcoma; Combined immunodeficiency for gene: TNFRSF4
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 TIRAP Ellen McDonagh Source Expert Review Green was added to TIRAP.
Added phenotypes Staphylococcal disease during childhood; Defects of TLR/NFkappa-B signalling; TIRAP deficiency; Defects in intrinsic and innate immunity; Defects in Intrinsic and Innate Immunity for gene: TIRAP
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 TGFB1 Ellen McDonagh Source Expert Review Green was added to TGFB1.
Added phenotypes Inflammatory bowel disease, immunodeficiency, and encephalopathy, 618213; IBD, immunodeficiency, recurrent viral infections, microcephaly, and encephalopathy; TGFB1 deficiency; Diseases of Immune Dysregulation for gene: TGFB1
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 TFRC Ellen McDonagh Source Expert Review Green was added to TFRC.
Added phenotypes Recurrent infections, neutropenia, thrombocytopenia; Recurrent infections, thrombocytopenia; Immunodeficiencies affecting cellular and humoral immunity for gene: TFRC
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 TCIRG1 Ellen McDonagh Source Expert Review Green was added to TCIRG1.
Added phenotypes Defects in intrinsic and innate immunity; Osteopetrosis with hypocalcemia; Defects in Intrinsic and Innate Immunity for gene: TCIRG1
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 STN1 Ellen McDonagh Source Expert Review Green was added to STN1.
Added phenotypes Combined immunodeficiencies with associated or syndromic features; Bone marrow failure; Intrauterine growth retardation, premature aging, pancytopenia, hypocellular bone marrow, gastrointestinal hemorrhage due to vascular ectasia, intracranial calcification, abnormal telomeres for gene: STN1
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 SNX10 Ellen McDonagh Source Expert Review Green was added to SNX10.
Added phenotypes Defects in intrinsic and innate immunity; Osteopetrosis with visual impairment; Defects in Intrinsic and Innate Immunity for gene: SNX10
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 SMARCD2 Ellen McDonagh Source Expert Review Green was added to SMARCD2.
Added phenotypes Congenital defects of phagocyte number or function; Neutropenia, developmental aberrations, skeletal abnormalities, hematopoietic stem cells, myelodysplasia for gene: SMARCD2
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 SLC7A7 Ellen McDonagh Source Expert Review Green was added to SLC7A7.
Added phenotypes Lysinuric protein intolerance, 222700; Severe bacterial infections; Lysinuric protein intolerance SLC7A7 deficiency; Predominantly Antibody Deficiencies for gene: SLC7A7
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 SLC39A7 Ellen McDonagh Source Expert Review Green was added to SLC39A7.
Added phenotypes Agammaglobulinemia; B cell deficiency; Early onset infections, blistering dermatosis, failure to thrive, thrombocytopenia; Predominantly Antibody Deficiencies for gene: SLC39A7
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 RNU4ATAC Ellen McDonagh Source Expert Review Green was added to RNU4ATAC.
Added phenotypes Recurrent bacterial infections, lymphadenopathy, Spondyloepiphyseal dysplasia, extreme intrauterine growth retardation, retinal dystrophy, facial dysmorphism, may present with microcephaly; Combined immunodeficiencies with associated or syndromic features; Recurrent bacterial infections, lymphadenopathy, Spondyloepiphyseal dysplasia, extreme intrauterine growth retardation, retinal dystrophy, facial dysmorphism, may present with microcephaly, short stature for gene: RNU4ATAC
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 RNF31 Ellen McDonagh Source Expert Review Green was added to RNF31.
Added phenotypes Polyglucosan body myopathy, early-onset, with or without immunodeficiency; Autoinflammatory syndrome with pyogenic bacterial infection and amylopectinosis; autoinflammation and combined immunodeficiency; Combined immunodeficiencies with associated or syndromic features; Bacterial infections, autoinflammation, amylopectinosis, lymphangiectasia for gene: RNF31
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 RELB Ellen McDonagh Source Expert Review Green was added to RELB.
Added phenotypes Immunodeficiencies affecting cellular and humoral immunity; Recurrent infectionsImmunodeficiencies affecting cellular and humoral immunity; Recurrent infections; ?Immunodeficiency 53, 617585 for gene: RELB
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 REL Ellen McDonagh Source Expert Review Green was added to REL.
Added phenotypes Recurrent infections with bacteria, mycobacteria, salmonella and opportunistic infections; Immunodeficiencies affecting cellular and humoral immunity; c-Rel deficiency for gene: REL
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 PSMG2 Ellen McDonagh Source Expert Review Green was added to PSMG2.
Added phenotypes Panniculitis, lipodystrophy, autoimmune hemolytic anemia; CANDLE (chronic atypical neutrophilic dermatitis with lipodystrophy); Autoinflammatory Disorders for gene: PSMG2
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 POLE2 Ellen McDonagh Source Expert Review Green was added to POLE2.
Added phenotypes Recurrent infections, disseminated BCG infections, autoimmunity (type 1 diabetes, hypothyroidism, facial dysmorphism); Combined immunodeficiencies with associated or syndromic features; Recurrent infections, disseminated BCG infections, autoimmunity (type 1 diabetes, hypothyroidism, facial dysmorphism for gene: POLE2
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 POLD2 Ellen McDonagh Source Expert Review Green was added to POLD2.
Added phenotypes Immunodeficiencies affecting cellular and humoral immunity; Polymerase d 2 deficiency; Recurrent respiratory tract infections, skin infections, warts and molluscum, short stature, intellectual disability for gene: POLD2
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 POLD1 Ellen McDonagh Source Expert Review Green was added to POLD1.
Added phenotypes Immunodeficiencies affecting cellular and humoral immunity; Recurrent respiratory tract infections, skin infections, warts and molluscum, short stature, intellectual disability; Polymerase d 1 deficiency for gene: POLD1
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 PLEKHM1 Ellen McDonagh Source Expert Review Green was added to PLEKHM1.
Added phenotypes Osteopetrosis; Defects in intrinsic and innate immunity; Defects in Intrinsic and Innate Immunity for gene: PLEKHM1
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 OSTM1 Ellen McDonagh Source Expert Review Green was added to OSTM1.
Added phenotypes Defects in intrinsic and innate immunity; Defects in Intrinsic and Innate Immunity; Osteopetrosis with hypocalcemia, neurologic features for gene: OSTM1
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 NBAS Ellen McDonagh Source Expert Review Green was added to NBAS.
Added phenotypes Infantile liver failure syndrome 2, 616483; Defects in intrinsic and innate immunity; Fever induced liver failure; Defects in Intrinsic and Innate Immunity; Fever induces liver failure for gene: NBAS
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 MSH6 Ellen McDonagh Source Expert Review Green was added to MSH6.
Added phenotypes Colorectal cancer, hereditary nonpolyposis, type 5 614350; Endometrial cancer, familial 608089; Predominantly Antibody Deficiencies; Family or personal history of cancer; Mismatch repair cancer syndrome 276300 for gene: MSH6
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 MS4A1 Ellen McDonagh Source Expert Review Green was added to MS4A1.
Added phenotypes Predominantly Antibody Deficiencies; Recurrent infections; Common variable immunodeficiency disorders (CVID); Immunodeficiency, common variable, 5 613495 for gene: MS4A1
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 MKL1 Ellen McDonagh Source Expert Review Green was added to MKL1.
Added phenotypes Susceptibility to severe bacterial infection; Mild thrombocytopenia; Congenital defects of phagocyte number or function for gene: MKL1
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 MASP2 Ellen McDonagh Source Expert Review Green was added to MASP2.
Added phenotypes Complement Deficiencies; MASP2 deficiency 613791; Mannan-binding lectin serine protease (MASP) deficiency; Pyogenic infections, inflammatory lung disease, autoimmunity for gene: MASP2
Publications for gene MASP2 were updated from 24658431; 32086639; 32048120; 19405982 to 24658431; 32086639; 32048120; 19405982
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 LIG1 Ellen McDonagh Source Expert Review Green was added to LIG1.
Added phenotypes DNA ligase I deficiency; Combined immunodeficiencies with associated or syndromic features; DNA-ligase 1 ATP-dependent deficiency (LIG1); Recurrent respiratory infections, growth retardation, sun sensitivity, lymphoma, radiation sensitivity for gene: LIG1
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 IL6ST Ellen McDonagh Source Expert Review Green was added to IL6ST.
Added phenotypes Eczema; Abnormal acute-phase responses; Recurrent infections; Bacterial infections, boiles, eczema, pulmonary abscesses, pneumatoceles, bone fractures, scoliosis, retention of primary teeth, craniosynostosis; Eosinophilia; Elevated IgE; Combined immunodeficiencies with associated or syndromic features for gene: IL6ST
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 IL6R Ellen McDonagh Source Expert Review Green was added to IL6R.
Added phenotypes Eczema; Recurrent infections; Recurrent pyogenic infections, cold abscesses, high circulating IL-6 levels; Hyper-IgE; Combined immunodeficiencies with associated or syndromic features for gene: IL6R
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 IL2RB Ellen McDonagh Source Expert Review Green was added to IL2RB.
Added phenotypes Lymphoproliferation, lymphadenopathy, hepatosplenomegaly, autoimmune hemolytic anemia, dermatitis, enteropathy, recurrent viral (EBV, CMV) infections; Immunodeficiency 63 with lymphoproliferation and autoimmunity, 618495; CD122 deficiency for gene: IL2RB
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 IFNAR2 Ellen McDonagh Source Expert Review Green was added to IFNAR2.
Added phenotypes ?Immunodeficiency 45, 616669; Severe viral infections (disseminated vaccine-strain measles, HHV6); Defects in Intrinsic and Innate Immunity for gene: IFNAR2
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 ICOSLG Ellen McDonagh Source Expert Review Green was added to ICOSLG.
Added phenotypes Immunodeficiencies affecting cellular and humoral immunity; Recurrent bacterial and viral infections for gene: ICOSLG
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 HYOU1 Ellen McDonagh Source Expert Review Green was added to HYOU1.
Added phenotypes Hypoglycemia, inflammatory complications; Congenital defects of phagocyte number or function for gene: HYOU1
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 HMOX1 Ellen McDonagh Source Expert Review Green was added to HMOX1.
Added phenotypes amyloidosis; Hemolysis, nephritis, inflammation; Defects in Intrinsic and Innate Immunity for gene: HMOX1
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 HAVCR2 Ellen McDonagh Source Expert Review Green was added to HAVCR2.
Added phenotypes T-cell lymphoma, subcutaneous panniculitis-like, 618398; Tim-3 deficiency; T-cell lymphoma, subcutaneous panniculitis-like, HLH; Autoinflammatory Disorders for gene: HAVCR2
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 FERMT1 Ellen McDonagh Source Expert Review Green was added to FERMT1.
Added phenotypes FERMT1 deficiency (Kindler syndrome); Diseases of Immune Dysregulation; Kindler syndrome, 173650; Dermatosis characterized by congenital blistering, skin atrophy, photosensitivity, skin fragility, and scaling for gene: FERMT1
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 FCN3 Ellen McDonagh Source Expert Review Green was added to FCN3.
Added phenotypes Respiratory infections, abscesses; Complement Deficiencies; Ficolin3 deficiency; Immunodeficiency due to ficolin 3 deficiency, 613860 for gene: FCN3
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 FCHO1 Ellen McDonagh Source Expert Review Green was added to FCHO1.
Added phenotypes Recurrent infections, lymphoproliferation, increased activation-induced T-cell death, defective clathrin-mediated endocytosis; FCHO1 deficiency; Immunodeficiencies affecting cellular and humoral immunity for gene: FCHO1
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 FANCM Ellen McDonagh Source Expert Review Green was added to FANCM.
Added phenotypes Fanconi Anemia Type M; Bone marrow failure; Normal to low NK, CNS, skeletal, skin, cardiac, GI, urogenital anomalies, increased chromosomal breakage for gene: FANCM
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 FANCI Ellen McDonagh Source Expert Review Green was added to FANCI.
Added phenotypes Fanconi anemia, complementation group I, 609053; Bone marrow failure; Fanconi Anemia Type I; Normal to low NK, CNS, skeletal, skin, cardiac, GI, urogenital anomalies, increased chromosomal breakage for gene: FANCI
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 FANCF Ellen McDonagh Source Expert Review Green was added to FANCF.
Added phenotypes Normal to low NK, CNS, skeletal, skin, cardiac, GI, urogenital anomalies, increased chromosomal breakage; Fanconi anemia, complementation group F, 603467; Bone marrow failure; Fanconi Anemia Type F for gene: FANCF
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 FAAP24 Ellen McDonagh Source Expert Review Green was added to FAAP24.
Added phenotypes EBV infection-driven lymphoproliferative disease; Diseases of Immune Dysregulation for gene: FAAP24
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 ERCC4 Ellen McDonagh Source Expert Review Green was added to ERCC4.
Added phenotypes Fanconi anemia, complementation group Q, 615272; Normal to low NK, CNS, skeletal, skin, cardiac, GI, urogenital anomalies, increased chromosomal breakage; Fanconi Anemia Type Q; Bone marrow failure for gene: ERCC4
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 DEF6 Ellen McDonagh Source Expert Review Green was added to DEF6.
Added phenotypes DEF6 deficiency; Diseases of Immune Dysregulation; Enteropathy, hepatosplenomegaly, cardiomyopathy, recurrent infections for gene: DEF6
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 DBR1 Ellen McDonagh Source Expert Review Green was added to DBR1.
Added phenotypes DBR1 deficiency; HSE of the brainstem. Other viral infections of the brainstem; Defects in intrinsic and innate immunity for gene: DBR1
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 CLCN7 Ellen McDonagh Source Expert Review Green was added to CLCN7.
Added phenotypes Defects in Intrinsic and Innate Immunity; Osteopetrosis with hypocalcemia, neurologic features for gene: CLCN7
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 C8G Ellen McDonagh Source Expert Review Green was added to C8G.
Added phenotypes Complement Deficiencies; Complement factor 8 defect; Complement component 8 deficiency; Disseminated neisserial infections for gene: C8G
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 C17orf62 Ellen McDonagh Source Expert Review Green was added to C17orf62.
Added phenotypes Autosomal recessive CGD EROS; Congenital defects of phagocyte number or function for gene: C17orf62
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 BRCA2 Ellen McDonagh Source Expert Review Green was added to BRCA2.
Added phenotypes Fanconi anemia, complementation group D1, 605724; Normal to low NK, CNS, skeletal, skin, cardiac, GI, urogenital anomalies, increased chromosomal breakage; Fanconi Anemia Type D1; Bone marrow failure for gene: BRCA2
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 BRCA1 Ellen McDonagh Source Expert Review Green was added to BRCA1.
Added phenotypes Fanconi Anemia Type S; Fanconi anemia, complementation group S, 617883; normal to low NK, CNS, skeletal, skin, cardiac, GI, urogenital anomalies, increased chromosomal breakage; Bone marrow failure for gene: BRCA1
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 ARHGEF1 Ellen McDonagh Source Expert Review Green was added to ARHGEF1.
Added phenotypes Recurrent infections, bronchiectasis; Immunodeficiency 62, 618459; ARHGEF1 deficiency; Predominantly Antibody Deficiencies for gene: ARHGEF1
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 AP3D1 Ellen McDonagh Source Expert Review Green was added to AP3D1.
Added phenotypes neutropenia; Immunodeficient HPS; seizures; Diseases of Immune Dysregulation; Hermansky-Pudlak syndrome with neutropenia; neuordevelopmental delay; albinism; ?Hermansky-Pudlak syndrome 10, 617050; Hermansky-Pudlak syndrome; Oculocutaneous albinism, recurrent infections, seizures, hearing loss and neurodevelopmental delay; Oculocutaneous albinism, severe neutropenia, recurrent infections, seizures, hearing loss and neurodevelopmental delay; HSP10 for gene: AP3D1
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 ALPI Ellen McDonagh Source Expert Review Green was added to ALPI.
Added phenotypes Inflammatory bowel disease; ALPI deficiency; Autoinflammatory Disorders for gene: ALPI
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 TINF2 Ellen McDonagh Source Expert Review Green was added to TINF2.
Added phenotypes microcephaly, neurodevelopmental delay exudative retinopathy; Bone marrow failure, pulmonary and hepatic fibrosis, nail dystrophy, leukoplakia, reticulate skin pigmentation; microcephaly, neurodevelopmental delay for gene: TINF2
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 TERC Ellen McDonagh Source Expert Review Green was added to TERC.
Added phenotypes Dyskeratosis congenita; Bone marrow failure; Bone marrow failure, pulmonary and hepatic fibrosis, nail dystrophy, leukoplakia, reticulate skin pigmentation; Dyskeratosis congenita 1; Intrauterine growth retardation, microcephaly, nail dystrophy, sparse scalp hair and eyelashes, hyperpigmentation of skin, palmar hyperkeratosis, premalignant oral leukoplakia, pancytopenia, myelodysplasia, +/- recurrent infections. A severe phenotype with developmental delay and cerebellar hypoplasia known as Hoyeraal-Hreidarsson Syndrome (HHS) may occur in some DKC patients; Combined immunodeficiencies with associated or syndromic features; Hoyeraal-Hreidarsson syndrome; microcephaly, neurodevelopmental delay for gene: TERC
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 TBX1 Ellen McDonagh Source Expert Review Green was added to TBX1.
Added phenotypes Hypoparathyroidism, conotruncal cardiac malformation, velopalatal insufficiency, abnormal facies, intellectual disability; DiGeorge syndrome 188400; Di George syndrome; T-B+ SCID; Severe combined immunodeficiency (SCID); Combined immunodeficiencies with associated or syndromic features for gene: TBX1
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 SAMD9L Ellen McDonagh Source Expert Review Green was added to SAMD9L.
Added phenotypes Cytopenia, predisposition to MDS with chromosome 7 aberrations, immunodeficiency, and progressive cerebellar dysfunction; Combined immunodeficiencies with associated or syndromic features; MDS, neurological features; Bone marrow failure for gene: SAMD9L
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 SAMD9 Ellen McDonagh Source Expert Review Green was added to SAMD9.
Added phenotypes IUGR with gonadal abnormalities, adrenal failure, MDS with chromosome 7 aberrations, predisposition to infections, enteropathy, absent spleen; MIRAGE syndrome (Myelodysplasia, Infection, Restriction of growth, Adrenal insufficiency, Genital phenotypes, and Enteropathy); ataxia-thrombocytopenia syndrome; Bone marrow failure; Combined immunodeficiencies with associated or syndromic features for gene: SAMD9
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 PTEN Ellen McDonagh Source Expert Review Green was added to PTEN.
Added phenotypes Recurrent infections, Lymphoproliferation, Autoimmunity; Lymphoproliferation, Autoimmunity; developmental delay; Predominantly Antibody Deficiencies for gene: PTEN
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 PSENEN Ellen McDonagh Source Expert Review Green was added to PSENEN.
Added phenotypes Acne inversa, familial, 2, with or without Dowling-Degos disease 613736; Defects in intrinsic and innate immunity; Defects in Intrinsic and Innate Immunity; Hidradenitis suppurativa for gene: PSENEN
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 NCSTN Ellen McDonagh Source Expert Review Green was added to NCSTN.
Added phenotypes Hidradenitis suppurativa with acne, 142690; Defects in intrinsic and innate immunity; familial hydradenitis suppurativa; Defects in Intrinsic and Innate Immunity; Hidradenitis suppurativa with acne for gene: NCSTN
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 IRF3 Ellen McDonagh Source Expert Review Green was added to IRF3.
Added phenotypes {Encephalopathy, acute, infection-induced (herpes-specific), susceptibility to, 7}, 616532; Herpes simplex virus 1 encephalitis; Defects in Intrinsic and Innate Immunity for gene: IRF3
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 IL17F Ellen McDonagh Source Expert Review Green was added to IL17F.
Added phenotypes CMC, folliculitis; Candidiasis, familial, 6, 613956; Defects in Intrinsic and Innate Immunity; Chronic mucocutaneous candidiasis (CMC) for gene: IL17F
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 TERT Ellen McDonagh Source Expert Review Green was added to TERT.
Added phenotypes Bone marrow failure; Bone marrow failure, pulmonary and hepatic fibrosis, nail dystrophy, leukoplakia, reticulate skin pigmentation; microcephaly, neurodevelopmental delay for gene: TERT
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 RAC2 Ellen McDonagh Source Expert Review Green was added to RAC2.
Added phenotypes Reticular dysgenesis; poststreptococcal glomerulonephritis; Congenital defects of phagocyte number or function; Neutrophil immunodeficiency syndrome; RAS-related C3 Bolutinum toxin substrate 2 deficiency (RAC2); T-B+ SCID; Neutrophil immunodeficiency syndrome 608203; Recurrent sinopulmonary infections, selective IgA defiency; urticaria; T-B- SCID; Poor wound healing, leukocytosis for gene: RAC2
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 NLRP1 Ellen McDonagh Source Expert Review Green was added to NLRP1.
Added phenotypes Dyskeratosis, autoimmunity and arthritis; Palmoplantar carcinoma, corneal scarring; Autoinflammation with arthritis and dyskeratosis; Autoinflammatory Disorders for gene: NLRP1
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 CFHR5 Ellen McDonagh Source Expert Review Green was added to CFHR5.
Added phenotypes Atypical hemolytic-uremic syndrome with anti-factor H antibodies; Atypical hemolytic uremic syndrome susceptibility; Nephropathy due to CFHR5 deficiency, 614809; Complement Deficiencies; Older onset atypical hemolytic-uremic syndrome, disseminated neisserial infections for gene: CFHR5
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 CFHR4 Ellen McDonagh Source Expert Review Green was added to CFHR4.
Added phenotypes Complement Deficiencies; Age related macular degeneration; Atypical hemolytic uremic syndrome susceptibility; Older onset atypical hemolytic-uremic syndrome, disseminated neisserial infections for gene: CFHR4
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 CFHR3 Ellen McDonagh Source Expert Review Green was added to CFHR3.
Added phenotypes Complement Deficiencies; Age related macular degeneration; Atypical hemolytic uremic syndrome susceptibility; Older onset atypical hemolytic-uremic syndrome, disseminated neisserial infections for gene: CFHR3
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 CFHR1 Ellen McDonagh Source Expert Review Green was added to CFHR1.
Added phenotypes Complement Deficiencies; Age related macular degeneration; Atypical hemolytic uremic syndrome susceptibility; Older onset atypical hemolytic-uremic syndrome, disseminated neisserial infections for gene: CFHR1
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 CFB Ellen McDonagh Source Expert Review Green was added to CFB.
Added phenotypes Infections with encapsulated organisms; Complement Deficiencies; complement factor B deficiency (AR); Atypical Hemolytic-uremic syndrome; Complement factor B deficiency, 615561; Susceptibility to atypical haemolytic uraemic syndrome 4 (AD) for gene: CFB
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 WDR1 Ellen McDonagh Source Expert Review Green was added to WDR1.
Added phenotypes Mild neutropenia, poor wound healing, severe stomatitis, neutrophil nuclei herniate; Congenital defects of phagocyte number or function for gene: WDR1
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 USP18 Ellen McDonagh Source Expert Review Green was added to USP18.
Added phenotypes Pseudo-TORCH syndrome 2, 617397; Autoinflammatory Disorders; TORCH like syndrome for gene: USP18
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 TNFRSF13C Ellen McDonagh Source Expert Review Green was added to TNFRSF13C.
Added phenotypes Immunodeficiency, common variable, 4; Variable clinical expression; Isolated IgG subclass deficiency; Common variable immunodeficiency disorders (CVID); Predominantly Antibody Deficiencies for gene: TNFRSF13C
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 TNFRSF11A Ellen McDonagh Source Expert Review Green was added to TNFRSF11A.
Added phenotypes Osteopetrosis; Defects in intrinsic and innate immunity; Defects in Intrinsic and Innate Immunity for gene: TNFRSF11A
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 TAPBP Ellen McDonagh Source Expert Review Green was added to TAPBP.
Added phenotypes Bare lymphocyte syndrome, type I 604571; Vasculitis, pyoderma gangrenosum; HLA class I deficiency; Immunodeficiencies affecting cellular and humoral immunity; Vasculitis,pyoderma gangrenosum for gene: TAPBP
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 RHOH Ellen McDonagh Source Expert Review Green was added to RHOH.
Added phenotypes T cell deficiency and various infectious diseases; Combined immunodeficiency; HPV infection, lung granulomas, molluscum contagiosum, lymphoma; Epidermodysplasia verruciformis; Immunodeficiencies affecting cellular and humoral immunity; RhoH deficiency for gene: RHOH
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 POLE Ellen McDonagh Source Expert Review Green was added to POLE.
Added phenotypes Recurrent respiratory infections, meningitis, facial dysmorphism, livido, short stature; Combined immunodeficiencies with associated or syndromic features; FILS syndrome 615139; Facial dysmorphism, immunodeficiency, livedo, and short stature (FILS syndrome) for gene: POLE
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 PMS2 Ellen McDonagh Source Expert Review Green was added to PMS2.
Added phenotypes Recurrent infections, cafe-au-lait spots, lymphoma, colorectal carcinoma, brain tumors; Post-Meiotic Segregation 2 (PMS2) deficiency; Mismatch repair cancer syndrome 276300; Combined immunodeficiencies with associated or syndromic features; CSR defects and Hyper IgM (HIGM) syndromes; Recurrent infections, caf-au-lait spots, lymphoma, colorectal carcinoma, brain tumors for gene: PMS2
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 NOP10 Ellen McDonagh Source Expert Review Green was added to NOP10.
Added phenotypes Dyskeratosis congenita; Hoyeraal-Hreidarsson syndrome; Dyskeratosis congenita 1; Dyskeratosis congenita, autosomal recessive 1 224230; Combined immunodeficiencies with associated or syndromic features; Intrauterine growth retardation, microcephaly, nail dystrophy, sparse scalp hair and eyelashes, hyperpigmentation of skin, palmar hyperkeratosis, premalignant oral leukoplakia, pancytopenia, myelodysplasia, +/- recurrent infections. A severe phenotype with developmental delay and cerebellar hypoplasia known as Hoyeraal-Hreidarsson Syndrome (HHS) may occur in some DKC patients for gene: NOP10
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 IRF7 Ellen McDonagh Added phenotypes Severe influenza; ?Immunodeficiency 39, 616345; Severe influenza disease; IRF7 deficiency; Defects in Intrinsic and Innate Immunity for gene: IRF7
Publications for gene IRF7 were updated from 26761402; 9315633; 32086639; 25814066; 32048120; 26621750 to 26761402; 9315633; 32086639; 25814066; 32048120; 26621750
COVID-19 research v0.40 IL21 Ellen McDonagh Source Expert Review Green was added to IL21.
Added phenotypes Immunodeficiency, common variable, 11, 615767; Severe early onset colitis, recurrent sinopulmonary infections; Immunodeficiencies affecting cellular and humoral immunity for gene: IL21
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 IGKC Ellen McDonagh Source Expert Review Green was added to IGKC.
Added phenotypes Immunoglobulin chain deficiencies; Kappa light chain deficiency, 614102; Asymptomatic; Predominantly Antibody Deficiencies for gene: IGKC
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 FPR1 Ellen McDonagh Source Expert Review Green was added to FPR1.
Added phenotypes Periodontitis only; Congenital defects of phagocyte number or function; Periodontitis; Localized juvenile peridontitis for gene: FPR1
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 FCGR3A Ellen McDonagh Added phenotypes severe herpes viral infections, particularly VZV, Epstein Barr virus (EBV), and (HPV); CD16 deficiency; predisposition to severe viral infection; Immunodeficiency 20, 615707; Autosomal recessive primary immunodeficiency with defective spontaneous NK cell cytotoxicity; Defects in Intrinsic and Innate Immunity; Fc receptor deficiencies for gene: FCGR3A
COVID-19 research v0.40 DNASE1L3 Ellen McDonagh Source Expert Review Green was added to DNASE1L3.
Added phenotypes Systemic lupus erythematosus 16, 614420; Autoinflammatory Disorders; Diseases of Immune Dysregulation; familial early-onset SLE; Systemic lupus erythematosus, lupus nephritis, hypocomplementemic urticarial vasculitis for gene: DNASE1L3
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 CTC1 Ellen McDonagh Source Expert Review Green was added to CTC1.
Added phenotypes Cerebroretinal microangiopathy with calcifications and cysts, 612199; Combined immunodeficiencies with associated or syndromic features; Bone marrow failure; Intrauterine growth retardation, sparse graying hair, dystrophic nails, trilinear bone marrow failure, osteopenia, gastrointestinal hemorrhage due to vascular ectasia, retinal telangiectasia, intracranial calcification, abnormal telomeres for gene: CTC1
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 CR2 Ellen McDonagh Source Expert Review Green was added to CR2.
Added phenotypes Recurrent infections; Lupus; Isolated IgG subclass deficiency; Immunodeficiency, common variable, 7; Common variable immunodeficiency disorders (CVID); hypogammaglobulinaemia; Predominantly Antibody Deficiencies; Immunodeficiency, common variable, 7, 614699 for gene: CR2
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 CFTR Ellen McDonagh Source Expert Review Green was added to CFTR.
Added phenotypes Congenital defects of phagocyte number or function; Respiratory infections, pancreatic insufficiency, elevated sweat chloride; Cystic fibrosis, 219700 for gene: CFTR
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 CD8A Ellen McDonagh Source Expert Review Green was added to CD8A.
Added phenotypes Susceptibility to respiratory infections associated with CD8alpha chain mutation; Immunodeficiencies affecting cellular and humoral immunity; CD8 deficiency familial, 608957; Recurrent infections, may be asymptomatic for gene: CD8A
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 CD81 Ellen McDonagh Source Expert Review Green was added to CD81.
Added phenotypes CD81 deficiency; Isolated IgG subclass deficiency; Recurrent infections, may have glomerulonephritis; Common variable immunodeficiency disorders (CVID); hypogammaglobulinaemia; Predominantly Antibody Deficiencies; Immunodeficiency, common variable 6, 613496 for gene: CD81
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 CD247 Ellen McDonagh Source Expert Review Green was added to CD247.
Added phenotypes ?Immunodeficiency 25; T-B+ severe combined immunodeficiency due to CD3zeta; Immunodeficiency 25, 610163; Atypical Severe Combined Immunodeficiency (Atypical SCID); Nl NK, no g/d T cells; Immunodeficiencies affecting cellular and humoral immunity; T-B+ SCID; Severe combined immunodeficiency (SCID) for gene: CD247
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 BCL10 Ellen McDonagh Source Expert Review Green was added to BCL10.
Added phenotypes Combined immunodeficiency with B cell, T cell, and fibroblast defects; ?Immunodeficiency 37, 616098; Recurrent bacterial and viral infections, candidiasis, gastroenteritis; Immunodeficiencies affecting cellular and humoral immunity for gene: BCL10
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 AP1S3 Ellen McDonagh Source Expert Review Green was added to AP1S3.
Added phenotypes Pustular psoriasis, 616106; Autoinflammatory Disorders; Pustular psoriasis for gene: AP1S3
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 ADAM17 Ellen McDonagh Source Expert Review Green was added to ADAM17.
Added phenotypes IBD-1; ADAM17 deficiency; Inflammatory skin and bowel disease, neonatal, 1; Inflammatory skin and bowel disease, neonatal 1, 614328; Autoinflammatory Disorders; inflammatory skin; Early onset diarrhea and skin lesions for gene: ADAM17
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.39 FBF1 Catherine Snow reviewed gene: FBF1: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
COVID-19 research v0.39 IFNAR1 Sarah Leigh gene: IFNAR1 was added
gene: IFNAR1 was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: IFNAR1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IFNAR1 were set to 31270247; 26676772; 20020050
Phenotypes for gene: IFNAR1 were set to IFNAR1 associated adverse reactions to certain live attenuated viral vaccines
Review for gene: IFNAR1 was set to AMBER
Added comment: Hypothesis from Abdelazeem Elhabyan (Tanta University Hospitals): this gene is involved in the interferon-mediated immune response to viruses of those is SARS Coronavirus (2003) which down-regulates the IFNAR1 receptors through its 3a protein. Additionally, Influenzavirus A suppress immune response by downregulation of this gene. It has been also linked to adverse reactions to measles and yellow fever vaccines in healthy individuals.
Sources: Literature
Hereditary ataxia with onset in adulthood v2.8 RFC1 Zornitza Stark gene: RFC1 was added
gene: RFC1 was added to Hereditary ataxia - adult onset. Sources: Expert Review
Mode of inheritance for gene: RFC1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RFC1 were set to 30926972
Phenotypes for gene: RFC1 were set to Cerebellar ataxia, neuropathy, and vestibular areflexia syndrome OMIM 614575
Mode of pathogenicity for gene: RFC1 was set to Other
Review for gene: RFC1 was set to GREEN
gene: RFC1 was marked as current diagnostic
Added comment: 23 affected individuals from 11 families reported with biallelic AAGGG repeat expansion in intron 2. Expansion carrier frequency of 0.7% in Europeans.
Sources: Expert Review
Long QT syndrome v2.5 KCNE1 Claire Kirk commented on gene: KCNE1
Hereditary neuropathy or pain disorder v1.4 VAPB Zornitza Stark gene: VAPB was added
gene: VAPB was added to Hereditary neuropathy NOT PMP22 copy number. Sources: Expert list
Mode of inheritance for gene: VAPB was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: VAPB were set to 15372378; 32162544; 28993872; 28173107; 26566915
Phenotypes for gene: VAPB were set to Adult proximal spinal muscular atrophy, autosomal dominant; dHMN/dSMA; Spinal muscular atrophy, late-onset, Finkel type, MIM# 182980
Review for gene: VAPB was set to GREEN
Added comment: p.P56S variant found in multiple families from different ethnicities but additional variant also reported; functional data.
Sources: Expert list
Hereditary neuropathy or pain disorder v1.4 UBA1 Zornitza Stark gene: UBA1 was added
gene: UBA1 was added to Hereditary neuropathy NOT PMP22 copy number. Sources: Expert list
Mode of inheritance for gene: UBA1 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Publications for gene: UBA1 were set to 18179898
Phenotypes for gene: UBA1 were set to Spinal muscular atrophy, X-linked 2, infantile MIM#301830
Review for gene: UBA1 was set to GREEN
gene: UBA1 was marked as current diagnostic
Added comment: Five families reported, gene is Green on the Paediatric motor neuropathies panel.
Sources: Expert list
Hereditary neuropathy or pain disorder v1.4 SYT2 Zornitza Stark reviewed gene: SYT2: Rating: AMBER; Mode of pathogenicity: None; Publications: 25192047, 30533528, 26519543; Phenotypes: Myasthenic syndrome, congenital, 7, presynaptic, HMSN; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted; Current diagnostic: yes
Hereditary neuropathy or pain disorder v1.4 SCO2 Zornitza Stark gene: SCO2 was added
gene: SCO2 was added to Hereditary neuropathy NOT PMP22 copy number. Sources: Expert list
Mode of inheritance for gene: SCO2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SCO2 were set to 29351582
Phenotypes for gene: SCO2 were set to axonal Charcot-Marie-Tooth disease
Review for gene: SCO2 was set to AMBER
Added comment: Two unrelated cases with compound heterozygous variants and a CMT phenotype. Cardiomyopathy not present.
Sources: Expert list
COVID-19 research v0.36 NFKBID Ellen McDonagh gene: NFKBID was added
gene: NFKBID was added to Viral susceptibility. Sources: Expert Review Red,Victorian Clinical Genetics Services
Mode of inheritance for gene: NFKBID was set to Unknown
COVID-19 research v0.36 MPI Ellen McDonagh gene: MPI was added
gene: MPI was added to Viral susceptibility. Sources: Expert Review Red,Victorian Clinical Genetics Services
Mode of inheritance for gene: MPI was set to Unknown
COVID-19 research v0.36 MASP1 Ellen McDonagh gene: MASP1 was added
gene: MASP1 was added to Viral susceptibility. Sources: Expert Review Red,ESID Registry 20171117
Mode of inheritance for gene: MASP1 was set to Unknown
Phenotypes for gene: MASP1 were set to Mannan-binding lectin serine protease (MASP) deficiency
COVID-19 research v0.36 IL23A Ellen McDonagh gene: IL23A was added
gene: IL23A was added to Viral susceptibility. Sources: Expert Review Red,ESID Registry 20171117
Mode of inheritance for gene: IL23A was set to Unknown
Phenotypes for gene: IL23A were set to Defects with susceptibility to mycobacterial infection (MSMD)
COVID-19 research v0.36 IL18 Ellen McDonagh gene: IL18 was added
gene: IL18 was added to Viral susceptibility. Sources: Expert Review Red,ESID Registry 20171117
Mode of inheritance for gene: IL18 was set to Unknown
Phenotypes for gene: IL18 were set to Defects with susceptibility to mycobacterial infection (MSMD)
COVID-19 research v0.36 IL17A Ellen McDonagh gene: IL17A was added
gene: IL17A was added to Viral susceptibility. Sources: Expert Review Red,GRID V2.0
Mode of inheritance for gene: IL17A was set to Unknown
Phenotypes for gene: IL17A were set to Arthritis; Immunodeficiency 5
COVID-19 research v0.36 IGHG2 Ellen McDonagh gene: IGHG2 was added
gene: IGHG2 was added to Viral susceptibility. Sources: Expert Review Red,ESID Registry 20171117
Mode of inheritance for gene: IGHG2 was set to Unknown
Phenotypes for gene: IGHG2 were set to Immunoglobulin chain deficiencies
COVID-19 research v0.36 GTF2H5 Ellen McDonagh gene: GTF2H5 was added
gene: GTF2H5 was added to Viral susceptibility. Sources: North West GLH,NHS GMS,London North GLH
Mode of inheritance for gene: GTF2H5 was set to Unknown
COVID-19 research v0.36 FPR3 Ellen McDonagh gene: FPR3 was added
gene: FPR3 was added to Viral susceptibility. Sources: Expert Review Red,ESID Registry 20171117
Mode of inheritance for gene: FPR3 was set to Unknown
Phenotypes for gene: FPR3 were set to Localized juvenile peridontitis
COVID-19 research v0.36 FPR2 Ellen McDonagh gene: FPR2 was added
gene: FPR2 was added to Viral susceptibility. Sources: Expert Review Red,ESID Registry 20171117
Mode of inheritance for gene: FPR2 was set to Unknown
Phenotypes for gene: FPR2 were set to Localized juvenile peridontitis
COVID-19 research v0.36 FCGRT Ellen McDonagh gene: FCGRT was added
gene: FCGRT was added to Viral susceptibility. Sources: Expert Review Red,ESID Registry 20171117
Mode of inheritance for gene: FCGRT was set to Unknown
Phenotypes for gene: FCGRT were set to Fc receptor deficiencies
COVID-19 research v0.36 FCGR2B Ellen McDonagh gene: FCGR2B was added
gene: FCGR2B was added to Viral susceptibility. Sources: Expert Review Red,ESID Registry 20171117
Mode of inheritance for gene: FCGR2B was set to Unknown
Phenotypes for gene: FCGR2B were set to Fc receptor deficiencies
COVID-19 research v0.36 FCGR2A Ellen McDonagh Mode of inheritance for gene FCGR2A was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to Unknown
Added phenotypes Fc receptor deficiencies for gene: FCGR2A
COVID-19 research v0.36 FCGR1A Ellen McDonagh gene: FCGR1A was added
gene: FCGR1A was added to Viral susceptibility. Sources: Expert Review Red,ESID Registry 20171117
Mode of inheritance for gene: FCGR1A was set to Unknown
Phenotypes for gene: FCGR1A were set to Fc receptor deficiencies
COVID-19 research v0.36 FBF1 Ellen McDonagh gene: FBF1 was added
gene: FBF1 was added to Viral susceptibility. Sources: Expert Review Red,Victorian Clinical Genetics Services
Mode of inheritance for gene: FBF1 was set to Unknown
COVID-19 research v0.36 COLEC11 Ellen McDonagh gene: COLEC11 was added
gene: COLEC11 was added to Viral susceptibility. Sources: Expert Review Red,ESID Registry 20171117
Mode of inheritance for gene: COLEC11 was set to Unknown
Phenotypes for gene: COLEC11 were set to Mannan-binding lectin serine protease (MASP) deficiency
COVID-19 research v0.36 CNBP Ellen McDonagh gene: CNBP was added
gene: CNBP was added to Viral susceptibility. Sources: Expert Review Red,ESID Registry 20171117
Mode of inheritance for gene: CNBP was set to Unknown
Phenotypes for gene: CNBP were set to Steinert- myotonica dystrophia
COVID-19 research v0.36 CD4 Ellen McDonagh gene: CD4 was added
gene: CD4 was added to Viral susceptibility. Sources: Expert Review Red,ESID Registry 20171117
Mode of inheritance for gene: CD4 was set to Unknown
Phenotypes for gene: CD4 were set to Selective CD4 cell deficiency
COVID-19 research v0.36 PSMA3 Ellen McDonagh gene: PSMA3 was added
gene: PSMA3 was added to Viral susceptibility. Sources: Victorian Clinical Genetics Services,North West GLH,NHS GMS,London North GLH,Expert Review Amber
Mode of inheritance for gene: PSMA3 was set to Unknown
Publications for gene: PSMA3 were set to 26524591
Phenotypes for gene: PSMA3 were set to CANDLE syndrome (Autoinflammation, lipodystrophy, and dermatosis syndrome)
COVID-19 research v0.36 KDM6A Ellen McDonagh gene: KDM6A was added
gene: KDM6A was added to Viral susceptibility. Sources: Expert Review Red,IUIS Classification February 2018,IUIS Classification December 2019
Mode of inheritance for gene: KDM6A was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)
Publications for gene: KDM6A were set to 25142838; 25546742; 26411453; 32086639; 15887282; 15523604; 32048120
Phenotypes for gene: KDM6A were set to Combined immunodeficiencies with associated or syndromic features; Kabuki Syndrome 2 due to KDM6A deficiency; Typical facial abnormalities, cleft or high arched palate, skeletal abnormalities, short stature, intellectual disability, congenital heart defects, recurrent infections (otitis media, pneumonia) in 50% of patients. Autoimmunity may be present
COVID-19 research v0.36 XIAP Ellen McDonagh gene: XIAP was added
gene: XIAP was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: XIAP was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)
Publications for gene: XIAP were set to 25943627; 21119115; 17080092; 21173700; 22228567
Phenotypes for gene: XIAP were set to Lymphoproliferative syndrome, X-linked, 2 (XLP2); inflammatory bowel disease; 300635; splenomegaly; Diseases of Immune Dysregulation; X-linked lymphoproliferative syndrome (XLP); haemophagocytic lymphohistiocytosis; Lymphoproliferative syndrome, X-linked, 2; EBV infection, Splenomegaly, lymphoproliferation, HLH, Colitis, IBD, hepatitis, Low iNKT cells, hypogammaglobulinemia
COVID-19 research v0.36 CYBB Ellen McDonagh gene: CYBB was added
gene: CYBB was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CYBB was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)
Publications for gene: CYBB were set to 1710153; 2556453; 17293536
Phenotypes for gene: CYBB were set to Chronic granulomatous disease, X-linked, 306400; Defects with susceptibility to mycobacterial infection (MSMD); Congenital defects of phagocyte number or function; Immunodeficiency 34, mycobacteriosis, X-linked, 300645; Chronic granulomatous disease (CGD); Isolated susceptibility to mycobacteria; Infections, autoinflammatory phenotype, IBD, McLeod phenotype in patients with deletions extending into the contiguous Kell locus; Defects in Intrinsic and Innate Immunity
COVID-19 research v0.36 SH3KBP1 Ellen McDonagh gene: SH3KBP1 was added
gene: SH3KBP1 was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: SH3KBP1 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Publications for gene: SH3KBP1 were set to 32086639; 32048120; 29636373
Phenotypes for gene: SH3KBP1 were set to Predominantly Antibody Deficiencies; Severe bacterial infections; SH3KBP1 (CIN85) deficiency; Immunodeficiency 61, 300310
COVID-19 research v0.36 IRAK1 Ellen McDonagh gene: IRAK1 was added
gene: IRAK1 was added to Viral susceptibility. Sources: Expert Review Red,IUIS Classification February 2018,IUIS Classification December 2019
Mode of inheritance for gene: IRAK1 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Publications for gene: IRAK1 were set to 32086639; 32048120; 28069966
Phenotypes for gene: IRAK1 were set to Bacterial infections, X-linked MECP2 deficiency-related syndrome due to a large de novo Xq28 chromosomal deletion encompassing both MECP2 and IRAK1; Defects in Intrinsic and Innate Immunity
COVID-19 research v0.36 WAS Ellen McDonagh gene: WAS was added
gene: WAS was added to Viral susceptibility. Sources: Expert Review Green,Combined B and T cell defect v1.12,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,Congenital neutropaenia v1.22,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: WAS was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Publications for gene: WAS were set to 11242115; 16804117
Phenotypes for gene: WAS were set to Wiskott-Aldrich syndrome (WAS); Combined immunodeficiencies with associated or syndromic features; Neutropenia, myeloid maturation arrest, monocytopenia, variable lymphoid anomalies; Congenital neutropenia; X-linked thrombocytopenia; Congenital defects of phagocyte number or function; X-linked thrombocytopenia with mutations in WASP; Thrombocytopenia with small platelets, recurrent bacterial and viral infections, bloody diarrhea, eczema, lymphoma, autoimmune disease, IgA nephropathy, vasculitis; Neutropenia, severe congenital, X-linked, 300299; XL thrombocytopenia is a mild form of WAS, and XL neutropenia is caused by missense mutations in the GTPase binding domain of WASp; Wiskott-Aldrich syndrome
Mode of pathogenicity for gene: WAS was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
COVID-19 research v0.36 TAZ Ellen McDonagh gene: TAZ was added
gene: TAZ was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,Congenital neutropaenia v1.22,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: TAZ was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Phenotypes for gene: TAZ were set to Barth syndrome; 3-methylglutaconic aciduria, type II, 302060; Congenital defects of phagocyte number or function; Cardiomyopathy, myopathy, growth retardation, neutropenia; Cardioskeletal myopathy with neutropenia and abnormal mitochondria
COVID-19 research v0.36 SH2D1A Ellen McDonagh gene: SH2D1A was added
gene: SH2D1A was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: SH2D1A was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Publications for gene: SH2D1A were set to 10598819; 29670631; 10556288; 11049992; 9774102; 10694488; 9771704
Phenotypes for gene: SH2D1A were set to EBV, HLH, Lymphoproliferation, Aplastic anaemia, Lymphoma. Hypogammaglobulinemia, Absent iNKT cells; Lymphoproliferative syndrome, X-linked, 1 308240; Diseases of Immune Dysregulation; X-linked lymphoproliferative syndrome (XLP); Lymphoproliferative syndrome, X-linked, 1 (XLP1)
COVID-19 research v0.36 POLA1 Ellen McDonagh gene: POLA1 was added
gene: POLA1 was added to Viral susceptibility. Sources: Expert Review Green,North West GLH,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: POLA1 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Publications for gene: POLA1 were set to 27019227
Phenotypes for gene: POLA1 were set to Hyperpigmentation, characteristic facies, lung and GI involvement; Autoinflammatory Disorders; Pigmentary disorder, reticulate, with systemic manifestations, X-linked 301220; X-linked reticulate pigmentary disorder; x-linked cutaneous amyloidosis with systemic features
COVID-19 research v0.36 MSN Ellen McDonagh Added phenotypes Immunodeficiencies affecting cellular and humoral immunity; Recurrent infections with bacteria, varicella, neutropenia; Immunodeficiency 50, 300988; Combined immunodeficiency for gene: MSN
Publications for gene MSN were updated from to 29556235; 27405666
COVID-19 research v0.36 MAGT1 Ellen McDonagh gene: MAGT1 was added
gene: MAGT1 was added to Viral susceptibility. Sources: Expert Review Green,Combined B and T cell defect v1.12,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: MAGT1 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Publications for gene: MAGT1 were set to 21796205; 25504528; 25205404; 24550228; 23846901; 27095930; 23871722; 21983175; 25956530
Phenotypes for gene: MAGT1 were set to Chronic active EBV, lymphoproliferation, combined immunodeficiency, impaired t cell function; Combined immunodeficiency; Immunodeficiency, X-linked, with magnesium defect, Epstein-Barr virus infection and neoplasia; Immunodeficiency, X-linked, with magnesium defect; Diseases of Immune Dysregulation; Epstein-Barr virus infection and neoplasia (XMEN); EBV infection, lymphoma, viral infections, respiratory and GI infections; XMEN syndrome
COVID-19 research v0.36 IL2RG Ellen McDonagh gene: IL2RG was added
gene: IL2RG was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,SCID v1.6,IUIS Classification February 2018
Mode of inheritance for gene: IL2RG was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Phenotypes for gene: IL2RG were set to Severe combined immunodeficiency, X-linked; Combined immunodeficiency, X-linked, moderate; Severe Combined Immune Deficiency; Atypical Severe Combined Immunodeficiency (Atypical SCID); Immunodeficiencies affecting cellular and humoral immunity; SCID; Severe combined immunodeficiency, X-linked, 300400; T-B+ SCID; SCID (x-linked); Omenn syndrome; Severe combined immunodeficiency (SCID); Low NK
COVID-19 research v0.36 IKBKG Ellen McDonagh gene: IKBKG was added
gene: IKBKG was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: IKBKG was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Publications for gene: IKBKG were set to 11047757
Phenotypes for gene: IKBKG were set to Ectodermal, dysplasia, anhidrotic, lymphedema and immunodeficiency, 300301; Immunodeficiency 33, 300636; Invasive pneumococcal disease, recurrent isolated, 2,300640; Defects of TLR/NFkappa-B signalling; Anhidrotic ectodermal dysplasia (in some), various infections (bacteria, mycobacteria, viruses and fungi), colitis, conical teeth, variable defects of skin, hair and teeth, monocyte dysfunction; Ectodermal dysplasia, hypohidrotic, with immune deficiency 300291; Combined immunodeficiencies with associated or syndromic features; Immunodeficiency, isolated, 300584
COVID-19 research v0.36 GATA1 Ellen McDonagh gene: GATA1 was added
gene: GATA1 was added to Viral susceptibility. Sources: Expert Review Green,North West GLH,Congenital neutropaenia v1.22,NHS GMS,London North GLH
Mode of inheritance for gene: GATA1 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Publications for gene: GATA1 were set to 16783379; 22706301
Phenotypes for gene: GATA1 were set to neutropenia; dyserythropoietic anaemia; thrombocytopenia; Anemia, X-linked, with/without neutropenia and/or platelet abnormalities, 300835
COVID-19 research v0.36 G6PD Ellen McDonagh Mode of inheritance for gene G6PD was changed from X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Added phenotypes Infections; haemolytic anaemia; Congenital defects of phagocyte number or function; chronic granulomatous disease-like susceptibility to infection; Glucose-6-phosphate dehydrogenase deficiency (G6PD) for gene: G6PD
Publications for gene G6PD were updated from 26694452; 18269318; 27458052; 27914961 to 18269318; 3681550; 26694452; 12130518; 27914961; 27458052
COVID-19 research v0.36 FOXP3 Ellen McDonagh gene: FOXP3 was added
gene: FOXP3 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: FOXP3 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Publications for gene: FOXP3 were set to 17635943; 11120765; 11295725; 16741580; 14671208
Phenotypes for gene: FOXP3 were set to FOXP3 deficiency (IPEX); Immune dysregulation polyendocrinopathy enteropathy X-linked syndrome; Diseases of Immune Dysregulation; Immunodysregulation, polyendocrinopathy, and enteropathy, X-linked, 304790; IPEX; Autoimmune enteropathy, early onset diabetes, hyroiditis hemolytic anemia, thrombocytopenia, eczema, elevated IgE, IgA
COVID-19 research v0.36 DKC1 Ellen McDonagh gene: DKC1 was added
gene: DKC1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: DKC1 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Publications for gene: DKC1 were set to 9590285; 10583221; 10217077; 9590276
Phenotypes for gene: DKC1 were set to Dyskeratosis congenita, X-linked 305000; Severe phenotype with DD and cerebellar hypoplasia; Hoyeraal-Hreidarsson Syndrome (HHS) may occur in some DKC patients; Combined immunodeficiencies with associated or syndromic features; Hoyeraal-Hreidarsson syndrome; Intrauterine growth retardation, microcephaly, nail dystrophy, sparse scalp hair and eyelashes, hyperpigmentation of skin, palmar hyperkeratosis, premalignant oral leukoplakia, pancytopenia, myelodysplasia, recurrent infections
COVID-19 research v0.36 CFP Ellen McDonagh gene: CFP was added
gene: CFP was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CFP was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Publications for gene: CFP were set to 22229731; 10909851; 8530058; 7151327; 6903190
Phenotypes for gene: CFP were set to Neisserial infections; Complement Deficiencies; Properdin deficiency; Properdin P factor complement deficiency (PFC)
COVID-19 research v0.36 CD40LG Ellen McDonagh gene: CD40LG was added
gene: CD40LG was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CD40LG was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Publications for gene: CD40LG were set to 7678782; 7586644; 11875495; 20301576; 7882172; 17146684; 8094231; 7679206; 7679801
Phenotypes for gene: CD40LG were set to Hyper-IGM immunodeficiency, X-linked; HIGM; Hyper-IGM syndrome; Hyper-IgM syndrome type 1; Neutropenia, thrombocytopenia, hemolytic anemia, opportunistic infections, biliary tract and liver disease, Cryptosporidium infections; XHIM; Immunodeficiency, X-linked, with hyper-IgM; Immunodeficiencies affecting cellular and humoral immunity; Hyper-IgM syndrome due to CD40 ligand deficiency; Hyper-IgM syndrome due to CD40L deficiency; IHIS; HIGM1; IMD3; CSR defects and Hyper IgM (HIGM) syndromes; Immunodeficiency 3; CD40 ligand deficiency
COVID-19 research v0.36 BTK Ellen McDonagh gene: BTK was added
gene: BTK was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,A- or hypo-gammaglobulinaemia v1.25,IUIS Classification February 2018
Mode of inheritance for gene: BTK was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Publications for gene: BTK were set to 20301626
Phenotypes for gene: BTK were set to Agammaglobulinemia, X-linked 1, 300755; Agammaglobulinemia, X-linked; Agammaglobulinemia, X-linked 1 (XLA); Agammaglobulinemia; Severe bacterial infections, normal numbers of pro-B cells; agammaglobulinaemia; Agammaglobulinemia and isolated hormone deficiency, 307200; Agammaglobulinemia and isolated hormone deficiency; Predominantly Antibody Deficiencies; CVID
COVID-19 research v0.36 ATP6AP1 Ellen McDonagh gene: ATP6AP1 was added
gene: ATP6AP1 was added to Viral susceptibility. Sources: Expert Review Green,North West GLH,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: ATP6AP1 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Publications for gene: ATP6AP1 were set to 27231034
Phenotypes for gene: ATP6AP1 were set to Immunodeficiency and hepatopathy with or without neurologic features; Hepatopathy, leukopenia, low copper; Predominantly Antibody Deficiencies; Immunodeficiency 47, 300972
COVID-19 research v0.36 STAT5A Ellen McDonagh gene: STAT5A was added
gene: STAT5A was added to Viral susceptibility. Sources: Expert Review Red,ESID Registry 20171117,GOSH PID v.8.0
Mode of inheritance for gene: STAT5A was set to Unknown
Publications for gene: STAT5A were set to 16418296
Phenotypes for gene: STAT5A were set to Defects with susceptibility to mycobacterial infection (MSMD); Combined immunodeficiency
COVID-19 research v0.36 SART3 Ellen McDonagh gene: SART3 was added
gene: SART3 was added to Viral susceptibility. Sources: Expert Review Red,GRID V2.0
Mode of inheritance for gene: SART3 was set to Unknown
Phenotypes for gene: SART3 were set to Porokeratosis
COVID-19 research v0.36 ITGAM Ellen McDonagh gene: ITGAM was added
gene: ITGAM was added to Viral susceptibility. Sources: Expert Review Red,Victorian Clinical Genetics Services,GRID V2.0
Mode of inheritance for gene: ITGAM was set to Unknown
Phenotypes for gene: ITGAM were set to Systemic lupus erythematous
COVID-19 research v0.36 FCGR3B Ellen McDonagh gene: FCGR3B was added
gene: FCGR3B was added to Viral susceptibility. Sources: Expert Review Red,ESID Registry 20171117,GRID V2.0,Congenital neutropaenia v1.22
Mode of inheritance for gene: FCGR3B was set to Unknown
Publications for gene: FCGR3B were set to 1978690
Phenotypes for gene: FCGR3B were set to Neutropenia,alloimmuneneonatal; Neutropenia, autoimmune neonatal; Neutropenia, alloimmune neonatal; Fc receptor deficiencies
COVID-19 research v0.36 ERCC2 Ellen McDonagh gene: ERCC2 was added
gene: ERCC2 was added to Viral susceptibility. Sources: Victorian Clinical Genetics Services,North West GLH,Other,NHS GMS,London North GLH,Expert Review Red
Mode of inheritance for gene: ERCC2 was set to Unknown
Publications for gene: ERCC2 were set to 11737070
Phenotypes for gene: ERCC2 were set to Combined immunodeficiency (CID) in a child affected by trichothiodystrophy (TTD); CD4 + lymphopenia
COVID-19 research v0.36 ELF4 Ellen McDonagh gene: ELF4 was added
gene: ELF4 was added to Viral susceptibility. Sources: Expert Review Red,A- or hypo-gammaglobulinaemia v1.25
Mode of inheritance for gene: ELF4 was set to Unknown
Publications for gene: ELF4 were set to 16264330
Phenotypes for gene: ELF4 were set to X-linked hypogammaglobulinemia with isolated growth hormone deficiency
COVID-19 research v0.36 KRAS Ellen McDonagh gene: KRAS was added
gene: KRAS was added to Viral susceptibility. Sources: GRID V2.0,ESID Registry 20171117,Expert Review Amber
Mode of inheritance for gene: KRAS was set to Unknown
Publications for gene: KRAS were set to 21079152; 21063026
Phenotypes for gene: KRAS were set to RAS associated lymphoproliferative disease, 614470; RALD
Mode of pathogenicity for gene: KRAS was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
COVID-19 research v0.36 NRAS Ellen McDonagh gene: NRAS was added
gene: NRAS was added to Viral susceptibility. Sources: ESID Registry 20171117,North West GLH,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,Expert Review Amber
Mode of inheritance for gene: NRAS was set to Unknown
Publications for gene: NRAS were set to 21079152; 5896945; 17517660; 29141318
Phenotypes for gene: NRAS were set to Ras associated lymphoproliferative disease (RALD); Autoimmune lymphoproliferative syndrome type IV; RAS-associated autoimmune lymphoproliferative syndrome type IV, somatic 614470
COVID-19 research v0.36 LRRC8A Ellen McDonagh gene: LRRC8A was added
gene: LRRC8A was added to Viral susceptibility. Sources: Expert Review Red,ESID Registry 20171117,A- or hypo-gammaglobulinaemia v1.25
Mode of inheritance for gene: LRRC8A was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Phenotypes for gene: LRRC8A were set to Agammaglobulinemia 5, 613506; Agammaglobulinemia
COVID-19 research v0.36 STAT3 Ellen McDonagh gene: STAT3 was added
gene: STAT3 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: STAT3 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: STAT3 were set to 17676033; 17881745; 25038750; 25359994
Phenotypes for gene: STAT3 were set to Hyper-IgE recurrent infection syndrome 147060; Hyper IgE syndrome (HIES); Diseases of Immune Dysregulation; Early-onset multi-organ autoimmune disease; Autoimmune disease, multisystem, infantile-onset, 1 615952; Combined immunodeficiencies with associated or syndromic features; Autoimmune disease, multisystem, infantile-onset
Mode of pathogenicity for gene: STAT3 was set to Other - please provide details in the comments
COVID-19 research v0.36 POMP Ellen McDonagh gene: POMP was added
gene: POMP was added to Viral susceptibility. Sources: North West GLH,Expert Review Green,NHS GMS,London North GLH
Mode of inheritance for gene: POMP was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: POMP were set to 29805043; 26524591
Phenotypes for gene: POMP were set to Proteasome-associated autoinflammatory syndrome 2, 618048; CANDLE syndrome (Autoinflammation, lipodystrophy, and dermatosis syndrome); combined immunodeficiency with autoinflammation
COVID-19 research v0.36 PIK3CD Ellen McDonagh gene: PIK3CD was added
gene: PIK3CD was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,A- or hypo-gammaglobulinaemia v1.25,IUIS Classification February 2018
Mode of inheritance for gene: PIK3CD was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: PIK3CD were set to 24165795; 24136356; 29226301
Phenotypes for gene: PIK3CD were set to Combined immunodeficiency; Activated PI3K-delta syndrome (APDS); Unclassified antibody deficiency; decreased or absent pro-B cells, EBV; Predominantly Antibody Deficiencies; sinopulmonary infections, dysgammaglobulinaemia, lymphadenopathy, nodular lymphoid hyperplasia and herpesviremia; Severe bacterial infections; Immunodeficiency 14,615513
Mode of pathogenicity for gene: PIK3CD was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
COVID-19 research v0.36 IKZF1 Ellen McDonagh gene: IKZF1 was added
gene: IKZF1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,A- or hypo-gammaglobulinaemia v1.25,IUIS Classification February 2018
Mode of inheritance for gene: IKZF1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: IKZF1 were set to 29889099; 21548011; 26981933
Phenotypes for gene: IKZF1 were set to Immunodeficiency, common variable, 13, 616873; IKAROS deficiency; Immunodeficiency, common variable 13; Predominantly Antibody Deficiencies; Recurrent sinopulmonary infections
COVID-19 research v0.36 GFI1 Ellen McDonagh gene: GFI1 was added
gene: GFI1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,Congenital neutropaenia v1.22,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: GFI1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Phenotypes for gene: GFI1 were set to Neutropenia, severe congenital 2; Congenital neutropenia; Severe congenital 2, autosomal dominant, 613107; Congenital defects of phagocyte number or function; Neutropenia, nonimmune chronic idiopathic, of adults, 607847; Severe congenital neutropenia; B/T lymphopenia; Chronic non-immune neutropenia of adults
COVID-19 research v0.36 F12 Ellen McDonagh gene: F12 was added
gene: F12 was added to Viral susceptibility. Sources: Expert Review Green,Victorian Clinical Genetics Services,North West GLH,GRID V2.0,NHS GMS,London North GLH
Mode of inheritance for gene: F12 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: F12 were set to 17186468; 16638441; 19178938
Phenotypes for gene: F12 were set to hereditary angioedema; Angioedema, Hereditary, Type III
Mode of pathogenicity for gene: F12 was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
COVID-19 research v0.36 CTLA4 Ellen McDonagh gene: CTLA4 was added
gene: CTLA4 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,A- or hypo-gammaglobulinaemia v1.25,IUIS Classification February 2018
Mode of inheritance for gene: CTLA4 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: CTLA4 were set to 25213377; 25329329
Phenotypes for gene: CTLA4 were set to Autoimmune lymphoproliferative syndrome, type V; interstitual lung disease; autoimmunity; lymphadenopathy; T cell lymphopenia; Combined immunodeficiency; Immune dysregulation; a broad range of autoimmune phenomena have been described along with polyclonal lymphocytic infiltrates. Susceptibility to infection and hypogammaglobulinaemia are not usually present in isolation; Diseases of Immune Dysregulation; Early-onset multi-organ autoimmune disease; Autoimmune lymphoproliferative syndrome, type V 616100; hypogammaglobulinaemia; enteropathy; Autoimmune cytopenias, enteropathy, interstitial lung disease, extra-lymphoid lymphocytic infiltration recurrent infections; CVID
COVID-19 research v0.36 CARD14 Ellen McDonagh gene: CARD14 was added
gene: CARD14 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CARD14 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: CARD14 were set to 23648549; 23067081; 22703878; 29689250; 29980436; 29704870; 23711932; 22521418; 30248356
Phenotypes for gene: CARD14 were set to Other autoinflammatory diseases with known genetic defect; Psoriasis 2, 602723; Autoinflammatory Disorders; Pityriasis rubra pilaris,173200; immune dysregulation; CARD14 mediated psoriasis; Psoriasis
COVID-19 research v0.36 ISCA-37446-Loss Ellen McDonagh Region: ISCA-37446-Loss was added
Region: ISCA-37446-Loss was added to Viral susceptibility. Sources: Expert Review Green,ClinGen
Mode of inheritance for Region: ISCA-37446-Loss was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes for Region: ISCA-37446-Loss were set to 188400; clefting; Velocardiofacial syndrome; neonatal hypocalcemia, which may present as tetany or seizures, due to hypoplasia of the parathyroid glands, and susceptibility to infection due to a deficit of T cells; cardiac malformations; Hearing deficits; DiGeorge syndrome; micrognathia
COVID-19 research v0.36 ISCA-37433-Loss Ellen McDonagh Region: ISCA-37433-Loss was added
Region: ISCA-37433-Loss was added to Viral susceptibility. Sources: Expert Review Green,ClinGen
Mode of inheritance for Region: ISCA-37433-Loss was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for Region: ISCA-37433-Loss were set to 20301696; 15889418; 15545748
Phenotypes for Region: ISCA-37433-Loss were set to diaphragmatic hernia; facial dysmorphic features, high frequency of cardiac defects, including conotruncal defects, prematurity, growth restriction, microcephaly, and mild developmental delay; 192430; 188400; 22q11.2 deletion syndrome; renal anomalies; cleft palate, polydactyly; congenital heart disease; Learning difficulties; Velocardiofacial syndrome; polyhydramnios; DiGeorge syndrome; immune deficiency
COVID-19 research v0.36 UNC119 Ellen McDonagh gene: UNC119 was added
gene: UNC119 was added to Viral susceptibility. Sources: Expert Review Red,ESID Registry 20171117,GRID V2.0
Mode of inheritance for gene: UNC119 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: UNC119 were set to 22184408
Phenotypes for gene: UNC119 were set to Immunodeficiency 13 615518; Combined immunodeficiency; Immunodeficiency 13/ UNC119 deficiency
COVID-19 research v0.36 TRAF3 Ellen McDonagh Mode of inheritance for gene TRAF3 was changed from Unknown to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Added phenotypes Herpetic encephalitis (HSE); Herpes simplex virus 1 encephalitis; Defects in Intrinsic and Innate Immunity; Defects in intrinsic and innate immunity; {?Encephalopathy, acute, infection-induced (herpes-specific), susceptibility to, 5},614849; Herpes simplex encephalitis, susceptibility to, 3 for gene: TRAF3
Publications for gene TRAF3 were updated from to 24378539; 20832341; 32086639; 32048120; 11296228
COVID-19 research v0.36 TOP2B Ellen McDonagh gene: TOP2B was added
gene: TOP2B was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: TOP2B was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: TOP2B were set to 31409799; 32086639; 32048120
Phenotypes for gene: TOP2B were set to Recurrent infections, facial dysmorphism, limb anomalies; Hoffman syndrome/TOP2B deficiency; Predominantly Antibody Deficiencies
COVID-19 research v0.36 TNFSF12 Ellen McDonagh gene: TNFSF12 was added
gene: TNFSF12 was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,Expert Review Red,IUIS Classification February 2018
Mode of inheritance for gene: TNFSF12 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: TNFSF12 were set to 23493554; 32086639; 32048120
Phenotypes for gene: TNFSF12 were set to Immunodeficiency, common variable with lack of anti-pneumococcal antibody; Common variable immunodeficiency disorders (CVID); Predominantly Antibody Deficiencies; Pneumonia, bacterial infections, warts, thrombocytopenia. neutropenia; Pneumonia, bacterial infections, warts, thrombocytopenia
COVID-19 research v0.36 THBD Ellen McDonagh gene: THBD was added
gene: THBD was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,Expert Review Red,IUIS Classification February 2018
Mode of inheritance for gene: THBD was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: THBD were set to 32086639; 32048120
Phenotypes for gene: THBD were set to Complement Deficiencies; Thrombomodulin deficiency; Hemolytic uremic syndrome, atypical, susceptibility to, 6; Atypical hemolytic-uremic syndrome
COVID-19 research v0.36 TGFBR2 Ellen McDonagh gene: TGFBR2 was added
gene: TGFBR2 was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: TGFBR2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: TGFBR2 were set to 32086639; 32048120; 29392890
Phenotypes for gene: TGFBR2 were set to Recurrent respiratory infections, eczema, food allergies, hyperextensible joints, scoliosis, retention of primary teeths, aortic anuerysms; Combined immunodeficiencies with associated or syndromic features; ALPS-FAS
COVID-19 research v0.36 TGFBR1 Ellen McDonagh gene: TGFBR1 was added
gene: TGFBR1 was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: TGFBR1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: TGFBR1 were set to 32086639; 32048120; 29392890
Phenotypes for gene: TGFBR1 were set to Loeys-Dietz syndrome 1, 609192; Loeys Dietz syndrome due to TGFBR1 deficiency; Combined immunodeficiencies with associated or syndromic features; Recurrent respiratory infectons, eczema, food allergies, hyperextensible joints, scoliosis, retention of primary teeths, aortic anuerysms
COVID-19 research v0.36 SRP54 Ellen McDonagh gene: SRP54 was added
gene: SRP54 was added to Viral susceptibility. Sources: IUIS Classification February 2018,IUIS Classification December 2019
Mode of inheritance for gene: SRP54 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: SRP54 were set to 32086639; 28972538; 29914977; 32048120
Phenotypes for gene: SRP54 were set to Schwachman Diamond features; Congenital defects of phagocyte number or function
COVID-19 research v0.36 SNORA31 Ellen McDonagh gene: SNORA31 was added
gene: SNORA31 was added to Viral susceptibility. Sources: Expert Review Red,Literature
Mode of inheritance for gene: SNORA31 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: SNORA31 were set to 31806906
Phenotypes for gene: SNORA31 were set to Herpes simplex encephalitis
COVID-19 research v0.36 SH3BP2 Ellen McDonagh gene: SH3BP2 was added
gene: SH3BP2 was added to Viral susceptibility. Sources: ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification December 2019,Expert Review Red,IUIS Classification February 2018
Mode of inheritance for gene: SH3BP2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: SH3BP2 were set to 22640988; 28914985; 29669173; 11381256; 32086639; 32048120
Phenotypes for gene: SH3BP2 were set to Other autoinflammatory diseases with known genetic defect; Autoinflammatory Disorders; Cherubism 118400; Bone degeneration in jaws
COVID-19 research v0.36 SEMA3E Ellen McDonagh gene: SEMA3E was added
gene: SEMA3E was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,Expert Review Red,IUIS Classification February 2018
Mode of inheritance for gene: SEMA3E was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: SEMA3E were set to 21055784; 32086639; 1735828; 12144540; 32048120
Phenotypes for gene: SEMA3E were set to CHARGE syndrome; immune-mediated cerebellar ataxia; Coloboma, heart anomaly, choanal atresia, intellectual retardation, genital and ear anomalies, CNS malformation, some are SCID-like and have low TRECs; Charge syndrome 214800; Combined immunodeficiencies with associated or syndromic features
COVID-19 research v0.36 SEC61A1 Ellen McDonagh gene: SEC61A1 was added
gene: SEC61A1 was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: SEC61A1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: SEC61A1 were set to 28782633; 32086639; 32048120
Phenotypes for gene: SEC61A1 were set to Severe recurrent respiratory tract infections; Predominantly Antibody Deficiencies; Hyperuricemic nephropathy, familial juvenile, 4, 617056; SEC61A1 deficiency
COVID-19 research v0.36 SAMD3 Ellen McDonagh gene: SAMD3 was added
gene: SAMD3 was added to Viral susceptibility. Sources: Expert Review Red,NHS GMS,London North GLH
Mode of inheritance for gene: SAMD3 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes for gene: SAMD3 were set to HLH, abnormal GRA
COVID-19 research v0.36 RET Ellen McDonagh gene: RET was added
gene: RET was added to Viral susceptibility. Sources: North West GLH,NHS GMS,GOSH PID v.8.0,London North GLH,Expert Review Red
Mode of inheritance for gene: RET was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: RET were set to 12086152; 9497256
Phenotypes for gene: RET were set to Central hypoventilation syndrome, congenital 209880
COVID-19 research v0.36 RELA Ellen McDonagh gene: RELA was added
gene: RELA was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: RELA was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: RELA were set to 28600438; 32086639; 32048120; 29305315
Phenotypes for gene: RELA were set to RelA haplosufficiency; Mucosal ulceration, impaired NFkB activation; Mucocutaneous ulceration, chronic, 618287; Immunodeficiencies affecting cellular and humoral immunity
COVID-19 research v0.36 RANBP2 Ellen McDonagh gene: RANBP2 was added
gene: RANBP2 was added to Viral susceptibility. Sources: North West GLH,NHS GMS,London North GLH,IUIS Classification December 2019,IUIS Classification February 2018
Mode of inheritance for gene: RANBP2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: RANBP2 were set to 32086639; 32048120
Phenotypes for gene: RANBP2 were set to Fever induces acute encephalopathy; Defects in intrinsic and innate immunity; Defects in Intrinsic and Innate Immunity
COVID-19 research v0.36 PTPN22 Ellen McDonagh gene: PTPN22 was added
gene: PTPN22 was added to Viral susceptibility. Sources: North West GLH,Expert Review Red,NHS GMS,London North GLH
Mode of inheritance for gene: PTPN22 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes for gene: PTPN22 were set to Lupus susceptibility; {Systemic lupus erythematosus susceptibility to}
COVID-19 research v0.36 PSEN1 Ellen McDonagh gene: PSEN1 was added
gene: PSEN1 was added to Viral susceptibility. Sources: Expert Review Red,IUIS Classification February 2018
Mode of inheritance for gene: PSEN1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: PSEN1 were set to 20929727
Phenotypes for gene: PSEN1 were set to Hidradenitis suppurative with cutaneous hyperpigmentation; Acne inversa, familial, 3 613737; Defects in Intrinsic and Innate Immunity
COVID-19 research v0.36 OAS1 Ellen McDonagh gene: OAS1 was added
gene: OAS1 was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: OAS1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: OAS1 were set to 32086639; 29455859; 32048120
Phenotypes for gene: OAS1 were set to OAS1 GOF; Autoinflammatory Disorders; Pulmonary alveolar proteinosis, skin rash
COVID-19 research v0.36 NFE2L2 Ellen McDonagh gene: NFE2L2 was added
gene: NFE2L2 was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: NFE2L2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: NFE2L2 were set to 32086639; 32048120; 29018201
Phenotypes for gene: NFE2L2 were set to Recurrent respiratory and skin infections, growth retardation, , developmental delay; increased expression of stress response genes; Immunodeficiency, developmental delay, and hypohomocysteinemia, 617744; white matter cerebral lesions, increased level of homocysteine; Combined immunodeficiencies with associated or syndromic features; NFE2L2 GOF
COVID-19 research v0.36 NFAT5 Ellen McDonagh gene: NFAT5 was added
gene: NFAT5 was added to Viral susceptibility. Sources: Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,Expert Review Red,IUIS Classification February 2018
Mode of inheritance for gene: NFAT5 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: NFAT5 were set to 32086639; 32048120
Phenotypes for gene: NFAT5 were set to NFAT5 haploinsufficieny; IBD, recurrent sinopulmonary infections; Diseases of Immune Dysregulation
COVID-19 research v0.36 LYZ Ellen McDonagh gene: LYZ was added
gene: LYZ was added to Viral susceptibility. Sources: Expert Review Red,NHS GMS,London North GLH
Mode of inheritance for gene: LYZ was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes for gene: LYZ were set to Amyloidosis, renal, 105200
COVID-19 research v0.36 KMT2D Ellen McDonagh gene: KMT2D was added
gene: KMT2D was added to Viral susceptibility. Sources: Expert Review Red,IUIS Classification February 2018,IUIS Classification December 2019
Mode of inheritance for gene: KMT2D was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: KMT2D were set to 25142838; 26411453; 32086639; 15887282; 15523604; 32048120
Phenotypes for gene: KMT2D were set to Kabuki syndrome 1, 147920; Combined immunodeficiencies with associated or syndromic features; Typical facial abnormalities, cleft or high arched palate, skeletal abnormalities, short stature, intellectual disability, congenital heart defects, recurrent infections (otitis media, pneumonia) in 50% of patients. Autoimmunity may be present
COVID-19 research v0.36 KMT2A Ellen McDonagh gene: KMT2A was added
gene: KMT2A was added to Viral susceptibility. Sources: Expert Review Red,ESID Registry 20171117,IUIS Classification December 2019
Mode of inheritance for gene: KMT2A was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: KMT2A were set to 32086639; 32048120; 27320412
Phenotypes for gene: KMT2A were set to Wiedemann-Steiner syndrome with Congenital immunodeficiency; Combined immunodeficiencies with associated or syndromic features; Unclassified antibody deficiency; Respiratory infections, short stature, hypertelorism, hairy elbows, developmental delay, intellectual disability
COVID-19 research v0.36 JAK1 Ellen McDonagh gene: JAK1 was added
gene: JAK1 was added to Viral susceptibility. Sources: Expert Review Red,IUIS Classification February 2018,IUIS Classification December 2019
Mode of inheritance for gene: JAK1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: JAK1 were set to 28111307; 32086639; 32048120
Phenotypes for gene: JAK1 were set to Hypereosinophilic syndrome; HSM, eosinophilia, eosinophilic enteritis, thyroid disease, poor growth, viral infections; Diseases of Immune Dysregulation; Susceptibility to mycobacteria and viruses, urothelial carcinoma; Defects in Intrinsic and Innate Immunity; HSM, eosinophilic enteritis, thyroid disease, poor growth, viral infections
Mode of pathogenicity for gene: JAK1 was set to Other - please provide details in the comments
COVID-19 research v0.36 IRF2BP2 Ellen McDonagh gene: IRF2BP2 was added
gene: IRF2BP2 was added to Viral susceptibility. Sources: Expert Review Red,IUIS Classification February 2018,IUIS Classification December 2019
Mode of inheritance for gene: IRF2BP2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: IRF2BP2 were set to 27016798; 32086639; 32048120
Phenotypes for gene: IRF2BP2 were set to Recurrent infections, possible autoimmunity and inflammatory disease; Predominantly Antibody Deficiencies; CVID
COVID-19 research v0.36 IL31RA Ellen McDonagh gene: IL31RA was added
gene: IL31RA was added to Viral susceptibility. Sources: Expert Review Red,NHS GMS,London North GLH
Mode of inheritance for gene: IL31RA was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes for gene: IL31RA were set to ?Amyloidosis, primary localized cutaneous 2, 613955
COVID-19 research v0.36 ERBIN Ellen McDonagh gene: ERBIN was added
gene: ERBIN was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: ERBIN was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: ERBIN were set to 28126831; 32086639; 32048120
Phenotypes for gene: ERBIN were set to ERBIN deficiency; Combined immunodeficiencies with associated or syndromic features; Recurrent respiratory infections, susceptibility to S. aureus, eczema, hyperextensible joints, scoliosis, arterial dilatation in some
COVID-19 research v0.36 BCL11B Ellen McDonagh gene: BCL11B was added
gene: BCL11B was added to Viral susceptibility. Sources: Expert Review Red,IUIS Classification February 2018,IUIS Classification December 2019
Mode of inheritance for gene: BCL11B was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: BCL11B were set to 29296816; 32086639; 32048120; 27959755
Phenotypes for gene: BCL11B were set to Combined immunodeficiencies with associated or syndromic features; leaky SCID; ?Immunodeficiency 49, 617237; Immunodeficiencies affecting cellular and humoral immunity; Congenital abnormalities, neonatal teeth, dysmorphic facies, absent corpus callosum, neurocognitive deficits
COVID-19 research v0.36 APOL1 Ellen McDonagh gene: APOL1 was added
gene: APOL1 was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,Expert Review Red,IUIS Classification February 2018
Mode of inheritance for gene: APOL1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: APOL1 were set to 16720107; 15894515; 25100047; 28827791; 32086639; 29470556; 29077717; 32048120; 28537557
Phenotypes for gene: APOL1 were set to Defects in Intrinsic and Innate Immunity; Trypanosomiasis, susceptibility to; Trypanosomias; Trypanosomiasis
COVID-19 research v0.36 ACTB Ellen McDonagh gene: ACTB was added
gene: ACTB was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,Expert Review Red,IUIS Classification February 2018
Mode of inheritance for gene: ACTB was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: ACTB were set to 32086639; 32048120; 10411937
Phenotypes for gene: ACTB were set to Congenital defects of phagocyte number or function; neutrophil dysfunction; Mental retardation, short stature; Actin beta deficiency (ACTB); Phagocytic disorder; Poor neutrophil chemotaxis, oxidative burst and actin remodeling. Thrombocytopenia; Baraitser-Winter syndrome 1, 243310
COVID-19 research v0.36 TINF2 Ellen McDonagh gene: TINF2 was added
gene: TINF2 was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: TINF2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: TINF2 were set to 18252230; 21199492; 21477109; 18979121; 27033759; 18669893; 29742735
Phenotypes for gene: TINF2 were set to microcephaly, neurodevelopmental delay exudative retinopathy; Bone marrow failure, pulmonary and hepatic fibrosis, nail dystrophy, leukoplakia, reticulate skin pigmentation; microcephaly, neurodevelopmental delay
COVID-19 research v0.36 TERC Ellen McDonagh gene: TERC was added
gene: TERC was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: TERC was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: TERC were set to 16332973; 32086639; 12525685; 32048120; 11574891
Phenotypes for gene: TERC were set to Dyskeratosis congenita; Bone marrow failure; Bone marrow failure, pulmonary and hepatic fibrosis, nail dystrophy, leukoplakia, reticulate skin pigmentation; Dyskeratosis congenita 1; Intrauterine growth retardation, microcephaly, nail dystrophy, sparse scalp hair and eyelashes, hyperpigmentation of skin, palmar hyperkeratosis, premalignant oral leukoplakia, pancytopenia, myelodysplasia, +/- recurrent infections. A severe phenotype with developmental delay and cerebellar hypoplasia known as Hoyeraal-Hreidarsson Syndrome (HHS) may occur in some DKC patients; Combined immunodeficiencies with associated or syndromic features; Hoyeraal-Hreidarsson syndrome; microcephaly, neurodevelopmental delay
COVID-19 research v0.36 TBX1 Ellen McDonagh gene: TBX1 was added
gene: TBX1 was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,SCID v1.6,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: TBX1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: TBX1 were set to 11242110; 24198816; 14585638; 32086639; 32048120
Phenotypes for gene: TBX1 were set to Hypoparathyroidism, conotruncal cardiac malformation, velopalatal insufficiency, abnormal facies, intellectual disability; DiGeorge syndrome 188400; Di George syndrome; T-B+ SCID; Severe combined immunodeficiency (SCID); Combined immunodeficiencies with associated or syndromic features
COVID-19 research v0.36 SAMD9L Ellen McDonagh gene: SAMD9L was added
gene: SAMD9L was added to Viral susceptibility. Sources: North West GLH,NHS GMS,London North GLH,IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: SAMD9L was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: SAMD9L were set to 32086639; 32048120; 28202457
Phenotypes for gene: SAMD9L were set to Cytopenia, predisposition to MDS with chromosome 7 aberrations, immunodeficiency, and progressive cerebellar dysfunction; Combined immunodeficiencies with associated or syndromic features; MDS, neurological features; Bone marrow failure
COVID-19 research v0.36 SAMD9 Ellen McDonagh gene: SAMD9 was added
gene: SAMD9 was added to Viral susceptibility. Sources: IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: SAMD9 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: SAMD9 were set to 29175836; 32086639; 29266745; 29535429; 28487541; 32048120
Phenotypes for gene: SAMD9 were set to IUGR with gonadal abnormalities, adrenal failure, MDS with chromosome 7 aberrations, predisposition to infections, enteropathy, absent spleen; MIRAGE syndrome (Myelodysplasia, Infection, Restriction of growth, Adrenal insufficiency, Genital phenotypes, and Enteropathy); ataxia-thrombocytopenia syndrome; Bone marrow failure; Combined immunodeficiencies with associated or syndromic features
COVID-19 research v0.36 PTEN Ellen McDonagh gene: PTEN was added
gene: PTEN was added to Viral susceptibility. Sources: North West GLH,NHS GMS,London North GLH,IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: PTEN was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: PTEN were set to 32086639; 27426521; 32048120
Phenotypes for gene: PTEN were set to Recurrent infections, Lymphoproliferation, Autoimmunity; Lymphoproliferation, Autoimmunity; developmental delay; Predominantly Antibody Deficiencies
COVID-19 research v0.36 PSENEN Ellen McDonagh gene: PSENEN was added
gene: PSENEN was added to Viral susceptibility. Sources: IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: PSENEN was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: PSENEN were set to 23439959; 28601418; 28287404; 23020871; 20929727; 32086639; 21412258; 27900998; 32048120; 28922471
Phenotypes for gene: PSENEN were set to Acne inversa, familial, 2, with or without Dowling-Degos disease 613736; Defects in intrinsic and innate immunity; Defects in Intrinsic and Innate Immunity; Hidradenitis suppurativa
COVID-19 research v0.36 NCSTN Ellen McDonagh gene: NCSTN was added
gene: NCSTN was added to Viral susceptibility. Sources: IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: NCSTN was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: NCSTN were set to 20929727; 32086639; 32048120; 21412258
Phenotypes for gene: NCSTN were set to Hidradenitis suppurativa with acne, 142690; Defects in intrinsic and innate immunity; familial hydradenitis suppurativa; Defects in Intrinsic and Innate Immunity; Hidradenitis suppurativa with acne
COVID-19 research v0.36 IRF3 Ellen McDonagh Mode of inheritance for gene IRF3 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Added phenotypes {Encephalopathy, acute, infection-induced (herpes-specific), susceptibility to, 7}, 616532; Herpes simplex virus 1 encephalitis; Defects in Intrinsic and Innate Immunity for gene: IRF3
Publications for gene IRF3 were updated from to 32086639; 26513235; 32048120; 26216125
COVID-19 research v0.36 IL17F Ellen McDonagh gene: IL17F was added
gene: IL17F was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: IL17F was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: IL17F were set to 32086639; 32048120; 21350122
Phenotypes for gene: IL17F were set to CMC, folliculitis; Candidiasis, familial, 6, 613956; Defects in Intrinsic and Innate Immunity; Chronic mucocutaneous candidiasis (CMC)
COVID-19 research v0.36 TNFRSF1A Ellen McDonagh gene: TNFRSF1A was added
gene: TNFRSF1A was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: TNFRSF1A was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: TNFRSF1A were set to 11175303; 10199409; 10902757; 17360963
Phenotypes for gene: TNFRSF1A were set to Periodic fever, familial 142680; TNF-receptor associated periodic fever syndrome (TRAPS); Recurrent fever, serositis, rash, and ocular or joint inflammation; Autoinflammatory Disorders
COVID-19 research v0.36 TNFAIP3 Ellen McDonagh gene: TNFAIP3 was added
gene: TNFAIP3 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: TNFAIP3 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: TNFAIP3 were set to 27845235; 29572183; 26642243; 28659290; 29317407
Phenotypes for gene: TNFAIP3 were set to A20 deficiency; Autoimmune lymphoproliferative syndrome; Autoinflammatory Disorders; Autoinflammatory syndrome, familial, Behcet-like, 616744; Arthralgia, mucosal ulcers, ocular inflammation
COVID-19 research v0.36 TMEM173 Ellen McDonagh Mode of pathogenicity for gene TMEM173 was changed from None to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
Added phenotypes Autoinflammatory Disorders; Type 1 interferonopathies; Skin vasculopathy, inflammatory lung disease, systemic autoinflammation and ICC, FCL; STING-associated vasculopathy, infantile-onset 615934 for gene: TMEM173
Publications for gene TMEM173 were updated from 25029335; 25401470; 30705050; 29976662; 29491158; 29425920 to 29425920; 29976662; 29491158; 25029335; 25401470; 30705050
COVID-19 research v0.36 TCF3 Ellen McDonagh gene: TCF3 was added
gene: TCF3 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,NHS GMS,London North GLH,A- or hypo-gammaglobulinaemia v1.25,IUIS Classification February 2018
Mode of inheritance for gene: TCF3 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: TCF3 were set to 29114388; 28532655; 24216514
Phenotypes for gene: TCF3 were set to Agammaglobulinemia; Recurrent bacterial infections; Agammaglobulinemia 8, autosomal dominant, 616941; Primary immunodeficiency; Predominantly Antibody Deficiencies
Mode of pathogenicity for gene: TCF3 was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
COVID-19 research v0.36 TBK1 Ellen McDonagh Mode of inheritance for gene TBK1 was changed from Unknown to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Added phenotypes Herpetic encephalitis (HSE); Herpes simplex virus 1 encephalitis; {Encephalopathy, acute, infection-induced (herpes-specific), susceptibility to, 8} 617900; Herpes simplex encephalitis, susceptibility to; Defects in Intrinsic and Innate Immunity for gene: TBK1
Publications for gene TBK1 were updated from to 22851595; 26513235
COVID-19 research v0.36 RPSA Ellen McDonagh gene: RPSA was added
gene: RPSA was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: RPSA was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: RPSA were set to 22560297; 23579497
Phenotypes for gene: RPSA were set to Isolated congential asplenia 271400; Bacteremia (encapsulated bacteria); Defects in Intrinsic and Innate Immunity
COVID-19 research v0.36 PSTPIP1 Ellen McDonagh gene: PSTPIP1 was added
gene: PSTPIP1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: PSTPIP1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: PSTPIP1 were set to 28628471; 28960754; 29575118; 26025129; 28251506
Phenotypes for gene: PSTPIP1 were set to Pyogenic sterile arthritis, pyoderma gangrenosum, and acne 604416; Destructive arthritis, inflammatory skin rash, myositis; Hyperzincaemia hypercalprotectinaemia; Autoinflammatory Disorders; Proline/serine/threonine phosphatase-interacting protein 1 deficiency (PSTPIP1); PAPA syndrome
Mode of pathogenicity for gene: PSTPIP1 was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
COVID-19 research v0.36 PLCG2 Ellen McDonagh gene: PLCG2 was added
gene: PLCG2 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,A- or hypo-gammaglobulinaemia v1.25,IUIS Classification February 2018
Mode of inheritance for gene: PLCG2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: PLCG2 were set to 29538758; 23000145; 22236196
Phenotypes for gene: PLCG2 were set to Other autoinflammatory diseases with known genetic defect; Cold urticaria hypogammaglobulinemia, autoinflammation; Familial cold autoinflammatory syndrome 3 614468; Familial cold autoinflammatory syndrome 3; Autoinflammatory Disorders; Hypogammaglobulinaemia, cold induced urticaria, autoinflammatory; Autoinflammation, antibody deficiency, and immune dysregulation syndrome 614878
Mode of pathogenicity for gene: PLCG2 was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
COVID-19 research v0.36 NOD2 Ellen McDonagh gene: NOD2 was added
gene: NOD2 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: NOD2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: NOD2 were set to 18955195; 15459013; 11528384; 4056967
Phenotypes for gene: NOD2 were set to Blau syndrome 186580; Uveitis, granulomatous synovitis, camptodactyly, rash and cranial neuropathies, 30% develop Crohn colitis; Autoinflammatory Disorders; Caspase recruitment domain-containing protein 15 deficiency (CARD15)
COVID-19 research v0.36 NLRP3 Ellen McDonagh gene: NLRP3 was added
