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Primary immunodeficiency or monogenic inflammatory bowel disease v4.202 RNU4ATAC Arina Puzriakova Phenotypes for gene: RNU4ATAC were changed from Recurrent bacterial infections, lymphadenopathy, Spondyloepiphyseal dysplasia, extreme intrauterine growth retardation, retinal dystrophy, facial dysmorphism, may present with microcephaly, short stature; 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 to Roifman syndrome, OMIM:616651; Recurrent bacterial infections, lymphadenopathy, Spondyloepiphyseal dysplasia, extreme intrauterine growth retardation, retinal dystrophy, facial dysmorphism, may present with microcephaly
Primary immunodeficiency or monogenic inflammatory bowel disease v4.193 SMARCAL1 Arina Puzriakova Added comment: Comment on phenotypes: Previous (overwritten) phenotypes: Schimke disease;Short stature, spondiloepiphyseal dysplasia, intrauterine growth retardation, nephropathy, bacterial, viral, fungal infections, may present as SCID, bone marrow failure;Combined immunodeficiencies with associated or syndromic features
Primary immunodeficiency or monogenic inflammatory bowel disease v4.193 SMARCAL1 Arina Puzriakova Phenotypes for gene: SMARCAL1 were changed from Schimke immunoosseous dysplasia 242900; Schimke disease; Short stature, spondiloepiphyseal dysplasia, intrauterine growth retardation, nephropathy, bacterial, viral, fungal infections, may present as SCID, bone marrow failure; Combined immunodeficiencies with associated or syndromic features to Schimke immunoosseous dysplasia, OMIM:242900
Primary immunodeficiency or monogenic inflammatory bowel disease v4.192 NHEJ1 Arina Puzriakova Added comment: Comment on phenotypes: Previous (overwritten) phenotypes: Severe combined immunodeficiency with microcephaly, growth retardation, and sensitivity to ionizing radiation;Severe combined immunodeficiency with microcephaly, growth retardation and sensitivity to ionizing radiation, 611291;T-B- SCID;T-B+ SCID;Combined immunodeficiency;Cernunnos/XLF deficiency;Nl NK, radiation sensitive, microcephaly;Immunodeficiencies affecting cellular and humoral immunity
Primary immunodeficiency or monogenic inflammatory bowel disease v4.192 NHEJ1 Arina Puzriakova Phenotypes for gene: NHEJ1 were changed from Severe combined immunodeficiency with microcephaly, growth retardation, and sensitivity to ionizing radiation; Severe combined immunodeficiency with microcephaly, growth retardation and sensitivity to ionizing radiation, 611291; T-B- SCID; T-B+ SCID; Combined immunodeficiency; Cernunnos/XLF deficiency; Nl NK, radiation sensitive, microcephaly; Immunodeficiencies affecting cellular and humoral immunity to Severe combined immunodeficiency with microcephaly, growth retardation, and sensitivity to ionizing radiation, OMIM:611291
Primary immunodeficiency or monogenic inflammatory bowel disease v3.5 DCLRE1B Achchuthan Shanmugasundram Phenotypes for gene: DCLRE1B were changed from 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 Dyskeratosis congenita, autosomal recessive 8, OMIM:620133
Primary immunodeficiency or monogenic inflammatory bowel disease v2.581 TERT Arina Puzriakova Phenotypes for gene: TERT were changed from 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 to Dyskeratosis congenita, autosomal dominant 2, OMIM:613989; Dyskeratosis congenita, autosomal recessive 4, OMIM:613989
Primary immunodeficiency or monogenic inflammatory bowel disease v2.535 SLC9A3 Arina Puzriakova Added phenotypes Diarrhea 8, secretory sodium, congenital, OMIM:616868 for gene: SLC9A3
Publications for gene: SLC9A3 were updated from 26358773; 33346580 to 26358773; 31276831; 30633106; 33346580
Primary immunodeficiency or monogenic inflammatory bowel disease v2.511 NLRP12 Arina Puzriakova Phenotypes for gene: NLRP12 were changed from Familial cold autoinflammatory syndrome 2, 611762; preterm premature rupture of membranes (PPROM); Non-pruritic urticaria, arthritis, chills, fever and leukocytosis after cold exposure.; Autoinflammatory Disorders to Familial cold autoinflammatory syndrome 2, OMIM:611762; Non-pruritic urticaria, arthritis, chills, fever and leukocytosis after cold exposure; Preterm premature rupture of membranes (PPROM); Autoinflammatory Disorders
Primary immunodeficiency or monogenic inflammatory bowel disease v2.498 RHBDF2 Boaz Palterer gene: RHBDF2 was added
gene: RHBDF2 was added to Primary immunodeficiency. Sources: Literature
Mode of inheritance for gene: RHBDF2 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: RHBDF2 were set to Pneumonia; Colitis; Immunodeficiency
Penetrance for gene: RHBDF2 were set to unknown
Review for gene: RHBDF2 was set to RED
Added comment: iRHOM deficiency with Respiratory and Intestinal inflammation and cytokine Secretion defect’ (IRIS): Kubo et al. (https://www.nature.com/articles/s41590-021-01093-y) described a new immunodeficiency disease due to loss-of-function mutations in RHBDF2, the gene encoding iRHOM2, in 4 subjects across two kindreds with recurrent infections in different organs. The disease presentation is pleiotropic, with one patient with recurrent pneumonia but no colon involvement, another had recurrent infectious hemorrhagic colitis but no lung involvement and the other two experienced recurrent respiratory infections. They replicated the phenotype in a KO mouse model and provided functional data.
Sources: Literature
Primary immunodeficiency or monogenic inflammatory bowel disease v2.443 ATM Arina Puzriakova Phenotypes for gene: ATM were changed from Ataxia-telangiectasia, 208900; Ataxia telangiectasia (ATM); immunodeficiency; Ataxia, telangiectasia, pulmonary infections, lymphoreticular and other malignancies, increased alpha fetoprotein, increased radiosensitivity, chromosomal instability and chromosomal translocations; Combined immunodeficiencies with associated or syndromic features to Ataxia-telangiectasia, OMIM:208900; 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
Primary immunodeficiency or monogenic inflammatory bowel disease v2.434 IPO8 Ivone Leong Added comment: Comment on publications: PMID: 34010604. 12 individuals from 9 families. 11/12 dilatation of the ascending aorta, 6/12 other abnormalities in great vessels (including ascending aortic aneurysm and carotid artery tortuosity), 6/10 heart malformations, 9/12 dysmorphic features (including proptossi, micrognathia, hypertelorism, frontal bossing and abnormal palate), 12/12 skeletal abnormalities (including hyperlaxity, recurrent joint dislocations, scoliosis, pectus and arachnodactyly), 8/12 skin hyperextensibility, 11/12 umbilical hernia, 7/12 developmental delay or intellectual disability (did not mention severity), 2/12 retinal detachment, 3/12 bilateral cataract (one patient had it at age of 45), 3/3 hyperIgE and IgG, 3/4 hypoIgA, 4/5 hypereosinophilia, 5/12 intestinal inflammation and 6/12 allergic symptoms. Patients were aged between 1 year - 62 years old).