gene: NLRP3 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: NLRP3 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: NLRP3 were set to 28847925; 11687797; 11992256; 29366613; 12522564; 12032915
Phenotypes for gene: NLRP3 were set to CINCA syndrome 607115; Non-pruritic urticaria, arthritis, chills, fever and leukocytosis after cold exposure; Neonatal onset rash, chronic meningitis, and arthropathy with fever and inflammation; Urticaria, SNHL, amyloidosis; Muckle-Wells syndrome 191900; Autoinflammatory Disorders; Familial cold autoinflammatory syndrome 1 120100; Deafness, autosomal dominant 34, with or without inflammation 617772
COVID-19 research v0.36 NLRP12 Ellen McDonagh gene: NLRP12 was added
gene: NLRP12 was added to Viral susceptibility. Sources: Expert Review Green,Victorian Clinical Genetics Services,North West GLH,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: NLRP12 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: NLRP12 were set to 29248470; 29178652; 27633793; 18230725; 27779193
Phenotypes for gene: NLRP12 were set to Autoinflammatory Disorders; Non-pruritic urticaria, arthritis, chills, fever and leukocytosis after cold exposure.; preterm premature rupture of membranes (PPROM); Familial cold autoinflammatory syndrome 2, 611762
COVID-19 research v0.36 NLRC4 Ellen McDonagh gene: NLRC4 was added
gene: NLRC4 was added to Viral susceptibility. Sources: Expert Review Green,Victorian Clinical Genetics Services,North West GLH,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: NLRC4 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: NLRC4 were set to 25217960; 25217959; 25385754; 27876626
Phenotypes for gene: NLRC4 were set to Autoinflammatory Disorders; Severe enterocolitis and macrophage activation syndrome; Autoinflammation with infantile enterocolitis 616050; ?Familial cold autoinflammatory syndrome 4 616115
Mode of pathogenicity for gene: NLRC4 was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
COVID-19 research v0.36 NFKBIA Ellen McDonagh gene: NFKBIA was added
gene: NFKBIA was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: NFKBIA was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: NFKBIA were set to 18412279; 17931563; 14523047; 15337789
Phenotypes for gene: NFKBIA were set to Combined immunodeficiencies with associated or syndromic features; Anhidrotic ectodermal dysplasia, various infections (bacteria, mycobacteria, viruses and fungi), colitis, variable defects of skin, hair and teeth, T cell and monocyte dysfunction; Defects of TLR/NFkappa-B signalling; Ectodermal dysplasia, anhidrotic, with T-cell immunodeficiency 612132
Mode of pathogenicity for gene: NFKBIA was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
COVID-19 research v0.36 NFKB2 Ellen McDonagh gene: NFKB2 was added
gene: NFKB2 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,A- or hypo-gammaglobulinaemia v1.25,IUIS Classification February 2018
Mode of inheritance for gene: NFKB2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: NFKB2 were set to 25237204; 24140114; 25524009; 24888602
Phenotypes for gene: NFKB2 were set to Recurrent sinopulmonary infections, alopecia and endorinopathies; Immunodeficiency, common variable, 10 615577; Unclassified antibody deficiency; Hypogammaglobuliaemia; central adrenal insufficiency; immune dysregulation; Common variable immunodeficiency disorders (CVID); Predominantly Antibody Deficiencies
COVID-19 research v0.36 NFKB1 Ellen McDonagh gene: NFKB1 was added
gene: NFKB1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: NFKB1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: NFKB1 were set to 29477724; 26279205
Phenotypes for gene: NFKB1 were set to Unclassified antibody deficiency; Recurrent sinopulmonary infections, COPD, EBV proliferation, autoimmune cytopenias, alopecia and autoimmune thyroiditis; Common variable immunodeficiency disorders (CVID); Predominantly Antibody Deficiencies; Immunodeficiency, common variable, 12 616576
COVID-19 research v0.36 GATA2 Ellen McDonagh gene: GATA2 was added
gene: GATA2 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: GATA2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: GATA2 were set to 29588856; 21670465; 21765025; 2543925; 29724903
Phenotypes for gene: GATA2 were set to Susceptibility to mycobacteria, HPV, histoplasmosis, alveolar proteinosis, MDS/AML/CMMoL, lymphedema; Congenital neutropenia; Combined immunodeficiency with susceptibility to mycobacterial, viral and fungal infections; Immunodeficiency 21,614172; Congenital defects of phagocyte number or function; Monocytopenia and mycobacterial infection (MonoMAC); Monocytopenia with susceptibility to infections
COVID-19 research v0.36 ELANE Ellen McDonagh gene: ELANE was added
gene: ELANE was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,Congenital neutropaenia v1.22,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: ELANE was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes for gene: ELANE were set to Congenital neutropenia; Susceptibility to MDS/leukemia, Severe congenital neutropenia or cyclic neutropenia; Neutropenia, cyclic, 162800; Cyclic neutropenia; Congenital defects of phagocyte number or function; Neutropenia, severe congenital 1; Neutropenia, severe congenital 1, autosomal dominant, 202700
COVID-19 research v0.36 CXCR4 Ellen McDonagh Mode of inheritance for gene CXCR4 was changed from Unknown to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Mode of pathogenicity for gene CXCR4 was changed from to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
Added phenotypes Myelokathexis, isolated; Warts hypogammaglobulinemia infections and myelokathexis (WHIM); WHIM syndrome, 193670; WHIM syndrome; Warts (HPV) infection, neutropenia, low B cell number, hypogammaglobulinemia; Defects in Intrinsic and Innate Immunity for gene: CXCR4
Publications for gene CXCR4 were updated from to 12692554; 15536153
COVID-19 research v0.36 COPA Ellen McDonagh gene: COPA was added
gene: COPA was added to Viral susceptibility. Sources: Expert Review Green,Victorian Clinical Genetics Services,North West GLH,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: COPA was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: COPA were set to 28956095; 25894502; 29137621
Phenotypes for gene: COPA were set to Autoimmune interstitial lung disease-arthritis syndrome; Autoimmune inflammatory arthritis and interstitial lung disease with Th17 dysregulation and autoantibody production; Autoinflammatory Disorders; Autoimmune inflammatoy arthritis and interstial lung disease, 616414; COPA syndrome
COVID-19 research v0.36 CHD7 Ellen McDonagh gene: CHD7 was added
gene: CHD7 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CHD7 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: CHD7 were set to 15300250; 29159871; 25689927; 20052490; 18976358; 19403480; 26544072; 19187738; 29531775; 26563674; 21378379; 22461308; 18505430
Phenotypes for gene: CHD7 were set to CHARGE syndrome, 214800; Coloboma, heart anomaly, choanal atresia, intellectual disability, genital and ear anomalies, CNS malformation, some are SCID-like and have low TRECs; Immunodeficiency; Combined immunodeficiencies with associated or syndromic features; COLOBOMA, HEART ANOMALY, CHOANAL ATRESIA, RETARDATION, GENITAL AND EAR ANOMALIES; Charge syndrome
COVID-19 research v0.36 CASP10 Ellen McDonagh gene: CASP10 was added
gene: CASP10 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CASP10 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: CASP10 were set to 16446975; 9028957; 10412980; 25663566; 16611303; 21447005
Phenotypes for gene: CASP10 were set to Adenopathies, splenomegaly, autoimmunity; Autoimmune lymphoproliferative syndrome, type II, 603909; Autoimmune lymphoproliferative syndrome (ALPS); Diseases of Immune Dysregulation
COVID-19 research v0.36 BACH2 Ellen McDonagh gene: BACH2 was added
gene: BACH2 was added to Viral susceptibility. Sources: Expert Review Green,North West GLH,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: BACH2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: BACH2 were set to 27807919; 28530713; 27680876
Phenotypes for gene: BACH2 were set to Diseases of Immune Dysregulation; BACH2-related immunodeficiency and autoimmunity (BRIDA); hypogammaglobulinaemia; infantile onset enterocolitis; Lymphocytic colitis, sinopulmonary infections
COVID-19 research v0.36 TNFRSF13B Ellen McDonagh gene: TNFRSF13B was added
gene: TNFRSF13B was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,IUIS Classification December 2019,GRID V2.0,GOSH PID v.8.0,A- or hypo-gammaglobulinaemia v1.25,Expert Review Red,IUIS Classification February 2018
Mode of inheritance for gene: TNFRSF13B was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: TNFRSF13B were set to 29114388; 28834165; 16007086; 16007087; 32086639; 18981294; 32048120
Phenotypes for gene: TNFRSF13B were set to IgA with IgG subclass deficiency; Immunodeficiency, common variable, 2; Immunodeficiency, common variable, 2, 240500; Variable clinical expression; Isolated IgG subclass deficiency; IGAD; Selective IgA deficiency; Common variable immunodeficiency disorders (CVID); Predominantly Antibody Deficiencies; Immunoglobulin A deficiency 2, 609529; CVID
COVID-19 research v0.36 STAT4 Ellen McDonagh gene: STAT4 was added
gene: STAT4 was added to Viral susceptibility. Sources: Expert Review Red,NHS GMS,London North GLH
Mode of inheritance for gene: STAT4 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Phenotypes for gene: STAT4 were set to {Systemic lupus erythematosus, susceptibility to, 11}, 612253
COVID-19 research v0.36 CFHR2 Ellen McDonagh gene: CFHR2 was added
gene: CFHR2 was added to Viral susceptibility. Sources: Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,Expert Review Red,IUIS Classification February 2018
Mode of inheritance for gene: CFHR2 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: CFHR2 were set to 32086639; 32048120
Phenotypes for gene: CFHR2 were set to Complement Deficiencies; Age related macular degeneration; Atypical hemolytic uremic syndrome susceptibility; Older onset atypical hemolytic-uremic syndrome, disseminated neisserial infections
COVID-19 research v0.36 TERT Ellen McDonagh gene: TERT was added
gene: TERT was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: TERT was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: TERT were set to 16247010; 18460650; 15885610; 17785587
Phenotypes for gene: TERT were set to Bone marrow failure; Bone marrow failure, pulmonary and hepatic fibrosis, nail dystrophy, leukoplakia, reticulate skin pigmentation; microcephaly, neurodevelopmental delay
COVID-19 research v0.36 RAC2 Ellen McDonagh gene: RAC2 was added
gene: RAC2 was added to Viral susceptibility. Sources: Combined B and T cell defect v1.12,ESID Registry 20171117,Victorian Clinical Genetics Services,Congenital neutropaenia v1.22,GRID V2.0,SCID v1.6,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: RAC2 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: RAC2 were set to 21167572; 30654050; 30723080; 31071452; 25512081; 10758162; 31382036; 10961859
Phenotypes for gene: RAC2 were set to Reticular dysgenesis; poststreptococcal glomerulonephritis; Congenital defects of phagocyte number or function; Neutrophil immunodeficiency syndrome; RAS-related C3 Bolutinum toxin substrate 2 deficiency (RAC2); T-B+ SCID; Neutrophil immunodeficiency syndrome 608203; Recurrent sinopulmonary infections, selective IgA defiency; urticaria; T-B- SCID; Poor wound healing, leukocytosis
COVID-19 research v0.36 NLRP1 Ellen McDonagh gene: NLRP1 was added
gene: NLRP1 was added to Viral susceptibility. Sources: North West GLH,NHS GMS,London North GLH,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: NLRP1 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: NLRP1 were set to 29850521; 27662089; 31484767; 27965258
Phenotypes for gene: NLRP1 were set to Dyskeratosis, autoimmunity and arthritis; Palmoplantar carcinoma, corneal scarring; Autoinflammation with arthritis and dyskeratosis; Autoinflammatory Disorders
COVID-19 research v0.36 MBL2 Ellen McDonagh Mode of inheritance for gene MBL2 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Added phenotypes Mannose-binding lectin deficiency (MBL); Chronic infections, due to MBL deficiency; Mannose-Binding Protein Deficiency, 614372 for gene: MBL2
Publications for gene MBL2 were updated from 16170752; 19405982; 25818534; 16185324; 15838797 to 16185324; 28347655; 10888598; 19405982; 1458688; 16170752; 15838797; 7707811; 25818534
COVID-19 research v0.36 GUCY2C Ellen McDonagh gene: GUCY2C was added
gene: GUCY2C was added to Viral susceptibility. Sources: North West GLH,NHS GMS,GOSH PID v.8.0,London North GLH,Expert Review Amber
Mode of inheritance for gene: GUCY2C was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Phenotypes for gene: GUCY2C were set to meconium ileus, 614665; Diarrhea 6, 614616
COVID-19 research v0.36 CFHR5 Ellen McDonagh gene: CFHR5 was added
gene: CFHR5 was added to Viral susceptibility. Sources: Victorian Clinical Genetics Services,North West GLH,GRID V2.0,NHS GMS,London North GLH,IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: CFHR5 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: CFHR5 were set to 28673452; 20800271; 32086639; 22503529; 32048120
Phenotypes for gene: CFHR5 were set to Atypical hemolytic-uremic syndrome with anti-factor H antibodies; Atypical hemolytic uremic syndrome susceptibility; Nephropathy due to CFHR5 deficiency, 614809; Complement Deficiencies; Older onset atypical hemolytic-uremic syndrome, disseminated neisserial infections
COVID-19 research v0.36 CFHR4 Ellen McDonagh gene: CFHR4 was added
gene: CFHR4 was added to Viral susceptibility. Sources: Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: CFHR4 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: CFHR4 were set to 32086639; 32048120
Phenotypes for gene: CFHR4 were set to Complement Deficiencies; Age related macular degeneration; Atypical hemolytic uremic syndrome susceptibility; Older onset atypical hemolytic-uremic syndrome, disseminated neisserial infections
COVID-19 research v0.36 CFHR3 Ellen McDonagh gene: CFHR3 was added
gene: CFHR3 was added to Viral susceptibility. Sources: Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: CFHR3 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: CFHR3 were set to 32086639; 32048120
Phenotypes for gene: CFHR3 were set to Complement Deficiencies; Age related macular degeneration; Atypical hemolytic uremic syndrome susceptibility; Older onset atypical hemolytic-uremic syndrome, disseminated neisserial infections
COVID-19 research v0.36 CFHR1 Ellen McDonagh gene: CFHR1 was added
gene: CFHR1 was added to Viral susceptibility. Sources: Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: CFHR1 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: CFHR1 were set to 32086639; 32048120
Phenotypes for gene: CFHR1 were set to Complement Deficiencies; Age related macular degeneration; Atypical hemolytic uremic syndrome susceptibility; Older onset atypical hemolytic-uremic syndrome, disseminated neisserial infections
COVID-19 research v0.36 CFB Ellen McDonagh gene: CFB was added
gene: CFB was added to Viral susceptibility. Sources: ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: CFB was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: CFB were set to 4109808; 24152280
Phenotypes for gene: CFB were set to Infections with encapsulated organisms; Complement Deficiencies; complement factor B deficiency (AR); Atypical Hemolytic-uremic syndrome; Complement factor B deficiency, 615561; Susceptibility to atypical haemolytic uraemic syndrome 4 (AD)
COVID-19 research v0.36 TREX1 Ellen McDonagh gene: TREX1 was added
gene: TREX1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: TREX1 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: TREX1 were set to 20799324; 21808053; 16845398; 25604658
Phenotypes for gene: TREX1 were set to Aicardi-Goutieres syndrome 1, dominant and recessive; Autoinflammatory Disorders; Type 1 interferonopathies; Classical AGS, SLE, FCL
COVID-19 research v0.36 TLR3 Ellen McDonagh Mode of inheritance for gene TLR3 was changed from Unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Mode of pathogenicity for gene TLR3 was changed from to Other - please provide details in the comments
Added phenotypes Herpetic encephalitis (HSE); Herpes simplex virus 1 encephalitis (incomplete clinical penetrance for all etiologies listed here); Defects in Intrinsic and Innate Immunity; Herpes simplex encephalitis, susceptibility to, 2 for gene: TLR3
Publications for gene TLR3 were updated from to 28368532; 21911422; 25339207
COVID-19 research v0.36 TICAM1 Ellen McDonagh Mode of inheritance for gene TICAM1 was changed from Unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Added phenotypes Encephalopathy, acute, infection-induced, susceptibility to, 6 614850; Herpes simplex virus 1 encephalitis; Herpetic encephalitis (HSE); Defects in Intrinsic and Innate Immunity for gene: TICAM1
Publications for gene TICAM1 were updated from to 22105173; 26513235
COVID-19 research v0.36 SERPING1 Ellen McDonagh gene: SERPING1 was added
gene: SERPING1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: SERPING1 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: SERPING1 were set to 1597123; 7883978
Phenotypes for gene: SERPING1 were set to Angioedema, hereditary, types I and II 106100; Complement component 4, partial deficiency of 120790; Complement Deficiencies; Hereditary Angioedema (C1inh); Hereditary angioedema
COVID-19 research v0.36 RTEL1 Ellen McDonagh gene: RTEL1 was added
gene: RTEL1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: RTEL1 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: RTEL1 were set to 23959892; 23453664; 23591994
Phenotypes for gene: RTEL1 were set to Combined immunodeficiencies with associated or syndromic features; Hoyeraal-Hreidarsson syndrome/ Dyskeratosis congenita, 4 615190; Intrauterine growth retardation, microcephaly, nail dystrophy, sparse scalp hair and eyelashes, hyperpigmentation of skin, palmar hyperkeratosis, premalignant oral leukoplakia, pancytopenia, myelodysplasia, +/- recurrent infections. A severe phenotype with developmental delay and cerebellar hypoplasia known as Hoyeraal-Hreidarsson Syndrome (HHS) may occur in some DKC patients; Dyskeratosis congenita, 5 615190
COVID-19 research v0.36 PARN Ellen McDonagh gene: PARN was added
gene: PARN was added to Viral susceptibility. Sources: Expert Review Green,Victorian Clinical Genetics Services,North West GLH,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: PARN was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: PARN were set to 25848748; 26342108; 25893599
Phenotypes for gene: PARN were set to Pulmonary fibrosis and/or bone marrow failure,telomere-related, 4 616371; Dyskeratosis congenita, autosomal recessive 6 616353; Intrauterine growth retardation, microcephaly, nail dystrophy, sparse scalp hair and eyelashes, hyperpigmentation of skin, palmar hyperkeratosis, premalignant oral leukoplakia, pancytopenia, myelodysplasia, +/- recurrent infections. A severe phenotype with developmental delay and cerebellar hypoplasia known as Hoyeraal-Hreidarsson Syndrome (HHS) may occur in some DKC patients; Combined immunodeficiencies with associated or syndromic features
COVID-19 research v0.36 MEFV Ellen McDonagh gene: MEFV was added
gene: MEFV was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: MEFV was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: MEFV were set to 11242116; 14679589; 9668175; 9288094; 10787449; 10090880; 11903360
Phenotypes for gene: MEFV were set to Familial mediterranean fever defect; Recurrent fever, serositis and inflammation responsive to colchicine. Predisoposes to vasculitis and inflammatory bowel disease.; Autoinflammatory Disorders; Familial Mediterranean fever, AD 134610; Familial Mediterranean fever, AR 249100
COVID-19 research v0.36 IRF8 Ellen McDonagh Mode of inheritance for gene IRF8 was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Added phenotypes Immunodeficiency 32B, monocyte and dendritic cell deficiency, autosomal recessive, 226990; Susceptibility to mycobacteria and multiple other infectious agents; Immunodeficiency 32A, mycobacteriosis, autosomal dominant, 614893; Defects with susceptibility to mycobacterial infection (MSMD); Susceptibility to mycobacteria; Defects in Intrinsic and Innate Immunity for gene: IRF8
Publications for gene IRF8 were updated from 27893462 to 25122610; 22464253; 21524210; 22046141; 27893462
COVID-19 research v0.36 IFNGR2 Ellen McDonagh gene: IFNGR2 was added
gene: IFNGR2 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: IFNGR2 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: IFNGR2 were set to 9616207; 18625743; 30264912; 15924140
Phenotypes for gene: IFNGR2 were set to Susceptibility to mycobacteria and Salmonella; Defects with susceptibility to mycobacterial infection (MSMD); Immunodeficiency 28, Mycobacteriosis, 614889; Defects in Intrinsic and Innate Immunity
COVID-19 research v0.36 IFIH1 Ellen McDonagh Mode of inheritance for gene IFIH1 was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Mode of pathogenicity for gene IFIH1 was changed from None to Other - please provide details in the comments
Added phenotypes Rhinovirus and other RNA viruses (AR); Classical AGS, SLE, SP, SMS; Autoinflammatory Disorders; Defects in Intrinsic and Innate Immunity; Aicardi-Goutieres syndrome 7 (AD); susceptibility to RNA viruses for gene: IFIH1
Publications for gene IFIH1 were updated from 29018476; 28606988 to 29018476; 28606988; 28716935
COVID-19 research v0.36 FAS Ellen McDonagh gene: FAS was added
gene: FAS was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: FAS was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: FAS were set to 10709732; 15459302; 26258116; 8929361; 9927496; 7540117; 28668589; 9028321; 9821419
Phenotypes for gene: FAS were set to Splenomegaly, adenopathies, autoimmune cytopenias, increased lymphoma risk, IgG and A normal or increased, elevated serum FasL and IL-10, vitamin B12; Diseases of Immune Dysregulation; Autoimmune lymphoproliferative syndrome, type IA (ALPS-FAS); Autoimmune lymphoproliferative syndrome type IA, 601859; Autoimmune lymphoproliferative syndrome (ALPS)
COVID-19 research v0.36 CFH Ellen McDonagh gene: CFH was added
gene: CFH was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,Inherited complement deficiency v0.11,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CFH was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: CFH were set to 14978182; 9312129; 24722444; 2966809; 1701856; 10803850; 16612335; 7742208
Phenotypes for gene: CFH were set to Complement Deficiencies; Complement factor H deficiency, 609814; Infections, disseminated neisserial infections, atypical Hemolytic-uremic syndrome, preeclampsia, dense deposit disease
COVID-19 research v0.36 CEBPE Ellen McDonagh gene: CEBPE was added
gene: CEBPE was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CEBPE was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: CEBPE were set to 11313242; 29651288; 10359588
Phenotypes for gene: CEBPE were set to Specific granule deficiency 1; Recurrent infection due to specific granule deficiency; Congenital defects of phagocyte number or function; Specific granule deficiency, 245480; Neutrophils with bilobed nuclei; neutrophil lactoferrin deficiency; CCAAT/enhancer binding protein epsilon deficiency (CEBPE)
COVID-19 research v0.36 CD46 Ellen McDonagh gene: CD46 was added
gene: CD46 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CD46 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: CD46 were set to 16621965; 14566051; 14615110
Phenotypes for gene: CD46 were set to Hemolytic uremic syndrome, atypical, susceptibility to, 2, 612922; atypical HUS; Membrane Cofactor Protein (CD46) deficiency; Complement Deficiencies; Atypical hemolytic-uremic syndrome, infections, preeclampsia
COVID-19 research v0.36 CARD11 Ellen McDonagh gene: CARD11 was added
gene: CARD11 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CARD11 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: CARD11 were set to 25352053; 23374270; 29074947; 23129749; 23561803; 30170123; 28628108; 28826773
Phenotypes for gene: CARD11 were set to immunodeficiency 11B with atopic dermatitis (AD), 617638; CARD11 deficiency; Combined immunodeficiency; Autoimmune lymphoproliferative syndrome (ALPS); Pneumocystis jirovecii pneumonia, bacterial and viral infections; Severe atopy, recurrent infections; B cell expansion with NFKB and T cell anergy (BENTA) (AD), 616452; Atypical Severe Combined Immunodeficiency (Atypical SCID); Splenomegaly, lymphadenopathy, poor vaccine response; Immunodeficiencies affecting cellular and humoral immunity; Predominantly Antibody Deficiencies; Predominantly antibody deficiencies; Combined immunodeficiencies with associated or syndromic features; Immunodeficiency 11A, 615206 (AR)
Mode of pathogenicity for gene: CARD11 was set to Other - please provide details in the comments
COVID-19 research v0.36 STAT1 Ellen McDonagh Mode of inheritance for gene STAT1 was changed from Unknown to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
Mode of pathogenicity for gene STAT1 was changed from to Other - please provide details in the comments
Added phenotypes Immunodeficiency 31A, mycobacteriosis; Combined immunodeficiency; Immunodeficiency 31B, mycobacterial and viral infections, autosomal recessive 613796; Defects with susceptibility to mycobacterial infection (MSMD); Candidiasis, familial, 7; Severe viral infections, mycobacterial infection; Chronic mucocutaneous candidiasis (CMC); Susceptibility to mycobacteria, Salmonella; Immunodeficiency 31A, mycobacteriosis, autosomal dominant 614892; CMC, various fungal, bacterial and viral (HSV) infections, auto-immunity (thyroiditis, diabetes, cytopenias), enteropathy; Immunodeficiency 31C, autosomal dominant 614162; Defects in Intrinsic and Innate Immunity for gene: STAT1
Publications for gene STAT1 were updated from to 26513235; 29702748; 11452125; 23541320; 23709754; 23534974; 21727188; 12590259
COVID-19 research v0.36 PIK3R1 Ellen McDonagh gene: PIK3R1 was added
gene: PIK3R1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,A- or hypo-gammaglobulinaemia v1.25,IUIS Classification February 2018
Mode of inheritance for gene: PIK3R1 was set to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
Publications for gene: PIK3R1 were set to 25133428; 22351933; 9888855; 25488983
Phenotypes for gene: PIK3R1 were set to Agammaglobulinemia; Severe bacterial infections, decreased or absent pro-B cells; Combined immunodeficiency; Immunodeficiency 36; Activated PI3K-delta syndrome (APDS); immunodeficiency with hypogammaglobulinaemia, lymphoproliferation and inflammatory disease (AD); Agammaglobulinemia 7, autosomal recessive, 615214; Agammaglobulinemia 7; Immunodeficiency 36, 616005; Predominantly Antibody Deficiencies; SHORT syndrome, 269880; Severe bacterial infections, pro-B cells present and low numbers of memory B cells, EBV
COVID-19 research v0.36 IFNGR1 Ellen McDonagh gene: IFNGR1 was added
gene: IFNGR1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: IFNGR1 was set to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
Publications for gene: IFNGR1 were set to 8960473; 8960475; 9389728; 9497247
Phenotypes for gene: IFNGR1 were set to Immunodeficiency 27A, (AR) 209950; Susceptibility to mycobacteria and Salmonella; Mycobacteriosis; Defects with susceptibility to mycobacterial infection (MSMD); Defects in Intrinsic and Innate Immunity; Immunodeficiency 27B, (AD) 615978
COVID-19 research v0.36 AIRE Ellen McDonagh gene: AIRE was added
gene: AIRE was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: AIRE was set to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
Publications for gene: AIRE were set to 9888391; 19807739; 11600535; 11836330; 10677297; 29437776; 29108822; 19758376; 9398839; 9837820; 28911151
Phenotypes for gene: AIRE were set to Autoimmune polyendocrinopathy syndrome, type I, with or without reversible metaphyseal dysplasia, 240300; Multiple endocrine deficiency Addison disease candidiasis syndrome; Autoimmune hypoparathyroidism chronic candidiasis Addison disease syndrome; Diseases of Immune Dysregulation; Chronic mucocutaneous candidiasis (CMC); Autoimmunity: hypoparathyroidism hypothyroidism, adrenal insufficiency, diabetes, gonadal dysfunction and other endocrine abnormalities, chronic mucocutaneous candidiasis, dental enamel hypoplasia, alopecia areata enteropathy, pernicious anemia; Hypoparathyroidism Addison disease mucocutaneous candidiasis syndrome; Autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED)
COVID-19 research v0.36 ACD Ellen McDonagh gene: ACD was added
gene: ACD was added to Viral susceptibility. Sources: Expert Review Green,North West GLH,GRID V2.0,NHS GMS,London North GLH
Mode of inheritance for gene: ACD was set to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
Publications for gene: ACD were set to 25205116; 25233904
Phenotypes for gene: ACD were set to Dyskeratosis congenita 6, 616553; Dyskeratosis congenita 7, 616553; Hoyeraal-Hreidarsson syndrome
COVID-19 research v0.36 ZNF341 Ellen McDonagh gene: ZNF341 was added
gene: ZNF341 was added to Viral susceptibility. Sources: Expert Review Red,Literature,IUIS Classification December 2019
Mode of inheritance for gene: ZNF341 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ZNF341 were set to 32086639; 29907691; 32048120; 29907690
Phenotypes for gene: ZNF341 were set to Hyper-IgE syndrome; Combined immunodeficiencies with associated or syndromic features; Bacterial infections, mild facial dysmorphism, pneumatoceles, hyperextensible joints, bone fractures, retention of primary teeth
COVID-19 research v0.36 WRAP53 Ellen McDonagh gene: WRAP53 was added
gene: WRAP53 was added to Viral susceptibility. Sources: IUIS Classification February 2018,IUIS Classification December 2019
Mode of inheritance for gene: WRAP53 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: WRAP53 were set to 32086639; 32048120
Phenotypes for gene: WRAP53 were set to Bone marrow failure; Bone marrow failure, pulmonary and hepatic fibrosis, nail dystrophy, leukoplakia, reticulate skin pigmentation; Combined immunodeficiencies with associated or syndromic features; Intrauterine growth retardation, microcephaly, nail dystrophy, sparse scalp hair and eyelashes, hyperpigmentation of skin, palmar hyperkeratosis, premalignant oral leukoplakia, pancytopenia, myelodysplasia, +/- recurrent infections. A severe phenotype with developmental delay and cerebellar hypoplasia known as Hoyeraal-Hreidarsson Syndrome (HHS) may occur in some DKC patients; microcephaly, neurodevelopmental delay
COVID-19 research v0.36 TRIM22 Ellen McDonagh gene: TRIM22 was added
gene: TRIM22 was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: TRIM22 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TRIM22 were set to 26836588; 32086639; 32048120
Phenotypes for gene: TRIM22 were set to TRIM22; Granulomatous colitis; Autoinflammatory Disorders; Diseases of Immune Dysregulation
COVID-19 research v0.36 TRAF3IP2 Ellen McDonagh gene: TRAF3IP2 was added
gene: TRAF3IP2 was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,Expert Review Red,IUIS Classification February 2018
Mode of inheritance for gene: TRAF3IP2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TRAF3IP2 were set to 32086639; 24120361; 32048120
Phenotypes for gene: TRAF3IP2 were set to Defects in Intrinsic and Innate Immunity; Chronic mucocutaneous candidiasis (CMC); Defects in intrinsic and innate immunity; Candidiasis, familial, 8 615527; CMC, blepharitis, folliculitis and macroglossia
COVID-19 research v0.36 TNFSF11 Ellen McDonagh gene: TNFSF11 was added
gene: TNFSF11 was added to Viral susceptibility. Sources: IUIS Classification February 2018,IUIS Classification December 2019
Mode of inheritance for gene: TNFSF11 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TNFSF11 were set to 32086639; 32048120
Phenotypes for gene: TNFSF11 were set to Osteopetrosis with severe growth retardation; Defects in intrinsic and innate immunity; Defects in Intrinsic and Innate Immunity
COVID-19 research v0.36 TNFRSF9 Ellen McDonagh gene: TNFRSF9 was added
gene: TNFRSF9 was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: TNFRSF9 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TNFRSF9 were set to 30872117; 32086639; 31537641; 31501153; 32048120
Phenotypes for gene: TNFRSF9 were set to EBV lymphoproliferation, B-cell lymphoma; CD137 deficiency (41BB)
COVID-19 research v0.36 TNFRSF4 Ellen McDonagh gene: TNFRSF4 was added
gene: TNFRSF4 was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,Expert Review Red,IUIS Classification February 2018
Mode of inheritance for gene: TNFRSF4 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TNFRSF4 were set to 32086639; 32048120
Phenotypes for gene: TNFRSF4 were set to Kaposi's Sarcoma, impaired immunity to HHV8, OX40 deficiency; Immunodeficiencies affecting cellular and humoral immunity; Impaired immunity to HHV8, Kaposis sarcoma; Combined immunodeficiency
COVID-19 research v0.36 TIRAP Ellen McDonagh gene: TIRAP was added
gene: TIRAP was added to Viral susceptibility. Sources: Expert Review Red,ESID Registry 20171117,IUIS Classification February 2018,IUIS Classification December 2019
Mode of inheritance for gene: TIRAP was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TIRAP were set to 32086639; 32048120; 28235196
Phenotypes for gene: TIRAP were set to Staphylococcal disease during childhood; Defects of TLR/NFkappa-B signalling; TIRAP deficiency; Defects in intrinsic and innate immunity; Defects in Intrinsic and Innate Immunity
COVID-19 research v0.36 TGFB1 Ellen McDonagh gene: TGFB1 was added
gene: TGFB1 was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: TGFB1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TGFB1 were set to 32086639; 32048120; 29483653
Phenotypes for gene: TGFB1 were set to Inflammatory bowel disease, immunodeficiency, and encephalopathy, 618213; IBD, immunodeficiency, recurrent viral infections, microcephaly, and encephalopathy; TGFB1 deficiency; Diseases of Immune Dysregulation
COVID-19 research v0.36 TFRC Ellen McDonagh gene: TFRC was added
gene: TFRC was added to Viral susceptibility. Sources: IUIS Classification February 2018,IUIS Classification December 2019
Mode of inheritance for gene: TFRC was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TFRC were set to 32086639; 32048120
Phenotypes for gene: TFRC were set to Recurrent infections, neutropenia, thrombocytopenia; Recurrent infections, thrombocytopenia; Immunodeficiencies affecting cellular and humoral immunity
COVID-19 research v0.36 TCIRG1 Ellen McDonagh gene: TCIRG1 was added
gene: TCIRG1 was added to Viral susceptibility. Sources: IUIS Classification February 2018,IUIS Classification December 2019
Mode of inheritance for gene: TCIRG1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TCIRG1 were set to 32086639; 32048120
Phenotypes for gene: TCIRG1 were set to Defects in intrinsic and innate immunity; Osteopetrosis with hypocalcemia; Defects in Intrinsic and Innate Immunity
COVID-19 research v0.36 STN1 Ellen McDonagh gene: STN1 was added
gene: STN1 was added to Viral susceptibility. Sources: IUIS Classification February 2018,IUIS Classification December 2019
Mode of inheritance for gene: STN1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: STN1 were set to 32086639; 32048120
Phenotypes for gene: STN1 were set to Combined immunodeficiencies with associated or syndromic features; Bone marrow failure; Intrauterine growth retardation, premature aging, pancytopenia, hypocellular bone marrow, gastrointestinal hemorrhage due to vascular ectasia, intracranial calcification, abnormal telomeres
COVID-19 research v0.36 SNX10 Ellen McDonagh gene: SNX10 was added
gene: SNX10 was added to Viral susceptibility. Sources: IUIS Classification February 2018,IUIS Classification December 2019
Mode of inheritance for gene: SNX10 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SNX10 were set to 32086639; 32048120
Phenotypes for gene: SNX10 were set to Defects in intrinsic and innate immunity; Osteopetrosis with visual impairment; Defects in Intrinsic and Innate Immunity
COVID-19 research v0.36 SMARCD2 Ellen McDonagh gene: SMARCD2 was added
gene: SMARCD2 was added to Viral susceptibility. Sources: IUIS Classification February 2018,IUIS Classification December 2019
Mode of inheritance for gene: SMARCD2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SMARCD2 were set to 32086639; 32048120
Phenotypes for gene: SMARCD2 were set to Congenital defects of phagocyte number or function; Neutropenia, developmental aberrations, skeletal abnormalities, hematopoietic stem cells, myelodysplasia
COVID-19 research v0.36 SLC7A7 Ellen McDonagh gene: SLC7A7 was added
gene: SLC7A7 was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: SLC7A7 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SLC7A7 were set to 28057010; 32086639; 32048120
Phenotypes for gene: SLC7A7 were set to Lysinuric protein intolerance, 222700; Severe bacterial infections; Lysinuric protein intolerance SLC7A7 deficiency; Predominantly Antibody Deficiencies
COVID-19 research v0.36 SLC39A7 Ellen McDonagh gene: SLC39A7 was added
gene: SLC39A7 was added to Viral susceptibility. Sources: Expert Review Red,Literature,IUIS Classification December 2019
Mode of inheritance for gene: SLC39A7 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SLC39A7 were set to 32086639; 32048120; 30718914
Phenotypes for gene: SLC39A7 were set to Agammaglobulinemia; B cell deficiency; Early onset infections, blistering dermatosis, failure to thrive, thrombocytopenia; Predominantly Antibody Deficiencies
COVID-19 research v0.36 RNU4ATAC Ellen McDonagh gene: RNU4ATAC was added
gene: RNU4ATAC was added to Viral susceptibility. Sources: IUIS Classification February 2018,IUIS Classification December 2019
Mode of inheritance for gene: RNU4ATAC was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RNU4ATAC were set to 32086639; 32048120
Phenotypes for gene: RNU4ATAC were set to Recurrent bacterial infections, lymphadenopathy, Spondyloepiphyseal dysplasia, extreme intrauterine growth retardation, retinal dystrophy, facial dysmorphism, may present with microcephaly; Combined immunodeficiencies with associated or syndromic features; Recurrent bacterial infections, lymphadenopathy, Spondyloepiphyseal dysplasia, extreme intrauterine growth retardation, retinal dystrophy, facial dysmorphism, may present with microcephaly, short stature
COVID-19 research v0.36 RNF31 Ellen McDonagh gene: RNF31 was added
gene: RNF31 was added to Viral susceptibility. Sources: Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,Expert Review Red,IUIS Classification February 2018
Mode of inheritance for gene: RNF31 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RNF31 were set to 32086639; 32048120; 26008899
Phenotypes for gene: RNF31 were set to Polyglucosan body myopathy, early-onset, with or without immunodeficiency; Autoinflammatory syndrome with pyogenic bacterial infection and amylopectinosis; autoinflammation and combined immunodeficiency; Combined immunodeficiencies with associated or syndromic features; Bacterial infections, autoinflammation, amylopectinosis, lymphangiectasia
COVID-19 research v0.36 RELB Ellen McDonagh gene: RELB was added
gene: RELB was added to Viral susceptibility. Sources: Combined B and T cell defect v1.12,Expert Review Red,IUIS Classification February 2018,IUIS Classification December 2019
Mode of inheritance for gene: RELB was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RELB were set to 32086639; 32048120; 26385063
Phenotypes for gene: RELB were set to Immunodeficiencies affecting cellular and humoral immunity; Recurrent infectionsImmunodeficiencies affecting cellular and humoral immunity; Recurrent infections; ?Immunodeficiency 53, 617585
COVID-19 research v0.36 REL Ellen McDonagh gene: REL was added
gene: REL was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: REL was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: REL were set to 32086639; 31103457; 32048120
Phenotypes for gene: REL were set to Recurrent infections with bacteria, mycobacteria, salmonella and opportunistic infections; Immunodeficiencies affecting cellular and humoral immunity; c-Rel deficiency
COVID-19 research v0.36 RECQL4 Ellen McDonagh gene: RECQL4 was added
gene: RECQL4 was added to Viral susceptibility. Sources: Expert Review Red,ESID Registry 20171117
Mode of inheritance for gene: RECQL4 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RECQL4 were set to 16630167
Phenotypes for gene: RECQL4 were set to Rothmund-Thomson syndrome, 268400; Combined immunodeficiency
COVID-19 research v0.36 RC3H1 Ellen McDonagh gene: RC3H1 was added
gene: RC3H1 was added to Viral susceptibility. Sources: Expert Review Red,Literature
Mode of inheritance for gene: RC3H1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RC3H1 were set to PMID: 31636267
Phenotypes for gene: RC3H1 were set to Hemophagocytic lymphohistiocytosis
COVID-19 research v0.36 PSMG2 Ellen McDonagh gene: PSMG2 was added
gene: PSMG2 was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: PSMG2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PSMG2 were set to 30664889; 32086639; 32048120
Phenotypes for gene: PSMG2 were set to Panniculitis, lipodystrophy, autoimmune hemolytic anemia; CANDLE (chronic atypical neutrophilic dermatitis with lipodystrophy); Autoinflammatory Disorders
COVID-19 research v0.36 PSMB10 Ellen McDonagh gene: PSMB10 was added
gene: PSMB10 was added to Viral susceptibility. Sources: Expert Review Red,Literature
Mode of inheritance for gene: PSMB10 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PSMB10 were set to 31783057
Phenotypes for gene: PSMB10 were set to Proteasome-associated autoinflammatory syndrome
COVID-19 research v0.36 POLE2 Ellen McDonagh gene: POLE2 was added
gene: POLE2 was added to Viral susceptibility. Sources: Expert Review Red,IUIS Classification February 2018,IUIS Classification December 2019
Mode of inheritance for gene: POLE2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: POLE2 were set to 32086639; 32048120
Phenotypes for gene: POLE2 were set to Recurrent infections, disseminated BCG infections, autoimmunity (type 1 diabetes, hypothyroidism, facial dysmorphism); Combined immunodeficiencies with associated or syndromic features; Recurrent infections, disseminated BCG infections, autoimmunity (type 1 diabetes, hypothyroidism, facial dysmorphism
COVID-19 research v0.36 POLD2 Ellen McDonagh gene: POLD2 was added
gene: POLD2 was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: POLD2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: POLD2 were set to 31449058; 32086639; 32048120
Phenotypes for gene: POLD2 were set to Immunodeficiencies affecting cellular and humoral immunity; Polymerase d 2 deficiency; Recurrent respiratory tract infections, skin infections, warts and molluscum, short stature, intellectual disability
COVID-19 research v0.36 POLD1 Ellen McDonagh gene: POLD1 was added
gene: POLD1 was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: POLD1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: POLD1 were set to 31449058; 32086639; 32048120; 31629014
Phenotypes for gene: POLD1 were set to Immunodeficiencies affecting cellular and humoral immunity; Recurrent respiratory tract infections, skin infections, warts and molluscum, short stature, intellectual disability; Polymerase d 1 deficiency
COVID-19 research v0.36 PLEKHM1 Ellen McDonagh gene: PLEKHM1 was added
gene: PLEKHM1 was added to Viral susceptibility. Sources: Expert Review Red,IUIS Classification February 2018,IUIS Classification December 2019
Mode of inheritance for gene: PLEKHM1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PLEKHM1 were set to 32086639; 32048120
Phenotypes for gene: PLEKHM1 were set to Osteopetrosis; Defects in intrinsic and innate immunity; Defects in Intrinsic and Innate Immunity
COVID-19 research v0.36 OSTM1 Ellen McDonagh gene: OSTM1 was added
gene: OSTM1 was added to Viral susceptibility. Sources: Expert Review Red,IUIS Classification February 2018,IUIS Classification December 2019
Mode of inheritance for gene: OSTM1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: OSTM1 were set to 32086639; 32048120
Phenotypes for gene: OSTM1 were set to Defects in intrinsic and innate immunity; Defects in Intrinsic and Innate Immunity; Osteopetrosis with hypocalcemia, neurologic features
COVID-19 research v0.36 NBAS Ellen McDonagh gene: NBAS was added
gene: NBAS was added to Viral susceptibility. Sources: Expert Review Red,IUIS Classification February 2018,IUIS Classification December 2019
Mode of inheritance for gene: NBAS was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: NBAS were set to 32086639; 32048120
Phenotypes for gene: NBAS were set to Infantile liver failure syndrome 2, 616483; Defects in intrinsic and innate immunity; Fever induced liver failure; Defects in Intrinsic and Innate Immunity; Fever induces liver failure
COVID-19 research v0.36 MSH6 Ellen McDonagh gene: MSH6 was added
gene: MSH6 was added to Viral susceptibility. Sources: Expert Review Red,IUIS Classification February 2018,GRID V2.0,IUIS Classification December 2019
Mode of inheritance for gene: MSH6 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MSH6 were set to 32086639; 32048120
Phenotypes for gene: MSH6 were set to Colorectal cancer, hereditary nonpolyposis, type 5 614350; Endometrial cancer, familial 608089; Predominantly Antibody Deficiencies; Family or personal history of cancer; Mismatch repair cancer syndrome 276300
COVID-19 research v0.36 MS4A1 Ellen McDonagh gene: MS4A1 was added
gene: MS4A1 was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,Expert Review Red,IUIS Classification February 2018
Mode of inheritance for gene: MS4A1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MS4A1 were set to 27250108; 32086639; 32048120; 20038800
Phenotypes for gene: MS4A1 were set to Predominantly Antibody Deficiencies; Recurrent infections; Common variable immunodeficiency disorders (CVID); Immunodeficiency, common variable, 5 613495
COVID-19 research v0.36 MRE11 Ellen McDonagh gene: MRE11 was added
gene: MRE11 was added to Viral susceptibility. Sources: Expert Review Red,ESID Registry 20171117,GRID V2.0
Mode of inheritance for gene: MRE11 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MRE11 were set to 10612394; 8445618
Phenotypes for gene: MRE11 were set to AT-like disorder; Ataxia-telangiectasia-like disorder 1 604391
COVID-19 research v0.36 MPO Ellen McDonagh gene: MPO was added
gene: MPO was added to Viral susceptibility. Sources: Expert Review Red,ESID Registry 20171117,GRID V2.0
Mode of inheritance for gene: MPO was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MPO were set to 9354683; 15108282; 9637725
Phenotypes for gene: MPO were set to Myeloperoxidase deficiency 254600
COVID-19 research v0.36 MKL1 Ellen McDonagh gene: MKL1 was added
gene: MKL1 was added to Viral susceptibility. Sources: Expert Review Red,IUIS Classification February 2018,IUIS Classification December 2019
Mode of inheritance for gene: MKL1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MKL1 were set to 26224645; 32086639; 32048120
Phenotypes for gene: MKL1 were set to Susceptibility to severe bacterial infection; Mild thrombocytopenia; Congenital defects of phagocyte number or function
COVID-19 research v0.36 MASP2 Ellen McDonagh Mode of inheritance for gene MASP2 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to BIALLELIC, autosomal or pseudoautosomal
Added phenotypes Complement Deficiencies; MASP2 deficiency 613791; Mannan-binding lectin serine protease (MASP) deficiency; Pyogenic infections, inflammatory lung disease, autoimmunity for gene: MASP2
Publications for gene MASP2 were updated from 19405982 to 24658431; 32086639; 32048120; 19405982
COVID-19 research v0.36 LIG1 Ellen McDonagh gene: LIG1 was added
gene: LIG1 was added to Viral susceptibility. Sources: Emory Genetics Laboratory,Expert Review,Other,IUIS Classification December 2019,Expert Review Red,Literature,IUIS Classification February 2018
Mode of inheritance for gene: LIG1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: LIG1 were set to 30395541; 1581963; 32086639; 32048120
Phenotypes for gene: LIG1 were set to DNA ligase I deficiency; Combined immunodeficiencies with associated or syndromic features; DNA-ligase 1 ATP-dependent deficiency (LIG1); Recurrent respiratory infections, growth retardation, sun sensitivity, lymphoma, radiation sensitivity
COVID-19 research v0.36 IL6ST Ellen McDonagh gene: IL6ST was added
gene: IL6ST was added to Viral susceptibility. Sources: Expert Review Red,Literature,IUIS Classification December 2019
Mode of inheritance for gene: IL6ST was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IL6ST were set to 31235509; 32086639; 30309848; 28747427; 32048120
Phenotypes for gene: IL6ST were set to Eczema; Abnormal acute-phase responses; Recurrent infections; Bacterial infections, boiles, eczema, pulmonary abscesses, pneumatoceles, bone fractures, scoliosis, retention of primary teeth, craniosynostosis; Eosinophilia; Elevated IgE; Combined immunodeficiencies with associated or syndromic features
COVID-19 research v0.36 IL6R Ellen McDonagh gene: IL6R was added
gene: IL6R was added to Viral susceptibility. Sources: Expert Review Red,Literature,IUIS Classification December 2019
Mode of inheritance for gene: IL6R was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IL6R were set to 31235509; 32086639; 32048120; 31778705
Phenotypes for gene: IL6R were set to Eczema; Recurrent infections; Recurrent pyogenic infections, cold abscesses, high circulating IL-6 levels; Hyper-IgE; Combined immunodeficiencies with associated or syndromic features
COVID-19 research v0.36 IL2RB Ellen McDonagh gene: IL2RB was added
gene: IL2RB was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: IL2RB was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IL2RB were set to 32086639; 31040185; 32048120; 31040184
Phenotypes for gene: IL2RB were set to Lymphoproliferation, lymphadenopathy, hepatosplenomegaly, autoimmune hemolytic anemia, dermatitis, enteropathy, recurrent viral (EBV, CMV) infections; Immunodeficiency 63 with lymphoproliferation and autoimmunity, 618495; CD122 deficiency
COVID-19 research v0.36 IL22 Ellen McDonagh gene: IL22 was added
gene: IL22 was added to Viral susceptibility. Sources: Expert Review Red,GRID V2.0
Mode of inheritance for gene: IL22 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: IL22 were set to AutoAb Chronic Mucocutaneous Candidiasis
COVID-19 research v0.36 IFNAR2 Ellen McDonagh gene: IFNAR2 was added
gene: IFNAR2 was added to Viral susceptibility. Sources: Expert Review Red,IUIS Classification February 2018,IUIS Classification December 2019
Mode of inheritance for gene: IFNAR2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IFNAR2 were set to 32086639; 32048120; 26424569
Phenotypes for gene: IFNAR2 were set to ?Immunodeficiency 45, 616669; Severe viral infections (disseminated vaccine-strain measles, HHV6); Defects in Intrinsic and Innate Immunity
COVID-19 research v0.36 ICOSLG Ellen McDonagh gene: ICOSLG was added
gene: ICOSLG was added to Viral susceptibility. Sources: Expert Review Red,Victorian Clinical Genetics Services,IUIS Classification December 2019
Mode of inheritance for gene: ICOSLG was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ICOSLG were set to 32086639; 32048120; 30498080
Phenotypes for gene: ICOSLG were set to Immunodeficiencies affecting cellular and humoral immunity; Recurrent bacterial and viral infections
COVID-19 research v0.36 HYOU1 Ellen McDonagh gene: HYOU1 was added
gene: HYOU1 was added to Viral susceptibility. Sources: Expert Review Red,IUIS Classification February 2018,IUIS Classification December 2019
Mode of inheritance for gene: HYOU1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: HYOU1 were set to 32086639; 32048120
Phenotypes for gene: HYOU1 were set to Hypoglycemia, inflammatory complications; Congenital defects of phagocyte number or function
COVID-19 research v0.36 HMOX1 Ellen McDonagh gene: HMOX1 was added
gene: HMOX1 was added to Viral susceptibility. Sources: Expert Review Red,IUIS Classification February 2018
Mode of inheritance for gene: HMOX1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: HMOX1 were set to 21088618; 9884342
Phenotypes for gene: HMOX1 were set to amyloidosis; Hemolysis, nephritis, inflammation; Defects in Intrinsic and Innate Immunity
COVID-19 research v0.36 HAVCR2 Ellen McDonagh gene: HAVCR2 was added
gene: HAVCR2 was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: HAVCR2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: HAVCR2 were set to 30792187; 32086639; 32048120; 30374066
Phenotypes for gene: HAVCR2 were set to T-cell lymphoma, subcutaneous panniculitis-like, 618398; Tim-3 deficiency; T-cell lymphoma, subcutaneous panniculitis-like, HLH; Autoinflammatory Disorders
COVID-19 research v0.36 GAD1 Ellen McDonagh gene: GAD1 was added
gene: GAD1 was added to Viral susceptibility. Sources: Expert Review Red,A- or hypo-gammaglobulinaemia v1.25
Mode of inheritance for gene: GAD1 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: GAD1 were set to ?Cerebral palsy, spastic quadriplegic, 1, 603513
COVID-19 research v0.36 FERMT1 Ellen McDonagh gene: FERMT1 was added
gene: FERMT1 was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: FERMT1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: FERMT1 were set to 32086639; 32048120; 21936020
Phenotypes for gene: FERMT1 were set to FERMT1 deficiency (Kindler syndrome); Diseases of Immune Dysregulation; Kindler syndrome, 173650; Dermatosis characterized by congenital blistering, skin atrophy, photosensitivity, skin fragility, and scaling
COVID-19 research v0.36 FCN3 Ellen McDonagh gene: FCN3 was added
gene: FCN3 was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,Expert Review Red,IUIS Classification February 2018
Mode of inheritance for gene: FCN3 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: FCN3 were set to 25662573; 19535802; 32086639; 32048120; 20971976; 22226667
Phenotypes for gene: FCN3 were set to Respiratory infections, abscesses; Complement Deficiencies; Ficolin3 deficiency; Immunodeficiency due to ficolin 3 deficiency, 613860
COVID-19 research v0.36 FCHO1 Ellen McDonagh gene: FCHO1 was added
gene: FCHO1 was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: FCHO1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: FCHO1 were set to 32086639; 30822429; 32048120
Phenotypes for gene: FCHO1 were set to Recurrent infections, lymphoproliferation, increased activation-induced T-cell death, defective clathrin-mediated endocytosis; FCHO1 deficiency; Immunodeficiencies affecting cellular and humoral immunity
COVID-19 research v0.36 FANCM Ellen McDonagh gene: FANCM was added
gene: FANCM was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: FANCM was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: FANCM were set to 32086639; 32048120
Phenotypes for gene: FANCM were set to Fanconi Anemia Type M; Bone marrow failure; Normal to low NK, CNS, skeletal, skin, cardiac, GI, urogenital anomalies, increased chromosomal breakage
COVID-19 research v0.36 FANCI Ellen McDonagh gene: FANCI was added
gene: FANCI was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: FANCI was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: FANCI were set to 32086639; 32048120
Phenotypes for gene: FANCI were set to Fanconi anemia, complementation group I, 609053; Bone marrow failure; Fanconi Anemia Type I; Normal to low NK, CNS, skeletal, skin, cardiac, GI, urogenital anomalies, increased chromosomal breakage
COVID-19 research v0.36 FANCF Ellen McDonagh gene: FANCF was added
gene: FANCF was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: FANCF was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: FANCF were set to 32086639; 32048120
Phenotypes for gene: FANCF were set to Normal to low NK, CNS, skeletal, skin, cardiac, GI, urogenital anomalies, increased chromosomal breakage; Fanconi anemia, complementation group F, 603467; Bone marrow failure; Fanconi Anemia Type F
COVID-19 research v0.36 FAAP24 Ellen McDonagh gene: FAAP24 was added
gene: FAAP24 was added to Viral susceptibility. Sources: Expert Review Red,IUIS Classification February 2018,IUIS Classification December 2019
Mode of inheritance for gene: FAAP24 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: FAAP24 were set to 32086639; 27473539; 32048120
Phenotypes for gene: FAAP24 were set to EBV infection-driven lymphoproliferative disease; Diseases of Immune Dysregulation
COVID-19 research v0.36 ERCC4 Ellen McDonagh gene: ERCC4 was added
gene: ERCC4 was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: ERCC4 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ERCC4 were set to 32086639; 32048120
Phenotypes for gene: ERCC4 were set to Fanconi anemia, complementation group Q, 615272; Normal to low NK, CNS, skeletal, skin, cardiac, GI, urogenital anomalies, increased chromosomal breakage; Fanconi Anemia Type Q; Bone marrow failure
COVID-19 research v0.36 ERCC3 Ellen McDonagh gene: ERCC3 was added
gene: ERCC3 was added to Viral susceptibility. Sources: Victorian Clinical Genetics Services,North West GLH,NHS GMS,London North GLH,Expert Review Red
Mode of inheritance for gene: ERCC3 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ERCC3 were set to none
Phenotypes for gene: ERCC3 were set to none
COVID-19 research v0.36 EPCAM Ellen McDonagh gene: EPCAM was added
gene: EPCAM was added to Viral susceptibility. Sources: Expert Review Red,GOSH PID v.8.0
Mode of inheritance for gene: EPCAM was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: EPCAM were set to Diarrhea 5, with tufting enteropathy, congenital
COVID-19 research v0.36 DEF6 Ellen McDonagh gene: DEF6 was added
gene: DEF6 was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: DEF6 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: DEF6 were set to 32086639; 31308374; 32048120
Phenotypes for gene: DEF6 were set to DEF6 deficiency; Diseases of Immune Dysregulation; Enteropathy, hepatosplenomegaly, cardiomyopathy, recurrent infections
COVID-19 research v0.36 DBR1 Ellen McDonagh gene: DBR1 was added
gene: DBR1 was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: DBR1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: DBR1 were set to 32086639; 32048120
Phenotypes for gene: DBR1 were set to DBR1 deficiency; HSE of the brainstem. Other viral infections of the brainstem; Defects in intrinsic and innate immunity
COVID-19 research v0.36 CLCN7 Ellen McDonagh gene: CLCN7 was added
gene: CLCN7 was added to Viral susceptibility. Sources: Expert Review Red,IUIS Classification February 2018,IUIS Classification December 2019
Mode of inheritance for gene: CLCN7 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CLCN7 were set to 32086639; 32048120
Phenotypes for gene: CLCN7 were set to Defects in Intrinsic and Innate Immunity; Osteopetrosis with hypocalcemia, neurologic features
COVID-19 research v0.36 C8G Ellen McDonagh gene: C8G was added
gene: C8G was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,Expert Review Red,IUIS Classification February 2018
Mode of inheritance for gene: C8G was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: C8G were set to 32086639; 32048120
Phenotypes for gene: C8G were set to Complement Deficiencies; Complement factor 8 defect; Complement component 8 deficiency; Disseminated neisserial infections
COVID-19 research v0.36 C17orf62 Ellen McDonagh gene: C17orf62 was added
gene: C17orf62 was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: C17orf62 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: C17orf62 were set to 30312704; 30361506; 32086639; 32048120
Phenotypes for gene: C17orf62 were set to Autosomal recessive CGD EROS; Congenital defects of phagocyte number or function
COVID-19 research v0.36 BRCA2 Ellen McDonagh gene: BRCA2 was added
gene: BRCA2 was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: BRCA2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: BRCA2 were set to 32086639; 32048120
Phenotypes for gene: BRCA2 were set to Fanconi anemia, complementation group D1, 605724; Normal to low NK, CNS, skeletal, skin, cardiac, GI, urogenital anomalies, increased chromosomal breakage; Fanconi Anemia Type D1; Bone marrow failure
COVID-19 research v0.36 BRCA1 Ellen McDonagh gene: BRCA1 was added
gene: BRCA1 was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: BRCA1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: BRCA1 were set to 32086639; 32048120
Phenotypes for gene: BRCA1 were set to Fanconi Anemia Type S; Fanconi anemia, complementation group S, 617883; normal to low NK, CNS, skeletal, skin, cardiac, GI, urogenital anomalies, increased chromosomal breakage; Bone marrow failure
COVID-19 research v0.36 BLOC1S6 Ellen McDonagh gene: BLOC1S6 was added
gene: BLOC1S6 was added to Viral susceptibility. Sources: Victorian Clinical Genetics Services, London North GLH,GRID V2.0,NHS GMS,GRID V2.0North West GLH,Expert Review Red
Mode of inheritance for gene: BLOC1S6 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: BLOC1S6 were set to 224,614,752,030,146,000,000,000
Phenotypes for gene: BLOC1S6 were set to Immune Dysregulation; Hermansky-pudlak syndrome 9, 614171; HPS9, palladin deficiency (NK cell defect)
COVID-19 research v0.36 ARHGEF1 Ellen McDonagh gene: ARHGEF1 was added
gene: ARHGEF1 was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: ARHGEF1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ARHGEF1 were set to 32086639; 30521495; 32048120
Phenotypes for gene: ARHGEF1 were set to Recurrent infections, bronchiectasis; Immunodeficiency 62, 618459; ARHGEF1 deficiency; Predominantly Antibody Deficiencies
COVID-19 research v0.36 AP3D1 Ellen McDonagh gene: AP3D1 was added
gene: AP3D1 was added to Viral susceptibility. Sources: Expert Review Red,Literature,IUIS Classification February 2018,IUIS Classification December 2019
Mode of inheritance for gene: AP3D1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: AP3D1 were set to 26744459; 32086639; 32048120
Phenotypes for gene: AP3D1 were set to neutropenia; Immunodeficient HPS; seizures; Diseases of Immune Dysregulation; Hermansky-Pudlak syndrome with neutropenia; neuordevelopmental delay; albinism; ?Hermansky-Pudlak syndrome 10, 617050; Hermansky-Pudlak syndrome; Oculocutaneous albinism, recurrent infections, seizures, hearing loss and neurodevelopmental delay; Oculocutaneous albinism, severe neutropenia, recurrent infections, seizures, hearing loss and neurodevelopmental delay; HSP10
COVID-19 research v0.36 ALPI Ellen McDonagh gene: ALPI was added
gene: ALPI was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: ALPI was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ALPI were set to 32086639; 32048120; 29567797
Phenotypes for gene: ALPI were set to Inflammatory bowel disease; ALPI deficiency; Autoinflammatory Disorders
COVID-19 research v0.36 WDR1 Ellen McDonagh gene: WDR1 was added
gene: WDR1 was added to Viral susceptibility. Sources: North West GLH,NHS GMS,London North GLH,IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: WDR1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: WDR1 were set to 32086639; 32048120; 27557945
Phenotypes for gene: WDR1 were set to Mild neutropenia, poor wound healing, severe stomatitis, neutrophil nuclei herniate; Congenital defects of phagocyte number or function
COVID-19 research v0.36 USP18 Ellen McDonagh gene: USP18 was added
gene: USP18 was added to Viral susceptibility. Sources: North West GLH,NHS GMS,London North GLH,IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: USP18 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: USP18 were set to 32086639; 32048120; 31272490; 27325888
Phenotypes for gene: USP18 were set to Pseudo-TORCH syndrome 2, 617397; Autoinflammatory Disorders; TORCH like syndrome
COVID-19 research v0.36 TNFRSF13C Ellen McDonagh gene: TNFRSF13C was added
gene: TNFRSF13C was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: TNFRSF13C was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TNFRSF13C were set to 32086639; 32048120
Phenotypes for gene: TNFRSF13C were set to Immunodeficiency, common variable, 4; Variable clinical expression; Isolated IgG subclass deficiency; Common variable immunodeficiency disorders (CVID); Predominantly Antibody Deficiencies
COVID-19 research v0.36 TNFRSF11A Ellen McDonagh gene: TNFRSF11A was added
gene: TNFRSF11A was added to Viral susceptibility. Sources: North West GLH,NHS GMS,London North GLH,IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: TNFRSF11A was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TNFRSF11A were set to 32086639; 32048120
Phenotypes for gene: TNFRSF11A were set to Osteopetrosis; Defects in intrinsic and innate immunity; Defects in Intrinsic and Innate Immunity
COVID-19 research v0.36 TAPBP Ellen McDonagh gene: TAPBP was added
gene: TAPBP was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,GRID V2.0,GOSH PID v.8.0,IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: TAPBP was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TAPBP were set to 32086639; 32048120; 12149238
Phenotypes for gene: TAPBP were set to Bare lymphocyte syndrome, type I 604571; Vasculitis, pyoderma gangrenosum; HLA class I deficiency; Immunodeficiencies affecting cellular and humoral immunity; Vasculitis,pyoderma gangrenosum
COVID-19 research v0.36 RHOH Ellen McDonagh gene: RHOH was added
gene: RHOH was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: RHOH was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RHOH were set to 22850876; 32086639; 32048120; 24189071
Phenotypes for gene: RHOH were set to T cell deficiency and various infectious diseases; Combined immunodeficiency; HPV infection, lung granulomas, molluscum contagiosum, lymphoma; Epidermodysplasia verruciformis; Immunodeficiencies affecting cellular and humoral immunity; RhoH deficiency
COVID-19 research v0.36 PSMB9 Ellen McDonagh gene: PSMB9 was added
gene: PSMB9 was added to Viral susceptibility. Sources: Victorian Clinical Genetics Services,North West GLH,NHS GMS,London North GLH,Expert Review Amber
Mode of inheritance for gene: PSMB9 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PSMB9 were set to 26524591
Phenotypes for gene: PSMB9 were set to CANDLE syndrome (Autoinflammation, lipodystrophy, and dermatosis syndrome); Autoinflammation, lipodystrophy, and dermatosis syndrome
COVID-19 research v0.36 PSMB4 Ellen McDonagh gene: PSMB4 was added
gene: PSMB4 was added to Viral susceptibility. Sources: Victorian Clinical Genetics Services,North West GLH,NHS GMS,London North GLH,Expert Review Amber
Mode of inheritance for gene: PSMB4 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PSMB4 were set to 26524591
Phenotypes for gene: PSMB4 were set to CANDLE syndrome (Autoinflammation, lipodystrophy, and dermatosis syndrome)
COVID-19 research v0.36 POLE Ellen McDonagh gene: POLE was added
gene: POLE was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: POLE was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: POLE were set to 23230001
Phenotypes for gene: POLE were set to Recurrent respiratory infections, meningitis, facial dysmorphism, livido, short stature; Combined immunodeficiencies with associated or syndromic features; FILS syndrome 615139; Facial dysmorphism, immunodeficiency, livedo, and short stature (FILS syndrome)
COVID-19 research v0.36 PMS2 Ellen McDonagh gene: PMS2 was added
gene: PMS2 was added to Viral susceptibility. Sources: ESID Registry 20171117,GRID V2.0,IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: PMS2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PMS2 were set to 7661930; 9488480; 15077197; 32086639; 16507833; 10763829; 32048120
Phenotypes for gene: PMS2 were set to Recurrent infections, cafe-au-lait spots, lymphoma, colorectal carcinoma, brain tumors; Post-Meiotic Segregation 2 (PMS2) deficiency; Mismatch repair cancer syndrome 276300; Combined immunodeficiencies with associated or syndromic features; CSR defects and Hyper IgM (HIGM) syndromes; Recurrent infections, caf-au-lait spots, lymphoma, colorectal carcinoma, brain tumors
COVID-19 research v0.36 NOP10 Ellen McDonagh gene: NOP10 was added
gene: NOP10 was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: NOP10 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: NOP10 were set to 17507419
Phenotypes for gene: NOP10 were set to Dyskeratosis congenita; Hoyeraal-Hreidarsson syndrome; Dyskeratosis congenita 1; Dyskeratosis congenita, autosomal recessive 1 224230; Combined immunodeficiencies with associated or syndromic features; Intrauterine growth retardation, microcephaly, nail dystrophy, sparse scalp hair and eyelashes, hyperpigmentation of skin, palmar hyperkeratosis, premalignant oral leukoplakia, pancytopenia, myelodysplasia, +/- recurrent infections. A severe phenotype with developmental delay and cerebellar hypoplasia known as Hoyeraal-Hreidarsson Syndrome (HHS) may occur in some DKC patients
COVID-19 research v0.36 IRF9 Ellen McDonagh gene: IRF9 was added
gene: IRF9 was added to Viral susceptibility. Sources: Expert Review,Expert Review Amber
Mode of inheritance for gene: IRF9 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IRF9 were set to 30143481; 30826365
Phenotypes for gene: IRF9 were set to Immunodeficiency 65, susceptibility to viral infections, 618648
COVID-19 research v0.36 IRF7 Ellen McDonagh Mode of inheritance for gene IRF7 was changed from Unknown to BIALLELIC, autosomal or pseudoautosomal
Added phenotypes Severe influenza; ?Immunodeficiency 39, 616345; Severe influenza disease; IRF7 deficiency; Defects in Intrinsic and Innate Immunity for gene: IRF7
Publications for gene IRF7 were updated from 26621750 to 26761402; 9315633; 32086639; 25814066; 32048120; 26621750
COVID-19 research v0.36 IL21 Ellen McDonagh gene: IL21 was added
gene: IL21 was added to Viral susceptibility. Sources: Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: IL21 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IL21 were set to 32086639; 24746753; 32048120
Phenotypes for gene: IL21 were set to Immunodeficiency, common variable, 11, 615767; Severe early onset colitis, recurrent sinopulmonary infections; Immunodeficiencies affecting cellular and humoral immunity
COVID-19 research v0.36 IGKC Ellen McDonagh gene: IGKC was added
gene: IGKC was added to Viral susceptibility. Sources: ESID Registry 20171117,GRID V2.0,IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: IGKC was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IGKC were set to 32086639; 32048120; 4185453
Phenotypes for gene: IGKC were set to Immunoglobulin chain deficiencies; Kappa light chain deficiency, 614102; Asymptomatic; Predominantly Antibody Deficiencies
COVID-19 research v0.36 FPR1 Ellen McDonagh gene: FPR1 was added
gene: FPR1 was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: FPR1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: FPR1 were set to 20203610; 28371599; 8224916; 29105764; 2910576; 10882119; 32086639; 32048120
Phenotypes for gene: FPR1 were set to Periodontitis only; Congenital defects of phagocyte number or function; Periodontitis; Localized juvenile peridontitis
COVID-19 research v0.36 FCGR3A Ellen McDonagh Mode of inheritance for gene FCGR3A was changed from Unknown to BIALLELIC, autosomal or pseudoautosomal
Added phenotypes severe herpes viral infections, particularly VZV, Epstein Barr virus (EBV), and (HPV); CD16 deficiency; predisposition to severe viral infection; Immunodeficiency 20, 615707; Autosomal recessive primary immunodeficiency with defective spontaneous NK cell cytotoxicity; Defects in Intrinsic and Innate Immunity; Fc receptor deficiencies for gene: FCGR3A
Publications for gene FCGR3A were updated from to 8609432; 23006327; 32086639; 8608639; 32048120; 8874200
COVID-19 research v0.36 DNASE1L3 Ellen McDonagh gene: DNASE1L3 was added
gene: DNASE1L3 was added to Viral susceptibility. Sources: North West GLH,NHS GMS,London North GLH,IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: DNASE1L3 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: DNASE1L3 were set to 27821515; 23666765; 22019780; 32086639; 32048120
Phenotypes for gene: DNASE1L3 were set to Systemic lupus erythematosus 16, 614420; Autoinflammatory Disorders; Diseases of Immune Dysregulation; familial early-onset SLE; Systemic lupus erythematosus, lupus nephritis, hypocomplementemic urticarial vasculitis
COVID-19 research v0.36 CTC1 Ellen McDonagh gene: CTC1 was added
gene: CTC1 was added to Viral susceptibility. Sources: North West GLH,NHS GMS,London North GLH,IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: CTC1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CTC1 were set to 22267198; 32086639; 32048120
Phenotypes for gene: CTC1 were set to Cerebroretinal microangiopathy with calcifications and cysts, 612199; Combined immunodeficiencies with associated or syndromic features; Bone marrow failure; Intrauterine growth retardation, sparse graying hair, dystrophic nails, trilinear bone marrow failure, osteopenia, gastrointestinal hemorrhage due to vascular ectasia, retinal telangiectasia, intracranial calcification, abnormal telomeres
COVID-19 research v0.36 CR2 Ellen McDonagh gene: CR2 was added
gene: CR2 was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,GRID V2.0,A- or hypo-gammaglobulinaemia v1.25,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: CR2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CR2 were set to 22035880; 26325596
Phenotypes for gene: CR2 were set to Recurrent infections; Lupus; Isolated IgG subclass deficiency; Immunodeficiency, common variable, 7; Common variable immunodeficiency disorders (CVID); hypogammaglobulinaemia; Predominantly Antibody Deficiencies; Immunodeficiency, common variable, 7, 614699
COVID-19 research v0.36 CFTR Ellen McDonagh gene: CFTR was added
gene: CFTR was added to Viral susceptibility. Sources: IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: CFTR was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CFTR were set to 32086639; 32048120
Phenotypes for gene: CFTR were set to Congenital defects of phagocyte number or function; Respiratory infections, pancreatic insufficiency, elevated sweat chloride; Cystic fibrosis, 219700
COVID-19 research v0.36 CD8A Ellen McDonagh gene: CD8A was added
gene: CD8A was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: CD8A was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CD8A were set to 11435463; 32086639; 32048120; 17658607
Phenotypes for gene: CD8A were set to Susceptibility to respiratory infections associated with CD8alpha chain mutation; Immunodeficiencies affecting cellular and humoral immunity; CD8 deficiency familial, 608957; Recurrent infections, may be asymptomatic
COVID-19 research v0.36 CD81 Ellen McDonagh gene: CD81 was added
gene: CD81 was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: CD81 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CD81 were set to 27250108; 32086639; 14530327; 32048120; 20237408
Phenotypes for gene: CD81 were set to CD81 deficiency; Isolated IgG subclass deficiency; Recurrent infections, may have glomerulonephritis; Common variable immunodeficiency disorders (CVID); hypogammaglobulinaemia; Predominantly Antibody Deficiencies; Immunodeficiency, common variable 6, 613496
COVID-19 research v0.36 CD247 Ellen McDonagh gene: CD247 was added
gene: CD247 was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,GRID V2.0,GOSH PID v.8.0,SCID v1.6,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: CD247 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CD247 were set to 26690594; 17170122; 16672702; 25688246; 27555457; https://doi.org/10.14785/lpsn-2014-0012
Phenotypes for gene: CD247 were set to ?Immunodeficiency 25; T-B+ severe combined immunodeficiency due to CD3zeta; Immunodeficiency 25, 610163; Atypical Severe Combined Immunodeficiency (Atypical SCID); Nl NK, no g/d T cells; Immunodeficiencies affecting cellular and humoral immunity; T-B+ SCID; Severe combined immunodeficiency (SCID)
COVID-19 research v0.36 BCL10 Ellen McDonagh gene: BCL10 was added
gene: BCL10 was added to Viral susceptibility. Sources: Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: BCL10 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: BCL10 were set to 32086639; 32048120; 25365219
Phenotypes for gene: BCL10 were set to Combined immunodeficiency with B cell, T cell, and fibroblast defects; ?Immunodeficiency 37, 616098; Recurrent bacterial and viral infections, candidiasis, gastroenteritis; Immunodeficiencies affecting cellular and humoral immunity
COVID-19 research v0.36 AP1S3 Ellen McDonagh gene: AP1S3 was added
gene: AP1S3 was added to Viral susceptibility. Sources: Victorian Clinical Genetics Services,North West GLH,NHS GMS,London North GLH,IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: AP1S3 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: AP1S3 were set to 32086639; 32048120
Phenotypes for gene: AP1S3 were set to Pustular psoriasis, 616106; Autoinflammatory Disorders; Pustular psoriasis
COVID-19 research v0.36 ADAM17 Ellen McDonagh gene: ADAM17 was added
gene: ADAM17 was added to Viral susceptibility. Sources: Victorian Clinical Genetics Services,North West GLH,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: ADAM17 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ADAM17 were set to 22010916; 20603312; 25058236; 32086639; 11149563; 28930861; 32048120; 25171914
Phenotypes for gene: ADAM17 were set to IBD-1; ADAM17 deficiency; Inflammatory skin and bowel disease, neonatal, 1; Inflammatory skin and bowel disease, neonatal 1, 614328; Autoinflammatory Disorders; inflammatory skin; Early onset diarrhea and skin lesions
COVID-19 research v0.36 ZBTB24 Ellen McDonagh gene: ZBTB24 was added
gene: ZBTB24 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: ZBTB24 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ZBTB24 were set to 21906047; 21596365
Phenotypes for gene: ZBTB24 were set to Combined immunodeficiencies with associated or syndromic features; Immunodeficiency-centromeric instability-facial anomalies syndrome-2 614069; Immunodeficiency centromeric instability facial anomalies syndrome (ICF); Facial dysmorphic features, macroglossia, bacterial/opportunistic infections, malabsorption, cytopenias, malignancies, multiradial configurations of chromosomes 1, 9, 16
COVID-19 research v0.36 ZAP70 Ellen McDonagh gene: ZAP70 was added
gene: ZAP70 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,SCID v1.6,IUIS Classification February 2018
Mode of inheritance for gene: ZAP70 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: ZAP70 were set to Selective T-cell defect; Combined immunodeficiency; Autoimmune disease, multisystem, infantile-onset, 2; Immunodeficiency 48; Severe Combined Immune Deficiency; Diseases of Immune Dysregulation; Immunodeficiencies affecting cellular and humoral immunity; Severe autoimmunity; Zap-70 deficiency; May have immune dysregulation, autoimmunity; Severe combined immunodeficiency (SCID)
COVID-19 research v0.36 WIPF1 Ellen McDonagh gene: WIPF1 was added
gene: WIPF1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: WIPF1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: WIPF1 were set to 11869681; 22231303; 9405671; 14757742; 27742395
Phenotypes for gene: WIPF1 were set to WIP deficiency; ?Wiskott-Aldrich syndrome 2 614493; Wiskott-Aldrich syndrome like, WIP deficiency; Combined immunodeficiencies with associated or syndromic features; Thrombocytopenia with or without small platelets, recurrent bacterial and viral infections, eczema, bloody diarrhea, WAS protein absent
COVID-19 research v0.36 VPS45 Ellen McDonagh gene: VPS45 was added
gene: VPS45 was added to Viral susceptibility. Sources: Expert Review Green,Victorian Clinical Genetics Services,North West GLH,Congenital neutropaenia v1.22,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: VPS45 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: VPS45 were set to 23599270; 23738510
Phenotypes for gene: VPS45 were set to VPS45 deficiency (SCN5); Neutropenia, severe congenital 5; Congenital defects of phagocyte number or function; Extramedullary hematopoiesis, bone marrow fibrosis, nephromegaly; Neutropenia, severe congenital, 5, autosomal recessive, 615285
COVID-19 research v0.36 VPS13B Ellen McDonagh gene: VPS13B was added
gene: VPS13B was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,Congenital neutropaenia v1.22,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: VPS13B was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: VPS13B were set to 24311531; 15211651; 12730828; 20461111; 15154116
Phenotypes for gene: VPS13B were set to Cohen syndrome, 216550; Congenital defects of phagocyte number or function; Dysmorphism, mental retardation, obesity, deafness, neutropenia; Cohen syndrome
COVID-19 research v0.36 USB1 Ellen McDonagh gene: USB1 was added
gene: USB1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: USB1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: USB1 were set to 20503306; 20004881
Phenotypes for gene: USB1 were set to Poikiloderma with neutropenia, 604173; Clericuzio-type poikiloderma with neutropenia syndrome; Congenital defects of phagocyte number or function; Retinopathy, developmental delay, facial dysmorphisms, poikiloderma
COVID-19 research v0.36 UNG Ellen McDonagh gene: UNG was added
gene: UNG was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,A- or hypo-gammaglobulinaemia v1.25,IUIS Classification February 2018
Mode of inheritance for gene: UNG was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: UNG were set to 12958596
Phenotypes for gene: UNG were set to Hyper IgM syndrome with lymphoid hyperplasia; Immunodeficiency with hyper IgM, type 5, 608106; Enlarged lymph nodes and germinal centers; Predominantly Antibody Deficiencies; CSR defects and Hyper IgM (HIGM) syndromes; Immunodeficiency with hyper IgM, type 5
COVID-19 research v0.36 UNC93B1 Ellen McDonagh Mode of inheritance for gene UNC93B1 was changed from Unknown to BIALLELIC, autosomal or pseudoautosomal
Added phenotypes Herpetic encephalitis (HSE); Herpes simplex virus 1 encephalitis; Herpes simplex encephalitis, susceptibility to, 1; {Encephalopathy, acute, infection-induced (herpes-specific), susceptibility to, 1} 610551; Defects in Intrinsic and Innate Immunity for gene: UNC93B1
Publications for gene UNC93B1 were updated from 26621750 to 16973841; 16415873; 29768176; 26621750
COVID-19 research v0.36 UNC13D Ellen McDonagh gene: UNC13D was added
gene: UNC13D was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: UNC13D was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: UNC13D were set to 15632205; 14622600; 16278825; 15703195; 17993578
Phenotypes for gene: UNC13D were set to Hemophagocytic lymphohistiocytosis, familial 3, 608898; Diseases of Immune Dysregulation; Familial hemophagocytic lymphohistiocytosis syndromes (FHLH); HPLH3; HLH3; FHL3; Fever, HSM, HLH, cytopenias,
COVID-19 research v0.36 TYK2 Ellen McDonagh gene: TYK2 was added
gene: TYK2 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: TYK2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TYK2 were set to 22402565; 17088085; 26304966
Phenotypes for gene: TYK2 were set to Hyper IgE syndrome (HIES); Defects in Intrinsic and Innate Immunity; Immunodeficiency 35 611521; Susceptibility to intracellular bacteria (mycobacteria, Salmonella), viruses, +/- elevated IgE
COVID-19 research v0.36 TTC7A Ellen McDonagh gene: TTC7A was added
gene: TTC7A was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: TTC7A was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TTC7A were set to 24292712; 23830146; 23423984; 24417819
Phenotypes for gene: TTC7A were set to Gastrointestinal defects and immunodeficiency syndrome, 243150; Immunodeficiencies with multiple intestinal atresias; Combined immunodeficiency; Combined immunodeficiency-enteropathy spectrum; Bacterial (sepsis), fungal, viral infections, multiple intestinal atresias, often with intrauterine polyhydramnios and early demise, some with SCID phenotype; Combined immunodeficiencies with associated or syndromic features; Multiple intestinal atresia and severe combined immunodeficiency
COVID-19 research v0.36 TTC37 Ellen McDonagh gene: TTC37 was added
gene: TTC37 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,A- or hypo-gammaglobulinaemia v1.25,IUIS Classification February 2018
Mode of inheritance for gene: TTC37 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TTC37 were set to 29383842; 25688341; 28292286; 21120949; 28944135; 20176027
Phenotypes for gene: TTC37 were set to Recurrent bacterial and viral infections, Abnormal hair findings: trichorrhexis nodosa; Trichohepatoenteric syndrome 1, 222470; Intrauterine growth retardation, woolly hair; intractable diarrhoea in infancy requiring total parenteral nutrition; Hypogammaglobulinaemia; Predominantly Antibody Deficiencies; facial dysmorphism; immune dysfunction; Trichohepatoenteric syndrome
COVID-19 research v0.36 TRNT1 Ellen McDonagh gene: TRNT1 was added
gene: TRNT1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: TRNT1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TRNT1 were set to 23553769; 29055896; 25193871
Phenotypes for gene: TRNT1 were set to Sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay, 616084; congenital sideroblastic anemia, deafness, developmental delay; Predominantly Antibody Deficiencies; Congenital sideroblastic anemia with immunodeficiency, fevers, and developmental delay (SIFD)
COVID-19 research v0.36 TRAC Ellen McDonagh gene: TRAC was added
gene: TRAC was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: TRAC was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TRAC were set to 3464003; 21206088
Phenotypes for gene: TRAC were set to Immunodeficiencies affecting cellular and humoral immunity; Recurrent viral, bacterial, fungal infections, immune dysregulation and autoimmunity, diarrhea; Immunodeficiency 7, TCR-alpha/beta deficient, 615387; Combined immunodeficiency
COVID-19 research v0.36 TPP2 Ellen McDonagh gene: TPP2 was added
gene: TPP2 was added to Viral susceptibility. Sources: Expert Review Green,Victorian Clinical Genetics Services,North West GLH,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: TPP2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TPP2 were set to 25525876; 25414442
Phenotypes for gene: TPP2 were set to immune thrombocytopenia and autoimmune hemolytic anemia; Autoimmune hemolytic anemia-autoimmune thrombocytopenia-primary immunodeficiency syndrome; TPP2 deficiency; Tripeptidyl-Peptidase II Deficiency; Diseases of Immune Dysregulation; Evans syndrome; Variable lymphoproliferation, severe autoimmune cytopenias, hypergammaglobulinemia, recurrent infections
COVID-19 research v0.36 TMC8 Ellen McDonagh Mode of inheritance for gene TMC8 was changed from Unknown to BIALLELIC, autosomal or pseudoautosomal
Added phenotypes HPV (group B1) infections and cancer of the skin (typical EV); Epidermodysplasia verruciformis, 226400; Defects in Intrinsic and Innate Immunity for gene: TMC8
Publications for gene TMC8 were updated from 26621750 to 15356576; 28196644; 12426567; 26997147; 28646613; 26621750
COVID-19 research v0.36 TMC6 Ellen McDonagh Mode of inheritance for gene TMC6 was changed from Unknown to BIALLELIC, autosomal or pseudoautosomal
Added phenotypes Human papillomavirus (HPV) (group B1) infections and cancer of the skin (typical EV); Epidermodysplasia verruciformis, 226400; Defects in Intrinsic and Innate Immunity for gene: TMC6
Publications for gene TMC6 were updated from 26621750 to 15356576; 28196644; 15042430; 12426567; 17008061; 26621750
COVID-19 research v0.36 TCN2 Ellen McDonagh gene: TCN2 was added
gene: TCN2 was added to Viral susceptibility. Sources: Expert Review Green,Agranulocytosis v1.3,Combined B and T cell defect v1.12,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,Congenital neutropaenia v1.22,GRID V2.0,NHS GMS,London North GLH,A- or hypo-gammaglobulinaemia v1.25,SCID v1.6,IUIS Classification February 2018
Mode of inheritance for gene: TCN2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TCN2 were set to 20352340; 24305960; 7849710; 7980584; 18956254
Phenotypes for gene: TCN2 were set to Transcobalamin-2 precursor; Transcobalamin II deficiency; Agammaglobulinemia; Megaloblastic anemia, pancytopenia, if untreated for prolonged periods results in intellectual disability; pancytopenia; Transcobalamin II deficiency, 275350; neutropenic colitis; Defects of Vitamin B12 and Folate metabolism; megaloblastic bone; can have a presentation similar to severe combined immunodeficiency; Combined immunodeficiencies with associated or syndromic features
COVID-19 research v0.36 TAP2 Ellen McDonagh gene: TAP2 was added
gene: TAP2 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: TAP2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TAP2 were set to 10560675; 11529920; 20083708; 7517574
Phenotypes for gene: TAP2 were set to Vasculitis, pyoderma gangrenosum; Bare lymphocyte syndrome, type I, due to TAP2 deficiency 604571; HLA class I deficiency; Immunodeficiencies affecting cellular and humoral immunity; Wegener-like granulomatosis
COVID-19 research v0.36 TAP1 Ellen McDonagh gene: TAP1 was added
gene: TAP1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: TAP1 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: TAP1 were set to HLA class I deficiency; Immunodeficiencies affecting cellular and humoral immunity; Vasculitis, pyoderma gangrenosum; Bare lymphocyte syndrome, type I 604571
COVID-19 research v0.36 STXBP2 Ellen McDonagh gene: STXBP2 was added
gene: STXBP2 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: STXBP2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: STXBP2 were set to 19804848; 19884660; 20301617; 20798128
Phenotypes for gene: STXBP2 were set to Hemophagocytic lymphohistiocytosis, familial 5, 613101; Diseases of Immune Dysregulation; Fever, HSM, cHLH, cytopenias, enteropathy; FHL5; Familial hemophagocytic lymphohistiocytosis syndromes (FHLH)
COVID-19 research v0.36 STX11 Ellen McDonagh gene: STX11 was added
gene: STX11 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: STX11 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: STX11 were set to 20301617; 24459464; 16582076; 16278825; 15703195
Phenotypes for gene: STX11 were set to HLH4; Hemophagocytic lymphohistiocytosis, familial 4, 603552; Diseases of Immune Dysregulation; Familial hemophagocytic lymphohistiocytosis syndromes (FHLH); FHL4; HPLH4; Fever, HSM, cHLH, cytopenias,
COVID-19 research v0.36 STK4 Ellen McDonagh gene: STK4 was added
gene: STK4 was added to Viral susceptibility. Sources: Expert Review Green,Combined B and T cell defect v1.12,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: STK4 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: STK4 were set to 26801501; 22294732; 26117625; 24453252; 22174160
Phenotypes for gene: STK4 were set to Hypergammaglobulinaemia, lymphopenia, combined immunodeficiency, congenital heart disease, autoimmunity; Intermittent neutropenia, bacterial, viral (HPV), candidal infections, EBV lymphoproliferation, autoimmune cytopenias, lymphoma, congenital heart disease; Combined immunodeficiency; T-cell immunodeficiency, recurrent infections, autoimmunity, and cardiac malformations; Immunodeficiencies affecting cellular and humoral immunity; AR hyperimmunoglobulin E syndrome
COVID-19 research v0.36 STIM1 Ellen McDonagh gene: STIM1 was added
gene: STIM1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,SCID v1.6,IUIS Classification February 2018
Mode of inheritance for gene: STIM1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: STIM1 were set to 20876309; 19420366; 24621671; 26560041; 22190180
Phenotypes for gene: STIM1 were set to Immunodeficiency 10, 612783; Combined immunodeficiency due to STIM1 deficiency ORPHA:317430; Combined immunodeficiency; Combined immunodeficiency due to STIM1 deficiency; Autoimmunity, EDA, non-progressive myopathy; T-B+ SCID; Combined immunodeficiencies with associated or syndromic features
COVID-19 research v0.36 STAT5B Ellen McDonagh gene: STAT5B was added
gene: STAT5B was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,SCID v1.6,IUIS Classification February 2018
Mode of inheritance for gene: STAT5B was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: STAT5B were set to 13679528; 20538865; 16787985; 17030597; 26703237; 15827093; 17389811; 16920911
Phenotypes for gene: STAT5B were set to Combined immunodeficiency; T-B+ SCID; Growth-hormone insensitive dwarfism, dysmorphic features, eczema, lymphocytic interstitial pneumonitis, autoimmunity; Growth hormone insensitivity with immunodeficiency 245590; Combined immunodeficiencies with associated or syndromic features
COVID-19 research v0.36 STAT2 Ellen McDonagh Mode of inheritance for gene STAT2 was changed from Unknown to BIALLELIC, autosomal or pseudoautosomal
Added phenotypes STAT2 deficiency; Predisposition to several viral infection; Severe viral infections (disseminated vaccine-strain measles); Defects in Intrinsic and Innate Immunity; Immunodeficiency 44, 616636 for gene: STAT2
Publications for gene STAT2 were updated from to 23391734; 26122121; 28087227
COVID-19 research v0.36 SPPL2A Ellen McDonagh gene: SPPL2A was added
gene: SPPL2A was added to Viral susceptibility. Sources: Expert Review Green,Expert Review,North West GLH,NHS GMS,London North GLH,Literature
Mode of inheritance for gene: SPPL2A was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SPPL2A were set to 30264912; 30127434
Phenotypes for gene: SPPL2A were set to Defects with susceptibility to mycobacterial infection (MSMD); Defects in Intrinsic and Innate Immunity; Susceptibility to mycobacteria
COVID-19 research v0.36 SPINK5 Ellen McDonagh gene: SPINK5 was added
gene: SPINK5 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: SPINK5 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SPINK5 were set to 19683336; 28943498; 10835624; 28832989; 28289593
Phenotypes for gene: SPINK5 were set to Combined immunodeficiencies with associated or syndromic features; Netherton syndrome 256500; Congenital ichthyosis, bamboo hair, atopic diathesis, increased bacterial infections, failure to thrive
COVID-19 research v0.36 SP110 Ellen McDonagh gene: SP110 was added
gene: SP110 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: SP110 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SP110 were set to 16648851