PMID: 34010605. 7 individuals from 6 families. 7/7 dysmorphic features (including frontal bossing, hypertelorism, retrognathia and palate abnormalities), 7/7 skeletal findings (including arachnodactyly, joint hypermobility, scoliosis, pectus excavatum and pes planum), 7/7 developmental delay, 2/7 ID (1 mild ID and no severity for the other patient), 5/7 atrial septal defect, 4/7 ventricular septal defect, 6/7 cardiovascular abnormalities with aortic root and/orascending aortic aneurysm, 2/7 marked arterial tortuosity, 5/7 umbilical hernia, 2/7 bruise easily. Authors noted that despite patients having severe aneurysm phenotype none experienced arterial or aortic dissection and concluded that it may be because of the patients' young age (1 year - 19 years old). The study did not look at the immunological profile of the patients. The study also describes a knockout mouse model which recapitulates the human phenotype.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.426 LRRC32 Arina Puzriakova Added comment: Comment on list classification: Novel candidate gene added by Boaz Palterer. Rating Red as currently there is not enough evidence to support this gene-disease association.

Lehmkuhl et al. 2021 (PMID: 34059789) - 2 unrelated patients with immunodeficiency were found to harbour two rare heterozygous missense variants each in the LRRC32 gene (p.Arg312Cys (recurring), p.Trp247Ter, p.Arg421Gln) - variants were in cis in one patient, but in trans in the other.