Phenotypes for gene: SP110 were set to Combined immunodeficiencies with associated or syndromic features; Hepatic veno-occlusive disease, Susceptibility to Pneumocystis jirovecii pneumonia, CMV, candida, thrombocytopenia, hepatosplenomegaly, cerebrospinal leukodystrophy; Hepatic venoocclusive disease with immunodeficiency 235550; Hepatic venoocclusive disease with immunodeficiency (VODI)
COVID-19 research v0.36 SMARCAL1 Ellen McDonagh gene: SMARCAL1 was added
gene: SMARCAL1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: SMARCAL1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SMARCAL1 were set to 17089404; 11799392
Phenotypes for gene: SMARCAL1 were set to Schimke disease; Combined immunodeficiencies with associated or syndromic features; Schimke immunoosseous dysplasia 242900; Short stature, spondiloepiphyseal dysplasia, intrauterine growth retardation, nephropathy, bacterial, viral, fungal infections, may present as SCID, bone marrow failure
COVID-19 research v0.36 SLC46A1 Ellen McDonagh gene: SLC46A1 was added
gene: SLC46A1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: SLC46A1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SLC46A1 were set to 17446347; 17129779; 27664775
Phenotypes for gene: SLC46A1 were set to Folate malabsorption, hereditary 229050; Congenital defect of folate absorption; Megaloblastic anemia, failure to thrive, if untreated for prolonged periods results in intellectual disability; Defects of Vitamin B12 and Folate metabolism; Combined immunodeficiencies with associated or syndromic features
COVID-19 research v0.36 SLC37A4 Ellen McDonagh gene: SLC37A4 was added
gene: SLC37A4 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,Congenital neutropaenia v1.22,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: SLC37A4 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SLC37A4 were set to 9428641; 10482962; 12576310
Phenotypes for gene: SLC37A4 were set to Glycogen storage disease Ib; Congenital defects of phagocyte number or function; Glycogen storage disease Ib, 232220; Glycogen storage disease type 1b (GS1b); Glycogen storage disease with or without neutropenia; Glycogen storage disease Ic; Fasting hypoglycemia, lactic acidosis, hyperlipidemia, hepatomegaly
COVID-19 research v0.36 SLC35C1 Ellen McDonagh gene: SLC35C1 was added
gene: SLC35C1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: SLC35C1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SLC35C1 were set to 11326279; 24403049; 11213799; 12116250; 11326280; 1279426
Phenotypes for gene: SLC35C1 were set to Mild LAD type 1 features with hh-blood group, growth retardation, developmental delay; Congenital defects of phagocyte number or function; Leukocyte adhesion deficiency (LAD); Congenital disorder of glycosylation, type IIc 266265
COVID-19 research v0.36 SLC29A3 Ellen McDonagh gene: SLC29A3 was added
gene: SLC29A3 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: SLC29A3 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SLC29A3 were set to 22875837; 16650224; 16155931; 20140240; 18947330; 17461801; 19336477; 16118898; 21178579; 19175903; 9545394; 21888995; 22238637; 23530176; 22653152; 18940313; 20619369
Phenotypes for gene: SLC29A3 were set to Other autoinflammatory diseases with known genetic defect; Hyperpigmentation hypertrichosis, histiocytosis-lymphadenopathy plus syndrome; Autoinflammatory Disorders; Histiocytosis-lymphadenopathy plus syndrome 602782
COVID-19 research v0.36 SKIV2L Ellen McDonagh gene: SKIV2L was added
gene: SKIV2L was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,NHS GMS,GOSH PID v.8.0,London North GLH
Mode of inheritance for gene: SKIV2L was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SKIV2L were set to 28944135; 29145277; 29484573
Phenotypes for gene: SKIV2L were set to Trichohepatoenteric syndrome 2,614602; Immune dysfunction; Trichohepatoenteric syndrome
COVID-19 research v0.36 SGPL1 Ellen McDonagh gene: SGPL1 was added
gene: SGPL1 was added to Viral susceptibility. Sources: Expert Review Green,Combined B and T cell defect v1.12,North West GLH,NHS GMS,London North GLH
Mode of inheritance for gene: SGPL1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SGPL1 were set to 28181337; 28165343; 28165339
Phenotypes for gene: SGPL1 were set to drenal insufficiency; focal segmental glomerulosclerosis; steroid-resistant nephrotic syndrome; Nephrotic syndrome 14, 617575; lymphopenia
COVID-19 research v0.36 SBDS Ellen McDonagh gene: SBDS was added
gene: SBDS was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,Congenital neutropaenia v1.22,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: SBDS was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SBDS were set to 14749921; 12496757; 11342425
Phenotypes for gene: SBDS were set to Shwachman-Bodian-Diamond syndrome; Shwachman-Diamond-syndrome; Shwachman-Diamond syndrome, 260400; Congenital defects of phagocyte number or function; Pancytopenia, exocrine pancreatic insufficiency, chondrodysplasia
COVID-19 research v0.36 SAMHD1 Ellen McDonagh gene: SAMHD1 was added
gene: SAMHD1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: SAMHD1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SAMHD1 were set to 19525956; 20358604; 21102625
Phenotypes for gene: SAMHD1 were set to Classical AGS, FCL; Autoinflammatory Disorders; Type 1 interferonopathies; Aicardi-Goutieres syndrome 5 612952
COVID-19 research v0.36 RORC Ellen McDonagh gene: RORC was added
gene: RORC was added to Viral susceptibility. Sources: Expert Review Green,Victorian Clinical Genetics Services,North West GLH,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: RORC was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RORC were set to 26160376
Phenotypes for gene: RORC were set to Immunodeficiency 42 616622; Susceptibility to mycobacteria and candida; Defects in Intrinsic and Innate Immunity; Susceptibility to candidasis & Mycobacterial infection
COVID-19 research v0.36 RNF168 Ellen McDonagh gene: RNF168 was added
gene: RNF168 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: RNF168 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RNF168 were set to 21394101; 19203578; 29255463
Phenotypes for gene: RNF168 were set to Combined immunodeficiencies with associated or syndromic features; RNF168 deficiency; Short stature, mild defect of motor control to ataxia, normal intelligence to learning difficulties, mild facial dysmorphism to microcephaly, increased radiosensitivity; RIDDLE syndrome 611943
COVID-19 research v0.36 RNASEH2C Ellen McDonagh gene: RNASEH2C was added
gene: RNASEH2C was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: RNASEH2C was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RNASEH2C were set to 23322642; 16845400; 25604658; 17846997
Phenotypes for gene: RNASEH2C were set to Aicardi-Goutieres syndrome 3 610329; Autoinflammatory Disorders; Type 1 interferonopathies; Classical AGS
COVID-19 research v0.36 RNASEH2B Ellen McDonagh gene: RNASEH2B was added
gene: RNASEH2B was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: RNASEH2B was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: RNASEH2B were set to Aicardi-Goutieres syndrome 2 610181; Autoinflammatory Disorders; Type 1 interferonopathies; Classical AGS, SP
COVID-19 research v0.36 RNASEH2A Ellen McDonagh gene: RNASEH2A was added
gene: RNASEH2A was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: RNASEH2A was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RNASEH2A were set to 23592335; 16845400; 21454563
Phenotypes for gene: RNASEH2A were set to Autoinflammatory Disorders; Classical AGS; Aicardi-Goutieres syndrome 4 610333, Lupus; Type 1 interferonopathies
COVID-19 research v0.36 RMRP Ellen McDonagh gene: RMRP was added
gene: RMRP was added to Viral susceptibility. Sources: Expert Review Green,Combined B and T cell defect v1.12,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: RMRP was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RMRP were set to 26830278; 2328993; 3582365; 24217815; 26279652; 25663137
Phenotypes for gene: RMRP were set to Short-limbed dwarfism with metaphyseal dysostosis, sparse hair, bone marrow failure, autoimmunity, susceptibility to lymphoma and other cancers, impaired spermatogenesis, neuronal dysplasia of the intestine; Cartilage hair hypoplasia; Cartilage-hair hypoplasia; Anauxetic dysplasia 1, 232220; Omenn syndrome; Cartilage-hair hypoplasia, with or without immunodeficiency; Combined immunodeficiencies with associated or syndromic features
COVID-19 research v0.36 RIPK1 Ellen McDonagh gene: RIPK1 was added
gene: RIPK1 was added to Viral susceptibility. Sources: Expert Review Green,North West GLH,NHS GMS,London North GLH,Literature
Mode of inheritance for gene: RIPK1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RIPK1 were set to 30026316
Phenotypes for gene: RIPK1 were set to Severe immunodeficiency, arthritis, and intestinal inflammation; Immunodeficiency 57, 618108
COVID-19 research v0.36 RFXAP Ellen McDonagh gene: RFXAP was added
gene: RFXAP was added to Viral susceptibility. Sources: Expert Review Green,Combined B and T cell defect v1.12,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: RFXAP was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RFXAP were set to 12498778; 9287230; 18336911; 22390233; 20197681; 9118943; 9806639
Phenotypes for gene: RFXAP were set to HLA class II deficiency; Combined immunodeficiency (MHC class II deficiency, bare lymphocyte syndrome); Bare lymphocyte syndrome, type II, complementation group D; Immunodeficiencies affecting cellular and humoral immunity; Respiratory and gastrointestinal infections, liver/biliary tract disease
COVID-19 research v0.36 RFXANK Ellen McDonagh gene: RFXANK was added
gene: RFXANK was added to Viral susceptibility. Sources: Expert Review Green,Combined B and T cell defect v1.12,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: RFXANK was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RFXANK were set to 22863278; 11313409; 12618906; 20414676; 9806546
Phenotypes for gene: RFXANK were set to HLA class II deficiency; Combined immunodeficiency (MHC class II deficiency, bare lymphocyte syndrome); MHC class II deficiency, complementation group B; Immunodeficiencies affecting cellular and humoral immunity; Respiratory and gastrointestinal infections, liver/biliary tract disease
COVID-19 research v0.36 RFX5 Ellen McDonagh gene: RFX5 was added
gene: RFX5 was added to Viral susceptibility. Sources: Expert Review Green,Combined B and T cell defect v1.12,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: RFX5 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RFX5 were set to 9401005; 7744245
Phenotypes for gene: RFX5 were set to HLA class II deficiency; Combined immunodeficiency; Bare lymphocyte syndrome (MHC class II deficiency); Bare lymphocyte syndrome, type II, complementation group E; Immunodeficiencies affecting cellular and humoral immunity; Respiratory and gastrointestinal infections, liver/biliary tract disease; Bare lymphocyte syndrome, type II, complementation group C
COVID-19 research v0.36 RBCK1 Ellen McDonagh gene: RBCK1 was added
gene: RBCK1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: RBCK1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RBCK1 were set to 23104095; 29260357
Phenotypes for gene: RBCK1 were set to Other autoinflammatory diseases with known genetic defect; HOIL1 deficiency; Polyglucosan body myopathy, early-onset, with or without immunodeficiency 615895; Bacterial infections, autoinflammation, amylopectinosis; Combined immunodeficiencies with associated or syndromic features
COVID-19 research v0.36 RASGRP1 Ellen McDonagh gene: RASGRP1 was added
gene: RASGRP1 was added to Viral susceptibility. Sources: Expert Review Green,North West GLH,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: RASGRP1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RASGRP1 were set to 27776107; 28822832; 30030704; 29282224; 29155103
Phenotypes for gene: RASGRP1 were set to Recurrent pneumonia, herpesvirus infections, EBV associated lymphoma; Immunodeficiency 64, 618534; Diseases of Immune Dysregulation; Immunodeficiency; EBV-induced lymphoma; immunde dysregulation
COVID-19 research v0.36 RAG2 Ellen McDonagh gene: RAG2 was added
gene: RAG2 was added to Viral susceptibility. Sources: Expert Review Green,Combined B and T cell defect v1.12,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,SCID v1.6,IUIS Classification February 2018
Mode of inheritance for gene: RAG2 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: RAG2 were set to Nl NK; Severe combined immunodeficiency, B cell-negative, 601457; Severe Combined Immune Deficiency; Atypical Severe Combined Immunodeficiency (Atypical SCID); Immunodeficiencies affecting cellular and humoral immunity; T-B+ SCID; Severe combined immunodeficiency, B cell-negative; Severe Combined Immunodeficiency, Autosomal Recessive, T Cell-Negative, B Cell-Negative, Nk Cell-Positive; Omenn syndrome; Severe combined immunodeficiency (SCID); T-B- SCID; RAG2 deficiency
COVID-19 research v0.36 RAG1 Ellen McDonagh gene: RAG1 was added
gene: RAG1 was added to Viral susceptibility. Sources: Expert Review Green,Combined B and T cell defect v1.12,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,SCID v1.6,IUIS Classification February 2018
Mode of inheritance for gene: RAG1 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: RAG1 were set to Nl NK; Severe combined immunodeficiency, B cell-negative, 601457; Severe Combined Immune Deficiency; Atypical Severe Combined Immunodeficiency (Atypical SCID); Immunodeficiencies affecting cellular and humoral immunity; T-B+ SCID; Severe combined immunodeficiency, B cell-negative; Omenn syndrome; Severe combined immunodeficiency (SCID); T-B- SCID; RAG1 deficiency
COVID-19 research v0.36 RAB27A Ellen McDonagh gene: RAB27A was added
gene: RAB27A was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: RAB27A was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RAB27A were set to 12058346; 12531900; 12522785; 15163896
Phenotypes for gene: RAB27A were set to Diseases of Immune Dysregulation; Partial albinism, fever, HSM, HLH, cytopenias; Griscelli syndrome, type 2 607624
COVID-19 research v0.36 PTPRC Ellen McDonagh gene: PTPRC was added
gene: PTPRC was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,SCID v1.6,IUIS Classification February 2018
Mode of inheritance for gene: PTPRC was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PTPRC were set to 11145714; 10700239; 22689986
Phenotypes for gene: PTPRC were set to Nl g/d T cells; {Hepatitic C virus, susceptibility to}, 609532; CD45 deficiency; Immunodeficiencies affecting cellular and humoral immunity; T-B+ SCID; Omenn syndrome; Severe combined immunodeficiency, T cell-negative, B-cell/natural killer-cell positive; Severe combined immunodeficiency (SCID)
COVID-19 research v0.36 PSMB8 Ellen McDonagh gene: PSMB8 was added
gene: PSMB8 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: PSMB8 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PSMB8 were set to 21129723; 21953331; 21852578; 21881205
Phenotypes for gene: PSMB8 were set to Other autoinflammatory diseases with known genetic defect; chronic atypical neutrophilic dermatosis with lipodystrophy and elevated temperature syndrome (CANDLE); Contractures, panniculitis, ICC, fevers; Autoinflammatory Disorders; Autoinflammation, lipodystrophy, and dermatosis syndrome 256040; CANDLE syndrome
COVID-19 research v0.36 PRKDC Ellen McDonagh gene: PRKDC was added
gene: PRKDC was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,SCID v1.6,IUIS Classification February 2018
Mode of inheritance for gene: PRKDC was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PRKDC were set to 23722905; 19075392; 25842288
Phenotypes for gene: PRKDC were set to Immunodeficiency 26, with or without neurologic abnormalities; DNA Pkcs deficiency; Combined immunodeficiency; Immunodeficiency, with or without neurologic abnormalities; Nl NK, radiation sensitive, microcephaly; Immunodeficiencies affecting cellular and humoral immunity; Severe combined immunodeficiency (SCID)
COVID-19 research v0.36 PRKCD Ellen McDonagh gene: PRKCD was added
gene: PRKCD was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: PRKCD was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PRKCD were set to 23430113; 23319571; 23666743
Phenotypes for gene: PRKCD were set to Recurrent infections, EBV chronic infection, lymphoproliferation, SLE-like autoimmunity (nephrotic and antiphospholipid syndromes), low IgG; Autoimmune lymphoproliferative syndrome, type III 615559; Diseases of Immune Dysregulation; Unclassified antibody deficiency; Immunodeficiency, common variable, 9; Autoimmune lymphoproliferative syndrome (ALPS)
COVID-19 research v0.36 PRF1 Ellen McDonagh gene: PRF1 was added
gene: PRF1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: PRF1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PRF1 were set to 15365097; 11179007; 15632205; 20301617; 10583959; 14757862; 12229880; 16860143
Phenotypes for gene: PRF1 were set to Fever, HSM, Hemophagocytic lymphohistiocytosis (HLH), cytopenias; FHL2; HPLH2; Familial hemophagocytic lymphohistiocytosis syndromes (FHLH); Diseases of Immune Dysregulation; Hemophagocytic lymphohistiocytosis, familial 2, 603553; HLH2
COVID-19 research v0.36 PNP Ellen McDonagh gene: PNP was added
gene: PNP was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,SCID v1.6,IUIS Classification February 2018
Mode of inheritance for gene: PNP was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: PNP were set to Combined immunodeficiency; Autoimmune haemolytic anemia, neurological impairment; Immunodeficiency due to purine nucleoside phosphorylase deficiency; Atypical Severe Combined Immunodeficiency (Atypical SCID); T-B+ SCID; Combined immunodeficiencies with associated or syndromic features
COVID-19 research v0.36 PGM3 Ellen McDonagh gene: PGM3 was added
gene: PGM3 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: PGM3 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PGM3 were set to 24698316; 24589341; 24931394
Phenotypes for gene: PGM3 were set to Immunodeficiency 23 615816; Combined immunodeficiencies with associated or syndromic features; Severe atopy, autoimmunity, bacterial and viral infections, skeletal anomalies dysplasia: short stature, brachydactyly, dysmorphic facial features, and intellectual disability cognitive impairment, hypomyelination; Combined immunodeficiency
COVID-19 research v0.36 PEPD Ellen McDonagh gene: PEPD was added
gene: PEPD was added to Viral susceptibility. Sources: Expert Review Green,North West GLH,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: PEPD was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PEPD were set to 6637477; 19308961; 15309682; 17142620; 8900231; 1972707; 2365824; 16470701
Phenotypes for gene: PEPD were set to Prolidase deficiency, 170100; Autoantibodies common, chronic skin ulcers, eczema, infections; Diseases of Immune Dysregulation
COVID-19 research v0.36 OTULIN Ellen McDonagh gene: OTULIN was added
gene: OTULIN was added to Viral susceptibility. Sources: Expert Review Green,Expert Review,Victorian Clinical Genetics Services,North West GLH,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: OTULIN was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: OTULIN were set to 27559085; 27523608
Phenotypes for gene: OTULIN were set to Autoinflammation, panniculitis, and dermatosis syndrome, 617099; Fever, diarrhea , dermatitis; Autoinflammatory Disorders
COVID-19 research v0.36 ORAI1 Ellen McDonagh gene: ORAI1 was added
gene: ORAI1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,SCID v1.6,IUIS Classification February 2018
Mode of inheritance for gene: ORAI1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ORAI1 were set to 16582901; 20004786
Phenotypes for gene: ORAI1 were set to Combined immunodeficiency; immunodeficiency, ectodermal dysplasia and myopathy; Immunodeficiency 9 612782; Autoimmunity, EDA, non-progressive myopathy; T-B+ SCID; Combined immunodeficiencies with associated or syndromic features
COVID-19 research v0.36 NSMCE3 Ellen McDonagh gene: NSMCE3 was added
gene: NSMCE3 was added to Viral susceptibility. Sources: Expert Review Green,North West GLH,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: NSMCE3 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: NSMCE3 were set to 27427983
Phenotypes for gene: NSMCE3 were set to Lung disease, immunodeficiency, and chromosome breakage syndrome, 617241; Combined immunodeficiencies with associated or syndromic features; Severe lung disease (possibly viral), thymic hypoplasia, Chromosomal breakage, radiation sensitivity
COVID-19 research v0.36 NHP2 Ellen McDonagh gene: NHP2 was added
gene: NHP2 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: NHP2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: NHP2 were set to 25182133; 18523010; 20301779; 20008900; 25907943
Phenotypes for gene: NHP2 were set to Dyskeratosis congenita; Hoyeraal-Hreidarsson syndrome; Dyskeratosis congenita, autosomal recessive 2 613987; Combined immunodeficiencies with associated or syndromic features; Intrauterine growth retardation, microcephaly, nail dystrophy, sparse scalp hair and eyelashes, hyperpigmentation of skin, palmar hyperkeratosis, premalignant oral leukoplakia, pancytopenia, myelodysplasia, +/- recurrent infections. A severe phenotype with developmental delay and cerebellar hypoplasia known as Hoyeraal-Hreidarsson Syndrome (HHS) may occur in some DKC patients
COVID-19 research v0.36 NHEJ1 Ellen McDonagh gene: NHEJ1 was added
gene: NHEJ1 was added to Viral susceptibility. Sources: Expert Review Green,Combined B and T cell defect v1.12,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,SCID v1.6,IUIS Classification February 2018
Mode of inheritance for gene: NHEJ1 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: NHEJ1 were set to Combined immunodeficiency; Severe combined immunodeficiency with microcephaly, growth retardation and sensitivity to ionizing radiation, 611291; Nl NK, radiation sensitive, microcephaly; Immunodeficiencies affecting cellular and humoral immunity; Severe combined immunodeficiency with microcephaly, growth retardation, and sensitivity to ionizing radiation; T-B+ SCID; Cernunnos/XLF deficiency; T-B- SCID
COVID-19 research v0.36 NCF4 Ellen McDonagh gene: NCF4 was added
gene: NCF4 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: NCF4 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: NCF4 were set to 29969437; 19692703
Phenotypes for gene: NCF4 were set to Infections, autoinflammatory phenotype; Congenital defects of phagocyte number or function; ?Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type III 613960; Chronic granulomatous disease (CGD); Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type III
COVID-19 research v0.36 NCF2 Ellen McDonagh gene: NCF2 was added
gene: NCF2 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: NCF2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: NCF2 were set to 9070911; 10498624; 7795241
Phenotypes for gene: NCF2 were set to Chronic granulomatous disease due to deficiency of NCF-2 233710; Chronic granulomatous disease (CGD); Congenital defects of phagocyte number or function; Infections, autoinflammatory phenotype
COVID-19 research v0.36 NCF1 Ellen McDonagh gene: NCF1 was added
gene: NCF1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: NCF1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: NCF1 were set to 16972229; 10706888; 11133775
Phenotypes for gene: NCF1 were set to Chronic granulomatous disease due to deficiency of NCF-1 233700; Chronic granulomatous disease (CGD); Congenital defects of phagocyte number or function; Infections, autoinflammatory phenotype
COVID-19 research v0.36 NBN Ellen McDonagh gene: NBN was added
gene: NBN was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: NBN was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: NBN were set to 9590180; 12447395; 11325820; 16415040
Phenotypes for gene: NBN were set to Nijmegen breakage syndrome (NBS1); Nijmegen breakage syndrome 251260; Aplastic anemia 609135; Microcephaly, dysmorphic facies, lymphomas, solid tumors, increased radiosensitivity, chromosomal instability; Combined immunodeficiencies with associated or syndromic features
COVID-19 research v0.36 MYSM1 Ellen McDonagh gene: MYSM1 was added
gene: MYSM1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: MYSM1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MYSM1 were set to 26220525; 28115216; 26474655; 28446309; 22184403; 24288411
Phenotypes for gene: MYSM1 were set to Bone marrow failure; immunodeficiency; Short stature, recurrent infections, congenital bone marrow failure, myelodysplasia, immunodeficiency affecting B-cells and granulocytes, skeletal anomalies, cataracts, developmental delay.; mid-face hypoplasia; MYSM1 deficiency; neurodevelopmental delay; Combined immunodeficiencies with associated or syndromic features
COVID-19 research v0.36 MYO5B Ellen McDonagh gene: MYO5B was added
gene: MYO5B was added to Viral susceptibility. Sources: Expert Review Green,North West GLH,NHS GMS,GOSH PID v.8.0,London North GLH
Mode of inheritance for gene: MYO5B was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MYO5B were set to 19006234; 18724368
Phenotypes for gene: MYO5B were set to Microvillus inclusion disease 251850
COVID-19 research v0.36 MYD88 Ellen McDonagh gene: MYD88 was added
gene: MYD88 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,A- or hypo-gammaglobulinaemia v1.25,IUIS Classification February 2018
Mode of inheritance for gene: MYD88 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MYD88 were set to 18669862; 23215570
Phenotypes for gene: MYD88 were set to recurrent pyogenic bacterial infection; Defects of TLR/NFkappa-B signalling; Defects in Intrinsic and Innate Immunity; Bacterial infections (pyogens); Pyogenic bacterial infections, recurrent, due to MYD88 deficiency 612260
COVID-19 research v0.36 MVK Ellen McDonagh gene: MVK was added
gene: MVK was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: MVK was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MVK were set to 10369261; 16435210
Phenotypes for gene: MVK were set to Hyper-IgD syndrome 260920; Autoinflammatory Disorders; Hyper IgD syndrome (MVK); Mevalonic aciduria 610377; Periodic fever and leukocytosis with high IgD levels
COVID-19 research v0.36 MTHFD1 Ellen McDonagh gene: MTHFD1 was added
gene: MTHFD1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: MTHFD1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MTHFD1 were set to 25633902; 27707659
Phenotypes for gene: MTHFD1 were set to Recurrent bacterial infection, Pneumocystis jirovecii, megaloblastic anemia, failure to thrive, neutropenia, seizures, intellectual disability, folate-responsive; Combined immunodeficiency and megaloblastic anemia with or without hyperhomocysteinemia 617780; Combined immunodeficiencies with associated or syndromic features; Defects of Vitamin B12 and Folate metabolism
COVID-19 research v0.36 MOGS Ellen McDonagh gene: MOGS was added
gene: MOGS was added to Viral susceptibility. Sources: Expert Review Green,Victorian Clinical Genetics Services,North West GLH,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: MOGS was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MOGS were set to 24716661; 29235540; 10788335
Phenotypes for gene: MOGS were set to Bacterial and viral infections, severe neurologic disease, also known as congenital disorder of glycosylation type IIb (CDG-IIb); Congenital disorder of glycosylation, type IIb 606056; Predominantly Antibody Deficiencies
COVID-19 research v0.36 MCM4 Ellen McDonagh gene: MCM4 was added
gene: MCM4 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: MCM4 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MCM4 were set to 22354167; 22499342; 22354170; 16532402
Phenotypes for gene: MCM4 were set to Combined immunodeficiencies with associated or syndromic features; Predisposition to several viral infection; Immunodeficiency 54, 609981; MCM4 deficiency; NK cells: low number and function. Viral infections (EBV, HSV, VZV), short stature, B cell lymphoma, adrenal failure; Natural killer cell and glucocorticoid deficiency with DNA repair defect
COVID-19 research v0.36 MAP3K14 Ellen McDonagh gene: MAP3K14 was added
gene: MAP3K14 was added to Viral susceptibility. Sources: Expert Review Green,Victorian Clinical Genetics Services,North West GLH,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: MAP3K14 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MAP3K14 were set to 29230214; 25406581; 29259025
Phenotypes for gene: MAP3K14 were set to Low NK number and function, recurrent bacterial, viral and Cryptosporidium infections; Recessive Atypical Combined Immunodeficiency; Primary Immunodeficiency with Multifaceted Aberrant Lymphoid Immunity; Immunodeficiencies affecting cellular and humoral immunity
COVID-19 research v0.36 MALT1 Ellen McDonagh gene: MALT1 was added
gene: MALT1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: MALT1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MALT1 were set to 25627829; 24332264; 23727036
Phenotypes for gene: MALT1 were set to Bacterial, fungal and viral infections; Immunodeficiency 12 615468; Immunodeficiencies affecting cellular and humoral immunity; Combined immunodeficiency
COVID-19 research v0.36 LYST Ellen McDonagh gene: LYST was added
gene: LYST was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: LYST was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: LYST were set to 9215679; 9215680; 10482950; 8896560
Phenotypes for gene: LYST were set to Chediak-Higashi syndrome 214500; Chediak Higashi syndrome; Partial albinism, recurrent infections, fever, HSM, HLH, giant lysosomes, neutropenia, cytopenias, bleeding tendency, progressive neurological dysfunction; Diseases of Immune Dysregulation
COVID-19 research v0.36 LRBA Ellen McDonagh gene: LRBA was added
gene: LRBA was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: LRBA was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: LRBA were set to 25468195; 22608502; 22721650
Phenotypes for gene: LRBA were set to Unclassified antibody deficiency; Recurrent infections, inflammatory bowel disease, autoimmunity, EBV infections; Diseases of Immune Dysregulation; Immunodeficiency, common variable, 8, with autoimmunity, 614700
COVID-19 research v0.36 LPIN2 Ellen McDonagh gene: LPIN2 was added
gene: LPIN2 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: LPIN2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: LPIN2 were set to 17330256; 29387759; 27860302; 15994876
Phenotypes for gene: LPIN2 were set to Other autoinflammatory diseases with known genetic defect; Chronic recurrent multifocal osteomyelitis, transfusion-dependent anemia, cutaneous inflammatory disorders; Autoinflammatory Disorders; Majeed syndrome 609628
COVID-19 research v0.36 LIG4 Ellen McDonagh gene: LIG4 was added
gene: LIG4 was added to Viral susceptibility. Sources: Expert Review Green,Combined B and T cell defect v1.12,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,SCID v1.6,IUIS Classification February 2018
Mode of inheritance for gene: LIG4 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: LIG4 were set to Combined immunodeficiency; LIG4 syndrome; DNA ligase IV deficiency; Nl NK, radiation sensitive, microcephaly; Immunodeficiencies affecting cellular and humoral immunity; T-B+ SCID; Severe combined immunodeficiency with sensitivity to ionizing radiation, 602450; Severe combined immunodeficiency (SCID); T-B- SCID; LIG4 syndrome, 606593{Multiple myeloma, resistance to}, 254500; Severe Combined Immunodeficiency with Sensitivity to Ionizing Radiation
COVID-19 research v0.36 LCK Ellen McDonagh gene: LCK was added
gene: LCK was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: LCK was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: LCK were set to 11351273; 9664084; 22985903
Phenotypes for gene: LCK were set to Severe combined immunodeficiency due to LCK deficiency; Recurrent infections, immune dysregulation, autoimmunity; Combined immunodeficiency; Immunodeficiency 22, 615758; Immunodeficiencies affecting cellular and humoral immunity; LCK deficiency
COVID-19 research v0.36 LAT Ellen McDonagh gene: LAT was added
gene: LAT was added to Viral susceptibility. Sources: Expert Review Green,Combined B and T cell defect v1.12,North West GLH,NHS GMS,London North GLH,A- or hypo-gammaglobulinaemia v1.25,SCID v1.6,IUIS Classification February 2018
Mode of inheritance for gene: LAT was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: LAT were set to 27522155; 27242165
Phenotypes for gene: LAT were set to Immunodeficiencies affecting cellular and humoral immunity; Immunodeficiency 52, 617514; Adenopathy, splenomegaly, recurrent infections, autoimmunity
COVID-19 research v0.36 LAMTOR2 Ellen McDonagh gene: LAMTOR2 was added
gene: LAMTOR2 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: LAMTOR2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: LAMTOR2 were set to 22427693; 17195838; 24092934; 28593997
Phenotypes for gene: LAMTOR2 were set to Neutropenia, Hypogammaglobulinemia CD8 cytotoxicity, partial albinism, growth failure; Congenital neutropenia; Congenital defects of phagocyte number or function; Primary immunodeficiency syndrome due to p14 deficiency; Immunodeficiency due to defect in MAPBP-interacting protein, 610798
COVID-19 research v0.36 JAK3 Ellen McDonagh gene: JAK3 was added
gene: JAK3 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,SCID v1.6,IUIS Classification February 2018
Mode of inheritance for gene: JAK3 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: JAK3 were set to SCID, autosomal recessive, T-negative/B-positive type; Severe Combined Immunodeficiency, Autosomal Recessive, T Cell-Negative, B Cell-Positive, Nk Cell-Negative; Severe Combined Immune Deficiency; Atypical Severe Combined Immunodeficiency (Atypical SCID); Immunodeficiencies affecting cellular and humoral immunity; JAK3 deficiency; T-B+ SCID; Omenn syndrome; Severe combined immunodeficiency (SCID); Low NK
COVID-19 research v0.36 JAGN1 Ellen McDonagh gene: JAGN1 was added
gene: JAGN1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: JAGN1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: JAGN1 were set to 25129144
Phenotypes for gene: JAGN1 were set to Congenital neutropenia; Myeloid maturation arrest, osteopenia; Congenital defects of phagocyte number or function; Neutropenia, severe congenital; Neutropenia, severe congenital, 6, autosomal recessive,616022; severe congenital neutropenia
COVID-19 research v0.36 ITK Ellen McDonagh gene: ITK was added
gene: ITK was added to Viral susceptibility. Sources: Expert Review Green,Combined B and T cell defect v1.12,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: ITK was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ITK were set to 21109689; 19425169; 22289921
Phenotypes for gene: ITK were set to EBV associated B cell lymphoproliferation, lymphoma, Nl or low IgG; Combined immunodeficiency; Diseases of Immune Dysregulation; ITK deficiency (HLH phenotype); EBV viraemia, HLH; Lymphoproliferative syndrome 1
COVID-19 research v0.36 ITGB2 Ellen McDonagh gene: ITGB2 was added
gene: ITGB2 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: ITGB2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ITGB2 were set to 1346613; 1968911; 1694220; 7472832
Phenotypes for gene: ITGB2 were set to Delayed cord separation, skin ulcers, periodontitis, leukocytosis; Leukocyte adhesion deficiency type I; Congenital defects of phagocyte number or function; LAD; Leukocyte adhesion deficiency, 116920
COVID-19 research v0.36 ITCH Ellen McDonagh gene: ITCH was added
gene: ITCH was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: ITCH was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ITCH were set to 26854353; 27322655; 20962770; 19592251; 20170897
Phenotypes for gene: ITCH were set to Early-onset chronic lung disease (interstitial pneumonitis), autoimmunity (thyroiditis, type I diabetes, chronic diarrhea/enteropathy, and hepatitis), failure to thrive, developmental delay, dysmorphic facial features; Diseases of Immune Dysregulation; Autoimmune disease, multisystem, with facial dysmorphism, 613385; Syndromic multisystem autoimmune disease due to Itch deficiency; Autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED)
COVID-19 research v0.36 ISG15 Ellen McDonagh gene: ISG15 was added
gene: ISG15 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: ISG15 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ISG15 were set to 22859821; 23579383; 25307056
Phenotypes for gene: ISG15 were set to Immunodeficiency 38, 616126; idiopathic basal ganglia calcification; Defects with susceptibility to mycobacterial infection (MSMD); Susceptibility to mycobacteria, brain calcifications; Defects in Intrinsic and Innate Immunity
COVID-19 research v0.36 IRAK4 Ellen McDonagh gene: IRAK4 was added
gene: IRAK4 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: IRAK4 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IRAK4 were set to 17878374; 17114497; 12637671; 16950813
Phenotypes for gene: IRAK4 were set to Defects with susceptibility to mycobacterial infection (MSMD); Defects of TLR/NFkappa-B signalling; Invasive pneumococcal disease, recurrent isolated, 1, 6107; IRAK4 deficiency, 610799; Defects in Intrinsic and Innate Immunity; Bacterial infections (pyogens)
COVID-19 research v0.36 INO80 Ellen McDonagh gene: INO80 was added
gene: INO80 was added to Viral susceptibility. Sources: Expert Review Green,Victorian Clinical Genetics Services,North West GLH,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: INO80 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: INO80 were set to 25883595; 25312759
Phenotypes for gene: INO80 were set to severe bacterial infections; Severe bacterial infections; Predominantly Antibody Deficiencies; INO80 deficiency, HIGM
COVID-19 research v0.36 IL7R Ellen McDonagh gene: IL7R was added
gene: IL7R was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,SCID v1.6,IUIS Classification February 2018
Mode of inheritance for gene: IL7R was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: IL7R were set to Severe combined immunodeficiency, T-cell negative, B-cell/natural killer cell-positive; Severe combined immunodeficiency, T-cell negative, B-cell/natural killer cell-positive type; Nl NK; Severe Combined Immune Deficiency; Atypical Severe Combined Immunodeficiency (Atypical SCID); Immunodeficiencies affecting cellular and humoral immunity; T-B+ SCID; Omenn syndrome; Severe combined immunodeficiency (SCID); IL7Ra deficiency
COVID-19 research v0.36 IL36RN Ellen McDonagh gene: IL36RN was added
gene: IL36RN was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: IL36RN was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IL36RN were set to 23303454; 22903787; 23698098
Phenotypes for gene: IL36RN were set to Other autoinflammatory diseases with known genetic defect; Psoriasis 14, generalized pustular 614204; Autoinflammatory Disorders; Pustular psoriasis
COVID-19 research v0.36 IL2RA Ellen McDonagh gene: IL2RA was added
gene: IL2RA was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: IL2RA was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IL2RA were set to 23416241; 9096364; 17196245; 24116927
Phenotypes for gene: IL2RA were set to Combined immunodeficiency; Immunodeficiency 41 with lymphoproliferation and autoimmunity, 606367; Interleukin 2 receptor alpha deficiency (CD25) (IPEX phenotype); Diseases of Immune Dysregulation; Interleukin-2 receptor, alpha chain, deficiency of; Omenn syndrome; Lymphoproliferation, autoimmunity, impaired T cell proliferation
COVID-19 research v0.36 IL21R Ellen McDonagh gene: IL21R was added
gene: IL21R was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: IL21R was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IL21R were set to 23440042; 12700598
Phenotypes for gene: IL21R were set to Combined immunodeficiency; Atypical Severe Combined Immunodeficiency (Atypical SCID); Immunodeficiency 56, 615207; Immunodeficiencies affecting cellular and humoral immunity; Omenn syndrome; Immunodeficiency, primary, autosomal recessive, IL21R-related; IL-21R deficiency; Severe combined immunodeficiency (SCID); Recurrent infections, Pneumocystis jiroveci, Cryptosporidium infections and liver disease
COVID-19 research v0.36 IL1RN Ellen McDonagh gene: IL1RN was added
gene: IL1RN was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: IL1RN was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IL1RN were set to 19494219; 19494218
Phenotypes for gene: IL1RN were set to Other autoinflammatory diseases with known genetic defect; DIRA; Interleukin 1 receptor antagonist deficiency 612852; Autoinflammatory Disorders; sterile multifocal osteomyelitis, periostitis, and pustulosis; Neonatal onset of sterile multifocal osteomyelitis, periostitis and pustulosis.
COVID-19 research v0.36 IL17RC Ellen McDonagh gene: IL17RC was added
gene: IL17RC was added to Viral susceptibility. Sources: Expert Review Green,Victorian Clinical Genetics Services,North West GLH,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: IL17RC was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IL17RC were set to 29076381; 25918342
Phenotypes for gene: IL17RC were set to Candidiasis, familial, 9 616445; Chronic Mucocutaneous Candidiasis; CMC; Defects in Intrinsic and Innate Immunity
COVID-19 research v0.36 IL17RA Ellen McDonagh gene: IL17RA was added
gene: IL17RA was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: IL17RA was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IL17RA were set to 27930337; 29076381; 21350122
Phenotypes for gene: IL17RA were set to Candidiasis, familial, 5; Chronic mucocutaneous candidiasis (CMC); Immunodeficiency 51, 613953; CMC, folliculitis; Defects in Intrinsic and Innate Immunity
COVID-19 research v0.36 IL12RB1 Ellen McDonagh gene: IL12RB1 was added
gene: IL12RB1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: IL12RB1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IL12RB1 were set to 11424023; 15736007; 9603733; 21487897; 15178580; 12594833
Phenotypes for gene: IL12RB1 were set to Susceptibility to mycobacteria and Salmonella; Immunodeficiency 30, 614891; Defects with susceptibility to mycobacterial infection (MSMD); Defects in Intrinsic and Innate Immunity
COVID-19 research v0.36 IL12B Ellen McDonagh gene: IL12B was added
gene: IL12B was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: IL12B was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IL12B were set to 11753820; 24127073; 9854038; 15322986
Phenotypes for gene: IL12B were set to Susceptibility to mycobacteria and Salmonella; Immunodeficiency 29, mycobacteriosis, 614890; Defects with susceptibility to mycobacterial infection (MSMD); Mendelian susceptibility to mycobacterial diseases due to complete IL12B deficiency; Defects in Intrinsic and Innate Immunity
COVID-19 research v0.36 IL10RB Ellen McDonagh gene: IL10RB was added
gene: IL10RB was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: IL10RB was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IL10RB were set to 21519361; 19890111; 27350736; 27302973; 28785144
Phenotypes for gene: IL10RB were set to Inflammatory bowel disease 25, early onset, autosomal recessive,612567; Immune dysregulation-inflammatory bowel disease-arthritis-recurrent infections syndrome; Diseases of Immune Dysregulation; IBD, folliculitis, recurrent respiratory diseases, arthritis, lymphoma
COVID-19 research v0.36 IL10RA Ellen McDonagh gene: IL10RA was added
gene: IL10RA was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: IL10RA was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IL10RA were set to 22476154; 21519361; 29059189; 28864178; 19890111; 29788474; 29248579; 29140941
Phenotypes for gene: IL10RA were set to IBD, Folliculitis, recurrent respiratory diseases, arthritis, lymphoma; Immune dysregulation-inflammatory bowel disease-arthritis-recurrent infections syndrome; Diseases of Immune Dysregulation; Inflammatory bowel disease 28, early onset, autosomal recessive, 613148
COVID-19 research v0.36 IL10 Ellen McDonagh gene: IL10 was added
gene: IL10 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: IL10 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IL10 were set to 19890111; 20951137
Phenotypes for gene: IL10 were set to Early-onset inflammatory bowel disease; Immune dysregulation-inflammatory bowel disease-arthritis-recurrent infections syndrome; Inflammatory bowel disease (IBD) Folliculitis, recurrent respiratory diseases, arthritis,; Diseases of Immune Dysregulation
COVID-19 research v0.36 IKBKB Ellen McDonagh gene: IKBKB was added
gene: IKBKB was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: IKBKB was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IKBKB were set to 25216719; 24369075; 30337470
Phenotypes for gene: IKBKB were set to Immunodeficiency 15, 615592; Immunodeficiencies affecting cellular and humoral immunity; Combined immunodeficiency; Recurrent bacterial, viral, fungal infections, opportunistic infections
COVID-19 research v0.36 IGLL1 Ellen McDonagh gene: IGLL1 was added
gene: IGLL1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,A- or hypo-gammaglobulinaemia v1.25,IUIS Classification February 2018
Mode of inheritance for gene: IGLL1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IGLL1 were set to 27576013; 9419212; 25502423
Phenotypes for gene: IGLL1 were set to Agammaglobulinemia; Severe bacterial infections, normal numbers of pro-B cells; Agammaglobulinemia 2, 613500; Agammaglobulinemia 2; Predominantly Antibody Deficiencies
COVID-19 research v0.36 IGHM Ellen McDonagh gene: IGHM was added
gene: IGHM was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,GRID V2.0,NHS GMS,London North GLH,A- or hypo-gammaglobulinaemia v1.25,IUIS Classification February 2018
Mode of inheritance for gene: IGHM was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IGHM were set to 8890099; 12370281
Phenotypes for gene: IGHM were set to Agammaglobulinemia 1; Agammaglobulinemia; Severe bacterial infections, normal numbers of pro-B cells; Predominantly Antibody Deficiencies; Agammaglobulinemia 1, 601495
COVID-19 research v0.36 ICOS Ellen McDonagh gene: ICOS was added
gene: ICOS was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,A- or hypo-gammaglobulinaemia v1.25,IUIS Classification February 2018
Mode of inheritance for gene: ICOS was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ICOS were set to 15507387; 12577056; 29867948; 29226302; 24795713; 26399252; 25678089; 19380800; 28861081; 10413651; 29226301
Phenotypes for gene: ICOS were set to combined immunodeficiency; Isolated IgG subclass deficiency; gammaglobulinaemia; Immunodeficiency, common variable, 1, 607594; Immunodeficiencies affecting cellular and humoral immunity; Common variable immunodeficiency disorders (CVID); hypogammaglobulinaemia; Immunodeficiency, common variable, 1; Recurrent infections, autoimmunity, gastroenteritis, granulomas
COVID-19 research v0.36 HTRA2 Ellen McDonagh gene: HTRA2 was added
gene: HTRA2 was added to Viral susceptibility. Sources: Expert Review Green,North West GLH,Congenital neutropaenia v1.22,NHS GMS,London North GLH
Mode of inheritance for gene: HTRA2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: HTRA2 were set to 27696117; 27208207
Phenotypes for gene: HTRA2 were set to 3-methylglutaconic aciduria, type VIII, 617248; early onset neurological syndrome; neutropenia
COVID-19 research v0.36 HPS6 Ellen McDonagh gene: HPS6 was added
gene: HPS6 was added to Viral susceptibility. Sources: Expert Review Green,North West GLH,NHS GMS,GOSH PID v.8.0,London North GLH
Mode of inheritance for gene: HPS6 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: HPS6 were set to Hermansky-Pudlak syndrome 6, 614075
COVID-19 research v0.36 HPS4 Ellen McDonagh gene: HPS4 was added
gene: HPS4 was added to Viral susceptibility. Sources: Expert Review Green,North West GLH,NHS GMS,GOSH PID v.8.0,London North GLH
Mode of inheritance for gene: HPS4 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: HPS4 were set to Hermansky-Pudlak syndrome 4, 614073
COVID-19 research v0.36 HPS1 Ellen McDonagh gene: HPS1 was added
gene: HPS1 was added to Viral susceptibility. Sources: Expert Review Green,North West GLH,NHS GMS,GOSH PID v.8.0,London North GLH
Mode of inheritance for gene: HPS1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: HPS1 were set to 9562579
Phenotypes for gene: HPS1 were set to inflammatory bowel disease; oculocutaneous albinism; Hermansky-Pudlak syndrome 1; bleeding; pulmonary fibrosis
COVID-19 research v0.36 HELLS Ellen McDonagh gene: HELLS was added
gene: HELLS was added to Viral susceptibility. Sources: Expert Review Green,North West GLH,NHS GMS,London North GLH,Literature,IUIS Classification February 2018
Mode of inheritance for gene: HELLS was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: HELLS were set to 28128455; 27328760; 17726103; 29339483; 11711429; 26216346; 14517253; 16395332
Phenotypes for gene: HELLS were set to ICF; Immunodeficiency-centromeric instability-facial anomalies syndrome 4, 616911; ICF4; Combined immunodeficiencies with associated or syndromic features; Facial dysmorphic features, macroglossia, bacterial/opportunistic infections, malabsorption, cytopenias, malignancies, multiradial configurations of chromosomes 1, 9, 16; Immunodeficiency-centromeric instability-facial anomalies syndrome
COVID-19 research v0.36 HAX1 Ellen McDonagh gene: HAX1 was added
gene: HAX1 was added to Viral susceptibility. Sources: Expert Review Green,Agranulocytosis v1.3,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,Congenital neutropaenia v1.22,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: HAX1 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: HAX1 were set to Congenital neutropenia; Cognitive and neurological defects in patients with defects in both HAX1 isoforms, susceptibility to MDS/leukemia; Neutropenia, severe congenital 3, autosomal recessive, 610738; Congenital defects of phagocyte number or function; Severe congenital neutropenia; Neutropenia, severe congenital 3
COVID-19 research v0.36 GINS1 Ellen McDonagh gene: GINS1 was added
gene: GINS1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: GINS1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: GINS1 were set to 28414293
Phenotypes for gene: GINS1 were set to Immunodeficiency 55, 617827; NK cell deficiency; chronic neutropenia; Neutropenia, IUGR, NK cells very low; GINS1 deficiency; Combined immunodeficiencies with associated or syndromic features; intrauterine growth retardation
COVID-19 research v0.36 G6PC3 Ellen McDonagh gene: G6PC3 was added
gene: G6PC3 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,Congenital neutropaenia v1.22,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: G6PC3 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: G6PC3 were set to 19118303; 20616219
Phenotypes for gene: G6PC3 were set to Structural heart defects, urogenital abnormalities, inner ear deafness, and venous angiectasias of trunks and limbs; Congenital neutropenia; Dursun syndrome, 612541; Severe Congenital Neutropenia; Neutropenia, severe congenital 4, autosomal recessive, 612541; Congenital defects of phagocyte number or function; Neutropenia, severe congenital 4
COVID-19 research v0.36 FOXN1 Ellen McDonagh gene: FOXN1 was added
gene: FOXN1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,SCID v1.6,IUIS Classification February 2018
Mode of inheritance for gene: FOXN1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: FOXN1 were set to 28636882; 15180707; 21507891; 11159512; 31447097; 10206641; 28077132; 29593714
Phenotypes for gene: FOXN1 were set to Nude severe combined immunodeficiency; T-cell immunodeficiency, congenital alopecia, and nail dystrophy; T-B+ SCID; Severe infections, abnormal thymic epithelium, immunodeficiency, congenital alopecia, nail dystrophy, neural tube defect; T-B+ SCID, congenital alopecia, nail dystrophy, 601705; Combined immunodeficiencies with associated or syndromic features
COVID-19 research v0.36 FERMT3 Ellen McDonagh gene: FERMT3 was added
gene: FERMT3 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: FERMT3 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: FERMT3 were set to 26729028; 27749372; 12511588; 17185466; 19234463; 21441448; 20357244
Phenotypes for gene: FERMT3 were set to LAD type 1 plus bleeding tendency; LAD; Congenital defects of phagocyte number or function; Leukocyte adhesion deficiency, type III, 612840
COVID-19 research v0.36 FAT4 Ellen McDonagh gene: FAT4 was added
gene: FAT4 was added to Viral susceptibility. Sources: Expert Review Green,Victorian Clinical Genetics Services,North West GLH,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: FAT4 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: FAT4 were set to 24913602; 25616299; 29681106
Phenotypes for gene: FAT4 were set to Lymphangiectasia and lymphedema with facial abnormalities and other dysmorphic features; Combined immunodeficiencies with associated or syndromic features; Hennekam lymphangiectasia-lymphedema syndrome 2, 616006
COVID-19 research v0.36 FASLG Ellen McDonagh gene: FASLG was added
gene: FASLG was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: FASLG was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: FASLG were set to 17605793; 8787672; 20301287; 27848183
Phenotypes for gene: FASLG were set to Autoimmune lymphoproliferative syndrome, type IB, 601859; Diseases of Immune Dysregulation; Autoimmune lymphoproliferative syndrome, type IB (ALPS-FASG); Splenomegaly, adenopathies, autoimmune cytopenias, SLE, soluble FasL is not elevated; Autoimmune lymphoproliferative syndrome (ALPS)
COVID-19 research v0.36 FADD Ellen McDonagh gene: FADD was added
gene: FADD was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: FADD was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: FADD were set to 21109225; 17656375; 25794656
Phenotypes for gene: FADD were set to para-infectious encephalopathy and hepatopathy; Functional hyposplenism, bacterial and viral infections, recurrent episodes of encephalopathy and liver dysfunction; Diseases of Immune Dysregulation; invasive pneumococcal disease; cardiovascular malformations; Infections, recurrent, with encephalopathy, hepatic dysfunction, and cardiovasuclar malformations, 613759; functional hyposplenism; ALPS-like disease
COVID-19 research v0.36 EXTL3 Ellen McDonagh gene: EXTL3 was added
gene: EXTL3 was added to Viral susceptibility. Sources: Expert Review Green,North West GLH,NHS GMS,London North GLH,A- or hypo-gammaglobulinaemia v1.25,IUIS Classification February 2018
Mode of inheritance for gene: EXTL3 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: EXTL3 were set to 28132690; 28148688
Phenotypes for gene: EXTL3 were set to Combined immunodeficiencies with associated or syndromic features; EXTL3 deficiency; Platyspondyly, kyphosis, variable skeletal dysplasias, developmental delay; Immunoskeletal dysplasia with neurodevelopmental abnormalities, 617425
COVID-19 research v0.36 ERCC6L2 Ellen McDonagh gene: ERCC6L2 was added
gene: ERCC6L2 was added to Viral susceptibility. Sources: Expert Review Green,North West GLH,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: ERCC6L2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ERCC6L2 were set to 27185855; 24507776
Phenotypes for gene: ERCC6L2 were set to Bone marrow failure syndrome 2, 615715; Combined immunodeficiencies with associated or syndromic features; Facial dysmorphism, microcephaly, bone marrow failure
COVID-19 research v0.36 EPG5 Ellen McDonagh gene: EPG5 was added
gene: EPG5 was added to Viral susceptibility. Sources: Expert Review Green,Combined B and T cell defect v1.12,Victorian Clinical Genetics Services,North West GLH,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: EPG5 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: EPG5 were set to 23222957; 23838600; 25331754; 26395118; 23674064; 26917586; 28624465
Phenotypes for gene: EPG5 were set to Vici syndrome; Vici syndrome due to EPG5 deficiency; Vici syndrome, 242840; Agenesis of the corpus callosum, cataracts, cardiomyopathy, skin hypopigmentation, intellectual disability, microcephaly, recurrent infections, chronic mucocutaneous candidiasis; Immunodeficiency with cleft lip/palate, cataract, hypopigmentation, and absent corpus callosum; syndromic phenotype (immunodeficiency variable); Combined immunodeficiencies with associated or syndromic features
COVID-19 research v0.36 DOCK8 Ellen McDonagh gene: DOCK8 was added
gene: DOCK8 was added to Viral susceptibility. Sources: Expert Review Green,Combined B and T cell defect v1.12,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: DOCK8 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: DOCK8 were set to 25724123; 19776401; 20004785; 25627830
Phenotypes for gene: DOCK8 were set to Combined immunodeficiency; Hyper-IgE recurrent infection syndrome, autosomal recessive; Hyper IgE syndrome (HIES); Immunodeficiencies affecting cellular and humoral immunity; Low NK cells with poor function, eosinophilia, recurrent infections, cutaneous viral, fungal and staphylococcal infections, severe atopy, cancer diathesis; Hyper-IgE recurrent infection syndrome; impaired T cell function, Atopy, cutaneous viral infections
COVID-19 research v0.36 DOCK2 Ellen McDonagh gene: DOCK2 was added
gene: DOCK2 was added to Viral susceptibility. Sources: Expert Review Green,Victorian Clinical Genetics Services,North West GLH,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: DOCK2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: DOCK2 were set to 28694805; 26083206; 29503648
Phenotypes for gene: DOCK2 were set to Dock 2 deficiency, Immunodeficiency 40; Immunodeficiencies affecting cellular and humoral immunity; Immunodeficiency 40, 616433; Nl NK cells, but defective function. Poor interferon responses in hematopoietic and non-hematopoietic cells
COVID-19 research v0.36 DNMT3B Ellen McDonagh gene: DNMT3B was added
gene: DNMT3B was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,A- or hypo-gammaglobulinaemia v1.25,IUIS Classification February 2018
Mode of inheritance for gene: DNMT3B was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: DNMT3B were set to 10647011
Phenotypes for gene: DNMT3B were set to Facial dysmorphic features, developmental delay, macroglossia, bacterial/opportunistic infections, malabsorption, cytopenias, malignancies, multiradial configurations of chromosomes 1, 9, 16; Immunodeficiency-centromeric instability-facial anomalies syndrome 1, 242860; Immunodeficiency centromeric instability facial anomalies syndrome (ICF); Immunodeficiency-centromeric instability-facial anomalies syndrome 1; Combined immunodeficiencies with associated or syndromic features
COVID-19 research v0.36 DNASE2 Ellen McDonagh gene: DNASE2 was added
gene: DNASE2 was added to Viral susceptibility. Sources: Expert Review Green,North West GLH,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: DNASE2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: DNASE2 were set to 29259162
Phenotypes for gene: DNASE2 were set to liver fibrosis; multisystem autoinflammatory syndrome; SLE; severe neonatal anemia; Autoinflammatory Disorders; deforming arthropathy; Glomerulonephritis, arthropathy, vasculitis; membranoproliferative glomerulonephritis
COVID-19 research v0.36 DNAJC21 Ellen McDonagh gene: DNAJC21 was added
gene: DNAJC21 was added to Viral susceptibility. Sources: Expert Review Green,North West GLH,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: DNAJC21 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: DNAJC21 were set to 27346687; 29700810; 28062395
Phenotypes for gene: DNAJC21 were set to Bone marrow failure syndrome 3, 617052; Metaphyseal changes, short stature, developmental delay, pancreatic dysfunction, bone marrow failure; Shwachman-Diamond syndrome-like; Congenital defects of phagocyte number or function
COVID-19 research v0.36 DCLRE1C Ellen McDonagh gene: DCLRE1C was added
gene: DCLRE1C was added to Viral susceptibility. Sources: Expert Review Green,Combined B and T cell defect v1.12,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,SCID v1.6,IUIS Classification February 2018
Mode of inheritance for gene: DCLRE1C was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: DCLRE1C were set to Severe combined immunodeficiency, Athabascan type, 602450; Severe combined immunodeficiency, Athabascan type; DCLRE1C (Artemis) deficiency; Combined immunodeficiency; Severe Combined Immunodeficiency With Sensitivity To Ionizing Radiation; Atypical Severe Combined Immunodeficiency (Atypical SCID); Immunodeficiencies affecting cellular and humoral immunity; Nl NK, radiation sensitive; T-B+ SCID; Omenn syndrome; Severe combined immunodeficiency (SCID); T-B- SCID
COVID-19 research v0.36 DCLRE1B Ellen McDonagh gene: DCLRE1B was added
gene: DCLRE1B was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: DCLRE1B was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: DCLRE1B were set to 20479256
Phenotypes for gene: DCLRE1B were set to Intrauterine growth retardation, microcephaly, nail dystrophy, sparse scalp hair and eyelashes, hyperpigmentation of skin, palmar hyperkeratosis, premalignant oral leukoplakia, pancytopenia, myelodysplasia, +/- recurrent infections. A severe phenotype with developmental delay and cerebellar hypoplasia known as Hoyeraal-Hreidarsson Syndrome (HHS) may occur in some DKC patients; Combined immunodeficiencies with associated or syndromic features; Hoyeraal-Hreidarsson syndrome
COVID-19 research v0.36 CYBA Ellen McDonagh gene: CYBA was added
gene: CYBA was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CYBA was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CYBA were set to 10759707; 12073015; 2243141; 1415254; 18422995
Phenotypes for gene: CYBA were set to Chronic granulomatous disease (CGD); Congenital defects of phagocyte number or function; Infections, autoinflammatory phenotype; Chronic granulomatous disease, autosomal, due to deficiency of CYBA,233690
COVID-19 research v0.36 CTSC Ellen McDonagh gene: CTSC was added
gene: CTSC was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CTSC was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CTSC were set to 10593994; 10662807; 11106356
Phenotypes for gene: CTSC were set to Severe periodontitis; Periodontitis, palmoplantar hyperkeratosis in some patients; Congenital defects of phagocyte number or function; Haim-Munk syndrome, 245010; palmoplantar keratoderma; Papillon-Lefevre syndrome, 245000
COVID-19 research v0.36 CTPS1 Ellen McDonagh gene: CTPS1 was added
gene: CTPS1 was added to Viral susceptibility. Sources: Expert Review Green,Victorian Clinical Genetics Services,North West GLH,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CTPS1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CTPS1 were set to 9536098; 24870241; 27638562; 26424649; 17576681
Phenotypes for gene: CTPS1 were set to Recurrent/chronic bacterial and viral infections (EBV, VZV), EBV lymphoproliferation, B-cell non-Hodgkin lymphoma; Severe combined immunodeficiency due to CTPS1 deficiency; Immunodeficiency 24, 615897; Patients develop Epstein-Barr Virus (EBV) driven Hemophagocytic Lymphohistiocytosis (HLH ); Diseases of Immune Dysregulation
COVID-19 research v0.36 CSF3R Ellen McDonagh gene: CSF3R was added
gene: CSF3R was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,Congenital neutropaenia v1.22,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CSF3R was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CSF3R were set to 24753537; 29070147; 19620628; 26324699
Phenotypes for gene: CSF3R were set to Congenital neutropenia; Congenital defects of phagocyte number or function; Neutropenia, severe congenital 7; N/A; Neutropenia, severe congenital, 7, autosomal recessive, 617014
COVID-19 research v0.36 CSF2RB Ellen McDonagh gene: CSF2RB was added
gene: CSF2RB was added to Viral susceptibility. Sources: Expert Review Green,North West GLH,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CSF2RB was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CSF2RB were set to 21205713; 21075760; 9410898
Phenotypes for gene: CSF2RB were set to Surfactant metabolism dysfunction, pulmonary, 5, 614370; Congenital defects of phagocyte number or function; Alveolar proteinosis
COVID-19 research v0.36 CSF2RA Ellen McDonagh gene: CSF2RA was added
gene: CSF2RA was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CSF2RA was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CSF2RA were set to 1972780; 18955570; 23632888; 18955567
Phenotypes for gene: CSF2RA were set to Congenital pulmonary alveolar proteinosis; Alveolar proteinosis; Congenital defects of phagocyte number or function; Pulmonary alveolar proteinosis; hypersensitivity; Surfactant metabolism dysfunction, pulmonary 4, 300770
COVID-19 research v0.36 CORO1A Ellen McDonagh gene: CORO1A was added
gene: CORO1A was added to Viral susceptibility. Sources: Expert Review Green,Combined B and T cell defect v1.12,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CORO1A was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CORO1A were set to 23522482; 18836449; 19097825
Phenotypes for gene: CORO1A were set to Combined immunodeficiency; Immunodeficiency 8; hypogammaglobulinaemia, combined immunodeficiency; Coronin-1A deficiency; Atypical Severe Combined Immunodeficiency (Atypical SCID); Detectable thymus, EBV; Immunodeficiencies affecting cellular and humoral immunity; Omenn syndrome; Severe combined immunodeficiency (SCID)
COVID-19 research v0.36 CLPB Ellen McDonagh gene: CLPB was added
gene: CLPB was added to Viral susceptibility. Sources: Expert Review Green,Victorian Clinical Genetics Services,North West GLH,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CLPB was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CLPB were set to 25650066; 25597510; 27891836; 28687938; 26916670; 25597511
Phenotypes for gene: CLPB were set to Neurocognitive developmental aberrations, microcephaly, hypoglycemia, hypotonia, ataxia, seizures, cataracts, IUGR; Congenital defects of phagocyte number or function; 3-methylglutaconic aciduria, type VII, with cataracts, neurologic involvement and neutropenia, 616271; 3-methylglutaconic aciduria, type VII; 3-methylglutaconic aciduria, type 7; Recurrent or severe infection
COVID-19 research v0.36 CIITA Ellen McDonagh gene: CIITA was added
gene: CIITA was added to Viral susceptibility. Sources: Expert Review Green,Combined B and T cell defect v1.12,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CIITA was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CIITA were set to 8402893; 11862382; 9099848
Phenotypes for gene: CIITA were set to HLA class II deficiency; Combined immunodeficiency (MHC class II deficiency, bare lymphocyte syndrome); Immunodeficiencies affecting cellular and humoral immunity; Respiratory and gastrointestinal infections, liver/biliary tract disease; Bare lymphocyte syndrome, type II, complementation group A
COVID-19 research v0.36 CFI Ellen McDonagh gene: CFI was added
gene: CFI was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,Inherited complement deficiency v0.11,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CFI was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CFI were set to 18374984; 24142231; 22710145; 19065647; 8613545; 12562389; 27091480; 3897024; 21316765; 25988862
Phenotypes for gene: CFI were set to {Macular degeneration, age-related, 13, susceptibility to}, 615439; Complement factor I deficiency; Factor I deficiency; {Hemolytic uremic syndrome, atypical, susceptibility to, 3}, 612923; Infections, disseminated neisserial infections, atypical Hemolytic-uremic syndrome, preeclampsia; Complement Deficiencies; Immunodeficiency with factor I anomaly; C3b inactivator deficiency; Complement factor I deficiency, 610984
COVID-19 research v0.36 CFD Ellen McDonagh gene: CFD was added
gene: CFD was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,Inherited complement deficiency v0.11,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CFD was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CFD were set to 29522842; 6568950; 16527897; 11457876
Phenotypes for gene: CFD were set to Complement factor D deficiency, 613912; Neisserial infections; Recurrent Neisseria infections due to factor D deficiency; Complement Deficiencies; Complement factor D deficiency; Factor D deficiency
COVID-19 research v0.36 CDCA7 Ellen McDonagh gene: CDCA7 was added
gene: CDCA7 was added to Viral susceptibility. Sources: Expert Review Green,North West GLH,NHS GMS,London North GLH,Literature,IUIS Classification February 2018
Mode of inheritance for gene: CDCA7 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CDCA7 were set to 28128455; 27328760; 15952214; 29339483; 29659838; 1999836; 26216346
Phenotypes for gene: CDCA7 were set to ICF; recurrent respiratory infections; ICF3; Immunodeficiency-centromeric instability-facial anomalies syndrome 3, 616910; immunodeficiency, centromeric instability, facial anomalies syndrome type 3; hypogammaglobulinaemia; enteropathy; Combined immunodeficiencies with associated or syndromic features; Facial dysmorphic features, macroglossia, bacterial/opportunistic infections, malabsorption, cytopenias, malignancies, multiradial configurations of chromosomes 1, 9, 16; Immunodeficiency-centromeric instability-facial anomalies syndrome
COVID-19 research v0.36 CD79B Ellen McDonagh gene: CD79B was added
gene: CD79B was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,A- or hypo-gammaglobulinaemia v1.25,IUIS Classification February 2018
Mode of inheritance for gene: CD79B was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CD79B were set to 17709424; 17675462; 24722855
Phenotypes for gene: CD79B were set to Agammaglobulinemia; Severe bacterial infections, normal numbers of pro-B cells; Agammaglobulinemia 6, 612692; CD79B deficiency, Agammaglobulinemia with autosomal recessive inheritance (ARA); Agammaglobulinemia 6; Predominantly Antibody Deficiencies
COVID-19 research v0.36 CD79A Ellen McDonagh gene: CD79A was added
gene: CD79A was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,A- or hypo-gammaglobulinaemia v1.25,IUIS Classification February 2018
Mode of inheritance for gene: CD79A was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CD79A were set to 19302039; 11920841; 24481606; 10525050; 29335801; 24909997
Phenotypes for gene: CD79A were set to Agammaglobulinemia; Agammaglobulinemia 3, 613501; Severe bacterial infections, normal numbers of pro-B cells; Agammaglobulinemia with autosomal recessive inheritance (ARA); Predominantly Antibody Deficiencies; CD79A deficiency; Agammaglobulinemia 3
COVID-19 research v0.36 CD70 Ellen McDonagh gene: CD70 was added
gene: CD70 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CD70 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CD70 were set to 28011864; 28011863; 29434583
Phenotypes for gene: CD70 were set to Combined immunodeficiency; CD70-deficiency; Diseases of Immune Dysregulation; EBV-related malignancy; EBV susceptibility, Hodgkin lymphoma
COVID-19 research v0.36 CD59 Ellen McDonagh gene: CD59 was added
gene: CD59 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CD59 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CD59 were set to 1382994; 1699124; 23149847; 24382084; 25716358
Phenotypes for gene: CD59 were set to Primary CD59 deficiency; paroxysmal nocturnal haemoglobinuria; CD59 antigen P18-20 deficiency (CD59); Hemolytic anemia, polyneuropathy; Hemolytic anemia, CD59-mediated, with or without immune-mediated polyneuropathy, 612300; childhood relapsing immune-mediated polyneuropathy; Complement Deficiencies; chronic hemolysis; Membrane Attack Complex Inhibitor (CD59) deficiency
COVID-19 research v0.36 CD55 Ellen McDonagh gene: CD55 was added
gene: CD55 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CD55 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CD55 were set to 28657829
Phenotypes for gene: CD55 were set to primary intestinal lymphangiectasia; protein-losing enteropathy; Protein losing enteropathy, thrombosis; Decay-accelerating factor for complement deficiency (DAF CD55); Complement Deficiencies; hypogammaglobulinaemia; angiopathic thrombosis
COVID-19 research v0.36 CD40 Ellen McDonagh gene: CD40 was added
gene: CD40 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CD40 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CD40 were set to 17502893; 20301287; 12584544; 11675497
Phenotypes for gene: CD40 were set to Immunodeficiency with hyper-IgM, type 3; Hyper-IgM syndrome due to CD40 deficiency; non-X-linked hyper IgM syndrome; Immunodeficiencies affecting cellular and humoral immunity; HIGM3; CD40 deficiency; Neutropenia, opportunistic infections, gastrointestinal and biliary tract and liver disease, Cryptosporidium infections; CSR defects and Hyper IgM (HIGM) syndromes
COVID-19 research v0.36 CD3G Ellen McDonagh gene: CD3G was added
gene: CD3G was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CD3G was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CD3G were set to 1635567; 17277165
Phenotypes for gene: CD3G were set to Combined immunodeficiency; Immunodeficiency 17, CD3 gamma deficient 615607; CD3z deficiency; Immunodeficiencies affecting cellular and humoral immunity; N/A
COVID-19 research v0.36 CD3E Ellen McDonagh gene: CD3E was added
gene: CD3E was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,SCID v1.6,IUIS Classification February 2018
Mode of inheritance for gene: CD3E was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: CD3E were set to Immunodeficiency due to defect in CD3-epsilon; Severe Combined Immune Deficiency; Atypical Severe Combined Immunodeficiency (Atypical SCID); Nl NK, no g/d T cells; Immunodeficiencies affecting cellular and humoral immunity; T-B+ SCID; Immunodeficiency 18, SCID variant; Severe combined immunodeficiency (SCID); CD3e deficiency
COVID-19 research v0.36 CD3D Ellen McDonagh gene: CD3D was added
gene: CD3D was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,SCID v1.6,IUIS Classification February 2018
Mode of inheritance for gene: CD3D was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: CD3D were set to CD3d deficiency; Severe Combined Immune Deficiency; Atypical Severe Combined Immunodeficiency (Atypical SCID); Nl NK, no g/d T cells; Immunodeficiency 19; Immunodeficiencies affecting cellular and humoral immunity; T-B+ SCID; Severe combined immunodeficiency, T cell-negative, B-cell/natural killer-cell positive; Severe combined immunodeficiency (SCID)
COVID-19 research v0.36 CD27 Ellen McDonagh gene: CD27 was added
gene: CD27 was added to Viral susceptibility. Sources: Expert Review Green,Combined B and T cell defect v1.12,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CD27 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CD27 were set to 22197273; 25843314; 22801960
Phenotypes for gene: CD27 were set to Lymphoproliferative syndrome 2; Combined immunodeficiency; Diseases of Immune Dysregulation; Features triggered by EBV infection, HLH, aplastic anemia, low iNKT cells, lymphoma; Combined immunodeficiency with EBV-associated lymphoproliferation; CD27 deficiency
COVID-19 research v0.36 CD19 Ellen McDonagh gene: CD19 was added
gene: CD19 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,A- or hypo-gammaglobulinaemia v1.25,IUIS Classification February 2018
Mode of inheritance for gene: CD19 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CD19 were set to 16672701; 21159371; 21330302
Phenotypes for gene: CD19 were set to Immunodeficiency, common variable, 3; Isolated IgG subclass deficiency; Recurrent infections, may have glomerulonephritis; Immunodeficiency, common variable, 3 613493; Common variable immunodeficiency disorders (CVID); Predominantly Antibody Deficiencies; hypogammaglobulinemia
COVID-19 research v0.36 CCBE1 Ellen McDonagh gene: CCBE1 was added
gene: CCBE1 was added to Viral susceptibility. Sources: Expert Review Green,Victorian Clinical Genetics Services,North West GLH,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CCBE1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CCBE1 were set to 24913602; 19911200; 19935664
Phenotypes for gene: CCBE1 were set to Lymphangiectasia and lymphedema with facial abnormalities and other dysmorphic features; Combined immunodeficiencies with associated or syndromic features; Hennekam lymphangiectasia-lymphedema syndrome 1, 235510
COVID-19 research v0.36 CASP8 Ellen McDonagh gene: CASP8 was added
gene: CASP8 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CASP8 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CASP8 were set to 24240292; 16157684; 12353035; 20301287
Phenotypes for gene: CASP8 were set to Caspase-8 deficiency state; Immunodeficiency due to CASP8 deficiency; CEDS; ?Autoimmune lymphoproliferative syndrome, type IIB, 607271; Diseases of Immune Dysregulation; Caspase 8 deficiency; Autoimmune lymphoproliferative syndrome (ALPS); Adenopathies, splenomegaly, bacterial and viral infections, hypogammaglobulinemia
COVID-19 research v0.36 CARMIL2 Ellen McDonagh gene: CARMIL2 was added
gene: CARMIL2 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CARMIL2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CARMIL2 were set to 27647349; 27896283; 28112205
Phenotypes for gene: CARMIL2 were set to warts, molluscum contagiosum, and T cell dysfunction; Combined immunodeficiency; Recurrent bacterial, fungal and mycobacterial infections, viral warts, molluscum and EBV lymphoproliferative and other malignancy, atopy; Diseases of Immune Dysregulation; EBV+ disseminated smooth muscle tumours
COVID-19 research v0.36 CARD9 Ellen McDonagh gene: CARD9 was added
gene: CARD9 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: CARD9 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CARD9 were set to 19864672; 23335372; 24131138
Phenotypes for gene: CARD9 were set to Predisposition to invasive fungal disease due to CARD9 deficiency; 212050; CARD9 deficiency; Invasive candidiasis infection, deep dermatophytoses, other invasive fungal infections; Candidiasis, familial, 2; Defects in Intrinsic and Innate Immunity
COVID-19 research v0.36 C9 Ellen McDonagh gene: C9 was added
gene: C9 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: C9 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: C9 were set to 9634479; 9570574; 9144525; 10072634
Phenotypes for gene: C9 were set to Mild susceptibility to disseminated neisserial infections; Complement component 9 deficiency; Complement Deficiencies; Susceptibility to invasive bacterial infection, especially meningococcal; C9 deficiency, 613825
COVID-19 research v0.36 C8B Ellen McDonagh gene: C8B was added
gene: C8B was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: C8B was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: C8B were set to 8098723; 19434484; 9476133; 27183977
Phenotypes for gene: C8B were set to Disseminated neisserial infections; C8 deficiency, type II, 613789; Complement component 8 deficiency; Complement Deficiencies; Susceptibility to invasive bacterial infection, especially meningococcal
COVID-19 research v0.36 C8A Ellen McDonagh gene: C8A was added
gene: C8A was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: C8A was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: C8A were set to 9759902
Phenotypes for gene: C8A were set to Disseminated neisserial infections; Complement component 8 deficiency; C8 deficiency, type I, 613790; Complement Deficiencies; Susceptibility to invasive bacterial infection, especially meningococcal
COVID-19 research v0.36 C7 Ellen McDonagh gene: C7 was added
gene: C7 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: C7 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: C7 were set to 16771861; 15554930; 9844043; 7762578
Phenotypes for gene: C7 were set to Disseminated neisserial infections; Complement component 7 deficiency; Complement Deficiencies; C7 deficiency, 610102; Susceptibility to invasive bacterial infection, especially meningococcal
COVID-19 research v0.36 C6 Ellen McDonagh gene: C6 was added
gene: C6 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: C6 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: C6 were set to 9472666; 8690922; 12653841
Phenotypes for gene: C6 were set to Disseminated neisserial infections; C6 deficiency, 612446; Complement Deficiencies; Susceptibility to invasive bacterial infection, especially meningococcal; Complement component 6 deficiency
COVID-19 research v0.36 C5 Ellen McDonagh gene: C5 was added
gene: C5 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: C5 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: C5 were set to 19375167; 25534848; 7730648
Phenotypes for gene: C5 were set to C5 deficiency, 609536; Disseminated neisserial infections; Complement Deficiencies; Complement component 5 deficiency; Susceptibility to invasive bacterial infection, especially meningococcal
COVID-19 research v0.36 C4B Ellen McDonagh gene: C4B was added
gene: C4B was added to Viral susceptibility. Sources: Expert Review Green,Victorian Clinical Genetics Services,North West GLH,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: C4B was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: C4B were set to 12626442; 2355198; 19062096; 1569346; 2788199
Phenotypes for gene: C4B were set to C4B deficiency, 614379; SLE, infections with encapsulated organisms , partial deficiency is common (either C4A or C4B) and appears to have a modest effect on host defense; Complement Deficiencies; SLE predisposition
COVID-19 research v0.36 C4A Ellen McDonagh gene: C4A was added
gene: C4A was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: C4A was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: C4A were set to 15294999; 2295875; 22482068
Phenotypes for gene: C4A were set to C4a deficiency, 614380; Complement Deficiencies; SLE, infections with encapsulated organisms , partial deficiency is common (either C4A or C4B) and appears to have a modest effect on host defense; Complement component 4 deficiency; SLE predisposition; Immunodeficiency due to a classical component pathway complement deficiency; infections with encapsulated organisms
COVID-19 research v0.36 C3 Ellen McDonagh gene: C3 was added
gene: C3 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: C3 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: C3 were set to 1350678; 1976733; 15781264; 4117597
Phenotypes for gene: C3 were set to Complement Deficiencies; Complement component 3 deficiency; Atypical hemolytic-uremic syndrome, dense deposit disease; Infections, glomerulonephritis, atypical hemolytic-uremic syndrome with GOF mutations; C3 deficiency, 613779
COVID-19 research v0.36 C2 Ellen McDonagh gene: C2 was added
gene: C2 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,Inherited complement deficiency v0.11,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: C2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: C2 were set to 1577763; 15643297; 11079100; 8621452; 7901282
Phenotypes for gene: C2 were set to Complement Component C2 Deficiency; Lupus; Complement Deficiencies; SLE, infections with encapsulated organisms, atherosclerosis; C2 deficiency, 217000; Immunodeficiency due to C1, C4, or C2 component complement deficiency
COVID-19 research v0.36 C1S Ellen McDonagh gene: C1S was added
gene: C1S was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: C1S was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: C1S were set to 27745832; 11390518; 20727163; 9856483
Phenotypes for gene: C1S were set to SLE; pyogenic infections; Complement component 1 deficiency; SLE, infections with encapsulated organisms, Ehlers Danlos phenotype; Complement Deficiencies; C1s deficiency, 613783; C1s deficiency, Lupus
COVID-19 research v0.36 C1R Ellen McDonagh gene: C1R was added
gene: C1R was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: C1R was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: C1R were set to 28544690; 21784777; 27745832; 29795138; 28711143
Phenotypes for gene: C1R were set to SLE; pyogenic infections; Complement component 1 deficiency; SLE, infections with encapsulated organisms, Ehlers Danlos phenotype; Complement Deficiencies; C1r/C1s deficiency, combined, Lupus; Immunodeficiency due to a classical component pathway complement deficiency
COVID-19 research v0.36 C1QC Ellen McDonagh gene: C1QC was added
gene: C1QC was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: C1QC was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: C1QC were set to 24157463; 8630118; 7900940; 21654842
Phenotypes for gene: C1QC were set to SLE, infections with encapsulated organisms; Complement component 1 deficiency; C1q deficiency, 613652; Complement Deficiencies; Immunodeficiency due to a classical component pathway complement deficiency
COVID-19 research v0.36 C1QB Ellen McDonagh gene: C1QB was added
gene: C1QB was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,Inherited complement deficiency v0.11,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: C1QB was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: C1QB were set to 9476130; 2894352; 24160257; 12133956; 25454803; 23651859; 17513176
Phenotypes for gene: C1QB were set to SLE, infections with encapsulated organisms; SLE; lupus-like disease; Complement component 1 deficiency; Immunodeficiency due to an early component of complement deficiency, 613652; C1q deficiency; susceptibility to invasive bacterial infection; Complement Deficiencies
COVID-19 research v0.36 C1QA Ellen McDonagh gene: C1QA was added
gene: C1QA was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: C1QA was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: C1QA were set to 7594474; 28601358; 25133636; 8840296; 26032012; 21654842
Phenotypes for gene: C1QA were set to SLE, infections with encapsulated organisms; Complement component 1 deficiency; C1q deficiency, 613652; Complement Deficiencies; Immunodeficiency due to a classical component pathway complement deficiency
COVID-19 research v0.36 BLNK Ellen McDonagh gene: BLNK was added
gene: BLNK was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,A- or hypo-gammaglobulinaemia v1.25,IUIS Classification February 2018
Mode of inheritance for gene: BLNK was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: BLNK were set to 19302039; 24582315; 25893637; 10583958
Phenotypes for gene: BLNK were set to Agammaglobulinemia; Agammaglobulinemia 4, 613502; Severe bacterial infections, normal numbers of pro-B cells; Agammaglobulinemia 4; Predominantly Antibody Deficiencies; agammaglobulinaemia with absent B cells
COVID-19 research v0.36 BLM Ellen McDonagh gene: BLM was added
gene: BLM was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: BLM was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: BLM were set to 17407155; 8231788; 9482582; 9285778; 7585968
Phenotypes for gene: BLM were set to Immunodeficiency; Combined immunodeficiencies with associated or syndromic features; Bloom syndrome, 210900; Short stature, dysmorphic facies, sun-sensitive erythema, marrow failure, leukemia, lymphoma, chromosomal instability
COVID-19 research v0.36 B2M Ellen McDonagh gene: B2M was added
gene: B2M was added to Viral susceptibility. Sources: Expert Review Green,Victorian Clinical Genetics Services,North West GLH,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: B2M was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: B2M were set to 25702838; 4186801
Phenotypes for gene: B2M were set to Immunodeficiency 43,241600; Immunodeficiency by defective expression of HLA class 1; Sinopulmonary infections, cutaneous granulomas. Absent _2m associated proteins MHC-I, CD1a, CD1b, CD1c; Immunodeficiencies affecting cellular and humoral immunity
COVID-19 research v0.36 ATM Ellen McDonagh gene: ATM was added
gene: ATM was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: ATM was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ATM were set to 27421701; 2136770; 27884168; 7792600; 2005780
Phenotypes for gene: ATM were set to Ataxia telangiectasia (ATM); immunodeficiency; Combined immunodeficiencies with associated or syndromic features; Ataxia, telangiectasia, pulmonary infections, lymphoreticular and other malignancies, increased alpha fetoprotein, increased radiosensitivity, chromosomal instability and chromosomal translocations; Ataxia-telangiectasia, 208900
COVID-19 research v0.36 ARPC1B Ellen McDonagh gene: ARPC1B was added
gene: ARPC1B was added to Viral susceptibility. Sources: Expert Review Green,North West GLH,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: ARPC1B was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ARPC1B were set to 29127144; 28368018; 27965109
Phenotypes for gene: ARPC1B were set to inflammatory predisposition; Platelet abnormalities with eosinophilia and immune-mediated inflammatory disease, 617718; Mild thrombocytopenia with normal sized platelets, recurrent invasive infections, colitis, vasculitis, autoantibodies (ANA, ANCA), eosinophilia, defective Arp2/3, filament branching; Immunodeficiency with thrombocytopenia; Combined immunodeficiencies with associated or syndromic features; Thrombocytopenia & Immune Deficiency
COVID-19 research v0.36 AP3B1 Ellen McDonagh gene: AP3B1 was added
gene: AP3B1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: AP3B1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: AP3B1 were set to 28585318; 16537806; 11809908; 16507770; 19679886; 14566336; 8042664; 23403622; 10024875
Phenotypes for gene: AP3B1 were set to Partial albinism, recurrent infections, pulmonary fibrosis, increased bleeding, neutropenia, HLH; Immunodeficient HPS; Hermansky-Pudlak syndrome 2; Diseases of Immune Dysregulation; Hermansky-Pudlak syndrome with neutropenia; Hermansky-Pudlak syndrome, 608233; HPS2
COVID-19 research v0.36 AK2 Ellen McDonagh gene: AK2 was added
gene: AK2 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,SCID v1.6,IUIS Classification February 2018
Mode of inheritance for gene: AK2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: AK2 were set to 19043417; 19043416
Phenotypes for gene: AK2 were set to Reticular dysgenesis, AK2 deficiency; Granulocytopenia and deafness; Reticular dysgenesis, 267500; Reticular dysgenesis with sensorineural deafness; Reticular Dysgenesis AK2 (SCID); Immunodeficiencies affecting cellular and humoral immunity
COVID-19 research v0.36 AICDA Ellen McDonagh gene: AICDA was added
gene: AICDA was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,A- or hypo-gammaglobulinaemia v1.25,IUIS Classification February 2018
Mode of inheritance for gene: AICDA was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: AICDA were set to 27701145; 21700883; 12958596
Phenotypes for gene: AICDA were set to Hyper IgM syndrome with lymphoid hyperplasia; Primary Immune Deficiencies; Immunodeficiency with hyper-IgM, type 2, 605258; Bacterial infections, enlarged lymph nodes and germinal centers; Predominantly Antibody Deficiencies; Immunodeficiency with hyper-IgM, type 2; CSR defects and Hyper IgM (HIGM) syndromes
COVID-19 research v0.36 ADAR Ellen McDonagh gene: ADAR was added
gene: ADAR was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: ADAR was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ADAR were set to 25604658; 24183309; 23001123; 24262145; 27643693; 25769924
Phenotypes for gene: ADAR were set to Fever Syndromes and Related Diseases, Aicardi-Goutieres syndrome 6, 615010; Type 1 interferonopathies; Autoinflammatory Disorders; AGS6; Classical AGS, BSN, SP
COVID-19 research v0.36 ADA2 Ellen McDonagh gene: ADA2 was added
gene: ADA2 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: ADA2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ADA2 were set to 24552284; 26922074; 24552285; 29564582
Phenotypes for gene: ADA2 were set to Other autoinflammatory diseases with known genetic defect; Evans' syndrome; Polyarteritis nodosa, childhood-onset, 615688; combined immunodeficiency; Polyarteritis nodosa; Deficiency of ADA2 (DADA2); Polyarteritis nodosa, childhood-onset, early-onset recurrent ischemic stroke and fever; Autoinflammatory Disorders; Fever with early onset stroke; ADA2 deficiency
COVID-19 research v0.36 ADA Ellen McDonagh gene: ADA was added
gene: ADA was added to Viral susceptibility. Sources: Expert Review Green,Combined B and T cell defect v1.12,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,SCID v1.6,IUIS Classification February 2018
Mode of inheritance for gene: ADA was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: ADA were set to Severe combined immunodeficiency due to ADA deficiency, 102700; Low NK, bone defects, may have pulmonary alveolar proteinosis, cognitive defects; Atypical Severe Combined Immunodeficiency (Atypical SCID); Immunodeficiencies affecting cellular and humoral immunity; Adenosine deaminase (ADA) deficiency; T-B+ SCID; Omenn syndrome; Severe combined immunodeficiency (SCID); T-B- SCID; Severe combined immunodeficiency due to ADA deficiency (some mosiacism noted)
COVID-19 research v0.36 ACP5 Ellen McDonagh gene: ACP5 was added
gene: ACP5 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: ACP5 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ACP5 were set to 21217752; 26789720; 21217755; 26951490; 18924170; 26346816
Phenotypes for gene: ACP5 were set to Spondyloenchondrodysplasia with immune dysregulation Type 1 interferonopathies; Short stature, SP, ICC, SLE, thrombocytopenia and autoimmune hemolytic anemia, possibly recurrent bacterial and viral infections; Spondyloenchondrodysplasia with immune dysregulation, 607944; Type 1 interferonopathies; Autoinflammatory Disorders
Primary immunodeficiency or monogenic inflammatory bowel disease v2.39 IRF9 Catherine Snow Classified gene: IRF9 as Amber List (moderate evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.39 IRF9 Catherine Snow Gene: irf9 has been classified as Amber List (Moderate Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.38 IRF9 Catherine Snow gene: IRF9 was added
gene: IRF9 was added to Primary immunodeficiency. Sources: Expert Review
Mode of inheritance for gene: IRF9 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IRF9 were set to 30143481; 30826365
Phenotypes for gene: IRF9 were set to Immunodeficiency 65, susceptibility to viral infections, 618648
Review for gene: IRF9 was set to AMBER
Added comment: Identified by external reviewer as not present in the Primary immunodeficiency (version 2.37) or the research Viral susceptibility panel (version 0.35).

PMID:30143481 - Life-threatening Influenza Pneumonitis in a Child With Inherited IRF9 Deficiency. 5 year old Algerian girl homozygous for LOF variant c.991G>A and was hospitalized for severe infection with IAV requiring mechanical ventilation and Tamiflu treatment, and who had a history of recurrent benign bronchiolitis, biliary perforation following measles-mumps-rubella (MMR) vaccination at 1 yr of age, and recurrent fevers without a causative pathogen identified.

PMID:30826365 - identifies a homozygous splicing mutation in the IRF9 gene in a family of Portugese origin. The variant, c.577+1G>T (NM_006084), which is located in the donor splice site of introns 5 and 6. The proband is was a 10-year-old boy born at term to healthy consanguineous parents (first cousins of Portuguese origin and residents of Venezuela). From the first year of life, the child displayed a marked susceptibility to viral infections with moderate-to-severe symptoms of disease that resulted in persistent neurological impairment and bronchiectasis. A six month old sibling who has the same homozygous variant has had preventative treatment with IVIG and cotrimoxazole and has not presented with infections.

PMID: 28878077 - During early viral infection, overwhelming antigen exposure can cause functional exhaustion of CD8+ T cells and lead to chronic infection this paper reports on a mouse study which demonstrates that IRF9 plays a role in preventing CD8+ T cell exhaustion.
Sources: Expert Review
COVID-19 research v0.35 TMEM173 Ellen McDonagh Classified gene: TMEM173 as Green List (high evidence)
COVID-19 research v0.35 TMEM173 Ellen McDonagh Added comment: Comment on list classification: Promoted to Green as clear evidence for this gene in viral susceptibility.
COVID-19 research v0.35 TMEM173 Ellen McDonagh Gene: tmem173 has been classified as Green List (High Evidence).
COVID-19 research v0.34 TMEM173 Ellen McDonagh commented on gene: TMEM173: Additional evidence added to the publication list, provided by Abdelazeem Elhabyan. Comments from Abdelazeem Elhabyan: GenBank - https://www.ncbi.nlm.nih.gov/gene?term=(human%5BOrganism%5D)%20AND%20TMEM173%5BGene%20Name%5D) This gene encodes a five transmembrane protein that functions as a major regulator of the innate immune response to viral and bacterial infections. The encoded protein is a pattern recognition receptor that detects cytosolic nucleic acids and transmits signals that activate type I interferon responses.