Note that a different homozygous founder variant was also found in 2 families with GDD, cleft palate, and proliferative retinopathy (PMID: 30976112) - none of these features were evident in the two cases discussed here.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.404 MAP1LC3B2 Arina Puzriakova Added comment: Comment on list classification: New gene added by Boaz Palterer. Single patient described in PMID:33310865 with recurrent herpes simplex virus 2-induced lymphocytic Mollaret's meningitis, and a MAP1LC3B2 variant (c.325C>A) supported by functional data. Rating Red, awaiting further evidence.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.403 ATG4A Arina Puzriakova Added comment: Comment on list classification: New gene added by Boaz Palterer. Single patient described in PMID:33310865 with recurrent herpes simplex virus 2-induced lymphocytic Mollaret's meningitis, and a ATG4A variant (c.268C>A) supported by functional data. Rating Red, awaiting further evidence.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.401 MAP1LC3B2 Boaz Palterer gene: MAP1LC3B2 was added
gene: MAP1LC3B2 was added to Primary immunodeficiency. Sources: Literature
Mode of inheritance for gene: MAP1LC3B2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: MAP1LC3B2 were set to 33310865
Phenotypes for gene: MAP1LC3B2 were set to Mollaret’s meningitis; recurrent HSV2 meningitis
Penetrance for gene: MAP1LC3B2 were set to unknown
Review for gene: MAP1LC3B2 was set to RED
Added comment: Hait et al. described a single patient with a rare heterozygous variant in MAP1LC3B2 presenting with recurrent HSV2 meningitis (Mollaret's meningitis). They showed that the mutations caused impaired HSV2-induced autophagy leading to increased viral replication and apoptosis of patient fibroblasts. The defect was rescued by the introduction of WT MAP1LC3B2 into patient fibroblasts.
Sources: Literature
Primary immunodeficiency or monogenic inflammatory bowel disease v2.401 ATG4A Boaz Palterer gene: ATG4A was added
gene: ATG4A was added to Primary immunodeficiency. Sources: Literature
Mode of inheritance for gene: ATG4A was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: ATG4A were set to 33310865
Phenotypes for gene: ATG4A were set to Mollaret’s meningitis; recurrent HSV2 meningitis
Penetrance for gene: ATG4A were set to unknown
Review for gene: ATG4A was set to RED
Added comment: Hait et al. described a single patient with a rare heterozygous variant in ATG4 presenting with recurrent HSV2 meningitis (Mollaret's meningitis). They showed that the mutations caused impaired HSV2-induced autophagy leading to increased viral replication and apoptosis of patient fibroblasts. The defect was rescued by the introduction of WT ATG4 into patient fibroblasts.
Sources: Literature
Primary immunodeficiency or monogenic inflammatory bowel disease v2.401 POU2AF1 Boaz Palterer gene: POU2AF1 was added
gene: POU2AF1 was added to Primary immunodeficiency. Sources: Literature
Mode of inheritance for gene: POU2AF1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: POU2AF1 were set to 33571536
Phenotypes for gene: POU2AF1 were set to Agammaglobulinemia; Immunodeficiency; Bob1 deficiency
Penetrance for gene: POU2AF1 were set to unknown
Review for gene: POU2AF1 was set to RED
Added comment: Kury et al. described a single patient from consanguineous parents carrying a homozygous frameshift mutation in POU2AF1, encoding for Bob1, presenting with agammaglobulinemia with normal B cells. Functional data showed that Bob1 deficiency ex vivo and in a mouse KO model reduced B-cell responsiveness, impaired plasmablast formation and immunoglobulin secretion.
Sources: Literature
Primary immunodeficiency or monogenic inflammatory bowel disease v2.399 SLC9A3 Ivone Leong Phenotypes for gene: SLC9A3 were changed from Very Early Onset Inflammatory Bowel Disease; Congenital sodium diarrhoea to Very Early Onset Inflammatory Bowel Disease; Diarrhea 8, secretory sodium, congenital, OMIM:616868
Primary immunodeficiency or monogenic inflammatory bowel disease v2.392 COL7A1 Kelsey Jones changed review comment from: Important monogenic cause of VEOIBD (recognised criteria for the R15 panel). In a retrospective case series, 9 of 57 (16%) children with recessive DEBP had diarrhoea with macroscopic/microscopic features of colitis (PMID: 18363753). Included on a monogenic IBD gene panel proposed by The Paediatric IBD Porto Group of ESPGHAN (PMID: 33346580). Not a recognised cause of immunodeficiency.
Sources: Expert Review; to: Important monogenic cause of VEOIBD (recognised criteria for the R15 panel). In a retrospective case series, 9 of 57 (16%) children with recessive DEBP had diarrhoea with macroscopic/microscopic features of colitis (PMID: 18363753). There is additionally a recognised association between Epidermolysis Bullosa Acquisita (an autoimmune condition directed against Type VII Collagen (the COL7A1 protein product) (PMID: 23517353). Included on a monogenic IBD gene panel proposed by The Paediatric IBD Porto Group of ESPGHAN (PMID: 33346580). Not a recognised cause of immunodeficiency.
Sources: Expert Review
Primary immunodeficiency or monogenic inflammatory bowel disease v2.392 COL7A1 Kelsey Jones gene: COL7A1 was added
gene: COL7A1 was added to Primary immunodeficiency. Sources: Expert Review
Mode of inheritance for gene: COL7A1 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: COL7A1 were set to PMID: 18363753
Phenotypes for gene: COL7A1 were set to Very Early Onset Inflammatory Bowel Disease; Dystrophic Epidermolysis Bullosa Pruriginosa
Penetrance for gene: COL7A1 were set to Incomplete
Review for gene: COL7A1 was set to AMBER