Hypothesis:
This gene is involved in interferon 1 pathway which is directly related to viral innate immune response. Upregulation may be associated with a protective effect or autoinflammatory response with aggravating effect. This is to be determined by clinical trials.

Highest organ of expression is the lung in genbank (Pneumonia caused by corona) RPKM ,\mean is 37

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7069765/

Extracellular vesicles released by virally infected cells(HSV) that carry STING can induce protective effect against viral replication in neighbouring non infected cells
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6146713/

Virulent Poxviruses Inhibit DNA Sensing by Preventing STING Activation
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5923072/
The gene is involved in acute pancreatitis in mice
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6112120/
COVID-19 research v0.33 TMEM173 Ellen McDonagh gene: TMEM173 was added
gene: TMEM173 was added to Viral susceptibility. Sources: Expert list
new-gene-name tags were added to gene: TMEM173.
Mode of inheritance for gene: TMEM173 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: TMEM173 were set to 25029335; 25401470; 30705050; 29976662; 29491158; 29425920
Phenotypes for gene: TMEM173 were set to STING-associated vasculopathy, infantile-onset 615934; Type 1 interferonopathies; Skin vasculopathy, inflammatory lung disease, systemic autoinflammation and ICC, FCL; Autoinflammatory Disorders
Added comment: This gene is Green on the Primary immunodeficiency (Version 2.37) gene panel.
Sources: Expert list
Primary immunodeficiency or monogenic inflammatory bowel disease v2.37 TMEM173 Ellen McDonagh Added comment: Comment on publications: Additional evidence added to the publication list, provided by Abdelazeem Elhabyan. Comments from Abdelazeem Elhabyan: GenBank - https://www.ncbi.nlm.nih.gov/gene?term=(human%5BOrganism%5D)%20AND%20TMEM173%5BGene%20Name%5D) This gene encodes a five transmembrane protein that functions as a major regulator of the innate immune response to viral and bacterial infections. The encoded protein is a pattern recognition receptor that detects cytosolic nucleic acids and transmits signals that activate type I interferon responses.

Hypothesis:
This gene is involved in interferon 1 pathway which is directly related to viral innate immune response. Upregulation may be associated with a protective effect or autoinflammatory response with aggravating effect. This is to be determined by clinical trials.

Highest organ of expression is the lung in genbank (Pneumonia caused by corona) RPKM ,\mean is 37

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7069765/

Extracellular vesicles released by virally infected cells(HSV) that carry STING can induce protective effect against viral replication in neighbouring non infected cells
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6146713/

Virulent Poxviruses Inhibit DNA Sensing by Preventing STING Activation
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5923072/
The gene is involved in acute pancreatitis in mice
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6112120/
Primary immunodeficiency or monogenic inflammatory bowel disease v2.37 TMEM173 Ellen McDonagh Publications for gene: TMEM173 were set to 25029335; 25401470
Intellectual disability v3.24 PIGK Zornitza Stark changed review comment from: 12 individuals from 9 unrelated families reported.
Sources: Expert list; to: 12 individuals from 9 unrelated families reported. Suggest adding to Genetic Epilepsy panel as well.
Sources: Expert list
Intellectual disability v3.24 PIGK Zornitza Stark gene: PIGK was added
gene: PIGK was added to Intellectual disability. Sources: Expert list
Mode of inheritance for gene: PIGK was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PIGK were set to 32220290
Phenotypes for gene: PIGK were set to Intellectual disability; seizures; cerebellar atrophy
Review for gene: PIGK was set to GREEN
gene: PIGK was marked as current diagnostic
Added comment: 12 individuals from 9 unrelated families reported.
Sources: Expert list
Intellectual disability v3.24 ADARB1 Zornitza Stark changed review comment from: Four unrelated individuals with bi-allelic variants in this gene.
Sources: Literature; to: Four unrelated individuals with bi-allelic variants in this gene. Suggest also adding to Genetic Epilepsy and Microcephaly panels.
Sources: Literature
Intellectual disability v3.24 ADARB1 Zornitza Stark gene: ADARB1 was added
gene: ADARB1 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: ADARB1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ADARB1 were set to 32220291
Phenotypes for gene: ADARB1 were set to Intellectual disability; microcephaly; seizures
Review for gene: ADARB1 was set to GREEN
gene: ADARB1 was marked as current diagnostic
Added comment: Four unrelated individuals with bi-allelic variants in this gene.
Sources: Literature
Hereditary neuropathy or pain disorder v1.4 PDK3 Zornitza Stark reviewed gene: PDK3: Rating: GREEN; Mode of pathogenicity: None; Publications: 23297365, 26801680, 27388934, 28902413; Phenotypes: Charcot-Marie-Tooth disease, X-linked dominant, 6 MIM#300905, HMSN; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females
Hereditary neuropathy or pain disorder v1.4 NTRK1 Zornitza Stark reviewed gene: NTRK1: Rating: AMBER; Mode of pathogenicity: None; Publications: ; Phenotypes: Insensitivity to pain, congenital, with anhidrosis, MIM# 256800; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Renal ciliopathies v1.12 KIF14 Catherine Snow changed review comment from: PMID:30388224 same authors as PMID: 24128419 identified two families and reported on two further families which had already previously been reported upon in PMID: 28566479. All fetuses had biallelic pathogenic variants.

PMID: 28892560 - Reported on four individuals with variants in KIF14. 3/4 had no problems with renal system, 1/4 a German boy, was identified who had small kidneys with increased echogenicity. WES of the German patient revealed 2 compound heterozygous missense variants of KIF14. One of these variants (NM_014875.2;c.2545C>G;p.His849Asp) replaces a histidine by aspartic acid and is predicted to be disease causing. (NM_014875.2;c.3662G>T;p.Gly1221Val) introduces valine at a position of glycine that is not conserved among different animals. This variant affects the first nucleotide of exon 24, a position that might impair splicing.

PMID: 29343805 - Biallelic Variants in KIF14 Cause Intellectual Disability With Microcephaly. 4 unrelated individuals identified but all asymptomatic in the Genitourinary system.

Rating as Amber and requesting support from clinical team as unsure of KIF14 and its broad phenotypes.; to: PMID:30388224 identified two families and reported on two further families which had already previously been reported upon in PMID: 28566479. All fetuses had biallelic pathogenic variants in KIF14 and had phenotypes within the spectrum of fetal forms of ciliopathies, Meckel–Gruber syndrome (MKS) - (intrauterine growth restriction, cystic kidneys and brain developmental defects, including cerebellar hypoplasia and vermis agenesis)

The paper also includes functional work on Zebrafish and reported that in vitro and in vivo analyses did not provide evidence of a direct role for KIF14 in ciliogenesis and suggested that loss of kif14 causes ciliopathy-like phenotypes through an accumulation of mitotic cells in ciliated tissues.

PMID: 28892560 - Reported on four individuals with variants in KIF14. 3/4 had no problems with renal system, 1/4 a German boy, was identified who had small kidneys with increased echogenicity. WES of the German patient revealed 2 compound heterozygous missense variants of KIF14. One of these variants (NM_014875.2;c.2545C>G;p.His849Asp) replaces a histidine by aspartic acid and is predicted to be disease causing. (NM_014875.2;c.3662G>T;p.Gly1221Val) introduces valine at a position of glycine that is not conserved among different animals. This variant affects the first nucleotide of exon 24, a position that might impair splicing.

PMID: 29343805 - Biallelic Variants in KIF14 Cause Intellectual Disability With Microcephaly. 4 unrelated individuals identified but all asymptomatic in the Genitourinary system.

Rating as Amber and requesting support from clinical team as unsure of KIF14 is relevant for this panel?
Renal ciliopathies v1.12 KIF14 Catherine Snow changed review comment from: PMID:30388224 same authors as PMID: 24128419 identified two families and reported on two further families which had already previously been reported upon in PMID: 28566479. All fetuses had biallelic pathogenic variants.

PMID: 28892560 - Reported on four individuals with variants in KIF14. 3/4 had no problems with renal system, 1/4 a German boy, was identified who had small kidneys with increased echogenicity. WES of the German patient revealed 2 compound heterozygous missense variants of KIF14. One of these variants (NM_014875.2;c.2545C>G;p.His849Asp) replaces a histidine by aspartic acid and is predicted to be disease causing. (NM_014875.2;c.3662G>T;p.Gly1221Val) introduces valine at a position of glycine that is not conserved among different animals. This variant affects the first nucleotide of exon 24, a position that might impair splicing.

PMID: 29343805 - Biallelic Variants in KIF14 Cause Intellectual Disability With Microcephaly. 4 unrelated individuals identified but all asymptomatic in the Genitourinary system.; to: PMID:30388224 same authors as PMID: 24128419 identified two families and reported on two further families which had already previously been reported upon in PMID: 28566479. All fetuses had biallelic pathogenic variants.

PMID: 28892560 - Reported on four individuals with variants in KIF14. 3/4 had no problems with renal system, 1/4 a German boy, was identified who had small kidneys with increased echogenicity. WES of the German patient revealed 2 compound heterozygous missense variants of KIF14. One of these variants (NM_014875.2;c.2545C>G;p.His849Asp) replaces a histidine by aspartic acid and is predicted to be disease causing. (NM_014875.2;c.3662G>T;p.Gly1221Val) introduces valine at a position of glycine that is not conserved among different animals. This variant affects the first nucleotide of exon 24, a position that might impair splicing.

PMID: 29343805 - Biallelic Variants in KIF14 Cause Intellectual Disability With Microcephaly. 4 unrelated individuals identified but all asymptomatic in the Genitourinary system.

Rating as Amber and requesting support from clinical team as unsure of KIF14 and its broad phenotypes.
Renal ciliopathies v1.12 KIF14 Catherine Snow reviewed gene: KIF14: Rating: AMBER; Mode of pathogenicity: None; Publications: 30388224, 28892560, 29343805; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Early onset or syndromic epilepsy v2.34 SETD1B Sarah Leigh changed review comment from: Comment on list classification: Associated with relevant phenotype in OMIM and as probable Gen2Phen gene for SETD1B associated intellectual disability, epilepsy and autism. At least 3 variants reported in at least 3 unrelated cases (PMID29322246; 31440728 31685013). Strucutral variants have also been reported that encompass SETD1B (PMID 20648245; 27106595; 25428890; 22369279).; to: Comment on list classification: Associated with relevant phenotype in OMIM and as probable Gen2Phen gene for SETD1B associated intellectual disability, epilepsy and autism. At least 3 variants reported in at least 3 unrelated cases who displayed epilepsy (PMID29322246; 31440728 31685013). Strucutral variants have also been reported that encompass SETD1B (PMID 20648245; 27106595; 25428890; 22369279).
Early onset or syndromic epilepsy v2.34 SETD1B Sarah Leigh changed review comment from: Comment on list classification: Associated with relevant phenotype in OMIM and as probable Gen2Phen gene for SETD1B associated intellectual disability, epilepsy and autism. At least 3 variants reported in at least 3 unrelated cases. Strucutral variants have also been reported that encompass SETD1B.; to: Comment on list classification: Associated with relevant phenotype in OMIM and as probable Gen2Phen gene for SETD1B associated intellectual disability, epilepsy and autism. At least 3 variants reported in at least 3 unrelated cases (PMID29322246; 31440728 31685013). Strucutral variants have also been reported that encompass SETD1B (PMID 20648245; 27106595; 25428890; 22369279).
Early onset or syndromic epilepsy v2.34 SETD1B Sarah Leigh Publications for gene: SETD1B were set to 29322246; 31440728; 31685013
Early onset or syndromic epilepsy v2.33 SETD1B Sarah Leigh Classified gene: SETD1B as Green List (high evidence)
Early onset or syndromic epilepsy v2.33 SETD1B Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as probable Gen2Phen gene for SETD1B associated intellectual disability, epilepsy and autism. At least 3 variants reported in at least 3 unrelated cases. Strucutral variants have also been reported that encompass SETD1B.
Early onset or syndromic epilepsy v2.33 SETD1B Sarah Leigh Gene: setd1b has been classified as Green List (High Evidence).
Early onset or syndromic epilepsy v2.32 SETD1B Sarah Leigh Phenotypes for gene: SETD1B were changed from to Epilepsy with myoclonic absences; intellectual disability
Early onset or syndromic epilepsy v2.31 SETD1B Sarah Leigh Added comment: Comment on mode of inheritance: Mode of inheritance obtained from Gen2Phen
Early onset or syndromic epilepsy v2.31 SETD1B Sarah Leigh Mode of inheritance for gene: SETD1B was changed from to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Early onset or syndromic epilepsy v2.30 SETD1B Sarah Leigh Publications for gene: SETD1B were set to
Early onset or syndromic epilepsy v2.29 SETD1A Sarah Leigh changed review comment from: Comment on list classification: Associated with relevant phenotype in OMIM and as probable Gen2Phen gene for intellectual disability. At least 4 variants reported, 3 de novo and 1 segrating in a family.; to: Comment on list classification: Associated with relevant phenotype in OMIM and as probable Gen2Phen gene for intellectual disability. At least 4 variants reported, 3 de novo and 1 segregating in a family.
Early onset or syndromic epilepsy v2.29 SETD1A Sarah Leigh Classified gene: SETD1A as Green List (high evidence)
Early onset or syndromic epilepsy v2.29 SETD1A Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as probable Gen2Phen gene for intellectual disability. At least 4 variants reported, 3 de novo and 1 segrating in a family.
Early onset or syndromic epilepsy v2.29 SETD1A Sarah Leigh Gene: setd1a has been classified as Green List (High Evidence).
CAKUT v1.58 CEP55 Rebecca Foulger Classified gene: CEP55 as Green List (high evidence)
CAKUT v1.58 CEP55 Rebecca Foulger Added comment: Comment on list classification: Updated rating from Grey to Green. Gene was added to the panel and rated Green by Zornitza Stark. 3 separate variants from 3 different ethnic groups (2 of the variants are likely Founder variants), plus zebrafish model. Most homozygous nonsense variants are embryonic lethal but PMID:28295209 report viable compound het missense variants.
CAKUT v1.58 CEP55 Rebecca Foulger Gene: cep55 has been classified as Green List (High Evidence).
CAKUT v1.57 CEP55 Rebecca Foulger Phenotypes for gene: CEP55 were changed from Multinucleated neurons, anhydramnios, renal dysplasia, cerebellar hypoplasia, and hydranencephaly, 236500 to Multinucleated neurons, anhydramnios, renal dysplasia, cerebellar hypoplasia, and hydranencephaly, 236500; MARCH syndrome; Meckel-like syndrome; lethal CEP55-related syndromes
CAKUT v1.56 CEP55 Rebecca Foulger Publications for gene: CEP55 were set to 30622327; 28264986
CAKUT v1.55 CEP55 Rebecca Foulger commented on gene: CEP55: PMID:32100459 (Barrie et al., 2020) describe 7 individuals from 5 families with biallelic CEP55 variants. This is the first reported case of missense variants in CEP55 (Previously only a prenatal lethal phenotype was reported due to homozygous CEP55 nonsense variants). The authors suggest that compound het cases with nonsense and missense CEP55 variants have a different viable phenotype. Homozgyosity for a splice variant in CEP55 is compatible with life. Renal abnormality was reported in Patient 3.
CAKUT v1.55 CEP55 Rebecca Foulger commented on gene: CEP55: PMID:28295209. Bondeson et al report a Swedish couple with 2 affected male fetuses homozygous for CEP55 p.Arg86*. Although the phenotype differed between fetuses, both exhibited kidney phenotypes (including renal dysplaisa). Segregation analysis supported the gene:disease association, and Haplotype analysis suggested a founder effect.
Unexplained young onset end-stage renal disease v1.7 CD151 Eleanor Williams Classified gene: CD151 as Amber List (moderate evidence)
Unexplained young onset end-stage renal disease v1.7 CD151 Eleanor Williams Added comment: Comment on list classification: Changing rating from red to amber as 2 cases have been reported with end stage renal disease, although the same variant is reported and the families are from the same ethnic origin. Also the presentation is syndromic so end-stage renal disease is unlikely to be the only phenotype picked up.
Unexplained young onset end-stage renal disease v1.7 CD151 Eleanor Williams Gene: cd151 has been classified as Amber List (Moderate Evidence).
Unexplained young onset end-stage renal disease v1.6 CD151 Eleanor Williams Phenotypes for gene: CD151 were changed from to Nephropathy with pretibial epidermolysis bullosa and deafness 609057
Unexplained young onset end-stage renal disease v1.5 CD151 Eleanor Williams Publications for gene: CD151 were set to
Unexplained young onset end-stage renal disease v1.4 CD151 Eleanor Williams Mode of inheritance for gene: CD151 was changed from Unknown to BIALLELIC, autosomal or pseudoautosomal
Unexplained young onset end-stage renal disease v1.3 CD151 Eleanor Williams edited their review of gene: CD151: Added comment: Associated with Nephropathy with pretibial epidermolysis bullosa and deafness #609057 in OMIM.

The 3 patients from 2 families described in PMID: 15265795 - Karamatic Crew et al 2004 all had end-stage kidney disease and homozygous insertion in the CD151 gene. Although they are described as unrelated both families are of Indian Jewish origin. The ages of the patients are not reported.

Another case is described in PMID: 29138120 - Vahidnezhad et al 2018 where the patient had history of nephropathy with proteinuria.

PMID: 17015618 - Sachs et al 2006 - report the generation of Cd151-null mice that recapitulate the renal pathology of human patients, i.e., with age they develop massive proteinuria; Changed publications: 15265795, 29138120, 17015618; Changed phenotypes: Nephropathy with pretibial epidermolysis bullosa and deafness 609057; Changed mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Unexplained kidney failure in young people v1.89 CD151 Eleanor Williams changed review comment from: Comment on list classification: Changing rating from red to amber as 2 cases have been reported with end stage renal disease, although the same variant is reported and the families are from the same ethnic origin.; to: Comment on list classification: Changing rating from red to amber as 2 cases have been reported with end stage renal disease, although the same variant is reported and the families are from the same ethnic origin. Also the presentation is syndromic so end-stage renal disease is unlikely to be the only phenotype picked up.
CAKUT v1.55 CEP55 Rebecca Foulger Publications for gene: CEP55 were set to 30622327
CAKUT v1.54 CEP55 Rebecca Foulger commented on gene: CEP55: PMID:28264986: Frosk et al, 2017 report a Dutch-German Mennonite family with 3 affected fetuses homozygous for CEP55 nonsense variant p.Ser425* presenting with MIM:236500 including renal dysplasia.
CAKUT v1.54 CEP55 Rebecca Foulger commented on gene: CEP55
Unexplained kidney failure in young people v1.89 CD151 Eleanor Williams Phenotypes for gene: CD151 were changed from Nephropathy with pretibial epidermolysis bullosa and deafness 609057 to Nephropathy with pretibial epidermolysis bullosa and deafness 609057
Unexplained kidney failure in young people v1.88 CD151 Eleanor Williams Phenotypes for gene: CD151 were changed from to Nephropathy with pretibial epidermolysis bullosa and deafness 609057
Unexplained kidney failure in young people v1.87 CD151 Eleanor Williams Publications for gene: CD151 were set to
Unexplained kidney failure in young people v1.86 CD151 Eleanor Williams Mode of inheritance for gene: CD151 was changed from to BIALLELIC, autosomal or pseudoautosomal
Unexplained kidney failure in young people v1.85 CD151 Eleanor Williams Classified gene: CD151 as Amber List (moderate evidence)
Unexplained kidney failure in young people v1.85 CD151 Eleanor Williams Added comment: Comment on list classification: Changing rating from red to amber as 2 cases have been reported with end stage renal disease, although the same variant is reported and the families are from the same ethnic origin.
Unexplained kidney failure in young people v1.85 CD151 Eleanor Williams Gene: cd151 has been classified as Amber List (Moderate Evidence).
Unexplained kidney failure in young people v1.84 CD151 Eleanor Williams changed review comment from: Associated with Nephropathy with pretibial epidermolysis bullosa and deafness #609057 in OMIM.

The 3 patients from 2 families described in PMID: 15265795 - Karamatic Crew et al 2004 all had end-stage kidney disease and homozygous insertion in the CD151 gene. Although they are described as unrelated both families are of Indian Jewish origin.; to: Associated with Nephropathy with pretibial epidermolysis bullosa and deafness #609057 in OMIM.

The 3 patients from 2 families described in PMID: 15265795 - Karamatic Crew et al 2004 all had end-stage kidney disease and homozygous insertion in the CD151 gene. Although they are described as unrelated both families are of Indian Jewish origin. The ages of the patients are not reported.

Another case is described in PMID: 29138120 - Vahidnezhad et al 2018 where the patient had history of nephropathy with proteinuria.

PMID: 17015618 - Sachs et al 2006 - report the generation of Cd151-null mice that recapitulate the renal pathology of human patients, i.e., with age they develop massive proteinuria
Unexplained kidney failure in young people v1.84 CD151 Eleanor Williams edited their review of gene: CD151: Changed publications: 15265795
Unexplained kidney failure in young people v1.84 CD151 Eleanor Williams commented on gene: CD151
Proteinuric renal disease v2.23 CD151 Eleanor Williams changed review comment from: Associated with Nephropathy with pretibial epidermolysis bullosa and deafness #609057 in OMIM (no inheritance pattern given). 2 patients are described as having proteinuria in the nephrotic range among other features.

3 cases plus mouse model that replicates the kidney phenotype:

PMID: 15265795 - Karamatic Crew et al 2004 - report two sibs and a third unrelated patient, all of Indian Jewish origin who lack the MER2 antigen and have made anti-MER2. All had end-stage kidney disease. The two sibs had other phenotypic features such as pretibial bullous skin lesions, neurosensory deafness, bilateral lacrimal duct stenosis, nail dystrophy, and β-thalassemia minor. Less information available about the 3rd patient. Direct sequencing of all CD151 exons revealed a homozygous single nucleotide insertion G383 which causes a frameshift after Lys127, introducing a premature stop signal at codon 140. Ages of patients are not given.

PMID: 29138120 - Vahidnezhad et al 2018 - report 1 consangineous family with Epidermolysis bullosa which was screened using a gene panel and NGS. A homozygous donor splice site mutation in CD151 (NM_139029; c.351+2T>C) was found. In this family the 33-year old proband, initially diagnosed as Kindler syndrome, had widespread blistering, poikiloderma, nail dystrophy, loss of teeth, early onset alopecia, and esophageal webbing and strictures. The patient also had history of nephropathy with proteinuria. (Abstract only accessed).

PMID: 17015618 - Sachs et al 2006 - report the generation of Cd151-null mice that recapitulate the renal pathology of human patients, i.e., with age they develop massive proteinuria caused by focal glomerulosclerosis, disorganization of the glomerular basement membrane, and tubular cystic dilation. The skin and hearing phenotypes were not observed.; to: Associated with Nephropathy with pretibial epidermolysis bullosa and deafness #609057 in OMIM (no inheritance pattern given). 2 patients are described as having proteinuria in the nephrotic range among other features.

3 cases (but 2 have the same variant - founder effect?) plus mouse model that replicates the kidney phenotype:

PMID: 15265795 - Karamatic Crew et al 2004 - report two sibs and a third unrelated patient, all of Indian Jewish origin who lack the MER2 antigen and have made anti-MER2. All had end-stage kidney disease. The two sibs had other phenotypic features such as pretibial bullous skin lesions, neurosensory deafness, bilateral lacrimal duct stenosis, nail dystrophy, and β-thalassemia minor. Less information available about the 3rd patient. Direct sequencing of all CD151 exons revealed a homozygous single nucleotide insertion G383 which causes a frameshift after Lys127, introducing a premature stop signal at codon 140. Ages of patients are not given.

PMID: 29138120 - Vahidnezhad et al 2018 - report 1 consangineous family with Epidermolysis bullosa which was screened using a gene panel and NGS. A homozygous donor splice site mutation in CD151 (NM_139029; c.351+2T>C) was found. In this family the 33-year old proband, initially diagnosed as Kindler syndrome, had widespread blistering, poikiloderma, nail dystrophy, loss of teeth, early onset alopecia, and esophageal webbing and strictures. The patient also had history of nephropathy with proteinuria. (Abstract only accessed).

PMID: 17015618 - Sachs et al 2006 - report the generation of Cd151-null mice that recapitulate the renal pathology of human patients, i.e., with age they develop massive proteinuria caused by focal glomerulosclerosis, disorganization of the glomerular basement membrane, and tubular cystic dilation. The skin and hearing phenotypes were not observed.
COVID-19 research v0.32 IFIH1 Ellen McDonagh Publications for gene: IFIH1 were set to 29018476
COVID-19 research v0.31 IFIH1 Ellen McDonagh Classified gene: IFIH1 as Green List (high evidence)
COVID-19 research v0.31 IFIH1 Ellen McDonagh Added comment: Comment on list classification: Biallelic variants associated with susceptibility to RNA viruses.
COVID-19 research v0.31 IFIH1 Ellen McDonagh Gene: ifih1 has been classified as Green List (High Evidence).
COVID-19 research v0.30 G6PD Ellen McDonagh Classified gene: G6PD as Green List (high evidence)
COVID-19 research v0.30 G6PD Ellen McDonagh Added comment: Comment on list classification: Promoted from Red to Green due to expert reviews from the Primary immunodeficiency panel.
COVID-19 research v0.30 G6PD Ellen McDonagh Gene: g6pd has been classified as Green List (High Evidence).
COVID-19 research v0.29 G6PD Ellen McDonagh Publications for gene: G6PD were set to 26694452; 18269318
Early onset or syndromic epilepsy v2.28 SERPINI1 Sarah Leigh Classified gene: SERPINI1 as Green List (high evidence)
Early onset or syndromic epilepsy v2.28 SERPINI1 Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 5 variants reported in unrelated cases.
Early onset or syndromic epilepsy v2.28 SERPINI1 Sarah Leigh Gene: serpini1 has been classified as Green List (High Evidence).
Early onset or syndromic epilepsy v2.27 SERPINI1 Sarah Leigh Phenotypes for gene: SERPINI1 were changed from Encephalopathy, familial, with neuroserpin inclusion bodies MIM#604218 to Encephalopathy, familial, with neuroserpin inclusion bodies 604218
CAKUT v1.54 CEP55 Rebecca Foulger Phenotypes for gene: CEP55 were changed from Multinucleated neurons, anhydramnios, renal dysplasia, cerebellar hypoplasia, and hydranencephaly, MIM# 236500 to Multinucleated neurons, anhydramnios, renal dysplasia, cerebellar hypoplasia, and hydranencephaly, 236500
CAKUT v1.53 CENPF Rebecca Foulger Classified gene: CENPF as Amber List (moderate evidence)
CAKUT v1.53 CENPF Rebecca Foulger Added comment: Comment on list classification: Updated rating from Grey to Amber. Gene was added to panel and rated Green by Zornitza Stark. Although CENPF has 'probable' disease confidence in Gene2Phenotype for Stromme syndrome, there are sufficient cases in OMIM and the literature to support the gene:disease association. Hydronephrosis/renal hypoplasia is seen in at least 2 Stromme families, but the phenotype is variable. CENPF is Green on the 'Renal ciliopathies' panel (Panel #725, V1.12). Rated as Amber awaiting further clinical feedback.
CAKUT v1.53 CENPF Rebecca Foulger Gene: cenpf has been classified as Amber List (Moderate Evidence).
Proteinuric renal disease v2.23 CD151 Eleanor Williams Publications for gene: CD151 were set to 15265795; 17015618; 29138120
Proteinuric renal disease v2.22 CD151 Eleanor Williams Publications for gene: CD151 were set to 15265795
Proteinuric renal disease v2.21 CD151 Eleanor Williams Mode of inheritance for gene: CD151 was changed from to BIALLELIC, autosomal or pseudoautosomal
Proteinuric renal disease v2.20 CD151 Eleanor Williams Classified gene: CD151 as Green List (high evidence)
Proteinuric renal disease v2.20 CD151 Eleanor Williams Added comment: Comment on list classification: 3 cases reported plus mouse model
Proteinuric renal disease v2.20 CD151 Eleanor Williams Gene: cd151 has been classified as Green List (High Evidence).
Proteinuric renal disease v2.19 CD151 Eleanor Williams commented on gene: CD151: Associated with Nephropathy with pretibial epidermolysis bullosa and deafness #609057 in OMIM (no inheritance pattern given). 2 patients are described as having proteinuria in the nephrotic range among other features.

3 cases plus mouse model that replicates the kidney phenotype:

PMID: 15265795 - Karamatic Crew et al 2004 - report two sibs and a third unrelated patient, all of Indian Jewish origin who lack the MER2 antigen and have made anti-MER2. All had end-stage kidney disease. The two sibs had other phenotypic features such as pretibial bullous skin lesions, neurosensory deafness, bilateral lacrimal duct stenosis, nail dystrophy, and β-thalassemia minor. Less information available about the 3rd patient. Direct sequencing of all CD151 exons revealed a homozygous single nucleotide insertion G383 which causes a frameshift after Lys127, introducing a premature stop signal at codon 140. Ages of patients are not given.

PMID: 29138120 - Vahidnezhad et al 2018 - report 1 consangineous family with Epidermolysis bullosa which was screened using a gene panel and NGS. A homozygous donor splice site mutation in CD151 (NM_139029; c.351+2T>C) was found. In this family the 33-year old proband, initially diagnosed as Kindler syndrome, had widespread blistering, poikiloderma, nail dystrophy, loss of teeth, early onset alopecia, and esophageal webbing and strictures. The patient also had history of nephropathy with proteinuria. (Abstract only accessed).

PMID: 17015618 - Sachs et al 2006 - report the generation of Cd151-null mice that recapitulate the renal pathology of human patients, i.e., with age they develop massive proteinuria caused by focal glomerulosclerosis, disorganization of the glomerular basement membrane, and tubular cystic dilation. The skin and hearing phenotypes were not observed.
CAKUT v1.52 CENPF Rebecca Foulger commented on gene: CENPF: PMID:26820108 (Filges et al., 2016) describe long-term clinical follow up for siblings reported by Stromme et al. (1993) with intestingal atresia, ocular anomalis and microcephaly. They detect truncating compound het variants in CENPF in the original family (Family A) and an additional sibling pair (Family B). The original siblings (Family A) had normal renal newborn ultrasounds. The additional siblings (Family B) had Hydronephrosis/bilateral renal hypoplasia in addition to Duodenal atresia and other gastrointestinal phenotypes.
CAKUT v1.52 CENPF Rebecca Foulger commented on gene: CENPF: PMID:25564561 (Waters et al., 2015) ientified a non-consagnuineous Caucasian kindred with 4 affected fetuses. Autopsy revealed phenotypes including Duodenal atresia and Bilateral renal hypolasia.
CAKUT v1.52 CENPF Rebecca Foulger commented on gene: CENPF: PMID:28407396 (Ozkinay et al., 2017) report a Stromme syndrome family with 2 affected individuals and a homozygous p.T1974Nfs*9 variant in CENPF. Renal phenotypes are not recorded in table 1.
CAKUT v1.52 CENPF Rebecca Foulger commented on gene: CENPF
CAKUT v1.52 CENPF Rebecca Foulger Publications for gene: CENPF were set to
CAKUT v1.51 CENPF Rebecca Foulger Phenotypes for gene: CENPF were changed from Stromme syndrome, 243605 to Stromme syndrome, 243605; bilateral renal hypoplasia; Duodenal atresia; Hydronephrosis
COVID-19 research v0.27 IRF3 Ellen McDonagh gene: IRF3 was added
gene: IRF3 was added to Viral susceptibility. Sources: Expert list,Expert Review Amber
Mode of inheritance for gene: IRF3 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Phenotypes for gene: IRF3 were set to {Encephalopathy, acute, infection-induced (herpes-specific), susceptibility to, 7}, MIM616532
COVID-19 research v0.27 UNC93B1 Ellen McDonagh Source Melbourne Genomics Health Alliance Immunology Flagship was added to UNC93B1.
Source Victorian Clinical Genetics Services was added to UNC93B1.
Source Expert Review Green was added to UNC93B1.
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.27 TRAF3 Ellen McDonagh gene: TRAF3 was added
gene: TRAF3 was added to Viral susceptibility. Sources: Melbourne Genomics Health Alliance Immunology Flagship,Victorian Clinical Genetics Services,Expert Review Green
Mode of inheritance for gene: TRAF3 was set to Unknown
COVID-19 research v0.27 TMC8 Ellen McDonagh Source Melbourne Genomics Health Alliance Immunology Flagship was added to TMC8.
Source Victorian Clinical Genetics Services was added to TMC8.
Source Expert Review Green was added to TMC8.
Mode of inheritance for gene TMC8 was changed from BIALLELIC, autosomal or pseudoautosomal to Unknown
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.27 TMC6 Ellen McDonagh Source Melbourne Genomics Health Alliance Immunology Flagship was added to TMC6.
Source Victorian Clinical Genetics Services was added to TMC6.
Source Expert Review Green was added to TMC6.
Mode of inheritance for gene TMC6 was changed from BIALLELIC, autosomal or pseudoautosomal to Unknown
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.27 TLR3 Ellen McDonagh gene: TLR3 was added
gene: TLR3 was added to Viral susceptibility. Sources: Melbourne Genomics Health Alliance Immunology Flagship,Victorian Clinical Genetics Services,Expert Review Green
Mode of inheritance for gene: TLR3 was set to Unknown
COVID-19 research v0.27 TICAM1 Ellen McDonagh gene: TICAM1 was added
gene: TICAM1 was added to Viral susceptibility. Sources: Melbourne Genomics Health Alliance Immunology Flagship,Victorian Clinical Genetics Services,Expert Review Green
Mode of inheritance for gene: TICAM1 was set to Unknown
COVID-19 research v0.27 TBK1 Ellen McDonagh gene: TBK1 was added
gene: TBK1 was added to Viral susceptibility. Sources: Melbourne Genomics Health Alliance Immunology Flagship,Victorian Clinical Genetics Services,Expert Review Green
Mode of inheritance for gene: TBK1 was set to Unknown
COVID-19 research v0.27 STAT2 Ellen McDonagh gene: STAT2 was added
gene: STAT2 was added to Viral susceptibility. Sources: Melbourne Genomics Health Alliance Immunology Flagship,Victorian Clinical Genetics Services,Expert Review Green
Mode of inheritance for gene: STAT2 was set to Unknown
COVID-19 research v0.27 STAT1 Ellen McDonagh gene: STAT1 was added
gene: STAT1 was added to Viral susceptibility. Sources: Melbourne Genomics Health Alliance Immunology Flagship,Victorian Clinical Genetics Services,Expert Review Green
Mode of inheritance for gene: STAT1 was set to Unknown
COVID-19 research v0.27 MSN Ellen McDonagh gene: MSN was added
gene: MSN was added to Viral susceptibility. Sources: Expert list,Expert Review Green
Mode of inheritance for gene: MSN was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Phenotypes for gene: MSN were set to Immunodeficiency 50, MIM300988
COVID-19 research v0.27 IRF7 Ellen McDonagh Source Melbourne Genomics Health Alliance Immunology Flagship was added to IRF7.
Source Victorian Clinical Genetics Services was added to IRF7.
Source Expert Review Green was added to IRF7.
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.27 FCGR3A Ellen McDonagh gene: FCGR3A was added
gene: FCGR3A was added to Viral susceptibility. Sources: Melbourne Genomics Health Alliance Immunology Flagship,Victorian Clinical Genetics Services,Expert Review Green
Mode of inheritance for gene: FCGR3A was set to Unknown
COVID-19 research v0.27 CXCR4 Ellen McDonagh gene: CXCR4 was added
gene: CXCR4 was added to Viral susceptibility. Sources: Melbourne Genomics Health Alliance Immunology Flagship,Victorian Clinical Genetics Services,Expert Review Green
Mode of inheritance for gene: CXCR4 was set to Unknown
Hereditary neuropathy or pain disorder v1.4 DRP2 Zornitza Stark reviewed gene: DRP2: Rating: GREEN; Mode of pathogenicity: None; Publications: 26227883, 11430802, 31217940, 22764250, 29473052; Phenotypes: X-linked Charcot-Marie-Tooth; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females
Hereditary neuropathy or pain disorder v1.4 DHTKD1 Zornitza Stark reviewed gene: DHTKD1: Rating: AMBER; Mode of pathogenicity: None; Publications: 23141294, 29661920, 28902413; Phenotypes: Charcot-Marie-Tooth disease, axonal, type 2Q, MIM#615025; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
CAKUT v1.50 CENPF Rebecca Foulger Phenotypes for gene: CENPF were changed from Stromme syndrome, MIM#243605 to Stromme syndrome, 243605
CAKUT v1.49 BMP7 Rebecca Foulger Classified gene: BMP7 as Red List (low evidence)
CAKUT v1.49 BMP7 Rebecca Foulger Added comment: Comment on list classification: BMP7 was added to CAKUT panel and rated Red by Zornitza Stark. Updated rating from Grey to Red to match Zornitza's review: There are additional functional papers reporting a role for BMP7 in renal tissues, but only one reported family plus a mouse model.
CAKUT v1.49 BMP7 Rebecca Foulger Gene: bmp7 has been classified as Red List (Low Evidence).
CAKUT v1.48 BMP7 Rebecca Foulger commented on gene: BMP7: PMID:7590254 (Dudley et al., 1995) report that mice lacking BMP7 display severe defects confined to the developing kidney and eye (renal dysplasia and anophthalmia at birth).
CAKUT v1.48 BMP7 Rebecca Foulger commented on gene: BMP7
Hereditary neuropathy or pain disorder v1.4 ARHGEF10 Zornitza Stark reviewed gene: ARHGEF10: Rating: GREEN; Mode of pathogenicity: None; Publications: 14508709, 21719701, 25025039, 25275565, 25091364; Phenotypes: Slowed nerve conduction velocity, MIM# 608236; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Arthrogryposis v3.3 MYH7 Zornitza Stark reviewed gene: MYH7: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Proteinuric renal disease v2.19 APOE Eleanor Williams commented on gene: APOE: Set Penetrance to incomplete as several reports of unaffected individuals who carry the same variants as affected individuals.
Proteinuric renal disease v2.19 APOE Eleanor Williams Source Expert list was removed from APOE.
Source Literature was added to APOE.
Penetrance for gene APOE was set from to None
Proteinuric renal disease v2.18 APOE Eleanor Williams Publications for gene: APOE were set to 10432380; 9176854; 18077821
Proteinuric renal disease v2.17 APOE Eleanor Williams Classified gene: APOE as Green List (high evidence)
Proteinuric renal disease v2.17 APOE Eleanor Williams Added comment: Comment on list classification: Changing rating from grey to green as many published cases of variants in APOE in patients with Lipoprotein glomerulopathy
Proteinuric renal disease v2.17 APOE Eleanor Williams Gene: apoe has been classified as Green List (High Evidence).
Proteinuric renal disease v2.16 APOE Eleanor Williams changed review comment from: Associated with Lipoprotein glomerulopathy #611771 in OMIM. No inheritance pattern listed.

Several publications report variants in the APOE gene in association with Lipoprotein glomerulopathy, mostly in individuals of Asian ethnicity but also in those with European ancestry for example (PMID: 18077821 - Rovin et al 2007). PMID: 31092271 - Xie et al 2019 lists many of the published variants (~12 to date, mostly point mutations, but also some deletions)

In several cases clinical asymptomatic carriers (all female?) also carry the same variants as probands e.g.
PMID: 18077821 - Rovin et al 2007
PMID: 10432380 - Matsunaga et al 1999
PMID: 31092271 - Xie et al 2019




; to: Associated with Lipoprotein glomerulopathy #611771 in OMIM. No inheritance pattern listed.

Several publications report variants in the APOE gene in association with Lipoprotein glomerulopathy, mostly in individuals of Asian ethnicity but also in those with European ancestry (for example PMID: 18077821 - Rovin et al 2007). PMID: 31092271 - Xie et al 2019 lists many of the published variants (~12 to date, mostly point mutations, but also some deletions)

In several cases clinical asymptomatic carriers (all female?) also carry the same variants as probands e.g.
PMID: 18077821 - Rovin et al 2007
PMID: 10432380 - Matsunaga et al 1999
PMID: 31092271 - Xie et al 2019
Proteinuric renal disease v2.16 APOE Eleanor Williams changed review comment from: Associated with Lipoprotein glomerulopathy #611771 in OMIM. No inheritance pattern listed.

PMID: 10432380 - Matsunaga et al 1999 - 32-year-old Japanese male patient with Lipoprotein glomerulopathy, whose history included proteinuria. A heterogyzous missense variant was identified termed apo E2 (Arg25Cys) Kyoto. His asymptomatic mother was also heterogyzous for this same variant.

PMID: 9176854 - Oikawa et al 1997 - report 3 patients with LPG from two families all with the same variant apo E Arg145Pro named APOE Sendai. Only the APOE gene was looked at.

PMID: 18077821 - Rovin et al 2007 - report two unrelated American men of European ancestry who presented with edema and proteinuria in the nephrotic range. Both patients had a heterozygous C→T transition resulting in an amino acid change Arg25Cys. Several female family members were heterozygous carriers of Arg25Cys, none had clinical evidence of lipoprotein glomerulopathy.

Review to be continued; to: Associated with Lipoprotein glomerulopathy #611771 in OMIM. No inheritance pattern listed.

Several publications report variants in the APOE gene in association with Lipoprotein glomerulopathy, mostly in individuals of Asian ethnicity but also in those with European ancestry for example (PMID: 18077821 - Rovin et al 2007). PMID: 31092271 - Xie et al 2019 lists many of the published variants (~12 to date, mostly point mutations, but also some deletions)

In several cases clinical asymptomatic carriers (all female?) also carry the same variants as probands e.g.
PMID: 18077821 - Rovin et al 2007
PMID: 10432380 - Matsunaga et al 1999
PMID: 31092271 - Xie et al 2019
Proteinuric renal disease v2.16 APOE Eleanor Williams commented on gene: APOE
CAKUT v1.48 ISL1 Rebecca Foulger gene: ISL1 was added
gene: ISL1 was added to CAKUT. Sources: Literature
Mode of inheritance for gene: ISL1 was set to Unknown
Publications for gene: ISL1 were set to 23641053
Phenotypes for gene: ISL1 were set to CAKUT
Review for gene: ISL1 was set to RED
Added comment: Added ISL1 to panel as a Red gene, based on PMID:23641053 which show that conditional deletion of Isl1 in mice caused kidney agenesis or hypoplasia and hydroureter, a phenotype resembling human congenital anomalies of the kidney and urinary tract (CAKUT). No further literature evidence at this time to increase rating.
Sources: Literature
COVID-19 research v0.26 G6PD Ellen McDonagh Phenotypes for gene: G6PD were changed from Susceptible to viral infection to Susceptibility to viral infection
COVID-19 research v0.25 FCGR2A Ellen McDonagh Phenotypes for gene: FCGR2A were changed from Severity of severe acute respiratory syndrome (SARS) SARS-Cov to Severity of severe acute respiratory syndrome (SARS)-Cov infection
COVID-19 research v0.24 FCGR2A Ellen McDonagh gene: FCGR2A was added
gene: FCGR2A was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: FCGR2A was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: FCGR2A were set to 16185324
Phenotypes for gene: FCGR2A were set to Severity of severe acute respiratory syndrome (SARS) SARS-Cov
Added comment: PMID: 16185324 reports an association between polymorphisms in this gene and the severity of SARS-Cov infection.
Sources: Literature
CAKUT v1.47 BMP4 Rebecca Foulger Classified gene: BMP4 as Amber List (moderate evidence)
CAKUT v1.47 BMP4 Rebecca Foulger Added comment: Comment on list classification: Updated rating from Red to Amber based on a number of papers linking BMP4 variants and renal phenotypes. Penetrance isn't complete (PMID:18305125), and phenotype is variable, even within families (PMID:30568244). However a mouse model supports a renal phenotype, and functional evidence shows expression in renal tissues. Therefore rated Amber awaiting further clinical review.
CAKUT v1.47 BMP4 Rebecca Foulger Gene: bmp4 has been classified as Amber List (Moderate Evidence).
Renal ciliopathies v1.12 ARMC9 Catherine Snow Classified gene: ARMC9 as Red List (low evidence)
Renal ciliopathies v1.12 ARMC9 Catherine Snow Added comment: Comment on list classification: ARMC9 appeared on the renal ciliopathies as it was imported from the Rare multisystem ciliopathy disorders panel version 1.86. Review from Zornitza Stark and also OMIM stating that ARMC9 has no hepatic or renal involvement.
Renal ciliopathies v1.12 ARMC9 Catherine Snow Gene: armc9 has been classified as Red List (Low Evidence).
CAKUT v1.46 BMP4 Rebecca Foulger Added comment: Comment on phenotypes: Not currently associated with a renal phenotype in OMIM or Gene2Phenotype.
CAKUT v1.46 BMP4 Rebecca Foulger Phenotypes for gene: BMP4 were changed from to CAKUT; renal maldevelopment; congenital renal dysplasia; Congenital Anomaly of the Kidneys and Urinary Tract
CAKUT v1.45 BMP4 Rebecca Foulger Publications for gene: BMP4 were set to
CAKUT v1.44 BMP4 Rebecca Foulger Mode of inheritance for gene: BMP4 was changed from to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
COVID-19 research v0.23 CCL5 Ellen McDonagh gene: CCL5 was added
gene: CCL5 was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: CCL5 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: CCL5 were set to 17540042
Phenotypes for gene: CCL5 were set to Susceptibility to Severe Acute Respiratory Syndrome Coronavirus Infection; Susceptibility to SARS-CoV
Added comment: PMID: 17540042 case-control study reporting an associated with a polymorphism in the CCL5 gene and admission to intensive care units or death due to SARS infection.
Sources: Literature
CAKUT v1.43 BMP4 Rebecca Foulger commented on gene: BMP4: Additional mouse model in PMID:18233958 where mutant mice result in uropathies resembling human CAKUT.
CAKUT v1.43 BMP4 Rebecca Foulger commented on gene: BMP4: PMID:30568244 (Nixon et al., 2019) investigate a BMP4 variant ( c. 130G>T, p.(Gly44Ter) with segregated in a family with Stickler syndrome. One male (age 20) also had congenital renal dysplasia. No other family members reported kidney disease.
COVID-19 research v0.22 CD14 Ellen McDonagh gene: CD14 was added
gene: CD14 was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: CD14 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: CD14 were set to 17913858
Phenotypes for gene: CD14 were set to Susceptibility to Severe Acute Respiratory Syndrome Coronavirus Infection; Susceptibility to SARS-CoV
Added comment: PMID: case-control study reporting association with a risk genotype of a polymorphism in this gene and severe SARS-CoV infection.
Sources: Literature
Renal ciliopathies v1.11 ADAMTS9 Catherine Snow Classified gene: ADAMTS9 as Amber List (moderate evidence)
Renal ciliopathies v1.11 ADAMTS9 Catherine Snow Added comment: Comment on list classification: Choi et al (PMID: 30609407) identified two unrelated individuals with ADAMTS9 variants (c.4575_4576del [p.Gln1525Hisfs∗60] and c.194C>G [p.Thr65Arg]) that appear to cause a Nephronophthisis-related ciliopathies (NPHP-RC)
The study also included functional work and knockdown of adamts9 in zebrafish recapitulated the NPHP-RC phenotypes.
Rating as Amber as only two individuals, where some clinical features differed between the two cases and although functional evidence present it is currently limited to this publication.
Renal ciliopathies v1.11 ADAMTS9 Catherine Snow Gene: adamts9 has been classified as Amber List (Moderate Evidence).
COVID-19 research v0.21 G6PD Ellen McDonagh Publications for gene: G6PD were set to 26694452
COVID-19 research v0.20 ACE Ellen McDonagh gene: ACE was added
gene: ACE was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: ACE was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: ACE were set to 15819995
Phenotypes for gene: ACE were set to Not associated with susceptibility to SARS-coronavirus infection and disease outcomes
Added comment: PMID: A case-control study found no association with the I/D polymorphism in this gene and increased susceptibility to SARS-coronavirus infection nor with poor outcomes after SARS-coronavirus infection (140 genetically unrelated Chinese SARS cases and 326 healthy volunteers were recruited).
Sources: Literature
Proteinuric renal disease v2.16 AMN Eleanor Williams Classified gene: AMN as Green List (high evidence)
Proteinuric renal disease v2.16 AMN Eleanor Williams Added comment: Comment on list classification: Changing rating from amber to green following expert review stating that proteinuria is a well known presenting feature of IMERSLUND-GRASBECK SYNDROME. At least 3 cases with variants in AMN and proteinuria are reported in the literature.
Proteinuric renal disease v2.16 AMN Eleanor Williams Gene: amn has been classified as Green List (High Evidence).
Proteinuric renal disease v2.15 AMN Eleanor Williams commented on gene: AMN: Associated with Megaloblastic anemia-1, Norwegian type #261100 (AR) in OMIM which is also known as IMERSLUND-GRASBECK SYNDROME (IGS).

PMID: 30691194 - Pacitto et al 2019 - describe a case of IGS with urinary tract infection and mild but persistent proteinuria at onset in an 11-month-old female child. The patient was found to be compound heterzygous for a novel intronic variant c.513+5G>A thought to affect a donor splice site, and the known pathogenetic variant c.1006+34_1007-31del. Parents each had one of the variants.

PMID: 26040326 - Montgomery et al 2015 - 2 half sisters with IGS and compound heterzygous variants in AMN are reported (c.35delA, p.Gln12Argfs*5) and (c.206 T > A, p.Met69Lys). Both presented with sub-nephrotic range proteinuria.

PMID: 22631584 - Densupsoontorn et al 2012 - report a Thai boy with IGS in whom a deleterious mutation in AMN was confirmed (homozygous c.663G>A; W221X). Persistent proteinuria was reported.

Note - not all patients are described as presenting with proteinuria e.g. PMID: 14593474 (Molecular cause of IGS unknown in this case).
COVID-19 research v0.19 CCL2 Ellen McDonagh gene: CCL2 was added
gene: CCL2 was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: CCL2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: CCL2 were set to 25818534
Phenotypes for gene: CCL2 were set to Susceptibility to Severe Acute Respiratory Syndrome Coronavirus Infection; Susceptibility to SARS-CoV
Added comment: PMID: 25818534 reports that the CCL2 G-2518A and MBL codon 54 variants have a significantly cumulative effect on increased risk of SARS-CoV infection.
Sources: Literature
COVID-19 research v0.18 G6PD Ellen McDonagh gene: G6PD was added
gene: G6PD was added to Viral susceptibility. Sources: Literature
Mode of inheritance for gene: G6PD was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)
Publications for gene: G6PD were set to 26694452
Phenotypes for gene: G6PD were set to Susceptible to viral infection
Added comment: PMID: 26694452 - a study that investigated the underlying mehanism of why glucose-6-phosphate dehydrogenase (G6PD)-deficient cells are highly susceptible to viral infection.
Sources: Literature
CAKUT v1.43 BMP4 Rebecca Foulger changed review comment from: PMID:18305125 (Weber et al., 2008) report 3 BMP4 variants in 5 unrelated Renal hypodysplasia (RH) patients (Ser91Cys, heterozygous in patients 6 and 7; Thr116Ser, heterozygous in patient 8; Asn150Lys, heterozygous in patient 9 and homozygous in patient 10). Patients were from Poland, Germany and Turkey. The father of patient 7 also had the variant but had normal renal ultrasound. The inheritance may be polygenic: the authors show expression of BMP4 in human renal tissue. PMID:19685083 (Tabatabaeifar et al., 2009) report functional evidence for these three missense mutations, and provide in vitro functional evidence in human cell lines that BMP4 mRNA is reduced in the mutants. ; to: PMID:18305125 (Weber et al., 2008) report 3 BMP4 variants in 5 unrelated CAKUT patients (Ser91Cys, heterozygous in patients 6 and 7; Thr116Ser, heterozygous in patient 8; Asn150Lys, heterozygous in patient 9 and homozygous in patient 10). Patients were from Poland, Germany and Turkey. All five affected patients presented with a spectrum of renal maldevelopment, ranging from kidney agenesis to hypoplasia and dysplasia (with or without
cysts). The father of patient 7 also had the variant but had normal renal ultrasound. The inheritance may be polygenic: the authors show expression of BMP4 in human renal tissue. PMID:19685083 (Tabatabaeifar et al., 2009) report functional evidence for these three missense mutations, and provide in vitro functional evidence in human cell lines that BMP4 mRNA is reduced in the mutants.
CAKUT v1.43 BMP4 Rebecca Foulger changed review comment from: PMID:18305125 (Weber et al., 2008) report 3 BMP4 variants in 5 unrelated Renal hypodysplasia (RH) patients (Ser91Cys, heterozygous in patients 6 and 7; Thr116Ser, heterozygous in patient 8; Asn150Lys, heterozygous in patient 9 and homozygous in patient 10). Patients were from Poland, Germany and Turkey. The father of patient 7 also had the variant but had normal renal ultrasound. The inheritance may be polygenic. the authors show expresson of BMP4 in human renal tissue.; to: PMID:18305125 (Weber et al., 2008) report 3 BMP4 variants in 5 unrelated Renal hypodysplasia (RH) patients (Ser91Cys, heterozygous in patients 6 and 7; Thr116Ser, heterozygous in patient 8; Asn150Lys, heterozygous in patient 9 and homozygous in patient 10). Patients were from Poland, Germany and Turkey. The father of patient 7 also had the variant but had normal renal ultrasound. The inheritance may be polygenic: the authors show expression of BMP4 in human renal tissue. PMID:19685083 (Tabatabaeifar et al., 2009) report functional evidence for these three missense mutations, and provide in vitro functional evidence in human cell lines that BMP4 mRNA is reduced in the mutants.
CAKUT v1.43 BMP4 Rebecca Foulger commented on gene: BMP4: PMID:18305125 (Weber et al., 2008) report 3 BMP4 variants in 5 unrelated Renal hypodysplasia (RH) patients (Ser91Cys, heterozygous in patients 6 and 7; Thr116Ser, heterozygous in patient 8; Asn150Lys, heterozygous in patient 9 and homozygous in patient 10). Patients were from Poland, Germany and Turkey. The father of patient 7 also had the variant but had normal renal ultrasound. The inheritance may be polygenic. the authors show expresson of BMP4 in human renal tissue.
Renal tubulopathies v2.13 VPS33B Eleanor Williams Classified gene: VPS33B as Green List (high evidence)
Renal tubulopathies v2.13 VPS33B Eleanor Williams Added comment: Comment on list classification: Changing rating from red to green. Sufficient cases and Renal tubular acidosis and Renal Fanconi syndrome are a feature of this syndrome
Renal tubulopathies v2.13 VPS33B Eleanor Williams Gene: vps33b has been classified as Green List (High Evidence).
Renal tubulopathies v2.12 VPS33B Eleanor Williams gene: VPS33B was added
gene: VPS33B was added to Renal tubulopathies. Sources: Literature
Mode of inheritance for gene: VPS33B was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: VPS33B were set to 8151641; 16155421; 16896922
Phenotypes for gene: VPS33B were set to Arthrogryposis, renal dysfunction, and cholestasis 1 #208085
Review for gene: VPS33B was set to GREEN
Added comment: Associated with Arthrogryposis, renal dysfunction, and cholestasis 1 #208085 (AR) in OMIM.
Many reported cases listed in OMIM. Renal tubular acidosis and Renal Fanconi syndrome are listed as clinical features. VIPAS39 & VPS33B form a complex.
Sources: Literature
CAKUT v1.43 BMP4 Rebecca Foulger commented on gene: BMP4: PMID:23641053 (Kaku et al., 2013). Indirect Animal study. Authors studied renal expression and phenotype of Isl1 in mice. Lack of Isl1 reduced the expression of mouse Bmp4.
CAKUT v1.43 BMP4 Rebecca Foulger commented on gene: BMP4
Renal tubulopathies v2.11 VIPAS39 Eleanor Williams Classified gene: VIPAS39 as Green List (high evidence)
Renal tubulopathies v2.11 VIPAS39 Eleanor Williams Added comment: Comment on list classification: Sufficient cases (>3) reported in PMID:20190753 with patients with different ethnicities, several variants are reported and functional studies support the phenotype.
Renal tubulopathies v2.11 VIPAS39 Eleanor Williams Gene: vipas39 has been classified as Green List (High Evidence).
Renal tubulopathies v2.10 VIPAS39 Eleanor Williams gene: VIPAS39 was added
gene: VIPAS39 was added to Renal tubulopathies. Sources: Expert Review
Mode of inheritance for gene: VIPAS39 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: VIPAS39 were set to 20190753
Phenotypes for gene: VIPAS39 were set to Arthrogryposis, renal dysfunction, and cholestasis 2 #613404
Review for gene: VIPAS39 was set to GREEN
Added comment: Reviewed by Zornitza Stark on the Unexplained kidney failure in young people panel (panel 156) where she notes that it is a syndromic disorder with a prominent renal phenotype renal tubular acidosis and Fanconi syndrome. Australian Genomics have this gene green on their renal tubulopathies panel.
Sources: Expert Review
Ataxia and cerebellar anomalies - narrow panel v2.6 SCN8A Sarah Leigh Mode of inheritance for gene: SCN8A was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Ataxia and cerebellar anomalies - narrow panel v2.5 SCN8A Sarah Leigh Deleted their comment
Ataxia and cerebellar anomalies - narrow panel v2.5 SCN8A Sarah Leigh Added comment: Comment on mode of inheritance: Based on report in PMID 31625145, reporting biallelic loss of function SCN8A variants in three cases in two families with severe developmental and epileptic encephalopathy. This differs from the previosly reported gain of function, monoallelic variants (PMID 24194747;22365152).
Ataxia and cerebellar anomalies - narrow panel v2.5 SCN8A Sarah Leigh Mode of inheritance for gene: SCN8A was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Renal ciliopathies v1.10 IFT140 Catherine Snow Classified gene: IFT140 as Green List (high evidence)
Renal ciliopathies v1.10 IFT140 Catherine Snow Added comment: Comment on list classification: Sufficient publications and external expert review an association of IFT140 variants and ciliopathic renal phenotype to rate IFT140 as Green.
Renal ciliopathies v1.10 IFT140 Catherine Snow Gene: ift140 has been classified as Green List (High Evidence).
Renal ciliopathies v1.10 IFT140 Catherine Snow Classified gene: IFT140 as Green List (high evidence)
Renal ciliopathies v1.10 IFT140 Catherine Snow Added comment: Comment on list classification: Sufficient publications and external expert review an association of IFT140 variants and ciliopathic renal phenotype to rate IFT140 as Green.
Renal ciliopathies v1.10 IFT140 Catherine Snow Gene: ift140 has been classified as Green List (High Evidence).
Renal ciliopathies v1.9 SLC41A1 Catherine Snow Deleted their comment
Renal ciliopathies v1.9 SLC41A1 Catherine Snow Deleted their comment
Renal ciliopathies v1.9 IFT172 Catherine Snow Classified gene: IFT172 as Green List (high evidence)
Renal ciliopathies v1.9 IFT172 Catherine Snow Added comment: Comment on list classification: A number of publications identify relationship of variants in IFT172 and phenotypes associated with Bardet-Biedl syndrome and Jeune and Mainzer-Saldino Syndromes, all are ciliopathy diseases. The range of phenotypes can result in serve skeletal and multiple affected organs but also includes a reported case of non-syndromic retinal dystrophy.
Sufficient numbers of unrelated individuals reported to have kidney dysfunction to include IFT172 as Green on the panel.
Renal ciliopathies v1.9 IFT172 Catherine Snow Gene: ift172 has been classified as Green List (High Evidence).
Renal ciliopathies v1.8 IFT172 Catherine Snow Publications for gene: IFT172 were set to
Intellectual disability v3.24 RNF13 Sarah Leigh Classified gene: RNF13 as Green List (high evidence)
Intellectual disability v3.24 RNF13 Sarah Leigh Gene: rnf13 has been classified as Green List (High Evidence).
Intellectual disability v3.23 RNF13 Sarah Leigh changed review comment from: Associated with relevant phenotype in OMIM and as probable Gen2Phen gene. At least 2 variants reported in 3 unrelated cases, together with supportive functional studies.; to: Associated with relevant phenotype in OMIM and as probable Gen2Phen gene. At least 2 variants reported in 3 unrelated cases, together with supportive functional studies.

Gain-of-function mechanism has been reported, therefore the mutational spectrum may be limited and is still to be determined through further cases or further functional studies (view of Helen Britain, GeL Clincial Fellow).
Early onset or syndromic epilepsy v2.26 RNF13 Sarah Leigh Classified gene: RNF13 as Green List (high evidence)
Early onset or syndromic epilepsy v2.26 RNF13 Sarah Leigh Gene: rnf13 has been classified as Green List (High Evidence).
Early onset or syndromic epilepsy v2.25 RNF13 Sarah Leigh changed review comment from: Associated with relevant phenotype in OMIM and as probable Gen2Phen gene. At least 2 variants reported in 3 unrelated cases, together with supportive functional studies.; to: Associated with relevant phenotype in OMIM and as probable Gen2Phen gene. At least 2 variants reported in 3 unrelated cases, together with supportive functional studies. Gain-of-function mechanism has been reported, therefore the mutational spectrum may be limited and is still to be determined through further cases or further functional studies (view of Helen Britain, GeL Clincial Fellow).
Intellectual disability v3.23 SCAMP5 Sarah Leigh Tag watchlist tag was added to gene: SCAMP5.
Intellectual disability v3.23 SCAMP5 Sarah Leigh changed review comment from: Comment on list classification: Not associated with phenotype in OMIM (last edited on 10/06/2014) or in Gen2Phen. Two variants have been identified in three unrelated cases (one monoallelic, one biallelic). Supportive functional studies have been reported.
It would appear that the two variants reported so far in this gene result in differing mode of pathogenicity and phenotypic features. With heterozygous c.538G>T, p.Gly180Trp seeming to have a dominant-negative effect resulting in autistic spectrum disorder, intellectual disability and seizures. While homozygous c.271C>T, p.R91W seems to have a loss of function effect resulting in early onset epilepsy and Parkinson’s disease. This may be due to different functional domains of the mature protein being altered.; to: Comment on list classification: Not associated with phenotype in OMIM (last edited on 10/06/2014) or in Gen2Phen. Two variants have been identified in three unrelated cases (one monoallelic, one biallelic). Supportive functional studies have been reported.
It would appear that the two variants reported so far in this gene result in differing mode of pathogenicity and phenotypic features. With heterozygous c.538G>T, p.Gly180Trp seeming to have a dominant-negative effect resulting in autistic spectrum disorder, intellectual disability and seizures. While homozygous c.271C>T, p.R91W seems to have a loss of function effect resulting in early onset epilepsy and Parkinson’s disease. This may be due to different functional domains of the mature protein being altered.
Based on this evidence, SCAMP5 is rated as Amber, with a Watchlist tag. This status may change if further cases are reported.
Early onset or syndromic epilepsy v2.25 SCAMP5 Sarah Leigh Tag watchlist tag was added to gene: SCAMP5.
Early onset or syndromic epilepsy v2.25 SCAMP5 Sarah Leigh changed review comment from: Comment on list classification: Not associated with phenotype in OMIM (last edited on 10/06/2014) or in Gen2Phen. Two variants have been identified in three unrelated cases (one monoallelic, one biallelic). Supportive functional studies have been reported.
It would appear that the two variants reported so far in this gene result in differing mode of pathogenicity and phenotypic features. With heterozygous c.538G>T, p.Gly180Trp seeming to have a dominant-negative effect resulting in autistic spectrum disorder, intellectual disability and seizures. While homozygous c.271C>T, p.R91W seems to have a loss of function effect resulting in early onset epilepsy and Parkinson’s disease. This may be due to different functional domains of the mature protein being altered. ; to: Comment on list classification: Not associated with phenotype in OMIM (last edited on 10/06/2014) or in Gen2Phen. Two variants have been identified in three unrelated cases (one monoallelic, one biallelic). Supportive functional studies have been reported.
It would appear that the two variants reported so far in this gene result in differing mode of pathogenicity and phenotypic features. With heterozygous c.538G>T, p.Gly180Trp seeming to have a dominant-negative effect resulting in autistic spectrum disorder, intellectual disability and seizures. While homozygous c.271C>T, p.R91W seems to have a loss of function effect resulting in early onset epilepsy and Parkinson’s disease. This may be due to different functional domains of the mature protein being altered.
Based on this evidence, SCAMP5 is rated as Amber, with a Watchlist tag. This status may change if further cases are reported.
Early onset or syndromic epilepsy v2.25 PTEN Rebecca Foulger changed review comment from: As discussed with members of the GMS Neurology Specialist Test Group on the Webex call Thursday 8th August 2019 for Clinical Indication R59 Early onset or syndromic epilepsy: Agreed to demote AKT1 from Green to Red. This panel is not the appropriate test for somatic variant detection due to the coverage. R110 Segmental overgrowth disorders (panel #98) should be used where megalencephaly is present to allow detection of somatic mosaic mutations.; to: As discussed with members of the GMS Neurology Specialist Test Group on the Webex call Thursday 8th August 2019 for Clinical Indication R59 Early onset or syndromic epilepsy: Agreed to demote PTEN from Green to Red. This panel is not the appropriate test for somatic variant detection due to the coverage. R110 Segmental overgrowth disorders (panel #98) should be used where megalencephaly is present to allow detection of somatic mosaic mutations.
Hyperthyroidism v2.3 TTR david halsall gene: TTR was added
gene: TTR was added to Hyperthyroidism. Sources: Literature
Mode of inheritance for gene: TTR was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: TTR were set to PMID: 31590893; 26522458
Phenotypes for gene: TTR were set to # 145680 HYPERTHYROXINEMIA, DYSTRANSTHYRETINEMIC; DTTRH
Penetrance for gene: TTR were set to unknown
Mode of pathogenicity for gene: TTR was set to Other
Review for gene: TTR was set to GREEN
Added comment: Specific gain of function sequence variants in TTE can cause method dependent factitious increases in serum free thyroxine when measured by commercial competive immunoassay methods. V30M, S77Y, I84S, V122I have been reported.
These varients need to be considered separately from loss of function at the locus which is associated with an amyloidogenic phenotype (familial transthyretin amyloidosis).
Sources: Literature
Retinal disorders v2.8 ABCC6 Gavin Arno reviewed gene: ABCC6: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: PSEUDOXANTHOMA ELASTICUM (PXE); Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Hereditary neuropathy or pain disorder v1.4 AIFM1 Zornitza Stark edited their review of gene: AIFM1: Changed publications: 22019070, 26173962, 25583628
Hereditary neuropathy or pain disorder v1.4 AIFM1 Zornitza Stark reviewed gene: AIFM1: Rating: AMBER; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Hereditary neuropathy or pain disorder v1.4 ABCA1 Zornitza Stark reviewed gene: ABCA1: Rating: AMBER; Mode of pathogenicity: None; Publications: ; Phenotypes: Tangier disease, MIM# 205400; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Childhood onset dystonia, chorea or related movement disorder v1.4 COL6A3 Zornitza Stark reviewed gene: COL6A3: Rating: AMBER; Mode of pathogenicity: None; Publications: 26004199, 32037012, 26872670; Phenotypes: Dystonia 27, MIM#616411; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary lymphoedema v2.4 CHD7 Zornitza Stark reviewed gene: CHD7: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: CHARGE syndrome, MIM# 214800; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
COVID-19 research v0.17 Ellen McDonagh Panel status changed from internal to public
COVID-19 research v0.16 Ellen McDonagh Panel name changed from Monogenic viral susceptibility to Viral susceptibility
Primary ciliary disorders v1.22 NEK10 Zerin Hyder gene: NEK10 was added
gene: NEK10 was added to Primary ciliary disorders. Sources: Other
Mode of inheritance for gene: NEK10 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: NEK10 were set to 31959991
Phenotypes for gene: NEK10 were set to primary ciliary dyskinesia; bronchiectasis
Penetrance for gene: NEK10 were set to unknown
Review for gene: NEK10 was set to GREEN
Added comment: In 9 patients from 5 unrelated consanguineous or likely consanguineous families with primary ciliary dyskinesia, Chivikula et al identified homozygous mutations in the NEK10 gene, which segregated with the disorder in all families and was confirmed by linkage analysis in 3 families. Analysis of human bronchial epithelial cells (HBECs) derived from 1 patient showed almost absent NEK10 protein expression, hypoplastic or shorter cilia, and reduced overall ciliary motion compared to controls, suggesting a loss-of-function effect. Detailed functional studies of these cells showed almost absent mucociliary transport, although cilia radial ultrastructure and beat frequency were normal. All individuals had previously unexplained bronchiectasis with CF excluded and no extrapulmonary features or situs inversus.
Sources: Other
Intellectual disability v3.23 SCN8A Sarah Leigh Added comment: Comment on mode of pathogenicity: Based on report in PMID 31625145, reporting biallelic loss of function SCN8A variants in three cases in two families with severe developmental and epileptic encephalopathy. This differs from the previosly reported gain of function monoallelic variants (PMID 24194747;22365152).
Intellectual disability v3.23 SCN8A Sarah Leigh Mode of pathogenicity for gene: SCN8A was changed from to Other
Early onset or syndromic epilepsy v2.25 SCN8A Sarah Leigh Added comment: Comment on mode of pathogenicity: Based on report in PMID 31625145, reporting biallelic loss of function SCN8A variants in three cases in two families with severe developmental and epileptic encephalopathy. This differs from the previosly reported gain of function, monoallelic variants (PMID 24194747;22365152).
Early onset or syndromic epilepsy v2.25 SCN8A Sarah Leigh Mode of pathogenicity for gene: SCN8A was changed from Other to Other
Early onset or syndromic epilepsy v2.24 SCN8A Sarah Leigh Added comment: Comment on mode of pathogenicity: Based on report in PMID 31625145, reporting biallelic loss of function SCN8A variants in three cases in two families with severe developmental and epileptic encephalopathy.
Early onset or syndromic epilepsy v2.24 SCN8A Sarah Leigh Mode of pathogenicity for gene: SCN8A was changed from None to Other
Renal ciliopathies v1.7 SCLT1 Catherine Snow Deleted their comment
Renal ciliopathies v1.7 SCLT1 Catherine Snow Deleted their comment
Renal ciliopathies v1.7 SCLT1 Catherine Snow Classified gene: SCLT1 as Amber List (moderate evidence)
Renal ciliopathies v1.7 SCLT1 Catherine Snow Added comment: Comment on list classification: PMID: 30425282 reports on individual who had compound heterozygous SCLT1 variants (c.1218 + 3insT and c.1631A > G) the patient was identified has having a form of ciliopathies that exhibits clinical features of Senior Løken syndrome. SLS is a syndromic form of retinal dystrophy associated with nephronophthisis.

PMID: 24285566 - Reported on a patient with a severe ciliopathy phenotype. A homozygous splice site mutation in the SCLT1 gene was detected, Adly et al. (2014) considered the severe ciliopathy phenotype of their patients to best fit oral–facial–digital syndrome (OFD) type IX in view of the prominent eye involvement no kidney involvement reported

PMID: 32055034 report on SCLT1 related to Bardet-Biedl syndrome is an autosomal recessive and genetically heterogeneous ciliopathy characterized by retinitis pigmentosa, obesity, kidney dysfunction, polydactyly, behavioral dysfunction, and hypogonadisma though clinical details on the individual are not provided

PMID: 28486600 - Li et al 2017 - report a mouse model with mutated Sclt1 gene. The Sclt1-/- mice exhibit typical ciliopathy phenotypes, including cystic kidney, cleft palate and polydactyly.

Rating gene as Amber as evidence of renal cillopathy phenotype is still limited.
Renal ciliopathies v1.7 SCLT1 Catherine Snow Gene: sclt1 has been classified as Amber List (Moderate Evidence).
Renal ciliopathies v1.6 SCLT1 Catherine Snow Classified gene: SCLT1 as Amber List (moderate evidence)
Renal ciliopathies v1.6 SCLT1 Catherine Snow Added comment: Comment on list classification: PMID: 30425282 reports on individual who had compound heterozygous SCLT1 variants (c.1218 + 3insT and c.1631A > G) the patient was identified has having a form of ciliopathies that exhibits clinical features of Senior Løken syndrome. SLS is a syndromic form of retinal dystrophy associated with nephronophthisis.

PMID: 24285566 - Reported on a patient with a severe ciliopathy phenotype. A homozygous splice site mutation in the SCLT1 gene was detected, Adly et al. (2014) considered the severe ciliopathy phenotype of their patients to best fit oral–facial–digital syndrome (OFD) type IX in view of the prominent eye involvement no kidney involvement reported

PMID: 32055034 report on SCLT1 related to Bardet-Biedl syndrome is an autosomal recessive and genetically heterogeneous ciliopathy characterized by retinitis pigmentosa, obesity, kidney dysfunction, polydactyly, behavioral dysfunction, and hypogonadisma though clinical details on the individual are not provided

PMID: 28486600 - Li et al 2017 - report a mouse model with mutated Sclt1 gene. The Sclt1-/- mice exhibit typical ciliopathy phenotypes, including cystic kidney, cleft palate and polydactyly.

Rating gene as Amber as evidence of renal cillopathy phenotype is still limited.
Renal ciliopathies v1.6 SCLT1 Catherine Snow Gene: sclt1 has been classified as Amber List (Moderate Evidence).
Renal ciliopathies v1.6 SCLT1 Catherine Snow Classified gene: SCLT1 as Amber List (moderate evidence)
Renal ciliopathies v1.6 SCLT1 Catherine Snow Added comment: Comment on list classification: PMID: 30425282 reports on individual who had compound heterozygous SCLT1 variants (c.1218 + 3insT and c.1631A > G) the patient was identified has having a form of ciliopathies that exhibits clinical features of Senior Løken syndrome. SLS is a syndromic form of retinal dystrophy associated with nephronophthisis.

PMID: 24285566 - Reported on a patient with a severe ciliopathy phenotype. A homozygous splice site mutation in the SCLT1 gene was detected, Adly et al. (2014) considered the severe ciliopathy phenotype of their patients to best fit oral–facial–digital syndrome (OFD) type IX in view of the prominent eye involvement no kidney involvement reported

PMID: 32055034 report on SCLT1 related to Bardet-Biedl syndrome is an autosomal recessive and genetically heterogeneous ciliopathy characterized by retinitis pigmentosa, obesity, kidney dysfunction, polydactyly, behavioral dysfunction, and hypogonadisma though clinical details on the individual are not provided

PMID: 28486600 - Li et al 2017 - report a mouse model with mutated Sclt1 gene. The Sclt1-/- mice exhibit typical ciliopathy phenotypes, including cystic kidney, cleft palate and polydactyly.

Rating gene as Amber as evidence of renal cillopathy phenotype is still limited
Renal ciliopathies v1.6 SCLT1 Catherine Snow Gene: sclt1 has been classified as Amber List (Moderate Evidence).
Early onset or syndromic epilepsy v2.23 SCN8A Sarah Leigh Added comment: Comment on mode of inheritance: Based on report in PMID 31625145, reporting biallelic loss of function SCN8A variants in three cases in two families with severe developmental and epileptic encephalopathy.
Early onset or syndromic epilepsy v2.23 SCN8A Sarah Leigh Mode of inheritance for gene: SCN8A was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Intellectual disability v3.22 SCN8A Sarah Leigh Added comment: Comment on mode of inheritance: Based on report in PMID 31625145, reporting biallelic loss of function SCN8A variants in three cases in two families with severe developmental and epileptic encephalopathy.
Intellectual disability v3.22 SCN8A Sarah Leigh Mode of inheritance for gene: SCN8A was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Intellectual disability v3.21 SCN8A Sarah Leigh Phenotypes for gene: SCN8A were changed from Cognitive impairment with or without cerebellar ataxia, 614306Epileptic encephalopathy, early infantile, 13, 614558; COGNITIVE IMPAIRMENT WITH OR WITHOUT CEREBELLAR ATAXIA to ?Cognitive impairment with or without cerebellar ataxia,614306; Epileptic encephalopathy, early infantile,614558; Seizures, benign familial infantile,617080
Early onset or syndromic epilepsy v2.22 SCN8A Sarah Leigh Phenotypes for gene: SCN8A were changed from Cognitive impairment with or without cerebellar ataxia; Intellectual disability; Epileptic encephalopathy, early infantile, 13 to ?Cognitive impairment with or without cerebellar ataxia,614306; Epileptic encephalopathy, early infantile,614558; Seizures, benign familial infantile,617080
Intellectual disability v3.20 SCN8A Sarah Leigh Publications for gene: SCN8A were set to
Early onset or syndromic epilepsy v2.21 SCN8A Sarah Leigh Publications for gene: SCN8A were set to Trudeau et al (2004) J Med Genet 43: 527_530; O'Brien and Meisler (2013) Frontiers in Genet 4(213): 1-9; Veeramah et al (2012) Am J Hum Genet 90: 502_510
Hereditary systemic amyloidosis v1.7 NLRP3 Rebecca Foulger Classified gene: NLRP3 as Green List (high evidence)
Hereditary systemic amyloidosis v1.7 NLRP3 Rebecca Foulger Added comment: Comment on list classification: Updated rating from Grey to Green. NLRP3 was added to panel and rated Green by Zornitza Stark. Not yet in G2P but sufficient cases to support gene:disease association for NLRP3:Muckle-Wells syndrome, and approx 25-30% of MWS cases have an AA amyloidosis phenotype. Cases of NRLP3 variants in amyloidosis patients reported in PMIDs 30431487, 11992256. In summary: sufficient evidence to support association with MWS, and 25-30% of MWS patients have amyloidosis.
Hereditary systemic amyloidosis v1.7 NLRP3 Rebecca Foulger Gene: nlrp3 has been classified as Green List (High Evidence).
Hereditary systemic amyloidosis v1.6 NLRP3 Rebecca Foulger commented on gene: NLRP3: PMID:11992256 (Dode et al., 2002) identify NLRP3 (CIAS1) variants in 9 unrelated families with MWS. AA amyloidosis is recorded amongst the phenotypes in family 1 (R260W variant).
Hereditary systemic amyloidosis v1.6 NLRP3 Rebecca Foulger commented on gene: NLRP3: PMID:30431487 (Pandiarajan et al., 2018) report a 10-yr old child with nephrotic syndrome. The patient had a NLRP3 variant (c.1055C>T, p.Ala352Val) and features including AA amyloidosis.
Hereditary systemic amyloidosis v1.6 NLRP3 Rebecca Foulger commented on gene: NLRP3: PMID:31057541 (Fingerhutová et al. 2019) report 1 family (11 individuals) with MWS and a p.Ala441Val variant in NLRP3. 2 patients aged over 50 years suffered with hearing loss and AA amyloidosis.
Hereditary systemic amyloidosis v1.6 NLRP3 Rebecca Foulger commented on gene: NLRP3: PMID:27435956 (Villalba et al., 2016) report a 5-year old MWS patient with T348M variant in NLRP3. They report that amyloidosis and hearing loss is seen in ~25% of patients.
Hereditary systemic amyloidosis v1.6 NLRP3 Rebecca Foulger commented on gene: NLRP3: PMID:28229991 (Hu et al., 2017) report a patient with periodic fever, arthralgia and skin lesions and an A92T variant in NLRP3 (p.D31V).
Hereditary systemic amyloidosis v1.6 NLRP3 Rebecca Foulger commented on gene: NLRP3
Hereditary systemic amyloidosis v1.6 NLRP3 Rebecca Foulger Phenotypes for gene: NLRP3 were changed from Muckle-Wells syndrome, 191900 to Muckle-Wells syndrome, 191900; AA amyloidosis; renal amyloidosis
Hereditary systemic amyloidosis v1.5 NLRP3 Rebecca Foulger Publications for gene: NLRP3 were set to 11687797; 28229991; 27435956; 31057541
Nephrocalcinosis or nephrolithiasis v2.9 SLC26A1 Eleanor Williams Publications for gene: SLC26A1 were set to 27210743; 20160351; 30383413; 27125215
Nephrocalcinosis or nephrolithiasis v2.8 SLC26A1 Eleanor Williams Publications for gene: SLC26A1 were set to 27210743; 27210743; 20160351; 30383413; 27125215
Nephrocalcinosis or nephrolithiasis v2.7 SLC26A1 Eleanor Williams Publications for gene: SLC26A1 were set to 27210743; 27210743; 20160351
Nephrocalcinosis or nephrolithiasis v2.6 SLC26A1 Eleanor Williams Classified gene: SLC26A1 as Amber List (moderate evidence)
Nephrocalcinosis or nephrolithiasis v2.6 SLC26A1 Eleanor Williams Added comment: Comment on list classification: Changing rating from grey to amber. Although there are several reported cases there is also evidence that the reported variants are not causative.
Nephrocalcinosis or nephrolithiasis v2.6 SLC26A1 Eleanor Williams Gene: slc26a1 has been classified as Amber List (Moderate Evidence).
Nephrocalcinosis or nephrolithiasis v2.5 SLC26A1 Eleanor Williams Classified gene: SLC26A1 as Amber List (moderate evidence)
Nephrocalcinosis or nephrolithiasis v2.5 SLC26A1 Eleanor Williams Added comment: Comment on list classification: Changing rating from grey to amber. Although there are several reported cases there is also evidence that the reported variants are not causative.
Nephrocalcinosis or nephrolithiasis v2.5 SLC26A1 Eleanor Williams Gene: slc26a1 has been classified as Amber List (Moderate Evidence).
Nephrocalcinosis or nephrolithiasis v2.4 SLC26A1 Eleanor Williams changed review comment from: Provisionally associated with ?Nephrolithiasis, calcium oxalate #167030 (AR) in OMIM.

PMID: 30383413 - Whittamore et al 2019 - were unable to were unable to reproduce the hyperoxaluria, hyperoxalemia, and urolithiasis of the original SAT-1-KO mouse model.

PMID: 27125215 - Wu et al 2016 - report that Human SLC26A1-mediated anion exchange differs from that of its rodent orthologs. Also using Xenopus oocytes they find that the C41W, A56T (also reported by Gee et al) variants found in a Mexican child with recessive proximal tubular Fanconi Syndrome and the Q566R and M132T variants from Dawson et al 2013 did not alter the functional properties tested of SLC26A1 and so the proposal that these are pathogenic variants for Renal Fanconi Syndrome disease or nephrolithiasis is NOT supported.

PMID: 27210743 - Gee et al 2016 - report 2 unrelated individuals. Case 1 - individual of Macedonian descent (A3054-21) who is from non-consanguineous parents and clinically presented with acute renal failure due to bilateral obstructive calculi, nephrocalcinosis, and bilateral ureteropelvic junction obstruction. Two compound heterozygous missense mutations (c.554C>T, p.Thr185Met and c.1073C>T, p.Ser358Leu) in SLC26A1 are reported. They have minor allele freq below 0.0006 in dbSNP. Case 2 - European-American boy (B641-12) who had nephrolithiasis and was born to consanguineous parents. A homozygous missense mutation (c.166G>A, p.Ala56Thr) in SLC26A1 was found. Its minor allele frequency is 0.0002 in dbSNP.

PMID: 24250268 - Dawson et al 2013 - screened the SLC26A1 gene in a cohort of 13 individuals with recurrent calcium oxalate urolithiasis. Found one individual was heterozygous R372H; 4 individuals were heterozygous Q556R; one patient was homozygous Q556R; and one patient with severe nephrocalcinosis (requiring nephrectomy) was homozygous Q556R and heterozygous M132T. The Q556R variant is found at a high allele frequency (0.3484 in NCBI).

PMID: 20160351 - Dawson et al 2010 - Sat1-/- mice (SLC26A1) exhibited hyperoxaluria with hyperoxalemia, nephrocalcinosis, and calcium oxalate stones in their renal tubules and bladder.

Summary:
Although there are 3+ cases (2 biallelic in Gee et al, 3 monalleleic and 2 biallelic in Dawson et al 2013), plus a mouse model (Dawson et all 2010), the high minor allele frequency of the Q556R variant and the lack of altered function in protein with the A56T and M132T variants (Wu et al), and the lack of reproducibility of the mouse model phenotype cast doubt on the causative role of these variants. Therefore this gene should be rated amber until more evidence for their role in nephrocalcinosis can be established.; to: Provisionally associated with ?Nephrolithiasis, calcium oxalate #167030 (AR) in OMIM.

PMID: 30383413 - Whittamore et al 2019 - were unable to reproduce the hyperoxaluria, hyperoxalemia, and urolithiasis of the original SAT-1-KO mouse model.

PMID: 27125215 - Wu et al 2016 - report that Human SLC26A1-mediated anion exchange differs from that of its rodent orthologs. Also using Xenopus oocytes they find that the C41W, A56T (also reported by Gee et al) variants found in a Mexican child with recessive proximal tubular Fanconi Syndrome and the Q566R and M132T variants from Dawson et al 2013 did not alter the functional properties tested of SLC26A1 and so the proposal that these are pathogenic variants for Renal Fanconi Syndrome disease or nephrolithiasis is NOT supported.

PMID: 27210743 - Gee et al 2016 - report 2 unrelated individuals. Case 1 - individual of Macedonian descent (A3054-21) who is from non-consanguineous parents and clinically presented with acute renal failure due to bilateral obstructive calculi, nephrocalcinosis, and bilateral ureteropelvic junction obstruction. Two compound heterozygous missense mutations (c.554C>T, p.Thr185Met and c.1073C>T, p.Ser358Leu) in SLC26A1 are reported. They have minor allele freq below 0.0006 in dbSNP. Case 2 - European-American boy (B641-12) who had nephrolithiasis and was born to consanguineous parents. A homozygous missense mutation (c.166G>A, p.Ala56Thr) in SLC26A1 was found. Its minor allele frequency is 0.0002 in dbSNP.

PMID: 24250268 - Dawson et al 2013 - screened the SLC26A1 gene in a cohort of 13 individuals with recurrent calcium oxalate urolithiasis. Found one individual was heterozygous R372H; 4 individuals were heterozygous Q556R; one patient was homozygous Q556R; and one patient with severe nephrocalcinosis (requiring nephrectomy) was homozygous Q556R and heterozygous M132T. The Q556R variant is found at a high allele frequency (0.3484 in NCBI).

PMID: 20160351 - Dawson et al 2010 - Sat1-/- mice (SLC26A1) exhibited hyperoxaluria with hyperoxalemia, nephrocalcinosis, and calcium oxalate stones in their renal tubules and bladder.

Summary:
Although there are 3+ cases (2 biallelic in Gee et al, 3 monalleleic and 2 biallelic in Dawson et al 2013), plus a mouse model (Dawson et all 2010), the high minor allele frequency of the Q556R variant and the lack of altered function in protein with the A56T and M132T variants (Wu et al), and the lack of reproducibility of the mouse model phenotype cast doubt on the causative role of these variants. Therefore this gene should be rated amber until more evidence for their role in nephrocalcinosis can be established.
Nephrocalcinosis or nephrolithiasis v2.4 SLC26A1 Eleanor Williams changed review comment from: Provisionally associated with ?Nephrolithiasis, calcium oxalate #167030 (AR) in OMIM.

PMID: 27125215 - Wu et al 2016 - report that Human SLC26A1-mediated anion exchange differs from that of its rodent orthologs. Also using Xenopus oocytes they find that the C41W, A56T (also reported by Gee et al) variants found in a Mexican child with recessive proximal tubular Fanconi Syndrome and the Q566R and M132T variants from Dawson et al 2013 did not alter the functional properties tested of SLC26A1 and so the proposal that these are pathogenic variants for Renal Fanconi Syndrome disease or nephrolithiasis is NOT supported.

PMID: 27210743 - Gee et al 2016 - report 2 unrelated individuals. Case 1 - individual of Macedonian descent (A3054-21) who is from non-consanguineous parents and clinically presented with acute renal failure due to bilateral obstructive calculi, nephrocalcinosis, and bilateral ureteropelvic junction obstruction. Two compound heterozygous missense mutations (c.554C>T, p.Thr185Met and c.1073C>T, p.Ser358Leu) in SLC26A1 are reported. They have minor allele freq below 0.0006 in dbSNP. Case 2 - European-American boy (B641-12) who had nephrolithiasis and was born to consanguineous parents. A homozygous missense mutation (c.166G>A, p.Ala56Thr) in SLC26A1 was found. Its minor allele frequency is 0.0002 in dbSNP.

PMID: 24250268 - Dawson et al 2013 - screened the SLC26A1 gene in a cohort of 13 individuals with recurrent calcium oxalate urolithiasis. Found one individual was heterozygous R372H; 4 individuals were heterozygous Q556R; one patient was homozygous Q556R; and one patient with severe nephrocalcinosis (requiring nephrectomy) was homozygous Q556R and heterozygous M132T. The Q556R variant is found at a high allele frequency (0.3484 in NCBI).

PMID: 20160351 - Dawson et al 2010 - Sat1-/- mice (SLC26A1) exhibited hyperoxaluria with hyperoxalemia, nephrocalcinosis, and calcium oxalate stones in their renal tubules and bladder.

Summary:
Although there are 3+ cases (2 biallelic in Gee et al, 3 monalleleic and 2 biallelic in Dawson et al 2013), plus a mouse model (Dawson et all 2010), the minor allele frequency of the Q556R variant and the lack of altered function for when protein with the A56T and M132T variants are expressed (Wu et al) cast doubt on the causative role of these variants. Therefore this gene should be rated amber until more evidence for their role in nephrocalcinosis can be established.; to: Provisionally associated with ?Nephrolithiasis, calcium oxalate #167030 (AR) in OMIM.

PMID: 30383413 - Whittamore et al 2019 - were unable to were unable to reproduce the hyperoxaluria, hyperoxalemia, and urolithiasis of the original SAT-1-KO mouse model.

PMID: 27125215 - Wu et al 2016 - report that Human SLC26A1-mediated anion exchange differs from that of its rodent orthologs. Also using Xenopus oocytes they find that the C41W, A56T (also reported by Gee et al) variants found in a Mexican child with recessive proximal tubular Fanconi Syndrome and the Q566R and M132T variants from Dawson et al 2013 did not alter the functional properties tested of SLC26A1 and so the proposal that these are pathogenic variants for Renal Fanconi Syndrome disease or nephrolithiasis is NOT supported.

PMID: 27210743 - Gee et al 2016 - report 2 unrelated individuals. Case 1 - individual of Macedonian descent (A3054-21) who is from non-consanguineous parents and clinically presented with acute renal failure due to bilateral obstructive calculi, nephrocalcinosis, and bilateral ureteropelvic junction obstruction. Two compound heterozygous missense mutations (c.554C>T, p.Thr185Met and c.1073C>T, p.Ser358Leu) in SLC26A1 are reported. They have minor allele freq below 0.0006 in dbSNP. Case 2 - European-American boy (B641-12) who had nephrolithiasis and was born to consanguineous parents. A homozygous missense mutation (c.166G>A, p.Ala56Thr) in SLC26A1 was found. Its minor allele frequency is 0.0002 in dbSNP.

PMID: 24250268 - Dawson et al 2013 - screened the SLC26A1 gene in a cohort of 13 individuals with recurrent calcium oxalate urolithiasis. Found one individual was heterozygous R372H; 4 individuals were heterozygous Q556R; one patient was homozygous Q556R; and one patient with severe nephrocalcinosis (requiring nephrectomy) was homozygous Q556R and heterozygous M132T. The Q556R variant is found at a high allele frequency (0.3484 in NCBI).

PMID: 20160351 - Dawson et al 2010 - Sat1-/- mice (SLC26A1) exhibited hyperoxaluria with hyperoxalemia, nephrocalcinosis, and calcium oxalate stones in their renal tubules and bladder.

Summary:
Although there are 3+ cases (2 biallelic in Gee et al, 3 monalleleic and 2 biallelic in Dawson et al 2013), plus a mouse model (Dawson et all 2010), the high minor allele frequency of the Q556R variant and the lack of altered function in protein with the A56T and M132T variants (Wu et al), and the lack of reproducibility of the mouse model phenotype cast doubt on the causative role of these variants. Therefore this gene should be rated amber until more evidence for their role in nephrocalcinosis can be established.
Nephrocalcinosis or nephrolithiasis v2.4 SLC26A1 Eleanor Williams commented on gene: SLC26A1
Renal ciliopathies v1.5 SLC41A1 Catherine Snow Classified gene: SLC41A1 as Red List (low evidence)
Renal ciliopathies v1.5 SLC41A1 Catherine Snow Added comment: Comment on list classification: SLC41A1 is associated with Mg2+ transport and a gene disease relationship was identified in PMID: 23661805. Since then no further cases reported and SLC41A1 has no phenotype MIM number.
Renal ciliopathies v1.5 SLC41A1 Catherine Snow Gene: slc41a1 has been classified as Red List (Low Evidence).
Renal ciliopathies v1.4 SLC41A1 Catherine Snow Classified gene: SLC41A1 as Red List (low evidence)
Renal ciliopathies v1.4 SLC41A1 Catherine Snow Added comment: Comment on list classification: SLC41A1 is associated with Mg2+ transport and a gene disease relationship was identified in PMID: 23661805. Since then no further cases reported and SLC41A1 has no phenotype MIM number.
Renal ciliopathies v1.4 SLC41A1 Catherine Snow Gene: slc41a1 has been classified as Red List (Low Evidence).
Renal ciliopathies v1.4 SLC41A1 Catherine Snow Classified gene: SLC41A1 as Red List (low evidence)
Renal ciliopathies v1.4 SLC41A1 Catherine Snow Added comment: Comment on list classification: SLC41A1 is associated with Mg2+ transport and a gene disease relationship was identified in PMID: 23661805. Since then no further cases reported and SLC41A1 has no phenotype MIM number.
Renal ciliopathies v1.4 SLC41A1 Catherine Snow Gene: slc41a1 has been classified as Red List (Low Evidence).
Nephrocalcinosis or nephrolithiasis v2.4 HNF4A Eleanor Williams Classified gene: HNF4A as Green List (high evidence)
Nephrocalcinosis or nephrolithiasis v2.4 HNF4A Eleanor Williams Added comment: Comment on list classification: Although only one variant reported in all cases, there are now 7 cases in which the R76W/R63W (depending on reference transcript used) variant has been found in patients with Fanconi renotubular syndrome and nephrocalcinosis is a feature. Fly model also supports a pathogenic role for this variant.
Nephrocalcinosis or nephrolithiasis v2.4 HNF4A Eleanor Williams Gene: hnf4a has been classified as Green List (High Evidence).
Nephrocalcinosis or nephrolithiasis v2.3 HNF4A Eleanor Williams changed review comment from: Note the same codon is reported as R76W and R63W in different paper depending on whether NM_000457 or NM_175914 is used as the reference transcript.

Additional papers including those cited by Zornitza Stark:

PMID: 31875549 - Marchesin et al 2019 - Fly model which shows that the R85W variant in Drosophila nephrocytes works in a dominant-negative and cytotoxic effect. Expression of dHNF4 harboring the FRTS mutation affects the catabolism of lipid droplets in nephrocytes by interfering with mitochondrial function. They also showed that the FRTS mutation caused nuclear depletion and cytosolic aggregation of a wild-type dHNF4 reporter protein. The cytosolic aggregates have a cytotoxic affect. By contrast, the expression of another known close mutation in the DNA-binding domain, R89W (that leads to MODY1 but not to FRTS; Hamilton et al., 2014), did not cause any dominant-negative or cytotoxic effects.

PMID: 30005691 - Liu et al 2018 1 case of a 10-year-old girl of Chinese Han ethnicity who presented with renal Fanconi syndrome, infantile hyperinsulinemic hypoglycemia, and transient cholestasis. In addition, she presented with bilateral severe hearing loss. Renal ultrasonography showed nephrocalcinosis. Gene analysis showed a heterozygous p.R63W mutation in the HNF4A gene that is responsible for Fanconi syndrome and hyperinsulinemic hypoglycemia. (NOTE: no transcript identifier given but they refer to this as the same variant as R76W).

PMID: 28693455 - Walsh et al 2917 - 1 case of mother and son with heterozygous c.187C > T; p.Arg63Trp in HNF4A and Renal Fanconi syndrome. Mother is reported to have mild nephrocalcinosis

PMID: 22802087 - Stanescu et al 2012 - 1 case that presented as a newborn with diazoxide-responsive hyperinsulinism and later developed renal Fanconi syndrome, hypophosphatemic rickets, and hepatic glycogenosis. Sequencing of HNF4A (MODY1) revealed a missense, de novo mutation (p.Arg76Trp, c.226C→T), (NM_000457) which is a known disease-causing MODY1 mutation in HNF4A. Nephrocalcinosis not specifically mentioned.

No nephrocalcinosis reported:
PMID: 28458902 - Clemente et al 2017 - 1 patient with congenital hyperinsulinaemic hypoglycaemia, rickets with craniotabes, wrist widening, genu varum and motor impairment. non-gap metabolic acidosis with acidified urine suggestive of proximal tubular acidosis, glycosuria with generalised aminoaciduria and tubular type proteinuria. Says this patient did NOT have the same ‘atypical’ Fanconi syndrome with hypercalciuria with relative hypocalcaemia, hypermagnesaemia, nephrocalcinosis and renal impairment as the patients reported by Hamilton et al 2014. A de novo variant p.Arg63Trp, c.187C > T (reference sequence: NM_175914.4) was found.

PMID: 27245055 - Improda et al 2016 - 2 infants with the p.R63W mutation HNF4A with macrosomia and atypical Fanconi syndrome, in addition to hyperinsulinaemic hypoglycaemia. No nephrocalcinosis reported but this may be due to young age.
; to: Note the same codon is reported as R76W and R63W in different paper depending on whether NM_000457 or NM_175914 is used as the reference transcript.

Additional papers including those cited by Zornitza Stark:

PMID: 31875549 - Marchesin et al 2019 - Fly model which shows that the R85W variant in Drosophila nephrocytes works in a dominant-negative and cytotoxic effect. Expression of dHNF4 harboring the FRTS mutation affects the catabolism of lipid droplets in nephrocytes by interfering with mitochondrial function. They also showed that the FRTS mutation caused nuclear depletion and cytosolic aggregation of a wild-type dHNF4 reporter protein. The cytosolic aggregates have a cytotoxic affect. By contrast, the expression of another known close mutation in the DNA-binding domain, R89W (that leads to MODY1 but not to FRTS; Hamilton et al., 2014), did not cause any dominant-negative or cytotoxic effects.

PMID: 31949432 - Anyiam et al 2019 - described patient with Renal Fanconi syndrome and R63W mutation through 3rd pregnancy. She had a history of progressive renal insufficiency, persistent proteinuria, nephrocalcinosis, and recurrent nephrolithiasis.

PMID: 30005691 - Liu et al 2018 1 case of a 10-year-old girl of Chinese Han ethnicity who presented with renal Fanconi syndrome, infantile hyperinsulinemic hypoglycemia, and transient cholestasis. In addition, she presented with bilateral severe hearing loss. Renal ultrasonography showed nephrocalcinosis. Gene analysis showed a heterozygous p.R63W mutation in the HNF4A gene that is responsible for Fanconi syndrome and hyperinsulinemic hypoglycemia. (NOTE: no transcript identifier given but they refer to this as the same variant as R76W).

PMID: 28693455 - Walsh et al 2917 - 1 case of mother and son with heterozygous c.187C > T; p.Arg63Trp in HNF4A and Renal Fanconi syndrome. Mother is reported to have mild nephrocalcinosis

PMID: 22802087 - Stanescu et al 2012 - 1 case that presented as a newborn with diazoxide-responsive hyperinsulinism and later developed renal Fanconi syndrome, hypophosphatemic rickets, and hepatic glycogenosis. Sequencing of HNF4A (MODY1) revealed a missense, de novo mutation (p.Arg76Trp, c.226C→T), (NM_000457) which is a known disease-causing MODY1 mutation in HNF4A. Nephrocalcinosis not specifically mentioned.

No nephrocalcinosis reported:
PMID: 28458902 - Clemente et al 2017 - 1 patient with congenital hyperinsulinaemic hypoglycaemia, rickets with craniotabes, wrist widening, genu varum and motor impairment. non-gap metabolic acidosis with acidified urine suggestive of proximal tubular acidosis, glycosuria with generalised aminoaciduria and tubular type proteinuria. Says this patient did NOT have the same ‘atypical’ Fanconi syndrome with hypercalciuria with relative hypocalcaemia, hypermagnesaemia, nephrocalcinosis and renal impairment as the patients reported by Hamilton et al 2014. A de novo variant p.Arg63Trp, c.187C > T (reference sequence: NM_175914.4) was found.

PMID: 27245055 - Improda et al 2016 - 2 infants with the p.R63W mutation HNF4A with macrosomia and atypical Fanconi syndrome, in addition to hyperinsulinaemic hypoglycaemia. No nephrocalcinosis reported but this may be due to young age.
Hereditary neuropathy v1.368 MAP1B Aleš Maver gene: MAP1B was added
gene: MAP1B was added to Hereditary neuropathy. Sources: Other
Mode of inheritance for gene: MAP1B was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MAP1B were set to https://n.neurology.org/content/92/15_Supplement/P3.4-037
Phenotypes for gene: MAP1B were set to Giant Axonal Neuropathy-like phenotype, polyneuropathy
Penetrance for gene: MAP1B were set to unknown
Review for gene: MAP1B was set to RED
Added comment: A single consanguineous family with three sibs affected by giant axonal neuropathy has been reported with walking difficulty, progressive lower extremity weakness and ataxia. All affected sibs were homozygous for the c.5521A>G, p.M1841V variant in MAP1B. Two brothers homozygous for the variant were also reported to have body mass index over 40. Nerve conduction studies revealed a severe sensory motor polyneuropathy.
Sources: Other
Nephrocalcinosis or nephrolithiasis v2.3 HNF4A Eleanor Williams changed review comment from: Summary
3 publications (Hamilton et al 2014, Lui et al 2018, Walsh et al 2017) report 6 cases of patients with R76W/R63W variants in which nephrocalcinosis is a feature. Fly model (Marchesin et al 2019) shows that the equivalent variant in Drosophila nephrocytes works in a dominant-negative and cytotoxic effect.; to: Summary
4 publications (Hamilton et al 2014, Lui et al 2018, Walsh et al 2017, Anyiam et al 2019) report 7 cases of patients with R76W/R63W variants in which nephrocalcinosis is a feature. Fly model (Marchesin et al 2019) shows that the equivalent variant in Drosophila nephrocytes works in a dominant-negative and cytotoxic effect.
Nephrocalcinosis or nephrolithiasis v2.3 HNF4A Eleanor Williams commented on gene: HNF4A: Summary
3 publications (Hamilton et al 2014, Lui et al 2018, Walsh et al 2017) report 6 cases of patients with R76W/R63W variants in which nephrocalcinosis is a feature. Fly model (Marchesin et al 2019) shows that the equivalent variant in Drosophila nephrocytes works in a dominant-negative and cytotoxic effect.
Nephrocalcinosis or nephrolithiasis v2.3 HNF4A Eleanor Williams changed review comment from: Note the same codon is reported as R76W and R63W in different paper depending on whether NM_000457 or NM_175914 is used as the reference transcript.

Additional papers cited by Zornitza Stark:

PMID: 31875549 - Marchesin et al 2019 - Fly model which shows that the R85W variant in Drosophila nephrocytes works in a dominant-negative and cytotoxic effect. Expression of dHNF4 harboring the FRTS mutation affects the catabolism of lipid droplets in nephrocytes by interfering with mitochondrial function. They also showed that the FRTS mutation caused nuclear depletion and cytosolic aggregation of a wild-type dHNF4 reporter protein. The cytosolic aggregates have a cytotoxic affect. By contrast, the expression of another known close mutation in the DNA-binding domain, R89W (that leads to MODY1 but not to FRTS; Hamilton et al., 2014), did not cause any dominant-negative or cytotoxic effects.

PMID: 30005691 - Liu et al 2018 1 case of a 10-year-old girl of Chinese Han ethnicity who presented with renal Fanconi syndrome, infantile hyperinsulinemic hypoglycemia, and transient cholestasis. In addition, she presented with bilateral severe hearing loss. Renal ultrasonography showed nephrocalcinosis. Gene analysis showed a heterozygous p.R63W mutation in the HNF4A gene that is responsible for Fanconi syndrome and hyperinsulinemic hypoglycemia. (NOTE: This seems to be the same codon as the R76W variant as the paper refers to it as such).


PMID: 22802087 - Stanescu et al 2012 - 1 case that presented as a newborn with diazoxide-responsive hyperinsulinism and later developed renal Fanconi syndrome, hypophosphatemic rickets, and hepatic glycogenosis. Sequencing of HNF4A (MODY1) revealed a missense, de novo mutation (p.Arg76Trp, c.226C→T), (NM_000457) which is a known disease-causing MODY1 mutation in HNF4A. Nephrocalcinosis not specifically mentioned.

No nephrocalcinosis reported:
PMID: 28458902 - Clemente et al 2017 - 1 patient with congenital hyperinsulinaemic hypoglycaemia, rickets with craniotabes, wrist widening, genu varum and motor impairment. non-gap metabolic acidosis with acidified urine suggestive of proximal tubular acidosis, glycosuria with generalised aminoaciduria and tubular type proteinuria. Says this patient did NOT have the same ‘atypical’ Fanconi syndrome with hypercalciuria with relative hypocalcaemia, hypermagnesaemia, nephrocalcinosis and renal impairment as the patients reported by Hamilton et al 2014. A de novo variant p.Arg63Trp, c.187C > T (reference sequence: NM_175914.4) was found.
; to: Note the same codon is reported as R76W and R63W in different paper depending on whether NM_000457 or NM_175914 is used as the reference transcript.

Additional papers including those cited by Zornitza Stark:

PMID: 31875549 - Marchesin et al 2019 - Fly model which shows that the R85W variant in Drosophila nephrocytes works in a dominant-negative and cytotoxic effect. Expression of dHNF4 harboring the FRTS mutation affects the catabolism of lipid droplets in nephrocytes by interfering with mitochondrial function. They also showed that the FRTS mutation caused nuclear depletion and cytosolic aggregation of a wild-type dHNF4 reporter protein. The cytosolic aggregates have a cytotoxic affect. By contrast, the expression of another known close mutation in the DNA-binding domain, R89W (that leads to MODY1 but not to FRTS; Hamilton et al., 2014), did not cause any dominant-negative or cytotoxic effects.

PMID: 30005691 - Liu et al 2018 1 case of a 10-year-old girl of Chinese Han ethnicity who presented with renal Fanconi syndrome, infantile hyperinsulinemic hypoglycemia, and transient cholestasis. In addition, she presented with bilateral severe hearing loss. Renal ultrasonography showed nephrocalcinosis. Gene analysis showed a heterozygous p.R63W mutation in the HNF4A gene that is responsible for Fanconi syndrome and hyperinsulinemic hypoglycemia. (NOTE: no transcript identifier given but they refer to this as the same variant as R76W).

PMID: 28693455 - Walsh et al 2917 - 1 case of mother and son with heterozygous c.187C > T; p.Arg63Trp in HNF4A and Renal Fanconi syndrome. Mother is reported to have mild nephrocalcinosis

PMID: 22802087 - Stanescu et al 2012 - 1 case that presented as a newborn with diazoxide-responsive hyperinsulinism and later developed renal Fanconi syndrome, hypophosphatemic rickets, and hepatic glycogenosis. Sequencing of HNF4A (MODY1) revealed a missense, de novo mutation (p.Arg76Trp, c.226C→T), (NM_000457) which is a known disease-causing MODY1 mutation in HNF4A. Nephrocalcinosis not specifically mentioned.

No nephrocalcinosis reported:
PMID: 28458902 - Clemente et al 2017 - 1 patient with congenital hyperinsulinaemic hypoglycaemia, rickets with craniotabes, wrist widening, genu varum and motor impairment. non-gap metabolic acidosis with acidified urine suggestive of proximal tubular acidosis, glycosuria with generalised aminoaciduria and tubular type proteinuria. Says this patient did NOT have the same ‘atypical’ Fanconi syndrome with hypercalciuria with relative hypocalcaemia, hypermagnesaemia, nephrocalcinosis and renal impairment as the patients reported by Hamilton et al 2014. A de novo variant p.Arg63Trp, c.187C > T (reference sequence: NM_175914.4) was found.

PMID: 27245055 - Improda et al 2016 - 2 infants with the p.R63W mutation HNF4A with macrosomia and atypical Fanconi syndrome, in addition to hyperinsulinaemic hypoglycaemia. No nephrocalcinosis reported but this may be due to young age.
Nephrocalcinosis or nephrolithiasis v2.3 HNF4A Eleanor Williams changed review comment from: Additional papers cited by Zornitza Stark:

PMID: 31875549 - Marchesin et al 2019 - Fly model which shows that the R85W variant in Drosophila nephrocytes works in a dominant-negative and cytotoxic effect. Expression of dHNF4 harboring the FRTS mutation affects the catabolism of lipid droplets in nephrocytes by interfering with mitochondrial function. They also showed that the FRTS mutation caused nuclear depletion and cytosolic aggregation of a wild-type dHNF4 reporter protein. The cytosolic aggregates have a cytotoxic affect. By contrast, the expression of another known close mutation in the DNA-binding domain, R89W (that leads to MODY1 but not to FRTS; Hamilton et al., 2014), did not cause any dominant-negative or cytotoxic effects.

PMID: 30005691 - Liu et al 2018 1 case of a 10-year-old girl of Chinese Han ethnicity who presented with renal Fanconi syndrome, infantile hyperinsulinemic hypoglycemia, and transient cholestasis. In addition, she presented with bilateral severe hearing loss. Gene analysis showed a heterozygous p.R63W mutation in the HNF4A gene that is responsible for Fanconi syndrome and hyperinsulinemic hypoglycemia.

PMID: 22802087 - Stanescu et al 2012 - 1 case that presented as a newborn with diazoxide-responsive hyperinsulinism and later developed renal Fanconi syndrome, hypophosphatemic rickets, and hepatic glycogenosis. Sequencing of HNF4A (MODY1) revealed a missense, de novo mutation (p.Arg76Trp, c.226C→T) which is a known disease-causing MODY1 mutation in HNF4A.

PMID: 28458902 - to be finished
; to: Note the same codon is reported as R76W and R63W in different paper depending on whether NM_000457 or NM_175914 is used as the reference transcript.

Additional papers cited by Zornitza Stark:

PMID: 31875549 - Marchesin et al 2019 - Fly model which shows that the R85W variant in Drosophila nephrocytes works in a dominant-negative and cytotoxic effect. Expression of dHNF4 harboring the FRTS mutation affects the catabolism of lipid droplets in nephrocytes by interfering with mitochondrial function. They also showed that the FRTS mutation caused nuclear depletion and cytosolic aggregation of a wild-type dHNF4 reporter protein. The cytosolic aggregates have a cytotoxic affect. By contrast, the expression of another known close mutation in the DNA-binding domain, R89W (that leads to MODY1 but not to FRTS; Hamilton et al., 2014), did not cause any dominant-negative or cytotoxic effects.

PMID: 30005691 - Liu et al 2018 1 case of a 10-year-old girl of Chinese Han ethnicity who presented with renal Fanconi syndrome, infantile hyperinsulinemic hypoglycemia, and transient cholestasis. In addition, she presented with bilateral severe hearing loss. Renal ultrasonography showed nephrocalcinosis. Gene analysis showed a heterozygous p.R63W mutation in the HNF4A gene that is responsible for Fanconi syndrome and hyperinsulinemic hypoglycemia. (NOTE: This seems to be the same codon as the R76W variant as the paper refers to it as such).


PMID: 22802087 - Stanescu et al 2012 - 1 case that presented as a newborn with diazoxide-responsive hyperinsulinism and later developed renal Fanconi syndrome, hypophosphatemic rickets, and hepatic glycogenosis. Sequencing of HNF4A (MODY1) revealed a missense, de novo mutation (p.Arg76Trp, c.226C→T), (NM_000457) which is a known disease-causing MODY1 mutation in HNF4A. Nephrocalcinosis not specifically mentioned.

No nephrocalcinosis reported:
PMID: 28458902 - Clemente et al 2017 - 1 patient with congenital hyperinsulinaemic hypoglycaemia, rickets with craniotabes, wrist widening, genu varum and motor impairment. non-gap metabolic acidosis with acidified urine suggestive of proximal tubular acidosis, glycosuria with generalised aminoaciduria and tubular type proteinuria. Says this patient did NOT have the same ‘atypical’ Fanconi syndrome with hypercalciuria with relative hypocalcaemia, hypermagnesaemia, nephrocalcinosis and renal impairment as the patients reported by Hamilton et al 2014. A de novo variant p.Arg63Trp, c.187C > T (reference sequence: NM_175914.4) was found.
Intellectual disability v3.19 SCAMP5 Sarah Leigh Added comment: Comment on mode of pathogenicity: Heterozygous c.538G>T, p.Gly180Trp seeming to have a dominant-negative effect resulting in autistic spectrum disorder, intellectual disability and seizures. While homozygous c.271C>T, p.R91W seems to have a loss of function effect resulting in early onset epilepsy and Parkinson’s disease.
Intellectual disability v3.19 SCAMP5 Sarah Leigh Mode of pathogenicity for gene: SCAMP5 was changed from Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments to Other
Early onset or syndromic epilepsy v2.20 SCAMP5 Sarah Leigh Added comment: Comment on mode of pathogenicity: Heterozygous c.538G>T, p.Gly180Trp seeming to have a dominant-negative effect resulting in autistic spectrum disorder, intellectual disability and seizures. While homozygous c.271C>T, p.R91W seems to have a loss of function effect resulting in early onset epilepsy and Parkinson’s disease.
Early onset or syndromic epilepsy v2.20 SCAMP5 Sarah Leigh Mode of pathogenicity for gene: SCAMP5 was changed from Other to Other
Intellectual disability v3.18 SCAMP5 Sarah Leigh Classified gene: SCAMP5 as Amber List (moderate evidence)
Intellectual disability v3.18 SCAMP5 Sarah Leigh Added comment: Comment on list classification: Not associated with phenotype in OMIM (last edited on 10/06/2014) or in Gen2Phen. Two variants have been identified in three unrelated cases (one monoallelic, one biallelic). Supportive functional studies have been reported.
It would appear that the two variants reported so far in this gene result in differing mode of pathogenicity and phenotypic features. With heterozygous c.538G>T, p.Gly180Trp seeming to have a dominant-negative effect resulting in autistic spectrum disorder, intellectual disability and seizures. While homozygous c.271C>T, p.R91W seems to have a loss of function effect resulting in early onset epilepsy and Parkinson’s disease. This may be due to different functional domains of the mature protein being altered.
Intellectual disability v3.18 SCAMP5 Sarah Leigh Gene: scamp5 has been classified as Amber List (Moderate Evidence).
Early onset or syndromic epilepsy v2.19 SCAMP5 Sarah Leigh changed review comment from: Comment on list classification: Not associated with phenotype in OMIM (last edited on 10/06/2014) or in Gen2Phen. Two variants have been identified in three unrelated cases (one monoallelic, one biallelic). Supportive functional studies have been reported.; to: Comment on list classification: Not associated with phenotype in OMIM (last edited on 10/06/2014) or in Gen2Phen. Two variants have been identified in three unrelated cases (one monoallelic, one biallelic). Supportive functional studies have been reported.
It would appear that the two variants reported so far in this gene result in differing mode of pathogenicity and phenotypic features. With heterozygous c.538G>T, p.Gly180Trp seeming to have a dominant-negative effect resulting in autistic spectrum disorder, intellectual disability and seizures. While homozygous c.271C>T, p.R91W seems to have a loss of function effect resulting in early onset epilepsy and Parkinson’s disease. This may be due to different functional domains of the mature protein being altered.
Membranoproliferative glomerulonephritis including C3 glomerulopathy v2.11 CFB Eleanor Williams changed review comment from: Comment on list classification: Downgrading from Green to Amber. Expert review highlights that some cases come from a gene panel screen with no segregation or additional functional data.; to: Comment on list classification: Downgrading from Green to Amber. Expert review highlights that some cases come from a gene panel screen with no segregation or additional functional data. This decision has been discussed with the Genomics England Clinical team
Membranoproliferative glomerulonephritis including C3 glomerulopathy v2.11 CFB Eleanor Williams Mode of pathogenicity for gene: CFB was changed from Other to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
Membranoproliferative glomerulonephritis including C3 glomerulopathy v2.10 CFB Eleanor Williams Classified gene: CFB as Amber List (moderate evidence)
Membranoproliferative glomerulonephritis including C3 glomerulopathy v2.10 CFB Eleanor Williams Added comment: Comment on list classification: Downgrading from Green to Amber. Expert review highlights that some cases come from a gene panel screen with no segregation or additional functional data.
Membranoproliferative glomerulonephritis including C3 glomerulopathy v2.10 CFB Eleanor Williams Gene: cfb has been classified as Amber List (Moderate Evidence).
Early onset or syndromic epilepsy v2.19 SCAMP5 Sarah Leigh Classified gene: SCAMP5 as Amber List (moderate evidence)
Early onset or syndromic epilepsy v2.19 SCAMP5 Sarah Leigh Gene: scamp5 has been classified as Amber List (Moderate Evidence).
Early onset or syndromic epilepsy v2.18 SCAMP5 Sarah Leigh commented on gene: SCAMP5: PMID 32020363 reports a homozygous variant (NM_001178111:c.271C>T, p.R91W rs747966691) in two sibs of a Chinese consanguienious family, with early onset epilepsy and Parkinson’s disease (the heterozygous parents had a normal phenotype). The p.R91W knock-in mouse showed typical early-onset epilepsy and functional studies showed dysfunction of SCAMP5 shifted the excitation/inhibition balance of the neuronal network in the brain. The patients with this variant did not show signs of autism, intellectual disability, or other growth and developmental disorders.
Early onset or syndromic epilepsy v2.18 SCAMP5 Sarah Leigh Classified gene: SCAMP5 as Green List (high evidence)
Early onset or syndromic epilepsy v2.18 SCAMP5 Sarah Leigh Added comment: Comment on list classification: Not associated with phenotype in OMIM (last edited on 10/06/2014) or in Gen2Phen. Two variants have been identified in three unrelated cases (one monoallelic, one biallelic). Supportive functional studies have been reported.
Early onset or syndromic epilepsy v2.18 SCAMP5 Sarah Leigh Gene: scamp5 has been classified as Green List (High Evidence).
Early onset or syndromic epilepsy v2.17 SCAMP5 Sarah Leigh Deleted their comment
Early onset or syndromic epilepsy v2.17 SCAMP5 Sarah Leigh Classified gene: SCAMP5 as Amber List (moderate evidence)
Early onset or syndromic epilepsy v2.17 SCAMP5 Sarah Leigh Added comment: Comment on list classification: Not associated with phenotype in OMIM (last edited on 10/06/2014) or in Gen2Phen. Two variants have been identified in three unrelated cases (one monoallelic, one biallelic). Supportive functional studies have been reported.
Early onset or syndromic epilepsy v2.17 SCAMP5 Sarah Leigh Gene: scamp5 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.17 SCAMP5 Sarah Leigh Added comment: Comment on mode of inheritance: Based on the reporting of a de novo heterozygous varaiant (NM_001178111.1:c.538G>T) in two unrelated cases (PMID: 31439720) and a homozygous variant (NM_001178111:c.271C>T, rs747966691) in two members of a Chinese consanguienious family (PMID: 32020363).
Intellectual disability v3.17 SCAMP5 Sarah Leigh Mode of inheritance for gene: SCAMP5 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Early onset or syndromic epilepsy v2.16 SCAMP5 Sarah Leigh Added comment: Comment on mode of inheritance: Based on the reporting of a de novo heterozygous varaiant (NM_001178111.1:c.538G>T) in two unrelated cases (PMID: 31439720) and a homozygous variant (NM_001178111:c.271C>T, rs747966691) in two members of a Chinese consanguienious family (PMID: 32020363).
Early onset or syndromic epilepsy v2.16 SCAMP5 Sarah Leigh Mode of inheritance for gene: SCAMP5 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Early onset or syndromic epilepsy v2.15 SCAMP5 Sarah Leigh Mode of inheritance for gene: SCAMP5 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
COVID-19 research v0.15 HLA-B Ellen McDonagh gene: HLA-B was added
gene: HLA-B was added to Monogenic viral susceptibility. Sources: Literature
Mode of inheritance for gene: HLA-B was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: HLA-B were set to 12969506
Phenotypes for gene: HLA-B were set to Susceptibility to Severe Acute Respiratory Syndrome Coronavirus Infection; Susceptibility to SARS-CoV
Added comment: PMID: 12969506 - HLA-B*4601 (OR = 2.08, P = 0.04, Pc = n.s.) and HLA-B*5401 (OR = 5.44, P = 0.02, Pc = n.s.) were associated with SARS coronavirus infection. Looking at the most severe cases of infection, the severity of SARS was shown to be significantly associated with HLA-B*4601 (P = 0.0008 or Pc = 0.0279).
Sources: Literature
COVID-19 research v0.14 MBL2 Ellen McDonagh commented on gene: MBL2: PMID: 25818534 reports that the CCL2 G-2518A and MBL codon 54 variants have a significantly cumulative effect on increased risk of SARS-CoV infection.
COVID-19 research v0.14 MBL2 Ellen McDonagh Phenotypes for gene: MBL2 were changed from Susceptibility to Severe Acute Respiratory Syndrome Coronavirus Infection to Susceptibility to Severe Acute Respiratory Syndrome Coronavirus Infection; susceptibility to SARS-CoV
COVID-19 research v0.13 MASP2 Ellen McDonagh gene: MASP2 was added
gene: MASP2 was added to Monogenic viral susceptibility. Sources: Literature
Mode of inheritance for gene: MASP2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: MASP2 were set to 19405982
Phenotypes for gene: MASP2 were set to Not associated with SARS-CoV susceptibility
Added comment: PMID: 19405982 find no association with SARS-CoV susceptibility.
Sources: Literature
COVID-19 research v0.12 MBL2 Ellen McDonagh commented on gene: MBL2
Intellectual disability v3.16 SCAMP5 Sarah Leigh Publications for gene: SCAMP5 were set to 31439720; 20071347
Early onset or syndromic epilepsy v2.14 SCAMP5 Sarah Leigh Publications for gene: SCAMP5 were set to 31439720; 20071347
COVID-19 research v0.12 MBL2 Ellen McDonagh gene: MBL2 was added
gene: MBL2 was added to Monogenic viral susceptibility. Sources: Literature
Mode of inheritance for gene: MBL2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: MBL2 were set to 16170752; 19405982; 25818534; 16185324; 15838797
Phenotypes for gene: MBL2 were set to Susceptibility to Severe Acute Respiratory Syndrome Coronavirus Infection
COVID-19 research v0.11 IL4 Ellen McDonagh gene: IL4 was added
gene: IL4 was added to Monogenic viral susceptibility. Sources: Literature
Mode of inheritance for gene: IL4 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: IL4 were set to 26524966
Phenotypes for gene: IL4 were set to Pooled results for susceptibility to tuberculosis, influenza, respiratory syncytial virus, SARS-Coronavirus and pneumonia infections
Added comment: PMID: 26524966 reported that the rs2070874 T allele was was significant for pooled respiratory infections (tuberculosis, influenza, respiratory syncytial virus, SARS-Coronavirus and pneumonia infections).
Sources: Literature
COVID-19 research v0.10 Ellen McDonagh Panel types changed to Research
Renal tubulopathies v2.9 CLDN10 Catherine Snow Classified gene: CLDN10 as Green List (high evidence)
Renal tubulopathies v2.9 CLDN10 Catherine Snow Added comment: Comment on list classification: Following additional review from Zornitza and review in PMID: 31671507 relating to CLDN10 and HELIX syndrome. Enough evidence to promote CLDN10 to Green.
Renal tubulopathies v2.9 CLDN10 Catherine Snow Gene: cldn10 has been classified as Green List (High Evidence).
Nephrocalcinosis or nephrolithiasis v2.3 HNF4A Eleanor Williams changed review comment from: Additional papers cited by Zornitza Stark:

PMID: 31875549 - Marchesin et al 2019 - Fly model. Used Drosophila nephrocytes as a model for proximal tubules to study the function of HNF4A and the impact of the FRTS-associated R85W mutation. Expression of dHNF4 harboring the FRTS mutation affects the catabolism of lipid droplets in nephrocytes by interfering with mitochondrial function. They also showed that the FRTS mutation promotes the nuclear export of a wild-type reporter protein, thereby reducing transcriptional output in a dominant-negative manner and promoting the formation of cytotoxic dHNF4 aggregates in the cytosol.
Review to be continued.

PMID: 22802087
PMID: 30005691
PMID: 28458902; to: Additional papers cited by Zornitza Stark:

PMID: 31875549 - Marchesin et al 2019 - Fly model which shows that the R85W variant in Drosophila nephrocytes works in a dominant-negative and cytotoxic effect. Expression of dHNF4 harboring the FRTS mutation affects the catabolism of lipid droplets in nephrocytes by interfering with mitochondrial function. They also showed that the FRTS mutation caused nuclear depletion and cytosolic aggregation of a wild-type dHNF4 reporter protein. The cytosolic aggregates have a cytotoxic affect. By contrast, the expression of another known close mutation in the DNA-binding domain, R89W (that leads to MODY1 but not to FRTS; Hamilton et al., 2014), did not cause any dominant-negative or cytotoxic effects.

PMID: 30005691 - Liu et al 2018 1 case of a 10-year-old girl of Chinese Han ethnicity who presented with renal Fanconi syndrome, infantile hyperinsulinemic hypoglycemia, and transient cholestasis. In addition, she presented with bilateral severe hearing loss. Gene analysis showed a heterozygous p.R63W mutation in the HNF4A gene that is responsible for Fanconi syndrome and hyperinsulinemic hypoglycemia.

PMID: 22802087 - Stanescu et al 2012 - 1 case that presented as a newborn with diazoxide-responsive hyperinsulinism and later developed renal Fanconi syndrome, hypophosphatemic rickets, and hepatic glycogenosis. Sequencing of HNF4A (MODY1) revealed a missense, de novo mutation (p.Arg76Trp, c.226C→T) which is a known disease-causing MODY1 mutation in HNF4A.

PMID: 28458902 - to be finished
Intellectual disability v3.15 RNF13 Sarah Leigh reviewed gene: RNF13: Rating: GREEN; Mode of pathogenicity: Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments; Publications: ; Phenotypes: ; Mode of inheritance: None
Early onset or syndromic epilepsy v2.13 RNF13 Sarah Leigh reviewed gene: RNF13: Rating: GREEN; Mode of pathogenicity: Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments; Publications: ; Phenotypes: ; Mode of inheritance: None
Intellectual disability v3.15 RNF113A Sarah Leigh Classified gene: RNF113A as Green List (high evidence)
Intellectual disability v3.15 RNF113A Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as possible Gen2Phen gene for X-linked trichothiodystrophy. At least 3 terminating variants reported in unrelated cases. Supportive functional studies also reported.
Intellectual disability v3.15 RNF113A Sarah Leigh Gene: rnf113a has been classified as Green List (High Evidence).
Intellectual disability v3.14 RNF113A Sarah Leigh Publications for gene: RNF113A were set to 25612912; 29144457
Early onset or syndromic epilepsy v2.13 RNF113A Sarah Leigh Classified gene: RNF113A as Green List (high evidence)
Early onset or syndromic epilepsy v2.13 RNF113A Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as possible Gen2Phen gene for X-linked trichothiodystrophy. At least 3 terminating variants reported in unrelated cases. Supportive functional studies also reported.
Early onset or syndromic epilepsy v2.13 RNF113A Sarah Leigh Gene: rnf113a has been classified as Green List (High Evidence).
Hereditary systemic amyloidosis v1.4 NLRP3 Rebecca Foulger Phenotypes for gene: NLRP3 were changed from Muckle-Wells syndrome, 191900 to Muckle-Wells syndrome, 191900
Hereditary systemic amyloidosis v1.4 NLRP3 Rebecca Foulger Phenotypes for gene: NLRP3 were changed from Muckle-Wells syndrome to Muckle-Wells syndrome, 191900
Intellectual disability v3.13 RARS Sarah Leigh Classified gene: RARS as Green List (high evidence)
Intellectual disability v3.13 RARS Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene. At least 19 variants reported in at least 13 cases of Hypomyelinating Leukodystrophy exhibinting intellectual disability to varying degrees. Supportive functional studies were also reported.
Intellectual disability v3.13 RARS Sarah Leigh Gene: rars has been classified as Green List (High Evidence).
Early onset or syndromic epilepsy v2.12 RARS Sarah Leigh Classified gene: RARS as Green List (high evidence)
Early onset or syndromic epilepsy v2.12 RARS Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene. At least 13 variants reported in at least 9 cases of Hypomyelinating Leukodystrophy exhibinting epilepsy. Supportive functional studies were also reported.
Early onset or syndromic epilepsy v2.12 RARS Sarah Leigh Gene: rars has been classified as Green List (High Evidence).
Intellectual disability v3.12 RARS Sarah Leigh commented on gene: RARS
Early onset or syndromic epilepsy v2.11 RARS Sarah Leigh commented on gene: RARS
Intellectual disability v3.12 RARS Sarah Leigh Tag new-gene-name tag was added to gene: RARS.
Early onset or syndromic epilepsy v2.11 RARS Sarah Leigh Tag new-gene-name tag was added to gene: RARS.
Intellectual disability v3.12 RALGAPA1 Sarah Leigh Classified gene: RALGAPA1 as Green List (high evidence)
Intellectual disability v3.12 RALGAPA1 Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as probable Gen2Phen gene for RALGAPA1-related neurodevelopmental disorder. At least 5 variants reported in at least 4 unrelated cases.
Intellectual disability v3.12 RALGAPA1 Sarah Leigh Gene: ralgapa1 has been classified as Green List (High Evidence).
Early onset or syndromic epilepsy v2.11 RALGAPA1 Sarah Leigh Classified gene: RALGAPA1 as Green List (high evidence)
Early onset or syndromic epilepsy v2.11 RALGAPA1 Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as probable Gen2Phen gene for RALGAPA1-related neurodevelopmental disorder. At least 5 variants reported in at least 4 unrelated cases.
Early onset or syndromic epilepsy v2.11 RALGAPA1 Sarah Leigh Gene: ralgapa1 has been classified as Green List (High Evidence).
Intellectual disability v3.11 RALGAPA1 Sarah Leigh Added comment: Comment on phenotypes: Intellectual disability;hypotonia;infantile spasms.
Intellectual disability v3.11 RALGAPA1 Sarah Leigh Phenotypes for gene: RALGAPA1 were changed from Intellectual disability; hypotonia; infantile spasms. to Neurodevelopmental disorder with hypotonia, neonatal respiratory insufficiency, and thermodysregulation 618797
Early onset or syndromic epilepsy v2.10 RALGAPA1 Sarah Leigh Added comment: Comment on phenotypes: Intellectual disability;hypotonia;infantile spasms
Early onset or syndromic epilepsy v2.10 RALGAPA1 Sarah Leigh Phenotypes for gene: RALGAPA1 were changed from Intellectual disability; hypotonia; infantile spasms. to .Neurodevelopmental disorder with hypotonia, neonatal respiratory insufficiency, and thermodysregulation 618797
Renal tubulopathies v2.8 CLDN10 Catherine Snow Publications for gene: CLDN10 were set to 19307729
Intellectual disability v3.10 PUM1 Sarah Leigh Classified gene: PUM1 as Green List (high evidence)
Intellectual disability v3.10 PUM1 Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 3 SNVs in at least 5 unrelated cases and CNVs spanning PUM1 in 9 cases. Supportive functional studies also reported.
Intellectual disability v3.10 PUM1 Sarah Leigh Gene: pum1 has been classified as Green List (High Evidence).
Early onset or syndromic epilepsy v2.9 PUM1 Sarah Leigh Classified gene: PUM1 as Green List (high evidence)
Early onset or syndromic epilepsy v2.9 PUM1 Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 3 SNVs in at least 5 unrelated cases and CNVs spanning PUM1 in 9 cases. Supportive functional studies also reported.
Early onset or syndromic epilepsy v2.9 PUM1 Sarah Leigh Gene: pum1 has been classified as Green List (High Evidence).
Nephrocalcinosis or nephrolithiasis v2.3 HNF4A Eleanor Williams commented on gene: HNF4A: Additional papers cited by Zornitza Stark:

PMID: 31875549 - Marchesin et al 2019 - Fly model. Used Drosophila nephrocytes as a model for proximal tubules to study the function of HNF4A and the impact of the FRTS-associated R85W mutation. Expression of dHNF4 harboring the FRTS mutation affects the catabolism of lipid droplets in nephrocytes by interfering with mitochondrial function. They also showed that the FRTS mutation promotes the nuclear export of a wild-type reporter protein, thereby reducing transcriptional output in a dominant-negative manner and promoting the formation of cytotoxic dHNF4 aggregates in the cytosol.
Review to be continued.

PMID: 22802087
PMID: 30005691
PMID: 28458902
Intellectual disability v3.9 PUM1 Sarah Leigh Added comment: Comment on phenotypes: Global developmental delay;Intellectual disability;Seizures;Abnormality of the face;Ataxia;Cryptorchidism
Intellectual disability v3.9 PUM1 Sarah Leigh Phenotypes for gene: PUM1 were changed from Global developmental delay; Intellectual disability; Seizures; Abnormality of the face; Ataxia; Cryptorchidism to Spinocerebellar ataxia 47 617931
Intellectual disability v3.8 PUM1 Sarah Leigh Publications for gene: PUM1 were set to 29474920; 30903679; 31859446
Early onset or syndromic epilepsy v2.8 PUM1 Sarah Leigh Added comment: Comment on phenotypes: Global developmental delay;Intellectual disability;Seizures;Abnormality of the face;Ataxia;Cryptorchidism
Early onset or syndromic epilepsy v2.8 PUM1 Sarah Leigh Phenotypes for gene: PUM1 were changed from Global developmental delay; Intellectual disability; Seizures; Abnormality of the face; Ataxia; Cryptorchidism to Spinocerebellar ataxia 47 617931
Early onset or syndromic epilepsy v2.7 PUM1 Sarah Leigh Publications for gene: PUM1 were set to 29474920; 30903679; 31859446
Tubulointerstitial kidney disease v1.9 SEC61A1 Eleanor Williams Classified gene: SEC61A1 as Green List (high evidence)
Tubulointerstitial kidney disease v1.9 SEC61A1 Eleanor Williams Added comment: Comment on list classification: Changing rating from Amber to Green. Two familial cases reported in Bolar publication plus animal model. Further case reported in Groopman.
Tubulointerstitial kidney disease v1.9 SEC61A1 Eleanor Williams Gene: sec61a1 has been classified as Green List (High Evidence).
Tubulointerstitial kidney disease v1.8 SEC61A1 Eleanor Williams Publications for gene: SEC61A1 were set to
Tubulointerstitial kidney disease v1.7 SEC61A1 Eleanor Williams commented on gene: SEC61A1: PMID: 30586318 - Groopman et al 2019 - Patient CKD184 in Table S7 has a heterozygous missense variant p.I428M in SEC61A1. The genetic diagnosis was Hyperuricemic nephropathy familial juvenile 4.