Added comment: Important monogenic cause of VEOIBD (recognised criteria for the R15 panel). In a retrospective case series, 9 of 57 (16%) children with recessive DEBP had diarrhoea with macroscopic/microscopic features of colitis (PMID: 18363753). Included on a monogenic IBD gene panel proposed by The Paediatric IBD Porto Group of ESPGHAN (PMID: 33346580). Not a recognised cause of immunodeficiency.
Sources: Expert Review
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
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.
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 v2.51 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 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.
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 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
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 v2.34 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 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 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 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 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 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 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 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 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 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 v2.28 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 v2.27 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 v2.14 NFE2L2 Louise Daugherty gene: NFE2L2 was added
gene: NFE2L2 was added to Primary immunodeficiency. 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 32048120; 32086639
Phenotypes for gene: NFE2L2 were set 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
Primary immunodeficiency or monogenic inflammatory bowel disease v2.13 TGFBR1 Louise Daugherty gene: TGFBR1 was added
gene: TGFBR1 was added to Primary immunodeficiency. 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 32048120; 32086639
Phenotypes for gene: TGFBR1 were set to Recurrent respiratory infectons, eczema, food allergies, hyperextensible joints, scoliosis, retention of primary teeths, aortic anuerysms; Loeys Dietz syndrome due to TGFBR1 deficiency; Loeys-Dietz syndrome 1, 609192; Combined immunodeficiencies with associated or syndromic features
Primary immunodeficiency or monogenic inflammatory bowel disease v2.13 TGFBR2 Louise Daugherty gene: TGFBR2 was added
gene: TGFBR2 was added to Primary immunodeficiency. 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 32048120; 32086639
Phenotypes for gene: TGFBR2 were set to Recurrent respiratory infections, eczema, food allergies, hyperextensible joints, scoliosis, retention of primary teeths, aortic anuerysms; ALPS-FAS; Combined immunodeficiencies with associated or syndromic features
Primary immunodeficiency or monogenic inflammatory bowel disease v1.132 STAT4 Louise Daugherty changed review comment from: New gene added after review of potential new genes for PID by the Immunology Test Group. This gene was noted as being only theoretical for PID so was rated as Red by the group.; to: Potential risk allele for SLE. New gene added after review of potential new genes for PID by the Immunology Test Group. This gene was noted as being only theoretical for PID so was rated as Red by the group.
Primary immunodeficiency or monogenic inflammatory bowel disease v1.132 IL31RA Louise Daugherty changed review comment from: Not clearly a primary immunodeficiency. New gene added after review of potential new genes for PID by the Immunology Test Group. This gene was noted as being only theoretical for PID.; to: Not clearly a primary immunodeficiency. New gene added after review of potential new genes for PID by the Immunology Test Group. This gene was noted as being only theoretical for PID so was rated as Red by the group.
Primary immunodeficiency or monogenic inflammatory bowel disease v1.132 IL31RA Louise Daugherty changed review comment from: New gene added after review of potential new genes for PID by the Immunology Test Group. This gene was noted as being only theoretical for PID.; to: Not clearly a primary immunodeficiency. New gene added after review of potential new genes for PID by the Immunology Test Group. This gene was noted as being only theoretical for PID.
Primary immunodeficiency or monogenic inflammatory bowel disease v1.132 IL31RA Louise Daugherty changed review comment from: New gene added after review of potential new genes for PID by the Immunology Test Group. This gene was noted as being only theoretical for PID.; to: New gene added after review of potential new genes for PID by the Immunology Test Group. This gene was noted as being only theoretical for PID.
Primary immunodeficiency or monogenic inflammatory bowel disease v1.130 RET Louise Daugherty commented on gene: RET: MEN2 / MTC - ?relevant phenotype / Hirschsprung in LOF
Primary immunodeficiency or monogenic inflammatory bowel disease v1.130 CTC1 Louise Daugherty commented on gene: CTC1: Cerebroretinal microangiopathy with calcifications and cysts: spasticity / dystonia / ataxia / seizures / cognitive decline (green association but ?phenotype)
Primary immunodeficiency or monogenic inflammatory bowel disease v1.127 RET Louise Daugherty commented on gene: RET: Gene rating submitted by Tracy Briggs, David Gokhale and Abigal Rousseau on behalf of North West GLH for the GMS Immunology specialist test group. As discussed with the GMS Immunology Specialist Test Group during webex call 28th March 2019 and confirmed in follow up email on 20th June the Specialist Test Group all agreed there is only enough evidence to rate this gene Red