PMID: 27392076 Bolar et al 2016 - report on two families with ADTKD and congenital anemia accompanied by either intrauterine growth retardation or neutropenia. Exclusion of known ADTKD genes coupled with linkage analysis, whole-exome sequencing, and targeted re-sequencing identified heterozygous missense variants in SEC61A1-c.553A>G (p.Thr185Ala) and c.200T>G (p.Val67Gly). Zebrafish model re-capitulated the phenotype and could not be rescued by mRNA with the pathogenic alleles.
Tubulointerstitial kidney disease v1.7 DNAJB11 Eleanor Williams Phenotypes for gene: DNAJB11 were changed from Polycystic kidney disease 6 with or without polycystic liver disease MIM 618061 to Polycystic kidney disease 6 with or without polycystic liver disease MIM 618061; Tubulointerstitial disease
Tubulointerstitial kidney disease v1.6 DNAJB11 Eleanor Williams Publications for gene: DNAJB11 were set to
Tubulointerstitial kidney disease v1.5 DNAJB11 Eleanor Williams Classified gene: DNAJB11 as Green List (high evidence)
Tubulointerstitial kidney disease v1.5 DNAJB11 Eleanor Williams Added comment: Comment on list classification: Changing rating from amber to green. Expert review indicates that there is sufficient phenotype overlap for this gene to be green on the Tubulointerstitial kidney disease panel.
Tubulointerstitial kidney disease v1.5 DNAJB11 Eleanor Williams Gene: dnajb11 has been classified as Green List (High Evidence).
Tubulointerstitial kidney disease v1.4 DNAJB11 Eleanor Williams commented on gene: DNAJB11: Associated with Polycystic kidney disease 6 with or without polycystic liver disease #618061 (AD) in OMIM.

PMID: 29706351 - Cornec-Le Gall et al 2018 - Initially identified DNAJB11 variants by WES in two families presenting with Autosomal-dominant polycystic kidney disease (ADPKD)-like features. In family 1 a missense variant (p.Pro54Arg) was found in two family members presenting with non-enlarged polycystic kidneys. In family 2 a frameshifting change (c.166_167insTT) was found; they presented with small renal and liver cysts. Five additional multigenerational families carrying DNAJB11 mutations were identified by targeted analysis. From analysis of the phenotype and functional studies from DNAJB11-null cells they conclude that DNAJB11-associated disease is a phenotypic hybrid of ADPKD and ADTKD, characterized by normal-sized cystic kidneys and progressive interstitial fibrosis resulting in late-onset ESRD.

PMID: 29777155 - Allison 2018 - research highlight about the Cornec-Le Gall et al 2018 paper.
Renal tubulopathies v2.7 SLC2A2 Catherine Snow Classified gene: SLC2A2 as Green List (high evidence)
Renal tubulopathies v2.7 SLC2A2 Catherine Snow Added comment: Comment on list classification: SLC2A2 (GLUT2) associated with Fanconi-Bickel syndrome which includes renal tubular dysfunction. Sufficient number of unrelated individuals reported to classify as Green. Identified in PMID: 32150856 as missing from the panel in 27/02/2020.
Renal tubulopathies v2.7 SLC2A2 Catherine Snow Gene: slc2a2 has been classified as Green List (High Evidence).
Membranoproliferative glomerulonephritis including C3 glomerulopathy v2.9 DGKE Eleanor Williams Added comment: Comment on mode of inheritance: Changing MOI to Biallelic only. All reported cases are homozygous.
Membranoproliferative glomerulonephritis including C3 glomerulopathy v2.9 DGKE Eleanor Williams Mode of inheritance for gene: DGKE was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal
Membranoproliferative glomerulonephritis including C3 glomerulopathy v2.8 CFI Eleanor Williams Classified gene: CFI as Amber List (moderate evidence)
Membranoproliferative glomerulonephritis including C3 glomerulopathy v2.8 CFI Eleanor Williams Added comment: Comment on list classification: Changing rating from Green to Amber. Expert review has rated this gene red. No famililal cases reported, and cases that are reported looked at candidate genes only.
Membranoproliferative glomerulonephritis including C3 glomerulopathy v2.8 CFI Eleanor Williams Gene: cfi has been classified as Amber List (Moderate Evidence).
Membranoproliferative glomerulonephritis including C3 glomerulopathy v2.7 CFH Eleanor Williams Added comment: Comment on mode of inheritance: Updating MOI to Biallelic only, after expert reviewer notes that only biallelic variants are associated with C3 glomerulopathy. They note monoalleleic defects are linked with aHUS but NOT MPGN
Membranoproliferative glomerulonephritis including C3 glomerulopathy v2.7 CFH Eleanor Williams Mode of inheritance for gene: CFH was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal
Membranoproliferative glomerulonephritis including C3 glomerulopathy v2.6 CFH Eleanor Williams Publications for gene: CFH were set to 24172683; 16612335; 24722444; 27458560
Membranoproliferative glomerulonephritis including C3 glomerulopathy v2.5 C3 Eleanor Williams Added comment: Comment on mode of pathogenicity: Gain of function mutations associated with familial C3G/MPGN
Membranoproliferative glomerulonephritis including C3 glomerulopathy v2.5 C3 Eleanor Williams Mode of pathogenicity for gene: C3 was changed from Other to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
Renal tubulopathies v2.6 SLC2A2 Catherine Snow Publications for gene: SLC2A2 were set to 32150856; 24175243
Renal tubulopathies v2.5 SLC2A2 Catherine Snow Publications for gene: SLC2A2 were set to
Mitochondrial disorders v2.5 COASY Zornitza Stark reviewed gene: COASY: Rating: GREEN; Mode of pathogenicity: None; Publications: 25778941, 24360804, 30089828, 28489334; Phenotypes: Neurodegeneration with brain iron accumulation 6 MIM#615643, Pontocerebellar hypoplasia, type 12 MIM#618266; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Mitochondrial disorders v2.5 NAXD Zornitza Stark reviewed gene: NAXD: Rating: GREEN; Mode of pathogenicity: None; Publications: 30576410; Phenotypes: Encephalopathy, progressive, early-onset, with brain edema and/or leukoencephalopathy, 2 MIM#618321; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Mitochondrial disorders v2.5 UQCRFS1 Zornitza Stark reviewed gene: UQCRFS1: Rating: GREEN; Mode of pathogenicity: None; Publications: 31883641; Phenotypes: Mitochondrial Complex III deficiency, lactic acidosis, fetal bradycardia, hypertrophic cardiomyopathy, alopecia totalis; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Mitochondrial disorders v2.5 SPATA5 Zornitza Stark reviewed gene: SPATA5: Rating: GREEN; Mode of pathogenicity: None; Publications: 30009132, 29343804; Phenotypes: Epilepsy, hearing loss, and mental retardation syndrome MIM#616577; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
Mitochondrial disorders v2.5 SLC52A3 Zornitza Stark reviewed gene: SLC52A3: Rating: GREEN; Mode of pathogenicity: None; Publications: 29053833, 29193829; Phenotypes: Brown-Vialetto-Van Laere syndrome 1, MIM#211530; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Mitochondrial disorders v2.5 SLC52A2 Zornitza Stark reviewed gene: SLC52A2: Rating: GREEN; Mode of pathogenicity: None; Publications: 29053833, 29193829; Phenotypes: Brown-Vialetto-Van Laere syndrome 2 MIM#614707; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Mitochondrial disorders v2.5 SLC39A8 Zornitza Stark reviewed gene: SLC39A8: Rating: AMBER; Mode of pathogenicity: None; Publications: 29453449, 27995398; Phenotypes: Congenital disorder of glycosylation, type IIn, MIM#616721; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Mitochondrial disorders v2.5 SLC25A24 Zornitza Stark reviewed gene: SLC25A24: Rating: GREEN; Mode of pathogenicity: None; Publications: 29100094, 29100093; Phenotypes: Fontaine progeroid syndrome, MIM#612289; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Mitochondrial disorders v2.5 SLC25A20 Zornitza Stark reviewed gene: SLC25A20: Rating: GREEN; Mode of pathogenicity: None; Publications: 9399886, 31108048, 25778941; Phenotypes: Carnitine-acylcarnitine translocase deficiency MIM#212138; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Mitochondrial disorders v2.5 SLC22A5 Zornitza Stark reviewed gene: SLC22A5: Rating: GREEN; Mode of pathogenicity: None; Publications: 9916797, 25778941, 17884651, 25778941; Phenotypes: Carnitine deficiency, systemic primary MIM#212140; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
Mitochondrial disorders v2.5 SDHAF4 Zornitza Stark reviewed gene: SDHAF4: Rating: RED; Mode of pathogenicity: None; Publications: 24954416; Phenotypes: ; Mode of inheritance: None
Mitochondrial disorders v2.5 SDHAF3 Zornitza Stark reviewed gene: SDHAF3: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Mitochondrial disorders v2.5 QARS Zornitza Stark edited their review of gene: QARS: Added comment: Encodes t-RNA synthetase, over 20 individuals reported, include in mito panel in line with other t-RNA synthetases.; Changed rating: GREEN; Changed publications: 28620870, 25471517, 25432320, 25041233, 24656866, 32042906; Changed phenotypes: Microcephaly, progressive, seizures, and cerebral and cerebellar atrophy, MIM# 615760
Mitochondrial disorders v2.5 PPOX Zornitza Stark reviewed gene: PPOX: Rating: GREEN; Mode of pathogenicity: None; Publications: 25778941, 9811936, 12859407, 30476629; Phenotypes: Porphyria variegata MIM#176200; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Mitochondrial disorders v2.5 POLRMT Zornitza Stark reviewed gene: POLRMT: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Mitochondrial disorders v2.5 PLA2G6 Zornitza Stark reviewed gene: PLA2G6: Rating: GREEN; Mode of pathogenicity: None; Publications: 25348461, 26001724, 26506412, 30528460, 16783378; Phenotypes: Infantile neuroaxonal dystrophy 1 MIM#256600, Neurodegeneration with brain iron accumulation 2B MIM#610217, Parkinson disease 14, autosomal recessive MIM#612953; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
Mitochondrial disorders v2.5 PITRM1 Zornitza Stark reviewed gene: PITRM1: Rating: GREEN; Mode of pathogenicity: None; Publications: 26697887, 29764912; Phenotypes: Cerebellar atrophy, mental retardation, spinocerebellar ataxia, cognitive decline, psychosis; Mode of inheritance: None; Current diagnostic: yes
Mitochondrial disorders v2.5 PANK2 Zornitza Stark reviewed gene: PANK2: Rating: GREEN; Mode of pathogenicity: None; Publications: 25778941, 11479594, 12510040, 28863176, 25778941; Phenotypes: HARP syndrome MIM#607236, Neurodegeneration with brain iron accumulation 1 MIM#234200; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
Mitochondrial disorders v2.5 OXCT1 Zornitza Stark reviewed gene: OXCT1: Rating: GREEN; Mode of pathogenicity: None; Publications: 25778941, 10964512, 8751852, 23420214, 25778941; Phenotypes: Succinyl CoA:3-oxoacid CoA transferase deficiency, MIM#245050; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
Mitochondrial disorders v2.5 OXA1L Zornitza Stark reviewed gene: OXA1L: Rating: AMBER; Mode of pathogenicity: None; Publications: 30201738, 16435202; Phenotypes: encephalopathy, hypotonia, developmental delay; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Mitochondrial disorders v2.5 NDUFB10 Zornitza Stark reviewed gene: NDUFB10: Rating: AMBER; Mode of pathogenicity: None; Publications: 28040730, 32025618; Phenotypes: fatal infantile lactic acidosis, cardiomyopathy; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Mitochondrial disorders v2.5 NDUFAF7 Zornitza Stark reviewed gene: NDUFAF7: Rating: RED; Mode of pathogenicity: None; Publications: 28837730; Phenotypes: Myopia; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Atypical haemolytic uraemic syndrome v2.7 ADAMTS13 Eleanor Williams Publications for gene: ADAMTS13 were set to
Atypical haemolytic uraemic syndrome v2.6 ADAMTS13 Eleanor Williams Classified gene: ADAMTS13 as Amber List (moderate evidence)
Atypical haemolytic uraemic syndrome v2.6 ADAMTS13 Eleanor Williams Gene: adamts13 has been classified as Amber List (Moderate Evidence).
Atypical haemolytic uraemic syndrome v2.5 ADAMTS13 Eleanor Williams commented on gene: ADAMTS13: Associated with Thrombotic thrombocytopenic purpura, hereditary #274150 (AR) in OMIM.

After consultation with the Genomics England clinical team it was decided to add this gene as Amber and discuss with the GMS group at the next update. ADAMTS13 may be responsible for a mimic of aHUS, that might be difficult to distinguish clinically. Therefore it is possible that inclusion in a differential diagnosis capacity is relevant.
Atypical haemolytic uraemic syndrome v2.5 ADAMTS13 Eleanor Williams changed review comment from: Consulting with the Genomics England clinical team as to whether to add this gene to the panel.; to: Consulting with the Genomics England clinical team as to whether to add this gene to the panel.
Atypical haemolytic uraemic syndrome v2.5 CFHR5 Eleanor Williams Classified gene: CFHR5 as Amber List (moderate evidence)
Atypical haemolytic uraemic syndrome v2.5 CFHR5 Eleanor Williams Added comment: Comment on list classification: Changing rating from grey to amber. Some evidence to suggest that variants in CFHR5 may be associated with aHUS but there are not 3 clear cases with variants only found in that gene and segregation data, or functional data
Atypical haemolytic uraemic syndrome v2.5 CFHR5 Eleanor Williams Gene: cfhr5 has been classified as Amber List (Moderate Evidence).
Atypical haemolytic uraemic syndrome v2.4 CFHR5 Eleanor Williams Publications for gene: CFHR5 were set to 22622361
Proteinuric renal disease v2.15 DGKE Eleanor Williams Classified gene: DGKE as Green List (high evidence)
Proteinuric renal disease v2.15 DGKE Eleanor Williams Added comment: Comment on list classification: Changing rating to green as multiple cases reported and expert review says proteinuria is a prominent feature
Proteinuric renal disease v2.15 DGKE Eleanor Williams Gene: dgke has been classified as Green List (High Evidence).
Proteinuric renal disease v2.14 DGKE Eleanor Williams Mode of inheritance for gene: DGKE was changed from to BIALLELIC, autosomal or pseudoautosomal
Proteinuric renal disease v2.13 TPRKB Eleanor Williams Classified gene: TPRKB as Green List (high evidence)
Proteinuric renal disease v2.13 TPRKB Eleanor Williams Added comment: Comment on list classification: Changing rating from red to green, as there are 3 reported cases.
Proteinuric renal disease v2.13 TPRKB Eleanor Williams Gene: tprkb has been classified as Green List (High Evidence).
Proteinuric renal disease v2.12 TPRKB Eleanor Williams Mode of inheritance for gene: TPRKB was changed from to BIALLELIC, autosomal or pseudoautosomal
Proteinuric renal disease v2.11 TPRKB Eleanor Williams Publications for gene: TPRKB were set to 28805828
Proteinuric renal disease v2.10 PTPRO Eleanor Williams Classified gene: PTPRO as Amber List (moderate evidence)
Proteinuric renal disease v2.10 PTPRO Eleanor Williams Added comment: Comment on list classification: Changing rating from red to amber. 2 families reported.
Proteinuric renal disease v2.10 PTPRO Eleanor Williams Gene: ptpro has been classified as Amber List (Moderate Evidence).
Proteinuric renal disease v2.9 KANK2 Eleanor Williams Classified gene: KANK2 as Amber List (moderate evidence)
Proteinuric renal disease v2.9 KANK2 Eleanor Williams Added comment: Comment on list classification: Changing rating from red to amber - 2 reported cases.
Proteinuric renal disease v2.9 KANK2 Eleanor Williams Gene: kank2 has been classified as Amber List (Moderate Evidence).
Mitochondrial disorders v2.5 MRM2 Zornitza Stark reviewed gene: MRM2: Rating: AMBER; Mode of pathogenicity: None; Publications: 28973171; Phenotypes: MELAS-like; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Mitochondrial disorders v2.5 MARS2 Zornitza Stark reviewed gene: MARS2: Rating: AMBER; Mode of pathogenicity: None; Publications: 25754315; Phenotypes: Combined oxidative phosphorylation deficiency 25, OMIM #616430, Spastic ataxia 3, autosomal recessive, OMIM #611390; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Hereditary ataxia with onset in adulthood v2.8 Ellen McDonagh Panel version has been signed off
Mitochondrial disorders v2.5 LYRM4 Zornitza Stark changed review comment from: Three individuals from two families reported.; to: Three individuals from two families reported. Amber on the other mito panel.
Mitochondrial disorders v2.5 LYRM4 Zornitza Stark reviewed gene: LYRM4: Rating: AMBER; Mode of pathogenicity: None; Publications: 23814038, 31497476; Phenotypes: Combined oxidative phosphorylation deficiency 19, MIM# 615595; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Mitochondrial disorders v2.5 IDH3A Zornitza Stark reviewed gene: IDH3A: Rating: GREEN; Mode of pathogenicity: None; Publications: 31012789, 30478029, 30058936, 28412069; Phenotypes: Retinitis pigmentosa; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Mitochondrial disorders v2.5 GATC Zornitza Stark reviewed gene: GATC: Rating: RED; Mode of pathogenicity: None; Publications: 30283131; Phenotypes: Mitochondrial cardiomyopathy; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Mitochondrial disorders v2.5 GATB Zornitza Stark reviewed gene: GATB: Rating: RED; Mode of pathogenicity: None; Publications: 30283131; Phenotypes: Mitochondrial cardiomyopathy; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Mitochondrial disorders v2.5 G6PC Zornitza Stark changed review comment from: Not a mitochondrial disorder.; to: Not a mitochondrial disorder. It is Red on the other mito panel.
Mitochondrial disorders v2.5 G6PC Zornitza Stark reviewed gene: G6PC: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Glycogen storage disease Ia, MIM# 232200; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Infantile enterocolitis & monogenic inflammatory bowel disease v1.16 ADAM17 Zornitza Stark reviewed gene: ADAM17: Rating: GREEN; Mode of pathogenicity: None; Publications: 22010916, 25804906, 21041656, 22236242; Phenotypes: Inflammatory neonatal-onset skin and bowel disease, MIM#614328; Mode of inheritance: None
Mitochondrial disorders v2.5 SSBP1 Zornitza Stark reviewed gene: SSBP1: Rating: GREEN; Mode of pathogenicity: None; Publications: 31298765, 31479473, 31550237, 31550240; Phenotypes: Optic atrophy with or without extraocular phenotypes; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal; Current diagnostic: yes
Unexplained kidney failure in young people v1.84 VIPAS39 Rebecca Foulger Classified gene: VIPAS39 as Green List (high evidence)
Unexplained kidney failure in young people v1.84 VIPAS39 Rebecca Foulger Added comment: Comment on list classification: Updated rating from Red to Green following review by Zornitza Stark, and curation of PMID:20190753. Sufficient (>3) cases of ARC being caused by VIPAS39 variants in PMID:20190753. Although only one paper, the patients are from multiple ethnicities and functional studies support the phenotype: VIPAS39 & VPS33B form a complex, and have roles in apical junction formation. Variants in VPS33B cause 'Arthrogryposis, renal dysfunction, and cholestasis 1, MIM:208085', and VPS33B is Green on this panel. VIPAS39-ARC also has a Confirmed Disease confidence in Gene2Phenotype.
Unexplained kidney failure in young people v1.84 VIPAS39 Rebecca Foulger Gene: vipas39 has been classified as Green List (High Evidence).
Unexplained kidney failure in young people v1.83 VIPAS39 Rebecca Foulger commented on gene: VIPAS39
Renal tubulopathies v2.4 HNF4A Catherine Snow Classified gene: HNF4A as Green List (high evidence)
Renal tubulopathies v2.4 HNF4A Catherine Snow Added comment: Comment on list classification: HNF4A sufficient individuals who are unrelated and from different populations in the literature to classify this as Green. Variable phenotype reported although currently only one variant p.R63W. PMID 28458902 reported a patients with the variant and reviewed other published case.
Renal tubulopathies v2.4 HNF4A Catherine Snow Gene: hnf4a has been classified as Green List (High Evidence).
Unexplained kidney failure in young people v1.83 VIPAS39 Rebecca Foulger Publications for gene: VIPAS39 were set to
Mitochondrial disorders v2.5 XPNPEP3 Zornitza Stark reviewed gene: XPNPEP3: Rating: RED; Mode of pathogenicity: None; Publications: 20179356; Phenotypes: Nephronophthisis-like nephropathy 1, MIM#613159; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Mitochondrial disorders v2.5 UQCR11 Zornitza Stark reviewed gene: UQCR11: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Mitochondrial disorders v2.5 UQCR10 Zornitza Stark reviewed gene: UQCR10: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Mitochondrial disorders v2.5 UQCC1 Zornitza Stark reviewed gene: UQCC1: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Mitochondrial disorders v2.5 ETFB Zornitza Stark reviewed gene: ETFB: Rating: GREEN; Mode of pathogenicity: None; Publications: 12815589, 7912128; Phenotypes: Glutaric acidemia IIB MIM#231680, Multiple acyl-CoA dehydrogenase deficiency (MADD); Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Mitochondrial disorders v2.5 ETFA Zornitza Stark reviewed gene: ETFA: Rating: GREEN; Mode of pathogenicity: None; Publications: 1882842, 12815589; Phenotypes: Glutaric acidemia IIA MIM#231680, Multiple acyl-CoA dehydrogenase deficiency (MADD); Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Mitochondrial disorders v2.5 ERAL1 Zornitza Stark reviewed gene: ERAL1: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Perrault syndrome 6, MIM# 617565; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Mitochondrial disorders v2.5 CYCS Zornitza Stark edited their review of gene: CYCS: Added comment: At least three families have been reported with this condition. CYCS is located in the mitochondria and is involved in the electron transport system that functions in oxidative phosphorylation.; Changed publications: 18345000, 24326104, 30051457
Mitochondrial disorders v2.5 COX6B2 Zornitza Stark reviewed gene: COX6B2: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Mitochondrial disorders v2.5 COX6A2 Zornitza Stark reviewed gene: COX6A2: Rating: GREEN; Mode of pathogenicity: None; Publications: 31155743, 23460811; Phenotypes: Mitochondrial complex IV deficiency, MIM# 220110; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Mitochondrial disorders v2.5 COX19 Zornitza Stark reviewed gene: COX19: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Mitochondrial disorders v2.5 COX18 Zornitza Stark reviewed gene: COX18: Rating: RED; Mode of pathogenicity: None; Publications: 19373256; Phenotypes: ; Mode of inheritance: None
Mitochondrial disorders v2.5 COX17 Zornitza Stark reviewed gene: COX17: Rating: RED; Mode of pathogenicity: None; Publications: 12370308; Phenotypes: ; Mode of inheritance: None
Mitochondrial disorders v2.5 COX16 Zornitza Stark reviewed gene: COX16: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Mitochondrial disorders v2.5 COX14 Zornitza Stark reviewed gene: COX14: Rating: AMBER; Mode of pathogenicity: None; Publications: 22243966; Phenotypes: Mitochondrial complex IV deficiency, MIM#220110; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Mitochondrial disorders v2.5 COX11 Zornitza Stark reviewed gene: COX11: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Mitochondrial disorders v2.5 COQ5 Zornitza Stark reviewed gene: COQ5: Rating: RED; Mode of pathogenicity: None; Publications: 29044765; Phenotypes: Cerebellar ataxia, encephalopathy, generalized tonic-clonic seizures, intellectual disability; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Mitochondrial disorders v2.5 COA4 Zornitza Stark reviewed gene: COA4: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Mitochondrial disorders v2.5 COA3 Zornitza Stark reviewed gene: COA3: Rating: RED; Mode of pathogenicity: None; Publications: 25604084; Phenotypes: Mitochondrial complex IV deficiency; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Mitochondrial disorders v2.5 BTD Zornitza Stark commented on gene: BTD: Can we please review the link to mitochondrial disease?
Mitochondrial disorders v2.5 ATPAF1 Zornitza Stark reviewed gene: ATPAF1: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Mitochondrial disorders v2.5 ATP5L2 Zornitza Stark reviewed gene: ATP5L2: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Mitochondrial disorders v2.5 ATP5L Zornitza Stark reviewed gene: ATP5L: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Mitochondrial disorders v2.5 ATP5J2 Zornitza Stark reviewed gene: ATP5J2: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Mitochondrial disorders v2.5 ATP5H Zornitza Stark reviewed gene: ATP5H: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Mitochondrial disorders v2.5 ATP5F1 Zornitza Stark reviewed gene: ATP5F1: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Mitochondrial disorders v2.5 ANO10 Zornitza Stark edited their review of gene: ANO10: Added comment: I don't think this is a mitochondrial disorder. The reported CoQ10 deficiency appears to be secondary.; Changed publications: 25778941; Changed phenotypes: Spinocerebellar ataxia, autosomal recessive 10, MIM# 613728
Intellectual disability v3.7 PIGP Sarah Leigh Classified gene: PIGP as Green List (high evidence)
Intellectual disability v3.7 PIGP Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 2 variants reported (rs768633670, rs778481061). rs768633670 were reported as a compound heterozygotes in one case and was present in at least two geographically separated consanguineous European families; suggesting a founder effect in the European population (PMID 32042915).
Supportive functional studies are also presented.
Intellectual disability v3.7 PIGP Sarah Leigh Gene: pigp has been classified as Green List (High Evidence).
Early onset or syndromic epilepsy v2.6 PIGP Sarah Leigh Classified gene: PIGP as Green List (high evidence)
Early onset or syndromic epilepsy v2.6 PIGP Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 2 variants reported (rs768633670, rs778481061). rs768633670 were reported as a compound heterozygotes in one case and was present in at least two geographically separated consanguineous European families; suggesting a founder effect in the European population (PMID 32042915).
Supportive functional studies are also presented.
Early onset or syndromic epilepsy v2.6 PIGP Sarah Leigh Gene: pigp has been classified as Green List (High Evidence).
Intellectual disability v3.6 PIGP Sarah Leigh Publications for gene: PIGP were set to 28334793; 31139695; 32042915
Intellectual disability v3.5 PIGP Sarah Leigh Phenotypes for gene: PIGP were changed from ?Epileptic encephalopathy, early infantile, 55, 617599; Generalized hypotonia; Global developmental delay; Seizures; Intellectual disability; Feeding difficulties; Cortical visual impairment to Epileptic encephalopathy, early infantile, 55, 617599; Generalized hypotonia; Global developmental delay; Seizures; Intellectual disability; Feeding difficulties; Cortical visual impairment
Intellectual disability v3.4 PIGP Sarah Leigh Publications for gene: PIGP were set to 28334793; 31139695; 32042915
Intellectual disability v3.4 PIGP Sarah Leigh Publications for gene: PIGP were set to 28334793; 31139695
Early onset or syndromic epilepsy v2.5 PIGP Sarah Leigh Phenotypes for gene: PIGP were changed from ?Epileptic encephalopathy, early infantile, 55, 617599; Generalized hypotonia; Global developmental delay; Seizures; Intellectual disability; Feeding difficulties; Cortical visual impairment to Epileptic encephalopathy, early infantile, 55, 617599; Generalized hypotonia; Global developmental delay; Seizures; Intellectual disability; Feeding difficulties; Cortical visual impairment
Early onset or syndromic epilepsy v2.4 PIGP Sarah Leigh Publications for gene: PIGP were set to 28334793; 31139695
Proteinuric renal disease v2.8 CD2AP Catherine Snow Mode of inheritance for gene: CD2AP was changed from to BIALLELIC, autosomal or pseudoautosomal
Proteinuric renal disease v2.7 CD2AP Catherine Snow Classified gene: CD2AP as Amber List (moderate evidence)
Proteinuric renal disease v2.7 CD2AP Catherine Snow Gene: cd2ap has been classified as Amber List (Moderate Evidence).
Proteinuric renal disease v2.6 DGKE Catherine Snow Classified gene: DGKE as Amber List (moderate evidence)
Proteinuric renal disease v2.6 DGKE Catherine Snow Gene: dgke has been classified as Amber List (Moderate Evidence).
Monogenic hearing loss v2.8 MITF Ellen McDonagh commented on gene: MITF: There is evidence to suggest there is reduced penetrance for this gene-disease association (PMID: 26100139). Due to feedback from Rowenna Roberts at GOSH, this gene has therefore been denoted as having incomplete pentrance.
Monogenic hearing loss v2.8 MITF Ellen McDonagh Publications for gene: MITF were set to 10578055; 10587587; 10760582; 10851256; 10942418; 11331755; 11929831; 11929848; 11930005; 12032083; 12086670; 12093801; 12235125; 12668617; 13985019; 15254223; 15623583; 15716956; 16001072; 16140982; 16998588; 17182868; 18316599; 18510545; 19188590; 22012259; 22080950; 26168401; 666627; 7874158; 7874167; 7874168; 8069297; 8578601; 8589691; 8659547; 8782819; 9158138; 9499424; 9500554; 9546825; 9677380; 9856573; 27889061
Monogenic hearing loss v2.7 MITF Ellen McDonagh Source Expert was removed from MITF.
Penetrance for gene MITF was set from to Complete
Ectodermal dysplasia v1.4 KREMEN1 Zornitza Stark reviewed gene: KREMEN1: Rating: AMBER; Mode of pathogenicity: None; Publications: 29526031; Phenotypes: Ectodermal dysplasia 13, hair/tooth type, 617392; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Pain syndromes v1.9 FAAH Tomislav Kokotovic reviewed gene: FAAH: Rating: AMBER; Mode of pathogenicity: None; Publications: 30929760; Phenotypes: insensitivity to pain, increased healing; Mode of inheritance: Unknown
Pain syndromes v1.9 FAAH Tomislav Kokotovic Deleted their review
Pain syndromes v1.9 FAAH Tomislav Kokotovic gene: FAAH was added
gene: FAAH was added to Pain syndromes. Sources: Other
Mode of inheritance for gene: FAAH was set to Unknown
Publications for gene: FAAH were set to 30929760
Phenotypes for gene: FAAH were set to insensitivity to pain, healing
Review for gene: FAAH was set to AMBER
Added comment: Sources: Other
Intellectual disability v3.3 SLC5A6 Zornitza Stark reviewed gene: SLC5A6: Rating: GREEN; Mode of pathogenicity: None; Publications: 31754459, 27904971, 31392107; Phenotypes: Developmental delay, epilepsy, neurodegeneration; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 RARS Zornitza Stark reviewed gene: RARS: Rating: GREEN; Mode of pathogenicity: None; Publications: 31814314; Phenotypes: Leukodystrophy, hypomyelinating, 9 (# 616140); Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 CXorf56 Zornitza Stark reviewed gene: CXorf56: Rating: GREEN; Mode of pathogenicity: None; Publications: 29374277, 31822863; Phenotypes: Mental retardation, X-linked 107, MIM# 301013; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females; Current diagnostic: yes
Hypogonadotropic hypogonadism v1.27 KLB Rachel Jones reviewed gene: KLB: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID: 28754744; Phenotypes: hypogonadotrophic hypogonadism; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v3.3 TNR Zornitza Stark gene: TNR was added
gene: TNR was added to Intellectual disability. Sources: Expert list
Mode of inheritance for gene: TNR was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TNR were set to 32099069
Phenotypes for gene: TNR were set to Spastic para- or tetraparesis; Axial muscular hypotonia; Intellectual disability; Transient opisthotonus
Review for gene: TNR was set to GREEN
gene: TNR was marked as current diagnostic
Added comment: 13 individuals from 8 unrelated families reported.
Sources: Expert list
Intellectual disability v3.3 RUSC2 Zornitza Stark gene: RUSC2 was added
gene: RUSC2 was added to Intellectual disability. Sources: Expert list
Mode of inheritance for gene: RUSC2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RUSC2 were set to 27612186
Phenotypes for gene: RUSC2 were set to Mental retardation, autosomal recessive 61, MIM# 617773
Review for gene: RUSC2 was set to AMBER
Added comment: Two unrelated families reported.
Sources: Expert list
Intellectual disability v3.3 RUNX2 Zornitza Stark reviewed gene: RUNX2: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Cleidocranial dysplasia, MIM# 119600; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v3.3 RSRC1 Zornitza Stark gene: RSRC1 was added
gene: RSRC1 was added to Intellectual disability. Sources: Expert list
Mode of inheritance for gene: RSRC1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RSRC1 were set to 28640246; 29522154
Phenotypes for gene: RSRC1 were set to Intellectual developmental disorder, autosomal recessive 70, MIM# 618402
Review for gene: RSRC1 was set to AMBER
Added comment: Two unrelated families reported, 8 affected individuals.
Sources: Expert list
Intellectual disability v3.3 RSPO4 Zornitza Stark reviewed gene: RSPO4: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Anonychia congenita, MIM# 206800; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 RSPH3 Zornitza Stark reviewed gene: RSPH3: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Ciliary dyskinesia, primary, 32, MIM# 616481; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 RSPH1 Zornitza Stark reviewed gene: RSPH1: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Ciliary dyskinesia, primary, 24, MIM# 615481; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 RPS19 Zornitza Stark reviewed gene: RPS19: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Diamond-Blackfan anemia 1, MIM#105650; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v3.3 RPGRIP1 Zornitza Stark reviewed gene: RPGRIP1: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Cone-rod dystrophy 13, MIM# 608194, Leber congenital amaurosis 6, MIM# 613826; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 RPE65 Zornitza Stark reviewed gene: RPE65: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Leber congenital amaurosis 2, MIM# 204100, Retinitis pigmentosa 20, MIM# 613794, Retinitis pigmentosa 87 with choroidal involvement, MIM# 618697; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Intellectual disability v3.3 ROBO3 Zornitza Stark reviewed gene: ROBO3: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Gaze palsy, familial horizontal, with progressive scoliosis, 1 607313; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 RNF13 Zornitza Stark reviewed gene: RNF13: Rating: GREEN; Mode of pathogenicity: None; Publications: 30595371; Phenotypes: Epileptic encephalopathy, early infantile, 73, MIM# 618379; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted; Current diagnostic: yes
Intellectual disability v3.3 RIC1 Zornitza Stark gene: RIC1 was added
gene: RIC1 was added to Intellectual disability. Sources: Expert list
Mode of inheritance for gene: RIC1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RIC1 were set to 31932796
Phenotypes for gene: RIC1 were set to Cleft lip; cataract; tooth abnormality; intellectual disability; facial dysmorphism; ADHD
Review for gene: RIC1 was set to AMBER
Added comment: Zebrafish model and consanguineous families but homozygous-by-descent. One to watch.
Sources: Expert list
Intellectual disability v3.3 RHEB Zornitza Stark reviewed gene: RHEB: Rating: GREEN; Mode of pathogenicity: None; Publications: 29051493; Phenotypes: Intellectual disability, Macrocephaly; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted; Current diagnostic: yes
Intellectual disability v3.3 RETREG1 Zornitza Stark reviewed gene: RETREG1: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Neuropathy, hereditary sensory and autonomic, type IIB, MIM# 613115; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 MYO5B Zornitza Stark reviewed gene: MYO5B: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Microvillus inclusion disease, MIM# 251850; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 MYH9 Zornitza Stark reviewed gene: MYH9: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss, MIM# 155100; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v3.3 MYH8 Zornitza Stark reviewed gene: MYH8: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Trismus-pseudocamptodactyly syndrome, MIM# 158300; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v3.3 MYH6 Zornitza Stark reviewed gene: MYH6: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: {Sick sinus syndrome 3} 614090 3 Atrial septal defect 3, MIM# 614089, Cardiomyopathy, dilated, 1EE, MIM# 613252, Cardiomyopathy, hypertrophic, 14, MIM# 613251; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v3.3 MTHFS Zornitza Stark reviewed gene: MTHFS: Rating: GREEN; Mode of pathogenicity: None; Publications: 30031689, 31844630, 22303332; Phenotypes: Neurodevelopmental disorder with microcephaly, epilepsy, and hypomyelination, 618367; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
Intellectual disability v3.3 MSX2 Zornitza Stark reviewed gene: MSX2: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Craniosynostosis 2, MIM# 604757, Parietal foramina 1, MIM# 168500, Parietal foramina with cleidocranial dysplasia, MIM# 168550; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v3.3 MSX1 Zornitza Stark reviewed gene: MSX1: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Ectodermal dysplasia 3, Witkop type 189500, Orofacial cleft 5 608874, Tooth agenesis, selective, 1, with or without orofacial cleft 106600; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v3.3 MPV17 Zornitza Stark reviewed gene: MPV17: Rating: GREEN; Mode of pathogenicity: None; Publications: 22593919; Phenotypes: Mitochondrial DNA depletion syndrome 6 (hepatocerebral type), OMIM #256810; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
Intellectual disability v3.3 MNX1 Zornitza Stark reviewed gene: MNX1: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Currarino syndrome, OMIM #176450; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v3.3 MN1 Zornitza Stark reviewed gene: MN1: Rating: GREEN; Mode of pathogenicity: None; Publications: 31834374, 31839203; Phenotypes: Intellectual disability, dysmophic features, rhombencephalosynapsis; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
Intellectual disability v3.3 MMP13 Zornitza Stark reviewed gene: MMP13: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Metaphyseal anadysplasia 1, MIM# 602111, Metaphyseal dysplasia, Spahr type, MIM# 250400, Spondyloepimetaphyseal dysplasia, Missouri type, MIM# 602111; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Intellectual disability v3.3 MGP Zornitza Stark reviewed gene: MGP: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Keutel syndrome, MIM# 245150; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 MFSD2A Zornitza Stark reviewed gene: MFSD2A: Rating: GREEN; Mode of pathogenicity: None; Publications: 26005865, 26005868, 24828044; Phenotypes: Microcephaly 15, primary, autosomal recessive, MIM# 616486; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 MFRP Zornitza Stark reviewed gene: MFRP: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Microphthalmia, isolated 5, MIM# 611040; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 METTL5 Zornitza Stark reviewed gene: METTL5: Rating: GREEN; Mode of pathogenicity: None; Publications: 29302074, 31564433; Phenotypes: Intellectual developmental disorder, autosomal recessive 72, MIM# 618665; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
Intellectual disability v3.3 MESP2 Zornitza Stark reviewed gene: MESP2: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Spondylocostal dysostosis 2, autosomal recessive, MIM# 608681; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 MC2R Zornitza Stark reviewed gene: MC2R: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Glucocorticoid deficiency, due to ACTH unresponsiveness, MIM# 202200; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 MATN3 Zornitza Stark reviewed gene: MATN3: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Spondyloepimetaphyseal dysplasia 608728, {Osteoarthritis susceptibility 2} 140600, Epiphyseal dysplasia, multiple, 5 607078; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Intellectual disability v3.3 MAPRE2 Zornitza Stark reviewed gene: MAPRE2: Rating: GREEN; Mode of pathogenicity: None; Publications: 26637975; Phenotypes: Symmetric circumferential skin creases, congenital, 2, MIM# 616734; Mode of inheritance: BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
Intellectual disability v3.3 MAPK10 Zornitza Stark reviewed gene: MAPK10: Rating: RED; Mode of pathogenicity: None; Publications: 23329067, 16249883; Phenotypes: Intellectual disability, seizures; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v3.3 MAP3K1 Zornitza Stark reviewed gene: MAP3K1: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: 46XY sex reversal 6, MIM# 613762; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v3.3 MAP1B Zornitza Stark reviewed gene: MAP1B: Rating: GREEN; Mode of pathogenicity: None; Publications: 31317654, 30150678, 30214071; Phenotypes: Intellectual disability, seizures, PVNH, dysmorphic features; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted; Current diagnostic: yes
Intellectual disability v3.3 MADD Zornitza Stark reviewed gene: MADD: Rating: GREEN; Mode of pathogenicity: None; Publications: 28940097; Phenotypes: Intellectual disability; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
Intellectual disability v3.3 NUP214 Zornitza Stark gene: NUP214 was added
gene: NUP214 was added to Intellectual disability. Sources: Expert list
Mode of inheritance for gene: NUP214 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: NUP214 were set to 31178128
Phenotypes for gene: NUP214 were set to developmental delay; intellectual disability; epileptic encephalopathy; developmental regression; microcephaly
Review for gene: NUP214 was set to GREEN
gene: NUP214 was marked as current diagnostic
Added comment: Three unrelated families reported, regression on background of pre-existing neurodisability.
Sources: Expert list
Intellectual disability v3.3 NUP107 Zornitza Stark reviewed gene: NUP107: Rating: AMBER; Mode of pathogenicity: None; Publications: ; Phenotypes: Galloway-Mowat syndrome 7, MIM# 618348, Nephrotic syndrome, type 11, MIM# 616730; Mode of inheritance: None
Intellectual disability v3.3 NRXN2 Zornitza Stark edited their review of gene: NRXN2: Added comment: One individual reported with autism and a paternally inherited variant in this gene, father had a language disorder. Another infant reported with severe EE and a maternally inherited variants in NRXN1 and a paternally inherited variant in NRXN2. Some animal data.; Changed publications: 21424692, 30709877, 25745399; Changed phenotypes: Autism
Intellectual disability v3.3 NR5A1 Zornitza Stark reviewed gene: NR5A1: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: 46XY sex reversal 3, 612965, Premature ovarian failure 7, 612964, Adrenocortical insufficiency, Spermatogenic failure 8, 613957; Mode of inheritance: None
Intellectual disability v3.3 NR2F2 Zornitza Stark reviewed gene: NR2F2: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Congenital heart defects, multiple types, 4, MIM# 615779; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v3.3 NPR2 Zornitza Stark reviewed gene: NPR2: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Acromesomelic dysplasia, Maroteaux type, MIM# 602875, Epiphyseal chondrodysplasia, Miura type MIM#615923, Short stature with nonspecific skeletal abnormalities 616255; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Intellectual disability v3.3 NPHS1 Zornitza Stark reviewed gene: NPHS1: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Nephrotic syndrome, type 1, MIM# 256300; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 NPHP4 Zornitza Stark reviewed gene: NPHP4: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Nephronophthisis 4, MIM# 606966, Senior-Loken syndrome 4, MIM# 606996; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 NPHP3 Zornitza Stark reviewed gene: NPHP3: Rating: GREEN; Mode of pathogenicity: None; Publications: 18371931; Phenotypes: Meckel syndrome 7, MIM# 267010; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 NOTCH2 Zornitza Stark reviewed gene: NOTCH2: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Alagille syndrome 2, MIM#610205, Hajdu-Cheney syndrome, MIM#102500; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v3.3 NOG Zornitza Stark reviewed gene: NOG: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Brachydactyly, type B2, MIM# 611377, Multiple synostoses syndrome 1, MIM# 186500, Stapes ankylosis with broad thumbs and toes, MIM# 184460, Symphalangism, proximal, 1A, MIM# 185800, Tarsal-carpal coalition syndrome, MIM# 186570; Mode of inheritance: None
Intellectual disability v3.3 NODAL Zornitza Stark reviewed gene: NODAL: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Heterotaxy, visceral, 5, MIM# 270100; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v3.3 NMNAT1 Zornitza Stark reviewed gene: NMNAT1: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Leber congenital amaurosis 9, MIM# 608553; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 NKX3-2 Zornitza Stark reviewed gene: NKX3-2: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Spondylo-megaepiphyseal-metaphyseal dysplasia, MIM# 613330; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 NHP2 Zornitza Stark reviewed gene: NHP2: Rating: AMBER; Mode of pathogenicity: None; Publications: 18523010, 31985013; Phenotypes: Dyskeratosis congenita, autosomal recessive 2, MIM# 613987, Høyeraal-Hreidarsson syndrome; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 NHEJ1 Zornitza Stark reviewed gene: NHEJ1: Rating: RED; Mode of pathogenicity: None; Publications: 16439204; Phenotypes: Severe combined immunodeficiency with microcephaly, growth retardation, and sensitivity to ionizing radiation; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 NGF Zornitza Stark reviewed gene: NGF: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Neuropathy, hereditary sensory and autonomic, type V, MIM# 608654; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 NEK1 Zornitza Stark reviewed gene: NEK1: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Short-rib thoracic dysplasia 6 with or without polydactyly, MIM# 263520; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Intellectual disability v3.3 NEDD4L Zornitza Stark reviewed gene: NEDD4L: Rating: GREEN; Mode of pathogenicity: None; Publications: 27694961; Phenotypes: Periventricular nodular heterotopia 7, MIM#617201; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted; Current diagnostic: yes
Intellectual disability v3.3 NDUFAF1 Zornitza Stark gene: NDUFAF1 was added
gene: NDUFAF1 was added to Intellectual disability. Sources: Expert list
Mode of inheritance for gene: NDUFAF1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: NDUFAF1 were set to 17557076; 21931170; 24963768
Phenotypes for gene: NDUFAF1 were set to Mitochondrial complex I deficiency, nuclear type 11, MIM#618234
Review for gene: NDUFAF1 was set to GREEN
gene: NDUFAF1 was marked as current diagnostic
Added comment: Three unrelated families described, DD/ID part of the phenotype, specifically mentioned in two families, child in third family died in infancy from HOCM.
Sources: Expert list
Cardiac arrhythmias v6.28 Sarah Leigh Panel version has been signed off
Hypotonic infant v9.42 Sarah Leigh Panel version has been signed off
Paediatric disorders v14.44 Sarah Leigh Panel version has been signed off
Childhood onset leukodystrophy v6.21 Eleanor Williams Panel version has been signed off
Cerebral malformation v5.18 Catherine Snow Panel version has been signed off
Hereditary ataxia and cerebellar anomalies - childhood onset v6.20 Catherine Snow Panel version has been signed off
Rare multisystem ciliopathy Super panel v4.22 Ellen McDonagh Panel version has been signed off
Cystic renal disease v3.20 Eleanor Williams Panel version has been signed off
Sudden unexplained death or survivors of a cardiac event v9.33 Ellen McDonagh Panel version has been signed off
Other rare neuromuscular disorders v5.44 Catherine Snow Panel version has been signed off
Intestinal failure or congenital diarrhoea v1.3 Ellen McDonagh Panel version has been signed off
Membranoproliferative glomerulonephritis including C3 glomerulopathy v2.4 Eleanor Williams Panel version has been signed off
Structural eye disease v1.4 Eleanor Williams Panel version has been signed off
Structural eye disease v1.3 Eleanor Williams Panel types changed to GMS Rare Disease Virtual; GMS Rare Disease; GMS signed-off
Polycystic liver disease v1.5 Catherine Snow Panel version has been signed off
Polycystic liver disease v1.4 Catherine Snow Panel types changed to GMS Rare Disease Virtual; GMS Rare Disease; GMS signed-off
Familial rhabdoid tumours v1.3 Catherine Snow Panel version has been signed off
Inherited pancreatic cancer v1.3 Catherine Snow Panel version has been signed off
Inherited predisposition to GIST v1.3 Catherine Snow Panel version has been signed off
Familial melanoma v1.3 Catherine Snow Panel version has been signed off
Haematuria v2.4 Eleanor Williams Panel version has been signed off
Haematuria v2.3 Eleanor Williams Panel version has been signed off
Cardiac arrhythmias - additional genes v1.7 Catherine Snow Panel version has been signed off
Neurological ciliopathies v1.6 Catherine Snow Panel version has been signed off
Neurological ciliopathies v1.5 Catherine Snow Panel types changed to GMS Rare Disease; Component Of Super Panel; GMS signed-off
Neurological segmental overgrowth v1.5 Catherine Snow Panel version has been signed off
Neurological segmental overgrowth v1.4 Catherine Snow Panel types changed to GMS Rare Disease; Component Of Super Panel; GMS signed-off
Hereditary ataxia with onset in adulthood v2.5 Catherine Snow Panel version has been signed off
Hereditary ataxia with onset in adulthood v2.4 Catherine Snow Panel types changed to GMS Rare Disease; GMS signed-off
Congenital disorders of glycosylation v2.5 Catherine Snow Panel version has been signed off
Congenital disorders of glycosylation v2.4 Catherine Snow Panel types changed to Rare Disease 100K; GMS Rare Disease; Component Of Super Panel; GMS signed-off
Paediatric motor neuronopathies v1.31 Catherine Snow Panel version has been signed off
Paediatric motor neuronopathies v1.30 Catherine Snow Panel types changed to Rare Disease 100K; GMS Rare Disease; Component Of Super Panel; GMS signed-off
Rhabdomyolysis and metabolic muscle disorders v1.36 Catherine Snow Panel version has been signed off
Rhabdomyolysis and metabolic muscle disorders v1.34 Catherine Snow Panel types changed to Rare Disease 100K; GMS Rare Disease; Component Of Super Panel; GMS signed-off
Renal ciliopathies v1.3 Eleanor Williams Panel version has been signed off
Renal ciliopathies v1.2 Eleanor Williams Panel types changed to GMS Rare Disease; Component Of Super Panel; GMS signed-off
Hypogonadotropic hypogonadism (GMS) v1.5 Ellen McDonagh Panel version has been signed off
Inherited renal cancer v1.3 Catherine Snow Panel version has been signed off
Inherited polyposis and early onset colorectal cancer - germline testing v1.3 Catherine Snow Panel version has been signed off
Inherited MMR deficiency (Lynch syndrome) v1.3 Catherine Snow Panel version has been signed off
Unexplained young onset end-stage renal disease v1.3 Eleanor Williams Panel version has been signed off
Pneumothorax - familial v2.20 Ellen McDonagh Panel version has been signed off
Unexplained young onset end-stage renal disease v1.2 Eleanor Williams Panel types changed to GMS Rare Disease Virtual; GMS Rare Disease; GMS signed-off
Pneumothorax - familial v2.19 Ellen McDonagh Panel version has been signed off
Pneumothorax - familial v2.18 Ellen McDonagh Panel version has been signed off
Inherited ovarian cancer (without breast cancer) v2.3 Catherine Snow Panel version has been signed off
Tubulointerstitial kidney disease v1.4 Eleanor Williams Panel version has been signed off
Tubulointerstitial kidney disease v1.3 Eleanor Williams Panel version has been signed off
Clefting v2.3 Eleanor Williams Panel version has been signed off
Ehlers Danlos syndrome with a likely monogenic cause v2.4 Eleanor Williams Panel version has been signed off
Ehlers Danlos syndrome with a likely monogenic cause v2.3 Eleanor Williams Panel types changed to Rare Disease 100K; GMS Rare Disease Virtual; GMS Rare Disease; GMS signed-off
Inherited breast cancer and ovarian cancer v0.7 Ellen McDonagh Panel status changed from public to internal
Childhood solid tumours v2.6 Eleanor Williams Panel version has been signed off
Childhood solid tumours v2.5 RET Eleanor Williams Added comment: Comment on mode of pathogenicity: Updating the mode of pathogenicity in line with the Adult solid tumours cancer susceptibility panel https://panelapp.genomicsengland.co.uk/panels/245/
Childhood solid tumours v2.5 RET Eleanor Williams Mode of pathogenicity for gene: RET was changed from to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
Intellectual disability v3.3 NDUFA2 Zornitza Stark gene: NDUFA2 was added
gene: NDUFA2 was added to Intellectual disability. Sources: Expert list
Mode of inheritance for gene: NDUFA2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: NDUFA2 were set to 18513682; 28857146
Phenotypes for gene: NDUFA2 were set to Mitochondrial complex I deficiency, nuclear type 13, MIM#618235
Review for gene: NDUFA2 was set to GREEN
gene: NDUFA2 was marked as current diagnostic
Added comment: Three unrelated families reported, DD/IDD in all.
Sources: Expert list
Intellectual disability v3.3 NCAPG2 Zornitza Stark gene: NCAPG2 was added
gene: NCAPG2 was added to Intellectual disability. Sources: Expert list
Mode of inheritance for gene: NCAPG2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: NCAPG2 were set to 30609410
Phenotypes for gene: NCAPG2 were set to Khan-Khan-Katsanis syndrome, MIM# 618460
Review for gene: NCAPG2 was set to GREEN
gene: NCAPG2 was marked as current diagnostic
Added comment: Two unrelated families and an animal model (zebrafish).
Sources: Expert list
Intellectual disability v3.3 NCAPD2 Zornitza Stark gene: NCAPD2 was added
gene: NCAPD2 was added to Intellectual disability. Sources: Expert list
Mode of inheritance for gene: NCAPD2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: NCAPD2 were set to 31056748; 27737959; 28097321
Phenotypes for gene: NCAPD2 were set to Microcephaly 21, primary, autosomal recessive, OMIM #617983
Review for gene: NCAPD2 was set to GREEN
gene: NCAPD2 was marked as current diagnostic
Added comment: 5 individuals from three unrelated families reported, some functional evidence.
Sources: Expert list
Intellectual disability v3.3 ZNF335 Zornitza Stark reviewed gene: ZNF335: Rating: GREEN; Mode of pathogenicity: None; Publications: 23178126, 27540107, 29652087; Phenotypes: Microcephaly 10, primary, autosomal recessive, OMIM #615095; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 ZNF148 Zornitza Stark reviewed gene: ZNF148: Rating: GREEN; Mode of pathogenicity: None; Publications: 27964749; Phenotypes: Global developmental delay, absent or hypoplastic corpus callosum, and dysmorphic facies, 617260; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted; Current diagnostic: yes
Intellectual disability v3.3 ZMPSTE24 Zornitza Stark reviewed gene: ZMPSTE24: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Mandibuloacral dysplasia with type B lipodystrophy, MIM# 608612, Restrictive dermopathy, lethal, MIM# 275210; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 ZIC3 Zornitza Stark reviewed gene: ZIC3: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Heterotaxy, visceral, 1, X-linked 306955, Congenital heart defects, nonsyndromic, 1, X-linked, 306955, VACTERL association, X-linked, 314390; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females
Intellectual disability v3.3 ZIC1 Zornitza Stark reviewed gene: ZIC1: Rating: GREEN; Mode of pathogenicity: None; Publications: 26340333, 30391508; Phenotypes: Structural brain anomalies with impaired intellectual development and craniosynostosis, OMIM #618736; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted; Current diagnostic: yes
Intellectual disability v3.3 XYLT1 Zornitza Stark reviewed gene: XYLT1: Rating: GREEN; Mode of pathogenicity: None; Publications: 24581741, 22711505, 23982343; Phenotypes: Desbuquois dysplasia 2, OMIM# 615777; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 XPC Zornitza Stark reviewed gene: XPC: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Xeroderma pigmentosum, group C, MIM# 278720; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 WRAP53 Zornitza Stark reviewed gene: WRAP53: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Dyskeratosis congenita, autosomal recessive 3, OMIM# 613988; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 WNT7A Zornitza Stark reviewed gene: WNT7A: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Fuhrmann syndrome, MIM# 228930, Ulna and fibula, absence of, with severe limb deficiency, MIM# 276820; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 WNT5A Zornitza Stark reviewed gene: WNT5A: Rating: AMBER; Mode of pathogenicity: None; Publications: 17256787; Phenotypes: Robinow syndrome, autosomal dominant 1, OMIM# 180700; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v3.3 WNT3 Zornitza Stark reviewed gene: WNT3: Rating: RED; Mode of pathogenicity: None; Publications: 14872406; Phenotypes: Tetra-amelia syndrome 1, MIM# 273395; Mode of inheritance: None
Intellectual disability v3.3 WNT10B Zornitza Stark reviewed gene: WNT10B: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Split-hand/foot malformation 6, MIM#225300; Mode of inheritance: None
Intellectual disability v3.3 WNT1 Zornitza Stark reviewed gene: WNT1: Rating: GREEN; Mode of pathogenicity: None; Publications: 26671912; Phenotypes: Osteogenesis imperfecta, type XV, OMIM# 615220; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 WFS1 Zornitza Stark reviewed gene: WFS1: Rating: AMBER; Mode of pathogenicity: None; Publications: ; Phenotypes: Wolfram syndrome 1, MIM# 222300, Wolfram-like syndrome, autosomal dominant, MIM# 614296; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Intellectual disability v3.3 WDR35 Zornitza Stark reviewed gene: WDR35: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Intellectual disability v3.3 WDR34 Zornitza Stark reviewed gene: WDR34: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Bleeding and platelet disorders v1.3 Catherine Snow Panel version has been signed off
Bleeding and platelet disorders v1.2 Catherine Snow Panel types changed to GMS Rare Disease Virtual; GMS Rare Disease; GMS signed-off
Inherited predisposition to acute myeloid leukaemia (AML) v1.3 Catherine Snow Panel version has been signed off
Cytopenia - NOT Fanconi anaemia v1.3 Catherine Snow Panel version has been signed off
Cytopenia - NOT Fanconi anaemia v1.2 Catherine Snow Panel types changed to GMS Rare Disease Virtual; GMS Rare Disease; GMS signed-off
Rare anaemia v1.3 Catherine Snow Panel version has been signed off
Rare anaemia v1.2 Catherine Snow Panel types changed to GMS Rare Disease Virtual; GMS Rare Disease; GMS signed-off
Combined factor V and VIII deficiency v1.3 Catherine Snow Panel version has been signed off
Thrombophilia with a likely monogenic cause v1.3 Catherine Snow Panel version has been signed off
Thrombophilia with a likely monogenic cause v1.2 Catherine Snow Panel types changed to GMS Rare Disease Virtual; GMS Rare Disease; GMS signed-off
Iron metabolism disorders - NOT common HFE mutations v1.3 Catherine Snow Panel version has been signed off
Iron metabolism disorders - NOT common HFE mutations v1.2 Catherine Snow Panel types changed to GMS Rare Disease Virtual; GMS Rare Disease; GMS signed-off
Confirmed Fanconi anaemia or Bloom syndrome v1.3 Catherine Snow Panel version has been signed off
Non-acute porphyrias v1.3 Catherine Snow Panel version has been signed off
Pancreatitis v2.3 Catherine Snow Panel version has been signed off
Pancreatitis v2.2 Catherine Snow Panel types changed to Rare Disease 100K; GMS Rare Disease Virtual; GMS Rare Disease; GMS signed-off
Congenital fibrosis of the extraocular muscles v1.3 Catherine Snow Panel version has been signed off
Congenital fibrosis of the extraocular muscles v1.2 Catherine Snow Panel types changed to GMS Rare Disease Virtual; GMS Rare Disease; GMS signed-off
Albinism or congenital nystagmus v1.3 Catherine Snow Panel version has been signed off
Albinism or congenital nystagmus v1.2 Catherine Snow Panel types changed to GMS Rare Disease Virtual; GMS Rare Disease; GMS signed-off
Sporadic aniridia v2.3 Catherine Snow Panel version has been signed off
Differences in sex development v2.3 Catherine Snow Panel version has been signed off
Pituitary hormone deficiency v2.3 Catherine Snow Panel version has been signed off
Hypophosphataemia or rickets v2.3 Catherine Snow Panel version has been signed off
Familial hyperparathyroidism or hypocalciuric hypercalcaemia v2.4 Catherine Snow Panel version has been signed off
Inherited breast cancer and ovarian cancer v0.5 Ellen McDonagh Panel status changed from internal to public
Inherited breast cancer and ovarian cancer v0.4 Ellen McDonagh List of related panels changed from to R208
Adult onset neurodegenerative disorder v2.3 APP alisdair mcneill reviewed gene: APP: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Cardiac arrhythmias - additional genes v1.5 Catherine Snow Panel version has been signed off
Cardiac arrhythmias - additional genes v1.4 Catherine Snow Panel types changed to Component Of Super Panel; GMS signed-off
Long QT syndrome v2.4 Catherine Snow Panel version has been signed off
Long QT syndrome v2.3 Catherine Snow Panel types changed to Rare Disease 100K; GMS Rare Disease; Component Of Super Panel; GMS signed-off
Primary lymphoedema v2.3 Catherine Snow Panel version has been signed off
Progressive cardiac conduction disease v1.3 Catherine Snow Panel version has been signed off
Progressive cardiac conduction disease v1.2 Catherine Snow Panel types changed to GMS Rare Disease; Component Of Super Panel; GMS signed-off
Hypertrophic cardiomyopathy v2.3 Catherine Snow Panel version has been signed off
Hypertrophic cardiomyopathy v2.2 Catherine Snow Panel types changed to Rare Disease 100K; GMS Rare Disease; Component Of Super Panel; GMS signed-off
Hereditary haemorrhagic telangiectasia v2.3 Catherine Snow Panel version has been signed off
Hereditary haemorrhagic telangiectasia v2.2 Catherine Snow Panel types changed to Rare Disease 100K; GMS Rare Disease Virtual; GMS Rare Disease; GMS signed-off
Pulmonary arterial hypertension v2.3 Catherine Snow Panel version has been signed off
Pulmonary arterial hypertension v2.2 Catherine Snow Panel types changed to Rare Disease 100K; GMS Rare Disease Virtual; GMS Rare Disease; GMS signed-off
Laterality disorders and isomerism v1.4 Catherine Snow Panel version has been signed off
Laterality disorders and isomerism v1.3 Catherine Snow Panel version has been signed off
Respiratory ciliopathies including non-CF bronchiectasis v1.4 Catherine Snow Panel version has been signed off
Respiratory ciliopathies including non-CF bronchiectasis v1.3 Catherine Snow Panel types changed to GMS Rare Disease Virtual; GMS Rare Disease; GMS signed-off
Surfactant deficiency v1.3 Catherine Snow Panel version has been signed off
Surfactant deficiency v1.2 Catherine Snow Panel types changed to GMS Rare Disease Virtual; GMS Rare Disease; GMS signed-off
Cerebral vascular malformations v2.3 Catherine Snow Panel version has been signed off
Severe microcephaly v2.3 Catherine Snow Panel version has been signed off
Hydrocephalus v2.4 Catherine Snow Panel version has been signed off
Limb girdle muscular dystrophies, myofibrillar myopathies and distal myopathies v2.5 Catherine Snow Panel version has been signed off
Limb girdle muscular dystrophies, myofibrillar myopathies and distal myopathies v2.4 Catherine Snow Panel types changed to Rare Disease 100K; GMS Rare Disease; Component Of Super Panel; GMS signed-off
Congenital muscular dystrophy v2.3 Catherine Snow Panel version has been signed off
Congenital muscular dystrophy v2.2 Catherine Snow Panel types changed to Rare Disease 100K; GMS Rare Disease; Component Of Super Panel; GMS signed-off
Congenital myopathy v2.3 Catherine Snow Panel version has been signed off
Congenital myopathy v2.2 Catherine Snow Panel types changed to Rare Disease 100K; GMS Rare Disease; Component Of Super Panel; GMS signed-off
Congenital myaesthenic syndrome v2.3 Catherine Snow Panel version has been signed off
Congenital myaesthenic syndrome v2.2 Catherine Snow Panel types changed to Rare Disease 100K; GMS Rare Disease; Component Of Super Panel; GMS signed-off
Distal myopathies v1.19 Catherine Snow Panel version has been signed off
Distal myopathies v1.19 Catherine Snow Panel version has been signed off
Congenital disorders of glycosylation v2.3 Catherine Snow Panel version has been signed off
Congenital disorders of glycosylation v2.2 Catherine Snow Panel types changed to Rare Disease 100K; Component Of Super Panel; GMS signed-off
Hereditary ataxia with onset in adulthood v2.3 Catherine Snow Panel version has been signed off
Hereditary ataxia with onset in adulthood v2.2 Catherine Snow Panel types changed to GMS signed-off
Adult onset neurodegenerative disorder v2.3 Catherine Snow Panel version has been signed off
Adult onset neurodegenerative disorder v2.2 Catherine Snow Panel types changed to GMS Rare Disease Virtual; GMS Rare Disease; GMS signed-off
White matter disorders and cerebral calcification - narrow panel v1.13 Catherine Snow Panel version has been signed off
White matter disorders and cerebral calcification - narrow panel v1.12 Catherine Snow Panel types changed to GMS Rare Disease; Component Of Super Panel; GMS signed-off
Ataxia and cerebellar anomalies - narrow panel v2.3 Catherine Snow Panel version has been signed off
Ataxia and cerebellar anomalies - narrow panel v2.2 Catherine Snow Panel types changed to GMS Rare Disease; Component Of Super Panel; GMS signed-off
Adult onset dystonia, chorea or related movement disorder v1.4 Catherine Snow Panel version has been signed off
Adult onset dystonia, chorea or related movement disorder v1.3 Catherine Snow Panel version has been signed off
Skeletal muscle channelopathy v1.3 Catherine Snow Panel version has been signed off
Skeletal muscle channelopathy v1.2 Catherine Snow Panel types changed to GMS Rare Disease Virtual; GMS Rare Disease; GMS signed-off
Adult onset hereditary spastic paraplegia v1.4 Catherine Snow Panel version has been signed off
Childhood onset hereditary spastic paraplegia v2.10 Catherine Snow Panel version has been signed off
Childhood onset hereditary spastic paraplegia v2.9 Catherine Snow Panel version has been signed off
Intellectual disability v3.3 WDR19 Zornitza Stark reviewed gene: WDR19: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Short-rib thoracic dysplasia 5 with or without polydactyly, OMIM #614376, Nephronophthisis 13, OMIM #614377, Senior-Loken syndrome 8, OMIM#616307; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 WDFY3 Zornitza Stark edited their review of gene: WDFY3: Added comment: >10 individuals with heterozygous variants in this gene and mild/moderate intellectual disability now described in the literature. Some evidence for opposing effects on brain size depending on variant location.; Changed rating: GREEN; Changed publications: 31327001, 27008544; Set current diagnostic: yes
Intellectual disability v3.3 VSX2 Zornitza Stark reviewed gene: VSX2: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Microphthalmia with coloboma 3, MIM# 610092, Microphthalmia, isolated 2, MIM# 610093; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Intellectual disability v3.3 VARS2 Zornitza Stark gene: VARS2 was added
gene: VARS2 was added to Intellectual disability. Sources: Expert list
Mode of inheritance for gene: VARS2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: VARS2 were set to 24827421; 25058219; 29137650; 29314548; 31064326
Phenotypes for gene: VARS2 were set to Combined oxidative phosphorylation deficiency 20, OMIM #615917
Review for gene: VARS2 was set to GREEN
gene: VARS2 was marked as current diagnostic
Added comment: ID is part of the phenotype of this metabolic disorder.
Sources: Expert list
Intellectual disability v3.3 VAMP1 Zornitza Stark reviewed gene: VAMP1: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Myasthenic syndrome, congenital, 25, MIM# 618323; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 UVSSA Zornitza Stark reviewed gene: UVSSA: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: UV-sensitive syndrome 3 614640; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 USP7 Zornitza Stark reviewed gene: USP7: Rating: GREEN; Mode of pathogenicity: None; Publications: 30679821; Phenotypes: ID, Autism; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted; Current diagnostic: yes
Intellectual disability v3.3 USP18 Zornitza Stark reviewed gene: USP18: Rating: GREEN; Mode of pathogenicity: None; Publications: 31940699, 12833411, 27325888; Phenotypes: Pseudo-TORCH syndrome 2, OMIM #617397; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 USB1 Zornitza Stark reviewed gene: USB1: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Poikiloderma with neutropenia, MIM# 604173; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 UROS Zornitza Stark reviewed gene: UROS: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Porphyria, congenital erythropoietic, MIM# 263700; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 UGT1A1 Zornitza Stark reviewed gene: UGT1A1: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Crigler-Najjar syndrome, type I, OMIM #218800, Crigler-Najjar syndrome, type II, OMIM #606785; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 UGP2 Zornitza Stark reviewed gene: UGP2: Rating: GREEN; Mode of pathogenicity: None; Publications: 31820119; Phenotypes: Epileptic encephalopathy, intellectual disability, microcephaly; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 TYRP1 Zornitza Stark reviewed gene: TYRP1: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Albinism, oculocutaneous, type III, 203290; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 TYR Zornitza Stark reviewed gene: TYR: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Albinism, oculocutaneous, type IA, 203100; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 TXNL4A Zornitza Stark reviewed gene: TXNL4A: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Burn-McKeown syndrome, MIM# 608572; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 TUBGCP2 Zornitza Stark gene: TUBGCP2 was added
gene: TUBGCP2 was added to Intellectual disability. Sources: Expert list
Mode of inheritance for gene: TUBGCP2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TUBGCP2 were set to 31630790
Phenotypes for gene: TUBGCP2 were set to Lissencephaly; pachygyria; subcortical band heterotopia; microcephaly; intellectual disability
Review for gene: TUBGCP2 was set to GREEN
gene: TUBGCP2 was marked as current diagnostic
Added comment: Four unrelated families reported.
Sources: Expert list
Fetal anomalies v1.3 TUBA8 Zornitza Stark reviewed gene: TUBA8: Rating: RED; Mode of pathogenicity: None; Publications: 19896110, 31481326, 28388629; Phenotypes: Cortical dysplasia, complex, with other brain malformations 8, MIM# 613180; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 TUBA8 Zornitza Stark reviewed gene: TUBA8: Rating: RED; Mode of pathogenicity: None; Publications: 19896110, 31481326, 28388629; Phenotypes: Cortical dysplasia, complex, with other brain malformations 8, MIM# 613180; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 TSHR Zornitza Stark reviewed gene: TSHR: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Hypothyroidism, congenital, nongoitrous, 1, MIM# 275200; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 TRPV4 Zornitza Stark reviewed gene: TRPV4: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Intellectual disability v3.3 TRPS1 Zornitza Stark reviewed gene: TRPS1: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Trichorhinophalangeal syndrome, type I (MIM 190350), Trichorhinophalangeal syndrome, type III (MIM 190351); Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Rare anaemia v1.1 RPL26 Zornitza Stark reviewed gene: RPL26: Rating: RED; Mode of pathogenicity: None; Publications: 22431104; Phenotypes: Diamond-Blackfan anemia 11, MIM# 614900; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v3.3 TRPM3 Zornitza Stark reviewed gene: TRPM3: Rating: GREEN; Mode of pathogenicity: None; Publications: 31278393; Phenotypes: Intellectual disability, epilepsy; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v3.3 TRPM1 Zornitza Stark reviewed gene: TRPM1: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Night blindness, congenital stationary (complete), 1C, autosomal recessive, MIM# 613216; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 TRNT1 Zornitza Stark gene: TRNT1 was added
gene: TRNT1 was added to Intellectual disability. Sources: Expert list
Mode of inheritance for gene: TRNT1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TRNT1 were set to 25193871; 23553769; 29170023; 27389523
Phenotypes for gene: TRNT1 were set to Sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay, OMIM #616084
Review for gene: TRNT1 was set to GREEN
gene: TRNT1 was marked as current diagnostic
Added comment: > 10 families reported with congenital sideroblastic anemia, B-cell deficiency, periodic fevers, and variable degrees of delayed psychomotor development.
Sources: Expert list
Intellectual disability v3.3 TRIP11 Zornitza Stark reviewed gene: TRIP11: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Achondrogenesis, type IA, MIM# 200600, Osteochondrodysplasia, MIM# 184260; Mode of inheritance: None
Intellectual disability v3.3 TRIM32 Zornitza Stark reviewed gene: TRIM32: Rating: RED; Mode of pathogenicity: None; Publications: 16606853; Phenotypes: Bardet-Biedl syndrome 11, MIM# 615988; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 TRAPPC4 Zornitza Stark reviewed gene: TRAPPC4: Rating: GREEN; Mode of pathogenicity: None; Publications: 31794024; Phenotypes: intellectual disability, epilepsy, spasticity, microcephaly; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 TRAPPC2 Zornitza Stark reviewed gene: TRAPPC2: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Spondyloepiphyseal dysplasia tarda, MIM# 313400; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females
Intellectual disability v3.3 TRAK1 Zornitza Stark reviewed gene: TRAK1: Rating: GREEN; Mode of pathogenicity: None; Publications: 28940097, 28364549, 29846532; Phenotypes: Epileptic encephalopathy, early infantile, 68, MIM# 618201; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 TP73 Zornitza Stark gene: TP73 was added
gene: TP73 was added to Intellectual disability. Sources: Expert list
Mode of inheritance for gene: TP73 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TP73 were set to 31130284
Phenotypes for gene: TP73 were set to Intellectual disability; lissencephaly
Review for gene: TP73 was set to AMBER
Added comment: Two unrelated families, no functional data.
Sources: Expert list
Intellectual disability v3.3 TP63 Zornitza Stark reviewed gene: TP63: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ADULT syndrome, OMIM #103285, Ectrodactyly, ectodermal dysplasia, and cleft lip/palate syndrome 3, OMIM #604292, Hay-Wells syndrome, OMIM #106260, Limb-mammary syndrome, OMIM #603543, Orofacial cleft 8, OMIM #618149, Rapp-Hodgkin syndrome, OMIM #129400, Split-hand/foot malformation 4, OMIM #605289; Mode of inheritance: None
Intellectual disability v3.3 SPOP Zornitza Stark gene: SPOP was added
gene: SPOP was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: SPOP was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: SPOP were set to 32109420
Phenotypes for gene: SPOP were set to Intellectual disability; dysmorphism; microcephaly; macrocephaly
Mode of pathogenicity for gene: SPOP was set to Other
Review for gene: SPOP was set to GREEN
gene: SPOP was marked as current diagnostic
Added comment: Seven individuals reported with de novo missense variants in this gene. Gain-of-function variants associated with microcephaly whereas dominant-negative variants associated with macrocephaly.
Sources: Literature
Intellectual disability v3.3 TMPRSS6 Zornitza Stark reviewed gene: TMPRSS6: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Iron-refractory iron deficiency anemia 206200; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 TMEM126B Zornitza Stark reviewed gene: TMEM126B: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Mitochondrial complex I deficiency, nuclear type 29, MIM# 618250; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 TINF2 Zornitza Stark reviewed gene: TINF2: Rating: GREEN; Mode of pathogenicity: None; Publications: 1404302, 18252230, 21477109; Phenotypes: Revesz syndrome, MIM# 268130; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted; Current diagnostic: yes
Intellectual disability v3.3 TGFB3 Zornitza Stark reviewed gene: TGFB3: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Arrhythmogenic right ventricular dysplasia 1, MIM# 107970, Loeys-Dietz syndrome 5, MIM# 615582; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v3.3 TGFB2 Zornitza Stark reviewed gene: TGFB2: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Loeys-Dietz syndrome 4, MIM# 614816; Mode of inheritance: None
Intellectual disability v3.3 TGFB1 Zornitza Stark reviewed gene: TGFB1: Rating: AMBER; Mode of pathogenicity: None; Publications: 29483653; Phenotypes: Inflammatory bowel disease, immunodeficiency, and encephalopathy, MIM# 618213; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 TET3 Zornitza Stark reviewed gene: TET3: Rating: GREEN; Mode of pathogenicity: None; Publications: 31928709; Phenotypes: Intellectual disability, dysmorphic features, abnormal growth, movement disorders; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Intellectual disability v3.3 TENM3 Zornitza Stark gene: TENM3 was added
gene: TENM3 was added to Intellectual disability. Sources: Expert list
Mode of inheritance for gene: TENM3 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TENM3 were set to 30513139; 22766609; 27103084; 29753094
Phenotypes for gene: TENM3 were set to Microphthalmia, syndromic 15, MIM#615145; coloboma
Review for gene: TENM3 was set to GREEN
gene: TENM3 was marked as current diagnostic
Added comment: At least four unrelated families described with syndromic microphthalmia and bi-allelic variants in this gene, ID is part of the phenotype.
Sources: Expert list
Intellectual disability v3.3 TEK Zornitza Stark reviewed gene: TEK: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Glaucoma 3, primary congenital, E , MIM#617272, Venous malformations, multiple cutaneous and mucosal, MIM# 600195; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v3.3 TCTN3 Zornitza Stark reviewed gene: TCTN3: Rating: GREEN; Mode of pathogenicity: None; Publications: 22883145, 25118024, 26092869; Phenotypes: Joubert syndrome 18, OMIM #614815, Orofaciodigital syndrome IV, OMIM #258860; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
Intellectual disability v3.3 TCF12 Zornitza Stark reviewed gene: TCF12: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Craniosynostosis 3, MIM# 615314; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v3.3 TBXAS1 Zornitza Stark reviewed gene: TBXAS1: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Ghosal hematodiaphyseal syndrome, MIM# 231095; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 TBX5 Zornitza Stark reviewed gene: TBX5: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Holt-Oram syndrome, MIM# 142900; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v3.3 TBX4 Zornitza Stark reviewed gene: TBX4: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Amelia, posterior, with pelvic and pulmonary hypoplasia syndrome, MIM# 601360, Ischiocoxopodopatellar syndrome with or without pulmonary arterial hypertension, MIM# 147891; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Intellectual disability v3.3 TBX3 Zornitza Stark reviewed gene: TBX3: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Ulnar-mammary syndrome, MIM# 181450; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v3.3 TBX22 Zornitza Stark reviewed gene: TBX22: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Abruzzo-Erickson syndrome, MIM# 302905, Cleft palate with ankyloglossia, MIM# 303400; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females
Intellectual disability v3.3 TBX20 Zornitza Stark reviewed gene: TBX20: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Atrial septal defect 4, MIM# 611363; Mode of inheritance: None
Intellectual disability v3.3 TBX15 Zornitza Stark reviewed gene: TBX15: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Cousin syndrome, MIM# 260660; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 TASP1 Zornitza Stark gene: TASP1 was added
gene: TASP1 was added to Intellectual disability. Sources: Expert list
Mode of inheritance for gene: TASP1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TASP1 were set to 31209944; 31350873
Phenotypes for gene: TASP1 were set to Developmental delay; microcephaly; dysmorphic features; congenital abnormalities
Review for gene: TASP1 was set to GREEN
gene: TASP1 was marked as current diagnostic
Added comment: Four unrelated families reported; two with founder mutation. Protein interacts with KMT2A and KMT2D. Another de novo missense variant reported in a single infant with multiple congenital abnormalities, insufficient evidence for mono allelic disease at present.
Sources: Expert list
Intellectual disability v3.3 TANC2 Zornitza Stark reviewed gene: TANC2: Rating: GREEN; Mode of pathogenicity: None; Publications: 31616000; Phenotypes: Intellectual disability, autism, epilepsy; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted; Current diagnostic: yes
Intellectual disability v3.3 TAB2 Zornitza Stark reviewed gene: TAB2: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Congenital heart defects, nonsyndromic, 2, MIM# 614980; Mode of inheritance: None
Intellectual disability v3.3 SUZ12 Zornitza Stark edited their review of gene: SUZ12: Changed phenotypes: Imagawa-Matsumoto syndrome, MIM# 618786, Intellectual disability, Overgrowth
Intellectual disability v3.3 SUZ12 Zornitza Stark reviewed gene: SUZ12: Rating: GREEN; Mode of pathogenicity: None; Publications: 31736240, 30019515, 28229514; Phenotypes: Intellectual disability, Overgrowth; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v3.3 SUCLA2 Zornitza Stark gene: SUCLA2 was added
gene: SUCLA2 was added to Intellectual disability. Sources: Expert list
Mode of inheritance for gene: SUCLA2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SUCLA2 were set to 27913098; 15877282; 23759946; 17287286; 17301081
Phenotypes for gene: SUCLA2 were set to Mitochondrial DNA depletion syndrome 5 (encephalomyopathic with or without methylmalonic aciduria); OMIM #612073
Review for gene: SUCLA2 was set to GREEN
Added comment: ID is part of the phenotype of this mitochondrial disorder.
Sources: Expert list
Intellectual disability v3.3 STT3A Zornitza Stark reviewed gene: STT3A: Rating: GREEN; Mode of pathogenicity: None; Publications: 23842455, 30701557, 28424003; Phenotypes: Congenital disorder of glycosylation, type Iw, OMIM #615596; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 STS Zornitza Stark reviewed gene: STS: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Intellectual disability v3.3 STAT1 Zornitza Stark reviewed gene: STAT1: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Intellectual disability v3.3 STAR Zornitza Stark reviewed gene: STAR: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Lipoid adrenal hyperplasia, MIM# 201710; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.3 SRY Zornitza Stark reviewed gene: SRY: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Early onset or syndromic epilepsy v2.3 SRPX2 Zornitza Stark reviewed gene: SRPX2: Rating: RED; Mode of pathogenicity: None; Publications: 16497722, 23933820, 23871722; Phenotypes: Rolandic epilepsy, mental retardation, and speech dyspraxia, MIM# 300643; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 ZNF341 Louise Daugherty edited their review of gene: ZNF341: Added comment: Added publication referenced by IUIS december 2019 update; Changed rating: AMBER; Changed publications: 29907691, 29907690
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 TRIM22 Louise Daugherty reviewed gene: TRIM22: Rating: AMBER; Mode of pathogenicity: ; Publications: 26836588; Phenotypes: ; Mode of inheritance:
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 TOP2B Louise Daugherty reviewed gene: TOP2B: Rating: AMBER; Mode of pathogenicity: ; Publications: 31409799; Phenotypes: ; Mode of inheritance:
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 TNFRSF9 Louise Daugherty reviewed gene: TNFRSF9: Rating: AMBER; Mode of pathogenicity: ; Publications: 31537641, 30872117, 31501153; Phenotypes: ; Mode of inheritance:
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 TGFBR2 Louise Daugherty reviewed gene: TGFBR2: Rating: AMBER; Mode of pathogenicity: ; Publications: 29392890; Phenotypes: ; Mode of inheritance:
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 TGFBR1 Louise Daugherty reviewed gene: TGFBR1: Rating: AMBER; Mode of pathogenicity: ; Publications: 29392890; Phenotypes: ; Mode of inheritance:
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 TGFB1 Louise Daugherty reviewed gene: TGFB1: Rating: AMBER; Mode of pathogenicity: ; Publications: 29483653; Phenotypes: ; Mode of inheritance:
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 SRP54 Louise Daugherty edited their review of gene: SRP54: Added comment: Added publication referenced by IUIS december 2019 update; Changed rating: AMBER; Changed publications: 28972538, 29914977
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 SLC7A7 Louise Daugherty reviewed gene: SLC7A7: Rating: AMBER; Mode of pathogenicity: ; Publications: 28057010; Phenotypes: ; Mode of inheritance:
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 SLC39A7 Louise Daugherty edited their review of gene: SLC39A7: Added comment: Added publication referenced by IUIS december 2019 update; Changed rating: AMBER; Changed publications: 30718914
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 SH3KBP1 Louise Daugherty reviewed gene: SH3KBP1: Rating: AMBER; Mode of pathogenicity: ; Publications: 29636373; Phenotypes: ; Mode of inheritance:
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 SEC61A1 Louise Daugherty reviewed gene: SEC61A1: Rating: AMBER; Mode of pathogenicity: ; Publications: 28782633; Phenotypes: ; Mode of inheritance:
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 RELA Louise Daugherty reviewed gene: RELA: Rating: AMBER; Mode of pathogenicity: ; Publications: 28600438, 29305315; Phenotypes: ; Mode of inheritance:
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 REL Louise Daugherty reviewed gene: REL: Rating: AMBER; Mode of pathogenicity: ; Publications: 31103457; Phenotypes: ; Mode of inheritance:
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 RAC2 Louise Daugherty edited their review of gene: RAC2: Added comment: Added publication referenced by IUIS december 2019 update; Changed publications: 25512081, 30723080, 30654050, 31071452, 31382036
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 PSMG2 Louise Daugherty reviewed gene: PSMG2: Rating: AMBER; Mode of pathogenicity: ; Publications: 30664889; Phenotypes: ; Mode of inheritance:
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 POLD2 Louise Daugherty reviewed gene: POLD2: Rating: AMBER; Mode of pathogenicity: ; Publications: 31449058; Phenotypes: ; Mode of inheritance:
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 POLD1 Louise Daugherty reviewed gene: POLD1: Rating: AMBER; Mode of pathogenicity: ; Publications: 31449058, 31629014; Phenotypes: ; Mode of inheritance:
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 OAS1 Louise Daugherty reviewed gene: OAS1: Rating: AMBER; Mode of pathogenicity: ; Publications: 29455859; Phenotypes: ; Mode of inheritance:
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 NLRP1 Louise Daugherty edited their review of gene: NLRP1: Added comment: Added publication referenced by IUIS december 2019 update; Changed publications: 27662089, 31484767
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 NFE2L2 Louise Daugherty reviewed gene: NFE2L2: Rating: AMBER; Mode of pathogenicity: ; Publications: 29018201; Phenotypes: ; Mode of inheritance:
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 LIG1 Louise Daugherty edited their review of gene: LIG1: Added comment: Added publication referenced by IUIS december 2019 update; Changed rating: AMBER; Changed publications: 30395541
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 IL6ST Louise Daugherty edited their review of gene: IL6ST: Added comment: Added publication referenced by IUIS december 2019 update; Changed rating: AMBER; Changed publications: 30309848, 28747427
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 IL6R Louise Daugherty edited their review of gene: IL6R: Added comment: Added publication referenced by IUIS december 2019 update; Changed rating: AMBER; Changed publications: 31235509, 31778705
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 IL2RB Louise Daugherty reviewed gene: IL2RB: Rating: AMBER; Mode of pathogenicity: ; Publications: 31040184, 31040185; Phenotypes: ; Mode of inheritance:
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 IKZF1 Louise Daugherty edited their review of gene: IKZF1: Added comment: Added publication referenced by IUIS december 2019 update; Changed rating: AMBER; Changed publications: 29889099
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 IKBKB Louise Daugherty edited their review of gene: IKBKB: Added comment: Added publication referenced by IUIS december 2019 update; Changed rating: AMBER; Changed publications: 30337470, 24369075
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 ICOSLG Louise Daugherty edited their review of gene: ICOSLG: Added comment: Added publication referenced by IUIS december 2019 update; Changed rating: AMBER; Changed publications: 30498080
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 HAVCR2 Louise Daugherty reviewed gene: HAVCR2: Rating: AMBER; Mode of pathogenicity: ; Publications: 30374066, 30792187; Phenotypes: ; Mode of inheritance:
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 FOXN1 Louise Daugherty edited their review of gene: FOXN1: Added comment: Added publication referenced by IUIS december 2019 update; Changed rating: AMBER; Changed publications: 31447097
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 FERMT1 Louise Daugherty reviewed gene: FERMT1: Rating: AMBER; Mode of pathogenicity: ; Publications: 21936020; Phenotypes: ; Mode of inheritance:
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 FCHO1 Louise Daugherty reviewed gene: FCHO1: Rating: AMBER; Mode of pathogenicity: ; Publications: 30822429; Phenotypes: ; Mode of inheritance:
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 ERBIN Louise Daugherty edited their review of gene: ERBIN: Added comment: Added publication referenced by IUIS december 2019 update; Changed rating: AMBER; Changed publications: 28126831
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 DNASE2 Louise Daugherty edited their review of gene: DNASE2: Added comment: Added publication referenced by IUIS december 2019 update; Changed rating: AMBER; Changed publications: 29259162
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 DNASE1L3 Louise Daugherty edited their review of gene: DNASE1L3: Added comment: Added publication referenced by IUIS december 2019 update; Changed publications: 22019780, 23666765, 27821515
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 DNAJC21 Louise Daugherty edited their review of gene: DNAJC21: Added comment: Added publication referenced by IUIS december 2019 update; Changed rating: AMBER; Changed publications: 28062395
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 DEF6 Louise Daugherty reviewed gene: DEF6: Rating: AMBER; Mode of pathogenicity: ; Publications: 31308374; Phenotypes: ; Mode of inheritance:
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 C17orf62 Louise Daugherty edited their review of gene: C17orf62: Added comment: Added publication referenced by IUIS december 2019 update; Changed rating: AMBER; Changed publications: 30361506, 30312704
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 CARD11 Louise Daugherty edited their review of gene: CARD11: Added comment: Added publication referenced by IUIS december 2019 update; Changed rating: AMBER; Changed publications: 30170123, 29074947
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 C1S Louise Daugherty edited their review of gene: C1S: Added comment: Added publication referenced by IUIS december 2019 update; Changed rating: AMBER; Changed publications: 27745832
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 C1R Louise Daugherty edited their review of gene: C1R: Added comment: Added publication referenced by IUIS december 2019 update; Changed rating: AMBER; Changed publications: 27745832
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 ARHGEF1 Louise Daugherty reviewed gene: ARHGEF1: Rating: AMBER; Mode of pathogenicity: ; Publications: 30521495; Phenotypes: ; Mode of inheritance:
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 ALPI Louise Daugherty reviewed gene: ALPI: Rating: AMBER; Mode of pathogenicity: ; Publications: 29567797; Phenotypes: ; Mode of inheritance:
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 ZNF341 Louise Daugherty Publications for gene ZNF341 were updated from 32048120; 29907691; 29907690; 32086639 to 32086639; 29907691; 32048120; 29907690
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 TRIM22 Louise Daugherty Publications for gene TRIM22 were updated from 32048120; 32086639 to 26836588; 32086639; 32048120
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 TOP2B Louise Daugherty Publications for gene TOP2B were updated from 32048120; 32086639 to 31409799; 32086639; 32048120
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 TNFRSF9 Louise Daugherty Publications for gene TNFRSF9 were updated from 32048120; 32086639 to 30872117; 32086639; 31537641; 31501153; 32048120
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 TGFBR2 Louise Daugherty Publications for gene TGFBR2 were updated from 32048120; 32086639 to 32086639; 32048120; 29392890
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 TGFBR1 Louise Daugherty Publications for gene TGFBR1 were updated from 32048120; 32086639 to 32086639; 32048120; 29392890
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 TGFB1 Louise Daugherty Publications for gene TGFB1 were updated from 32048120; 32086639 to 32086639; 32048120; 29483653
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 SRP54 Louise Daugherty Publications for gene SRP54 were updated from 32048120; 32086639 to 32086639; 28972538; 29914977; 32048120
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 SLC7A7 Louise Daugherty Publications for gene SLC7A7 were updated from 32086639; 32048120 to 28057010; 32086639; 32048120
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 SLC39A7 Louise Daugherty Publications for gene SLC39A7 were updated from 32048120; 30718914; 32086639 to 32086639; 32048120; 30718914
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 SH3KBP1 Louise Daugherty Publications for gene SH3KBP1 were updated from 32048120; 32086639 to 32086639; 32048120; 29636373
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 SEC61A1 Louise Daugherty Publications for gene SEC61A1 were updated from 32048120; 32086639 to 28782633; 32086639; 32048120
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 RELA Louise Daugherty Publications for gene RELA were updated from 32048120; 32086639 to 28600438; 32086639; 32048120; 29305315
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 REL Louise Daugherty Publications for gene REL were updated from 32048120; 32086639 to 32086639; 31103457; 32048120
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 RAC2 Louise Daugherty Publications for gene RAC2 were updated from 10961859; 10758162; 21167572; 25512081 to 21167572; 30654050; 30723080; 31071452; 25512081; 10758162; 31382036; 10961859
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 PSMG2 Louise Daugherty Publications for gene PSMG2 were updated from 32048120; 32086639 to 30664889; 32086639; 32048120
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 POLD2 Louise Daugherty Publications for gene POLD2 were updated from 32086639; 32048120 to 31449058; 32086639; 32048120
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 POLD1 Louise Daugherty Publications for gene POLD1 were updated from 32048120; 32086639 to 31449058; 32086639; 32048120; 31629014
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 OAS1 Louise Daugherty Publications for gene OAS1 were updated from 32048120; 32086639 to 32086639; 29455859; 32048120
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 NLRP1 Louise Daugherty Publications for gene NLRP1 were updated from 27965258; 29850521 to 29850521; 27662089; 31484767; 27965258
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 NFE2L2 Louise Daugherty Publications for gene NFE2L2 were updated from 32048120; 32086639 to 32086639; 32048120; 29018201
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 LIG1 Louise Daugherty Publications for gene LIG1 were updated from 32048120; 1581963; 32086639 to 30395541; 1581963; 32086639; 32048120
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 IL6ST Louise Daugherty Publications for gene IL6ST were updated from 32048120; 31235509; 32086639 to 31235509; 32086639; 30309848; 28747427; 32048120
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 IL6R Louise Daugherty Publications for gene IL6R were updated from 32048120; 31235509; 32086639 to 31235509; 32086639; 32048120; 31778705
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 IL2RB Louise Daugherty Publications for gene IL2RB were updated from 32086639; 32048120 to 32086639; 31040185; 32048120; 31040184
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 IKZF1 Louise Daugherty Publications for gene IKZF1 were updated from 21548011; 26981933 to 29889099; 21548011; 26981933
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 IKBKB Louise Daugherty Publications for gene IKBKB were updated from 24369075; 25216719 to 25216719; 24369075; 30337470
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 ICOSLG Louise Daugherty Publications for gene ICOSLG were updated from 32048120; 32086639 to 32086639; 32048120; 30498080
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 HAVCR2 Louise Daugherty Publications for gene HAVCR2 were updated from 32086639; 32048120 to 30792187; 32086639; 32048120; 30374066
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 FOXN1 Louise Daugherty Publications for gene FOXN1 were updated from 15180707; 10206641; 21507891; 28636882; 28077132; 29593714; 11159512 to 28636882; 15180707; 21507891; 11159512; 31447097; 10206641; 28077132; 29593714
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 FERMT1 Louise Daugherty Publications for gene FERMT1 were updated from 32048120; 32086639 to 32086639; 32048120; 21936020
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 FCHO1 Louise Daugherty Publications for gene FCHO1 were updated from 32048120; 32086639 to 32086639; 30822429; 32048120
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 ERBIN Louise Daugherty Publications for gene ERBIN were updated from 32086639; 32048120 to 28126831; 32086639; 32048120
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 DNASE1L3 Louise Daugherty Publications for gene DNASE1L3 were updated from 32048120; 22019780; 32086639 to 27821515; 23666765; 22019780; 32086639; 32048120
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 DNAJC21 Louise Daugherty Publications for gene DNAJC21 were updated from 27346687; 28062395; 29700810 to 27346687; 29700810; 28062395
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 DEF6 Louise Daugherty Publications for gene DEF6 were updated from 32086639; 32048120 to 32086639; 31308374; 32048120
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 C17orf62 Louise Daugherty Publications for gene C17orf62 were updated from 32086639; 32048120 to 30312704; 30361506; 32086639; 32048120
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 CARD11 Louise Daugherty Publications for gene CARD11 were updated from 23374270; 23561803; 28628108; 28826773; 23129749; 25352053 to 25352053; 23374270; 29074947; 23561803; 23129749; 30170123; 28628108; 28826773
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 C1S Louise Daugherty Publications for gene C1S were updated from 11390518; 9856483; 20727163 to 27745832; 11390518; 20727163; 9856483
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 C1R Louise Daugherty Publications for gene C1R were updated from 27745832; 29795138; 28711143; 21784777; 28544690 to 28544690; 21784777; 27745832; 29795138; 28711143
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 ARHGEF1 Louise Daugherty Publications for gene ARHGEF1 were updated from 32086639; 32048120 to 32086639; 30521495; 32048120
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 ALPI Louise Daugherty Publications for gene ALPI were updated from 32086639; 32048120 to 32086639; 32048120; 29567797
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 ZNF341 Louise Daugherty Source IUIS Classification December 2019 was added to ZNF341.
Added phenotypes Bacterial infections, mild facial dysmorphism, pneumatoceles, hyperextensible joints, bone fractures, retention of primary teeth; Combined immunodeficiencies with associated or syndromic features for gene: ZNF341
Publications for gene ZNF341 were updated from 29907690; 29907691 to 32048120; 29907691; 29907690; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 WRAP53 Louise Daugherty Source IUIS Classification December 2019 was added to WRAP53.
Mode of inheritance for gene WRAP53 was changed from to BIALLELIC, autosomal or pseudoautosomal
Added phenotypes Bone marrow failure, pulmonary and hepatic fibrosis, nail dystrophy, leukoplakia, reticulate skin pigmentation; microcephaly, neurodevelopmental delay; Bone marrow failure for gene: WRAP53
Publications for gene WRAP53 were updated from to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 WDR1 Louise Daugherty Source IUIS Classification December 2019 was added to WDR1.
Added phenotypes Mild neutropenia, poor wound healing, severe stomatitis, neutrophil nuclei herniate; Congenital defects of phagocyte number or function for gene: WDR1
Publications for gene WDR1 were updated from 27557945 to 32048120; 27557945; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 USP18 Louise Daugherty Source IUIS Classification December 2019 was added to USP18.
Added phenotypes Autoinflammatory Disorders; TORCH like syndrome for gene: USP18
Publications for gene USP18 were updated from 31272490; 27325888 to 32048120; 27325888; 31272490; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 TRAF3IP2 Louise Daugherty Source IUIS Classification December 2019 was added to TRAF3IP2.
Added phenotypes CMC, blepharitis, folliculitis and macroglossia; Defects in intrinsic and innate immunity for gene: TRAF3IP2
Publications for gene TRAF3IP2 were updated from 24120361 to 32048120; 24120361; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 TRAF3 Louise Daugherty Source IUIS Classification December 2019 was added to TRAF3.
Added phenotypes Defects in intrinsic and innate immunity; Herpes simplex virus 1 encephalitis for gene: TRAF3
Publications for gene TRAF3 were updated from 20832341; 11296228; 24378539 to 24378539; 20832341; 32048120; 11296228; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 TNFSF12 Louise Daugherty Source IUIS Classification December 2019 was added to TNFSF12.
Added phenotypes Predominantly Antibody Deficiencies; Pneumonia, bacterial infections, warts, thrombocytopenia for gene: TNFSF12
Publications for gene TNFSF12 were updated from 23493554 to 32048120; 23493554; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 TNFSF11 Louise Daugherty Source IUIS Classification December 2019 was added to TNFSF11.
Mode of inheritance for gene TNFSF11 was changed from to BIALLELIC, autosomal or pseudoautosomal
Added phenotypes Osteopetrosis with severe growth retardation; Defects in intrinsic and innate immunity for gene: TNFSF11
Publications for gene TNFSF11 were updated from to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 TNFRSF4 Louise Daugherty Source IUIS Classification December 2019 was added to TNFRSF4.
Added phenotypes Impaired immunity to HHV8, Kaposis sarcoma; Immunodeficiencies affecting cellular and humoral immunity for gene: TNFRSF4
Publications for gene TNFRSF4 were updated from to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 TNFRSF13C Louise Daugherty Source IUIS Classification December 2019 was added to TNFRSF13C.
Added phenotypes Variable clinical expression; Predominantly Antibody Deficiencies for gene: TNFRSF13C
Publications for gene TNFRSF13C were updated from to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 TNFRSF13B Louise Daugherty Source IUIS Classification December 2019 was added to TNFRSF13B.
Added phenotypes Variable clinical expression; Predominantly Antibody Deficiencies for gene: TNFRSF13B
Publications for gene TNFRSF13B were updated from 16007086; 16007087; 18981294; 28834165; 29114388 to 16007086; 18981294; 29114388; 16007087; 32048120; 28834165; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 TNFRSF11A Louise Daugherty Source IUIS Classification December 2019 was added to TNFRSF11A.
Added phenotypes Osteopetrosis; Defects in intrinsic and innate immunity for gene: TNFRSF11A
Publications for gene TNFRSF11A were updated from to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 TIRAP Louise Daugherty Source IUIS Classification December 2019 was added to TIRAP.
Mode of inheritance for gene TIRAP was changed from to BIALLELIC, autosomal or pseudoautosomal
Added phenotypes Defects in intrinsic and innate immunity; Staphylococcal disease during childhood for gene: TIRAP
Publications for gene TIRAP were updated from 28235196 to 32048120; 28235196; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 THBD Louise Daugherty Source IUIS Classification December 2019 was added to THBD.
Mode of inheritance for gene THBD was changed from Unknown to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Added phenotypes Atypical hemolytic-uremic syndrome; Complement Deficiencies for gene: THBD
Publications for gene THBD were updated from to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 TFRC Louise Daugherty Source IUIS Classification December 2019 was added to TFRC.
Mode of inheritance for gene TFRC was changed from to BIALLELIC, autosomal or pseudoautosomal
Added phenotypes Recurrent infections, thrombocytopenia; Immunodeficiencies affecting cellular and humoral immunity for gene: TFRC
Publications for gene TFRC were updated from to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 TERC Louise Daugherty Source IUIS Classification December 2019 was added to TERC.
Added phenotypes Bone marrow failure, pulmonary and hepatic fibrosis, nail dystrophy, leukoplakia, reticulate skin pigmentation; microcephaly, neurodevelopmental delay; Bone marrow failure for gene: TERC
Publications for gene TERC were updated from 16332973; 11574891; 12525685 to 32048120; 12525685; 16332973; 11574891; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 TCIRG1 Louise Daugherty Source IUIS Classification December 2019 was added to TCIRG1.
Mode of inheritance for gene TCIRG1 was changed from to BIALLELIC, autosomal or pseudoautosomal
Added phenotypes Defects in intrinsic and innate immunity; Osteopetrosis with hypocalcemia for gene: TCIRG1
Publications for gene TCIRG1 were updated from to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 TBX1 Louise Daugherty Source IUIS Classification December 2019 was added to TBX1.
Added phenotypes Hypoparathyroidism, conotruncal cardiac malformation, velopalatal insufficiency, abnormal facies, intellectual disability; Combined immunodeficiencies with associated or syndromic features for gene: TBX1
Publications for gene TBX1 were updated from 24198816; 14585638; 11242110 to 11242110; 14585638; 24198816; 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 TAPBP Louise Daugherty Source IUIS Classification December 2019 was added to TAPBP.
Added phenotypes Vasculitis,pyoderma gangrenosum; Immunodeficiencies affecting cellular and humoral immunity for gene: TAPBP
Publications for gene TAPBP were updated from 12149238 to 32048120; 12149238; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 STN1 Louise Daugherty Source IUIS Classification December 2019 was added to STN1.
Mode of inheritance for gene STN1 was changed from to BIALLELIC, autosomal or pseudoautosomal
Added phenotypes Intrauterine growth retardation, premature aging, pancytopenia, hypocellular bone marrow, gastrointestinal hemorrhage due to vascular ectasia, intracranial calcification, abnormal telomeres; Bone marrow failure for gene: STN1
Publications for gene STN1 were updated from to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 SRP54 Louise Daugherty Source IUIS Classification December 2019 was added to SRP54.
Mode of inheritance for gene SRP54 was changed from to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Added phenotypes Congenital defects of phagocyte number or function; Schwachman Diamond features for gene: SRP54
Publications for gene SRP54 were updated from to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 SNX10 Louise Daugherty Source IUIS Classification December 2019 was added to SNX10.
Mode of inheritance for gene SNX10 was changed from to BIALLELIC, autosomal or pseudoautosomal
Added phenotypes Osteopetrosis with visual impairment; Defects in intrinsic and innate immunity for gene: SNX10
Publications for gene SNX10 were updated from to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 SMARCD2 Louise Daugherty Source IUIS Classification December 2019 was added to SMARCD2.
Mode of inheritance for gene SMARCD2 was changed from to BIALLELIC, autosomal or pseudoautosomal
Added phenotypes Neutropenia, developmental aberrations, skeletal abnormalities, hematopoietic stem cells, myelodysplasia; Congenital defects of phagocyte number or function for gene: SMARCD2
Publications for gene SMARCD2 were updated from to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 SLC39A7 Louise Daugherty Source IUIS Classification December 2019 was added to SLC39A7.
Added phenotypes Early onset infections, blistering dermatosis, failure to thrive, thrombocytopenia; Predominantly Antibody Deficiencies for gene: SLC39A7
Publications for gene SLC39A7 were updated from 30718914 to 32048120; 30718914; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 SH3BP2 Louise Daugherty Source IUIS Classification December 2019 was added to SH3BP2.
Added phenotypes Bone degeneration in jaws; Autoinflammatory Disorders for gene: SH3BP2
Publications for gene SH3BP2 were updated from 22640988; 28914985; 11381256; 29669173 to 29669173; 22640988; 32048120; 28914985; 11381256; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 SEMA3E Louise Daugherty Source IUIS Classification December 2019 was added to SEMA3E.
Added phenotypes Coloboma, heart anomaly, choanal atresia, intellectual retardation, genital and ear anomalies, CNS malformation, some are SCID-like and have low TRECs; Combined immunodeficiencies with associated or syndromic features for gene: SEMA3E
Publications for gene SEMA3E were updated from 1735828; 21055784; 12144540 to 12144540; 1735828; 32048120; 21055784; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 SAMD9L Louise Daugherty Source IUIS Classification December 2019 was added to SAMD9L.
Added phenotypes Bone marrow failure; MDS, neurological features for gene: SAMD9L
Publications for gene SAMD9L were updated from 28202457 to 32048120; 28202457; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 SAMD9 Louise Daugherty Source IUIS Classification December 2019 was added to SAMD9.
Mode of inheritance for gene SAMD9 was changed from Other - please specifiy in evaluation comments to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Added phenotypes IUGR with gonadal abnormalities, adrenal failure, MDS with chromosome 7 aberrations, predisposition to infections, enteropathy, absent spleen; Bone marrow failure for gene: SAMD9
Publications for gene SAMD9 were updated from 28487541; 29175836; 29266745; 29535429 to 28487541; 29535429; 32048120; 29266745; 29175836; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 RNU4ATAC Louise Daugherty Source IUIS Classification December 2019 was added to RNU4ATAC.
Mode of inheritance for gene RNU4ATAC was changed from to BIALLELIC, autosomal or pseudoautosomal
Added phenotypes Recurrent bacterial infections, lymphadenopathy, Spondyloepiphyseal dysplasia, extreme intrauterine growth retardation, retinal dystrophy, facial dysmorphism, may present with microcephaly, short stature for gene: RNU4ATAC
Publications for gene RNU4ATAC were updated from to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 RNF31 Louise Daugherty Source IUIS Classification December 2019 was added to RNF31.
Added phenotypes Bacterial infections, autoinflammation, amylopectinosis, lymphangiectasia; Combined immunodeficiencies with associated or syndromic features for gene: RNF31
Publications for gene RNF31 were updated from 26008899 to 32048120; 26008899; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 RHOH Louise Daugherty Source IUIS Classification December 2019 was added to RHOH.
Added phenotypes HPV infection, lung granulomas, molluscum contagiosum, lymphoma; Immunodeficiencies affecting cellular and humoral immunity for gene: RHOH
Publications for gene RHOH were updated from 22850876; 24189071 to 32048120; 22850876; 24189071; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 RELB Louise Daugherty Source IUIS Classification December 2019 was added to RELB.
Added phenotypes Recurrent infectionsImmunodeficiencies affecting cellular and humoral immunity for gene: RELB
Publications for gene RELB were updated from 26385063 to 32048120; 26385063; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 RANBP2 Louise Daugherty Source IUIS Classification December 2019 was added to RANBP2.
Added phenotypes Defects in intrinsic and innate immunity; Fever induces acute encephalopathy for gene: RANBP2
Publications for gene RANBP2 were updated from to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 PTEN Louise Daugherty Source IUIS Classification December 2019 was added to PTEN.
Added phenotypes Recurrent infections, Lymphoproliferation, Autoimmunity; developmental delay; Predominantly Antibody Deficiencies for gene: PTEN
Publications for gene PTEN were updated from 27426521 to 32048120; 27426521; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 PSENEN Louise Daugherty Source IUIS Classification December 2019 was added to PSENEN.
Added phenotypes Defects in intrinsic and innate immunity; Hidradenitis suppurativa for gene: PSENEN
Publications for gene PSENEN were updated from 20929727; 21412258; 27900998; 28287404; 28601418; 23439959; 23020871; 28922471 to 21412258; 28601418; 23439959; 32048120; 27900998; 28287404; 20929727; 28922471; 23020871; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 POLE2 Louise Daugherty Source IUIS Classification December 2019 was added to POLE2.
Added phenotypes Recurrent infections, disseminated BCG infections, autoimmunity (type 1 diabetes, hypothyroidism, facial dysmorphism); Combined immunodeficiencies with associated or syndromic features for gene: POLE2
Publications for gene POLE2 were updated from to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 PMS2 Louise Daugherty Source IUIS Classification December 2019 was added to PMS2.
Mode of inheritance for gene PMS2 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal
Added phenotypes Recurrent infections, cafe-au-lait spots, lymphoma, colorectal carcinoma, brain tumors; Combined immunodeficiencies with associated or syndromic features for gene: PMS2
Publications for gene PMS2 were updated from 7661930; 15077197; 9488480; 10763829; 16507833 to 15077197; 32048120; 7661930; 9488480; 16507833; 10763829; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 PLEKHM1 Louise Daugherty Source IUIS Classification December 2019 was added to PLEKHM1.
Mode of inheritance for gene PLEKHM1 was changed from to BIALLELIC, autosomal or pseudoautosomal
Added phenotypes Osteopetrosis; Defects in intrinsic and innate immunity for gene: PLEKHM1
Publications for gene PLEKHM1 were updated from to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 OSTM1 Louise Daugherty Source IUIS Classification December 2019 was added to OSTM1.
Added phenotypes Osteopetrosis with hypocalcemia, neurologic features; Defects in intrinsic and innate immunity for gene: OSTM1
Publications for gene OSTM1 were updated from to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 NFAT5 Louise Daugherty Source IUIS Classification December 2019 was added to NFAT5.
Added phenotypes IBD, recurrent sinopulmonary infections; Diseases of Immune Dysregulation for gene: NFAT5
Publications for gene NFAT5 were updated from to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 NCSTN Louise Daugherty Source IUIS Classification December 2019 was added to NCSTN.
Added phenotypes Defects in intrinsic and innate immunity; Hidradenitis suppurativa with acne for gene: NCSTN
Publications for gene NCSTN were updated from 20929727; 21412258 to 32048120; 20929727; 21412258; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 NBAS Louise Daugherty Source IUIS Classification December 2019 was added to NBAS.
Added phenotypes Defects in intrinsic and innate immunity; Fever induces liver failure for gene: NBAS
Publications for gene NBAS were updated from to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 MSH6 Louise Daugherty Source IUIS Classification December 2019 was added to MSH6.
Mode of inheritance for gene MSH6 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal
Added phenotypes Predominantly Antibody Deficiencies; Family or personal history of cancer for gene: MSH6
Publications for gene MSH6 were updated from to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 MS4A1 Louise Daugherty Source IUIS Classification December 2019 was added to MS4A1.
Added phenotypes Recurrent infections; Predominantly Antibody Deficiencies for gene: MS4A1
Publications for gene MS4A1 were updated from 20038800; 27250108 to 32048120; 27250108; 20038800; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 MKL1 Louise Daugherty Source IUIS Classification December 2019 was added to MKL1.
Added phenotypes Mild thrombocytopenia; Congenital defects of phagocyte number or function for gene: MKL1
Publications for gene MKL1 were updated from 26224645 to 32048120; 26224645; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 MASP2 Louise Daugherty Source IUIS Classification December 2019 was added to MASP2.
Added phenotypes Pyogenic infections, inflammatory lung disease, autoimmunity; Complement Deficiencies for gene: MASP2
Publications for gene MASP2 were updated from 24658431 to 32048120; 24658431; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 LIG1 Louise Daugherty Source IUIS Classification December 2019 was added to LIG1.
Added phenotypes Recurrent respiratory infections, growth retardation, sun sensitivity, lymphoma, radiation sensitivity; Combined immunodeficiencies with associated or syndromic features for gene: LIG1
Publications for gene LIG1 were updated from 1581963 to 32048120; 1581963; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 KMT2D Louise Daugherty Source IUIS Classification December 2019 was added to KMT2D.
Added phenotypes Typical facial abnormalities, cleft or high arched palate, skeletal abnormalities, short stature, intellectual disability, congenital heart defects, recurrent infections (otitis media, pneumonia) in 50% of patients. Autoimmunity may be present; Combined immunodeficiencies with associated or syndromic features for gene: KMT2D
Publications for gene KMT2D were updated from 15887282; 25142838; 15523604; 26411453 to 25142838; 32048120; 15887282; 15523604; 26411453; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 KMT2A Louise Daugherty Source IUIS Classification December 2019 was added to KMT2A.
Added phenotypes Respiratory infections, short stature, hypertelorism, hairy elbows, developmental delay, intellectual disability; Combined immunodeficiencies with associated or syndromic features for gene: KMT2A
Publications for gene KMT2A were updated from 27320412 to 32048120; 27320412; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 KDM6A Louise Daugherty Source IUIS Classification December 2019 was added to KDM6A.
Added phenotypes Typical facial abnormalities, cleft or high arched palate, skeletal abnormalities, short stature, intellectual disability, congenital heart defects, recurrent infections (otitis media, pneumonia) in 50% of patients. Autoimmunity may be present; Combined immunodeficiencies with associated or syndromic features for gene: KDM6A
Publications for gene KDM6A were updated from 26411453; 25546742; 15887282; 25142838; 15523604 to 25546742; 25142838; 32048120; 15887282; 15523604; 26411453; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 JAK1 Louise Daugherty Source IUIS Classification December 2019 was added to JAK1.
Mode of inheritance for gene JAK1 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Added phenotypes Diseases of Immune Dysregulation; HSM, eosinophilic enteritis, thyroid disease, poor growth, viral infections for gene: JAK1
Publications for gene JAK1 were updated from 28111307 to 32048120; 28111307; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 IRF7 Louise Daugherty Source IUIS Classification December 2019 was added to IRF7.
Added phenotypes Severe influenza disease for gene: IRF7
Publications for gene IRF7 were updated from 25814066; 26761402; 9315633 to 26761402; 25814066; 9315633; 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 IRF3 Louise Daugherty Source IUIS Classification December 2019 was added to IRF3.
Added phenotypes Herpes simplex virus 1 encephalitis for gene: IRF3
Publications for gene IRF3 were updated from 26216125; 26513235 to 32048120; 26216125; 26513235; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 IRF2BP2 Louise Daugherty Source IUIS Classification December 2019 was added to IRF2BP2.
Added phenotypes Recurrent infections, possible autoimmunity and inflammatory disease; Predominantly Antibody Deficiencies for gene: IRF2BP2
Publications for gene IRF2BP2 were updated from 27016798 to 32048120; 27016798; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 IRAK1 Louise Daugherty Source IUIS Classification December 2019 was added to IRAK1.
Mode of inheritance for gene IRAK1 was changed from BIALLELIC, autosomal or pseudoautosomal to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Added phenotypes Bacterial infections, X-linked MECP2 deficiency-related syndrome due to a large de novo Xq28 chromosomal deletion encompassing both MECP2 and IRAK1 for gene: IRAK1
Publications for gene IRAK1 were updated from 28069966 to 32048120; 28069966; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 IL6ST Louise Daugherty Source IUIS Classification December 2019 was added to IL6ST.
Added phenotypes Bacterial infections, boiles, eczema, pulmonary abscesses, pneumatoceles, bone fractures, scoliosis, retention of primary teeth, craniosynostosis; Combined immunodeficiencies with associated or syndromic features for gene: IL6ST
Publications for gene IL6ST were updated from 31235509 to 32048120; 31235509; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 IL6R Louise Daugherty Source IUIS Classification December 2019 was added to IL6R.
Added phenotypes Recurrent pyogenic infections, cold abscesses, high circulating IL-6 levels; Combined immunodeficiencies with associated or syndromic features for gene: IL6R
Publications for gene IL6R were updated from 31235509 to 32048120; 31235509; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 IL21 Louise Daugherty Source IUIS Classification December 2019 was added to IL21.
Added phenotypes Severe early onset colitis, recurrent sinopulmonary infections; Immunodeficiencies affecting cellular and humoral immunity for gene: IL21
Publications for gene IL21 were updated from 24746753 to 32048120; 24746753; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 IL17F Louise Daugherty Source IUIS Classification December 2019 was added to IL17F.
Added phenotypes CMC, folliculitis for gene: IL17F
Publications for gene IL17F were updated from 21350122 to 32048120; 21350122; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 IGKC Louise Daugherty Source IUIS Classification December 2019 was added to IGKC.
Added phenotypes Asymptomatic; Predominantly Antibody Deficiencies for gene: IGKC
Publications for gene IGKC were updated from 4185453 to 32048120; 4185453; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 IFNAR2 Louise Daugherty Source IUIS Classification December 2019 was added to IFNAR2.
Added phenotypes Severe viral infections (disseminated vaccine-strain measles, HHV6) for gene: IFNAR2
Publications for gene IFNAR2 were updated from 26424569 to 32048120; 26424569; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 ICOSLG Louise Daugherty Source IUIS Classification December 2019 was added to ICOSLG.
Mode of inheritance for gene ICOSLG was changed from to BIALLELIC, autosomal or pseudoautosomal
Added phenotypes Recurrent bacterial and viral infections; Immunodeficiencies affecting cellular and humoral immunity for gene: ICOSLG
Publications for gene ICOSLG were updated from to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 HYOU1 Louise Daugherty Source IUIS Classification December 2019 was added to HYOU1.
Mode of inheritance for gene HYOU1 was changed from to BIALLELIC, autosomal or pseudoautosomal
Added phenotypes Hypoglycemia, inflammatory complications; Congenital defects of phagocyte number or function for gene: HYOU1
Publications for gene HYOU1 were updated from to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 FPR1 Louise Daugherty Source IUIS Classification December 2019 was added to FPR1.
Added phenotypes Periodontitis only; Congenital defects of phagocyte number or function for gene: FPR1
Publications for gene FPR1 were updated from 10882119; 20203610; 8224916; 2910576; 28371599; 29105764 to 20203610; 29105764; 8224916; 10882119; 32048120; 28371599; 2910576; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 FCN3 Louise Daugherty Source IUIS Classification December 2019 was added to FCN3.
Added phenotypes Respiratory infections, abscesses for gene: FCN3
Publications for gene FCN3 were updated from 19535802; 20971976; 22226667; 25662573 to 22226667; 32048120; 20971976; 19535802; 25662573; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 FCGR3A Louise Daugherty Source IUIS Classification December 2019 was added to FCGR3A.
Added phenotypes severe herpes viral infections, particularly VZV, Epstein Barr virus (EBV), and (HPV) for gene: FCGR3A
Publications for gene FCGR3A were updated from 8608639; 8874200; 23006327; 8609432 to 8874200; 23006327; 32048120; 8609432; 8608639; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 FAAP24 Louise Daugherty Source IUIS Classification December 2019 was added to FAAP24.
Added phenotypes Diseases of Immune Dysregulation; EBV infection-driven lymphoproliferative disease for gene: FAAP24
Publications for gene FAAP24 were updated from 27473539 to 32048120; 27473539; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 DNASE1L3 Louise Daugherty Source IUIS Classification December 2019 was added to DNASE1L3.
Added phenotypes Systemic lupus erythematosus, lupus nephritis, hypocomplementemic urticarial vasculitis; Autoinflammatory Disorders for gene: DNASE1L3
Publications for gene DNASE1L3 were updated from 22019780 to 32048120; 22019780; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 CTC1 Louise Daugherty Source IUIS Classification December 2019 was added to CTC1.
Added phenotypes Intrauterine growth retardation, sparse graying hair, dystrophic nails, trilinear bone marrow failure, osteopenia, gastrointestinal hemorrhage due to vascular ectasia, retinal telangiectasia, intracranial calcification, abnormal telomeres; Bone marrow failure for gene: CTC1
Publications for gene CTC1 were updated from 22267198 to 32048120; 22267198; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 CLCN7 Louise Daugherty Source IUIS Classification December 2019 was added to CLCN7.
Mode of inheritance for gene CLCN7 was changed from to BIALLELIC, autosomal or pseudoautosomal
Added phenotypes Osteopetrosis with hypocalcemia, neurologic features for gene: CLCN7
Publications for gene CLCN7 were updated from to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 CFTR Louise Daugherty Source IUIS Classification December 2019 was added to CFTR.
Added phenotypes Respiratory infections, pancreatic insufficiency, elevated sweat chloride; Congenital defects of phagocyte number or function for gene: CFTR
Publications for gene CFTR were updated from to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 CFHR5 Louise Daugherty Source IUIS Classification December 2019 was added to CFHR5.
Added phenotypes Older onset atypical hemolytic-uremic syndrome, disseminated neisserial infections for gene: CFHR5
Publications for gene CFHR5 were updated from 20800271; 22503529; 28673452 to 32048120; 28673452; 20800271; 22503529; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 CFHR4 Louise Daugherty Source IUIS Classification December 2019 was added to CFHR4.
Mode of inheritance for gene CFHR4 was changed from Unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Added phenotypes Older onset atypical hemolytic-uremic syndrome, disseminated neisserial infections for gene: CFHR4
Publications for gene CFHR4 were updated from to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 CFHR3 Louise Daugherty Source IUIS Classification December 2019 was added to CFHR3.
Added phenotypes Older onset atypical hemolytic-uremic syndrome, disseminated neisserial infections for gene: CFHR3
Publications for gene CFHR3 were updated from to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 CFHR2 Louise Daugherty Source IUIS Classification December 2019 was added to CFHR2.
Mode of inheritance for gene CFHR2 was changed from Unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Added phenotypes Older onset atypical hemolytic-uremic syndrome, disseminated neisserial infections for gene: CFHR2
Publications for gene CFHR2 were updated from to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 CFHR1 Louise Daugherty Source IUIS Classification December 2019 was added to CFHR1.
Added phenotypes Older onset atypical hemolytic-uremic syndrome, disseminated neisserial infections for gene: CFHR1
Publications for gene CFHR1 were updated from to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 CD8A Louise Daugherty Source IUIS Classification December 2019 was added to CD8A.
Added phenotypes Recurrent infections, may be asymptomatic; Immunodeficiencies affecting cellular and humoral immunity for gene: CD8A
Publications for gene CD8A were updated from 11435463; 17658607 to 32048120; 17658607; 11435463; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 CD81 Louise Daugherty Source IUIS Classification December 2019 was added to CD81.
Added phenotypes Recurrent infections, may have glomerulonephritis; Predominantly Antibody Deficiencies for gene: CD81
Publications for gene CD81 were updated from 20237408; 14530327; 27250108 to 27250108; 14530327; 20237408; 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 C8G Louise Daugherty Source IUIS Classification December 2019 was added to C8G.
Added phenotypes Disseminated neisserial infections for gene: C8G
Publications for gene C8G were updated from to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 BCL11B Louise Daugherty Source IUIS Classification December 2019 was added to BCL11B.
Added phenotypes Congenital abnormalities, neonatal teeth, dysmorphic facies, absent corpus callosum, neurocognitive deficits; Combined immunodeficiencies with associated or syndromic features for gene: BCL11B
Publications for gene BCL11B were updated from 29296816; 27959755 to 32048120; 27959755; 29296816; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 BCL10 Louise Daugherty Source IUIS Classification December 2019 was added to BCL10.
Added phenotypes Recurrent bacterial and viral infections, candidiasis, gastroenteritis; Immunodeficiencies affecting cellular and humoral immunity for gene: BCL10
Publications for gene BCL10 were updated from 25365219 to 32048120; 25365219; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 APOL1 Louise Daugherty Source IUIS Classification December 2019 was added to APOL1.
Mode of inheritance for gene APOL1 was changed from Unknown to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Added phenotypes Trypanosomiasis for gene: APOL1
Publications for gene APOL1 were updated from 25100047; 29470556; 16720107; 28537557; 15894515; 28827791; 29077717 to 28827791; 29470556; 32048120; 28537557; 16720107; 15894515; 25100047; 29077717; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 AP3D1 Louise Daugherty Source IUIS Classification December 2019 was added to AP3D1.
Added phenotypes Oculocutaneous albinism, recurrent infections, seizures, hearing loss and neurodevelopmental delay for gene: AP3D1
Publications for gene AP3D1 were updated from 26744459 to 32048120; 26744459; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 AP1S3 Louise Daugherty Source IUIS Classification December 2019 was added to AP1S3.
Added phenotypes Pustular psoriasis; Autoinflammatory Disorders for gene: AP1S3
Publications for gene AP1S3 were updated from to 32048120; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 ADAM17 Louise Daugherty Source IUIS Classification December 2019 was added to ADAM17.
Added phenotypes Early onset diarrhea and skin lesions; Autoinflammatory Disorders for gene: ADAM17
Publications for gene ADAM17 were updated from 25058236; 28930861; 22010916; 25171914; 11149563; 20603312 to 22010916; 28930861; 20603312; 32048120; 25171914; 11149563; 25058236; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.34 ACTB Louise Daugherty Source IUIS Classification December 2019 was added to ACTB.
Mode of inheritance for gene ACTB was changed from Unknown to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Added phenotypes Mental retardation, short stature; Congenital defects of phagocyte number or function for gene: ACTB
Publications for gene ACTB were updated from 10411937 to 32048120; 10411937; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.33 TINF2 Louise Daugherty Phenotypes for gene: TINF2 were changed from DBone marrow failure, pulmonary and hepatic fibrosis, nail dystrophy, leukoplakia, reticulate skin pigmentation; microcephaly, neurodevelopmental delay; Bone marrow failure, pulmonary and hepatic fibrosis, nail dystrophy, leukoplakia, reticulate skin pigmentation; microcephaly, neurodevelopmental delay exudative retinopathy to Bone marrow failure, pulmonary and hepatic fibrosis, nail dystrophy, leukoplakia, reticulate skin pigmentation; microcephaly, neurodevelopmental delay; Bone marrow failure, pulmonary and hepatic fibrosis, nail dystrophy, leukoplakia, reticulate skin pigmentation; microcephaly, neurodevelopmental delay exudative retinopathy
Primary immunodeficiency or monogenic inflammatory bowel disease v2.32 TINF2 Louise Daugherty Phenotypes for gene: TINF2 were changed from Dyskeratosis congenita 3; Dyskeratosis congenita; Hoyeraal-Hreidarsson syndrome; Intrauterine growth retardation, microcephaly, nail dystrophy, sparse scalp hair and eyelashes, hyperpigmentation of skin, palmar hyperkeratosis, premalignant oral leukoplakia, pancytopenia, myelodysplasia, +/- recurrent infections. A severe phenotype with developmental delay and cerebellar hypoplasia known as Hoyeraal-Hreidarsson Syndrome (HHS) may occur in some DKC patients; Combined immunodeficiencies with associated or syndromic features to DBone marrow failure, pulmonary and hepatic fibrosis, nail dystrophy, leukoplakia, reticulate skin pigmentation; microcephaly, neurodevelopmental delay; Bone marrow failure, pulmonary and hepatic fibrosis, nail dystrophy, leukoplakia, reticulate skin pigmentation; microcephaly, neurodevelopmental delay exudative retinopathy
Primary immunodeficiency or monogenic inflammatory bowel disease v2.31 TERT Louise Daugherty Phenotypes for gene: TERT were changed from Dyskeratosis congenita 2 613989, Dyskeratosis congenita 4 613989; Dyskeratosis congenita; Hoyeraal-Hreidarsson syndrome; Intrauterine growth retardation, microcephaly, nail dystrophy, sparse scalp hair and eyelashes, hyperpigmentation of skin, palmar hyperkeratosis, premalignant oral leukoplakia, pancytopenia, myelodysplasia, +/- recurrent infections. A severe phenotype with developmental delay and cerebellar hypoplasia known as Hoyeraal-Hreidarsson Syndrome (HHS) may occur in some DKC patients; Combined immunodeficiencies with associated or syndromic features to Bone marrow failure, pulmonary and hepatic fibrosis, nail dystrophy, leukoplakia, reticulate skin pigmentation; microcephaly, neurodevelopmental delay; Bone marrow failure, pulmonary and hepatic fibrosis, nail dystrophy, leukoplakia, reticulate skin pigmentation; microcephaly, neurodevelopmental delay; Bone marrow failure
Primary immunodeficiency or monogenic inflammatory bowel disease v2.30 RAC2 Louise Daugherty Phenotypes for gene: RAC2 were changed from T-B- SCID; T-B+ SCID; Neutrophil immunodeficiency syndrome 608203; Neutrophil immunodeficiency syndrome; RAS-related C3 Bolutinum toxin substrate 2 deficiency (RAC2); Poor wound healing, leukocytosis; Congenital defects of phagocyte number or function to T-B- SCID; T-B+ SCID; Neutrophil immunodeficiency syndrome 608203; Neutrophil immunodeficiency syndrome; RAS-related C3 Bolutinum toxin substrate 2 deficiency (RAC2); Poor wound healing, leukocytosis; Congenital defects of phagocyte number or function; Reticular dysgenesis; Recurrent sinopulmonary infections, selective IgA defiency; poststreptococcal glomerulonephritis; urticaria
Primary immunodeficiency or monogenic inflammatory bowel disease v2.29 NLRP1 Louise Daugherty Phenotypes for gene: NLRP1 were changed from Dyskeratosis, autoimmunity and arthritis; Autoinflammatory Disorders; Autoinflammation with arthritis and dyskeratosis to Dyskeratosis, autoimmunity and arthritis; Palmoplantar carcinoma, corneal scarring; Autoinflammatory Disorders; Autoinflammation with arthritis and dyskeratosis
Primary immunodeficiency or monogenic inflammatory bowel disease v2.28 TINF2 Louise Daugherty commented on gene: TINF2: OriginaI Metadata from IUIS classification table (December, 2019). IUIS Genetic defect (original gene symbol in IUIS download): TINF2. PanelApp HGNC gene symbol check: TINF2 . IUIS Disease: AD-DKC due to TINF2 deficiency . IUIS Inheritance: AD .T cells: normal to low / normal to low .B cells: normal to low / normal to low, .IUIS Other affected cells: Hematopoietic stem cell / Hematopoietic stem cell. IUIS Associated features: Bone marrow failure, pulmonary and hepatic fibrosis, nail dystrophy, leukoplakia, reticulate skin pigmentation; microcephaly, neurodevelopmental delay. IUIS Major category: Bone marrow failure IUIS Subcategory: none given
Primary immunodeficiency or monogenic inflammatory bowel disease v2.28 TERT Louise Daugherty commented on gene: TERT: OriginaI Metadata from IUIS classification table (December, 2019). IUIS Genetic defect (original gene symbol in IUIS download): TERT .PanelApp HGNC gene symbol check: TERT . IUIS Disease: AD/AR-DKC due to TERT deficiency . IUIS Inheritance: AD or AR .T cells: normal to low / normal to low, .B cells: Normal to low / normal to low, .IUIS Other affected cells: Hematopoietic stem cell / Hematopoietic stem cell. IUIS Associated features: Bone marrow failure, pulmonary and hepatic fibrosis, nail dystrophy, leukoplakia, reticulate skin pigmentation; microcephaly, neurodevelopmental delay / Bone marrow failure, pulmonary and hepatic fibrosis, nail dystrophy, leukoplakia, reticulate skin pigmentation; microcephaly, neurodevelopmental delay. IUIS Major category: Bone marrow failure, UIS Subcategory: none given
Primary immunodeficiency or monogenic inflammatory bowel disease v2.28 RAC2 Louise Daugherty Added comment: Comment on mode of inheritance: changed MOI due to IUIS December 2019 update
Primary immunodeficiency or monogenic inflammatory bowel disease v2.28 RAC2 Louise Daugherty Mode of inheritance for gene: RAC2 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.27 RAC2 Louise Daugherty commented on gene: RAC2: Original Metadata from IUIS classification table (December, 2019). IUIS Genetic defect (original gene symbol in IUIS download): RAC2 .PanelApp HGNC gene symbol check: RAC2 . IUIS Disease: RAC2 deficiency . IUIS Inheritance: AD GOF / AR / AD LOF, T cells: Very low / no data, .B cells: Very low / no data, Immunoglobulin levels: Low / low, Neutrophil count: Low / High.IUIS Other affected cells: N. IUIS Associated features: Reticular dysgenesis / Recurrent sinopulmonary infections, selective IgA defiency; poststreptococcal glomerulonephritis; urticaria Poor wound healing, leukocytosis, IUIS Major category: TImmunodeficiencies affecting cellular and humoral immunity / Predominantly Antibody Deficiencies / Congenital defects of phagocyte number or function. IUIS Subcategory: T-B- SCID / CVID Phenotype/ Defects of Motility
Primary immunodeficiency or monogenic inflammatory bowel disease v2.27 NLRP1 Louise Daugherty commented on gene: NLRP1: Original Metadata from IUIS classification table (December, 2019). IUIS Genetic defect (original gene symbol in IUIS download): NLRP1 .PanelApp HGNC gene symbol check: NLRP1 . IUIS Disease: NLRP1 deficiency . IUIS Inheritance: AR / AD GOF .T cells: Normal / Normal, .B cells: Normal / Normal, Immunoglobulin levels: Normal / Normal, Neutrophil count: Normal / Normal IUIS Other affected cells: leukocytes / Keratinocytes. IUIS Associated features: Dyskeratosis, autoimmunity and arthritis / Palmoplantar carcinoma, corneal scarring, IUIS Major category: Autoinflammatory Disorders. IUIS Subcategory: Defects Affecting the Inflammasome
Primary immunodeficiency or monogenic inflammatory bowel disease v2.27 CFB Louise Daugherty changed review comment from: OriginaI Metadata from IUIS classification table (December, 2019). IUIS Genetic defect (original gene symbol in IUIS download): CFB .PanelApp HGNC gene symbol check: CFB . IUIS Disease: Factor B . IUIS Inheritance: AD .T cells: N/A, .B cells: N/A, .IUIS Other affected cells: N/A. IUIS Associated features: Atypical Hemolytic-uremic syndrome. IUIS Major category: Complement Deficiencies. IUIS Subcategory: N/A. // OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): CFB .PanelApp HGNC gene symbol check: CFB . IUIS Disease: Factor B . IUIS Inheritance: AD GOF / AR .T cells: Normal / Normal , .B cells: Normal / Normal, Immunoglobulin levels:Normal / Normal, Neutrophil count: Normal / Normal .IUIS Other affected cells: N/A. IUIS Associated features: Infections with encapsulated organisms. IUIS Major category: Complement Deficiencies. IUIS Subcategory: N/A.; to: OriginaI Metadata from IUIS classification table (December, 2019). IUIS Genetic defect (original gene symbol in IUIS download): CFB .PanelApp HGNC gene symbol check: CFB . IUIS Disease: Factor B . IUIS Inheritance: AD .T cells: N/A, .B cells: N/A, .IUIS Other affected cells: N/A. IUIS Associated features: Atypical Hemolytic-uremic syndrome. IUIS Major category: Complement Deficiencies. IUIS Subcategory: N/A. // OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): CFB .PanelApp HGNC gene symbol check: CFB . IUIS Disease: Factor B . IUIS Inheritance: AD GOF / AR .T cells: Normal / Normal , .B cells: Normal / Normal, Immunoglobulin levels:Normal / Normal, Neutrophil count: Normal / Normal .IUIS Other affected cells: N/A. IUIS Associated features: Infections with encapsulated organisms. IUIS Major category: Complement Deficiencies. IUIS Subcategory: N/A.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.27 CFB Louise Daugherty commented on gene: CFB: OriginaI Metadata from IUIS classification table (December, 2019). IUIS Genetic defect (original gene symbol in IUIS download): CFB .PanelApp HGNC gene symbol check: CFB . IUIS Disease: Factor B . IUIS Inheritance: AD .T cells: N/A, .B cells: N/A, .IUIS Other affected cells: N/A. IUIS Associated features: Atypical Hemolytic-uremic syndrome. IUIS Major category: Complement Deficiencies. IUIS Subcategory: N/A. // OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): CFB .PanelApp HGNC gene symbol check: CFB . IUIS Disease: Factor B . IUIS Inheritance: AD GOF / AR .T cells: Normal / Normal , .B cells: Normal / Normal, Immunoglobulin levels:Normal / Normal, Neutrophil count: Normal / Normal .IUIS Other affected cells: N/A. IUIS Associated features: Infections with encapsulated organisms. IUIS Major category: Complement Deficiencies. IUIS Subcategory: N/A.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.27 SLC7A7 Louise Daugherty Publications for gene: SLC7A7 were set to
Primary immunodeficiency or monogenic inflammatory bowel disease v2.26 SLC7A7 Louise Daugherty Phenotypes for gene: SLC7A7 were changed from to Lysinuric protein intolerance SLC7A7 deficiency; Severe bacterial infections; Predominantly Antibody Deficiencies; Lysinuric protein intolerance, 222700
Primary immunodeficiency or monogenic inflammatory bowel disease v2.25 SLC7A7 Louise Daugherty Mode of inheritance for gene: SLC7A7 was changed from to BIALLELIC, autosomal or pseudoautosomal