Gene rating submitted by Kimberly Gilmour and Austen Worth on behalf of London North GLH for the GMS Immunology specialist test group. As discussed with the GMS Immunology Specialist Test Group during webex call 28th March 2019 and confirmed in follow up email 6th September the Specialist Test Group all agreed there is only enough evidence to rate this gene Red
Primary immunodeficiency or monogenic inflammatory bowel disease v1.127 RET Louise Daugherty commented on gene: RET: Genes with discrepant ratings (PID 100K vs sumbmitted LNGLH submitted Immunology lists)--agreed rating in webex call 28 March 2019
Primary immunodeficiency or monogenic inflammatory bowel disease v1.103 BLOC1S6 Louise Daugherty gene: BLOC1S6 was added
gene: BLOC1S6 was added to Primary immunodeficiency. Sources: Other
Mode of inheritance for gene: BLOC1S6 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: BLOC1S6 were set to Hermansky-pudlak syndrome 9, 614171; HPS9, palladin deficiency (NK cell defect); Immune Dysregulation
Review for gene: BLOC1S6 was set to RED
Added comment: 2 reviews
Sophie Hambleton (Newcastle University)
[email protected]
Red List (low evidence)

Only 1 reported patient (a previous report had to be retracted).
Created: 19 Jun 2018, 5:47 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Created: 19 Jun 2018, 5:47 a.m.

Panel version: 0.1006
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Your review
Louise Daugherty (Genomics England Curator)
[email protected]
I don't know

Comment on list classification: Changed from Amber to Red after external clinical review, only one bonafide case
Created: 20 Jun 2018, 3:10 p.m.

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After review decided to keep as Amber- currently there is only one case for HPS9 need more individuals to determine if immunodeficiency is a feature of BLOC-1 deficiency
Created: 11 May 2018, 4:31 p.m.

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Comment on publications: one one affected reported to date (2012). Added HPS gene review PMID: 20301464 (2017)
Created: 11 May 2018, 4:25 p.m.

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Comment on phenotypes: added PID phenotype
Created: 11 May 2018, 4:24 p.m.

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This gene was absent from the original PanelApp PID panel dataset (review April 2018). However it was listed in external expert immunodeficiency diagnostic gene list(s) GOSH or GRID. In this combined PID panel, this gene has been rated as AMBER and needs further curational review to assess pertinence prior to v1.
Created: 20 Apr 2018, 12:25 p.m.

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Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: BLOC1S6, GRID_Gene_Symbol: BLOC1S6, GRID_Transcript_ENS_Community submitted: ENST00000220531, GRID_Transcript_RefSeq: NM_012388.3, GRID_Transcript_ENS_used_on_Production: ENST00000220531
Created: 17 Apr 2018, 12:12 p.m.

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Created: 17 Apr 2018, 12:12 p.m.

Panel version: 0.679
Sources: Other
Primary immunodeficiency or monogenic inflammatory bowel disease v1.93 RET Louise Daugherty Source Expert Review Red was added to RET.
Source GOSH PID v.8.0 was added to RET.
Primary immunodeficiency or monogenic inflammatory bowel disease v1.89 RET Louise Daugherty Publications for gene: RET were set to
Primary immunodeficiency or monogenic inflammatory bowel disease v1.88 RET Louise Daugherty Phenotypes for gene: RET were changed from to Central hypoventilation syndrome, congenital 209880
Primary immunodeficiency or monogenic inflammatory bowel disease v1.87 RET Louise Daugherty Mode of inheritance for gene: RET was changed from to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Primary immunodeficiency or monogenic inflammatory bowel disease v1.67 RET Louise Daugherty Source London North GLH was added to RET.
Primary immunodeficiency or monogenic inflammatory bowel disease v1.66 RET Louise Daugherty Source NHS GMS was added to RET.
Primary immunodeficiency or monogenic inflammatory bowel disease v1.65 RET Louise Daugherty gene: RET was added
gene: RET was added to Primary immunodeficiency. Sources: North West GLH
Mode of inheritance for gene: RET was set to
Primary immunodeficiency or monogenic inflammatory bowel disease v1.64 PSMB4 Louise Daugherty RET was changed to PSMB4
Primary immunodeficiency or monogenic inflammatory bowel disease v1.64 RET Louise Daugherty Source North West GLH was added to RET.
Primary immunodeficiency or monogenic inflammatory bowel disease v1.20 NFAT5 Sarah Leigh Added comment: Comment on list classification: This rating of this gene has been returned to red. The amber rating was made in error as only one immunodeficiency associated variant has been reported in this gene.
Primary immunodeficiency or monogenic inflammatory bowel disease v1.16 RIPK1 Louise Daugherty edited their review of gene: RIPK1: Added comment: From OMIM : Lourenco et al. (2018) PMID: 30026316 reports 4 patients from 3 unrelated consanguineous families with immunodeficiency-57 identifying homozygous loss-of-function mutations in the RIPK1 gene. The variants segregated with the disorder in the families and were not found in the gnomAD database. Functional studies of patient cells showed impaired mitogen-activated protein kinase activation, impaired phosphorylation of downstream signaling molecules, impaired proinflammatory signaling downstream of TNFR1 and TLR3 and defective secretion of certain cytokines. Similar results were observed in vitro in a monocyte-like cell line with CRISPR/Cas9-mediated knockdown of RAPK1. The findings indicated that RIPK1 plays a critical role in the human immune system.; Changed rating: GREEN
Primary immunodeficiency or monogenic inflammatory bowel disease RET Louise Daugherty marked gene: RET as ready
Primary immunodeficiency or monogenic inflammatory bowel disease RET Louise Daugherty classified RET as Red List (low evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease RET Sophie Hambleton reviewed gene: RET
Primary immunodeficiency or monogenic inflammatory bowel disease RET Sarah Leigh classified RET as Amber List (moderate evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease RET Louise Daugherty reviewed RET
Primary immunodeficiency or monogenic inflammatory bowel disease RET Louise Daugherty Added gene to panel