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Undiagnosed metabolic disorders v1.614 ALAS2 Arina Puzriakova Phenotypes for gene: ALAS2 were changed from X-linked dominant protoporphyria (Porphyrias with acute painful photosensitivity); X-linked sideroblastic anaemia (XLSA) (Porphyrias with acute painful photosensitivity); Erythropoietic protoporphyria, mild variant to Anemia, sideroblastic, 1, OMIM:300751; Protoporphyria, erythropoietic, X-linked, OMIM:300752
Undiagnosed metabolic disorders v1.607 ATP5E Sarah Leigh edited their review of gene: ATP5E: Added comment: PMID: 34954817 reports two further cases of OMIM: 614053 who are both homozygous for ATP5E (new gene name: ATP5F1E) variant c.35A>G, p.Tyr12Cys (rs387906929), previously reported in PubMed: 20566710. Personal communication with the lead author of PMID: 34954817, confirmed that none of these cases were related to one another and so represent independent occurrences of this variant.; Changed rating: GREEN; Changed publications to: 27604308, 34954817, 20566710
Undiagnosed metabolic disorders v1.607 PIGM Sarah Leigh changed review comment from: A single PIGM variant (NM_145167.2(PIGM):c.-270C>G) has been associated with Glycosylphosphatidylinositol deficiency, (OMIM:610293) and as limited Gen2Phen gene for the same condition.
To date, this variant has only been reported in people of Arab or Turkish descent. Microsatellite- and SNP-based haplotypes encompassing PIGM reported in PMID:19168132, suggested that a founder effect in the two families (one Arab and one Turkish) was unlikely. However, subsequent occurrences of the variant in two additional unrelated Arab families (PMID: 31445883) might suggest that this variant is confined within the Middle Eastern populations.
Functional studies have shown that this variant reduces transcription of PIGM and blocks mannosylation of glycosylphosphatidylinositol anchor (PMID: 16767100).; to: A single PIGM variant (NM_145167.2(PIGM):c.-270C>G)(rs587776528) has been associated with Glycosylphosphatidylinositol deficiency, (OMIM:610293) and as limited Gen2Phen gene for the same condition.
To date, this variant has only been reported in people of Arab or Turkish descent. Microsatellite- and SNP-based haplotypes encompassing PIGM reported in PMID:19168132, suggested that a founder effect in the two families (one Arab and one Turkish) was unlikely. However, subsequent occurrences of the variant in two additional unrelated Arab families (PMID: 31445883) might suggest that this variant is confined within the Middle Eastern populations.
Functional studies have shown that this variant reduces transcription of PIGM and blocks mannosylation of glycosylphosphatidylinositol anchor (PMID: 16767100).
Undiagnosed metabolic disorders v1.606 PIGM Sarah Leigh edited their review of gene: PIGM: Added comment: A single PIGM variant (NM_145167.2(PIGM):c.-270C>G) has been associated with Glycosylphosphatidylinositol deficiency, (OMIM:610293) and as limited Gen2Phen gene for the same condition.
To date, this variant has only been reported in people of Arab or Turkish descent. Microsatellite- and SNP-based haplotypes encompassing PIGM reported in PMID:19168132, suggested that a founder effect in the two families (one Arab and one Turkish) was unlikely. However, subsequent occurrences of the variant in two additional unrelated Arab families (PMID: 31445883) might suggest that this variant is confined within the Middle Eastern populations.
Functional studies have shown that this variant reduces transcription of PIGM and blocks mannosylation of glycosylphosphatidylinositol anchor (PMID: 16767100).; Changed rating: GREEN
Undiagnosed metabolic disorders v1.603 SEC23B Arina Puzriakova Added comment: Comment on mode of inheritance: There is limited evidence linking this gene with Cowden syndrome (monoallelic variants). Only one family has been reported to date (PMID:26522472). This gene:disease association is provisional in OMIM, 'limited' disease confidence category in G2P and is not listed in ClinGen (whereas CDAII is). Biallelic phenotype remains relevant to this panel (PMID: 35163229).

On this basis, updating the MOI from 'Both mono- and biallelic' to 'Biallelic' only.
Undiagnosed metabolic disorders v1.594 SLC22A5 Sarah Leigh Phenotypes for gene: SLC22A5 were changed from Carnitine transporter deficiency (Disorders of carnitine transport and the carnitine cycle); Propionicacidemia to Carnitine deficiency, systemic primary, OMIM:212140; systemic primary carnitine deficiency disease, MONDO:0008919
Undiagnosed metabolic disorders v1.573 SPG7 Sarah Leigh edited their review of gene: SPG7: Added comment: Associated with relevant phenotype in OMIM and as definitive Gen2Phen gene. Numerous biallelic SPG7 variants have been reported (PMIDs: 9635427; 16534102; 17646629; 18200586, 20186691; 22571692) and at least five monoallelic SPG7 variants have been associated with Spastic paraplegia 7, autosomal recessive, OMIM:607259 (PMIDs: 18200586; 22571692). For this reason, the mode of inheritance for this gene should be BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form) autosomal or pseudoautosomal.; Changed rating: GREEN; Changed mode of inheritance: BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
Undiagnosed metabolic disorders v1.551 SDHA Arina Puzriakova Added comment: Comment on mode of inheritance: This gene was recently included on a gene list provided by Carl Fratter (Oxford University Hospitals NHS Trust) on behalf of GMS Mitochondrial providers, indicating that the MOI should be updated from 'biallelic' only to 'both mono- and biallelic' on Mitochondrial GMS panels (R354 and R63). As there was sufficient supporting evidence for the change, the MOI has also been updated to 'both' on this panel to ensure all panels reflect correct knowledge. Heterozygous variants can be associated with abnormal mitochondrial accumulation and therefore also within the scope of the panel.
Undiagnosed metabolic disorders v1.545 ATP5A1 Arina Puzriakova Added comment: Comment on list classification: There is now sufficient evidence to support this gene-disease association and therefore ATP5A1 has been promoted to Green.
Undiagnosed metabolic disorders v1.543 ATP5A1 Arina Puzriakova Added comment: Comment on mode of inheritance: Two families (with two affected sibs each) reported with recessive variants and supported by functional studies (PMIDs: 23599390; 23596069). Six unrelated patients have been reported with heterozygous variants; including one recurrent variant c.620G>A in four cases, c.545G>A and c.1037C>T in the remaining two, respectively (PMIDs: 34483339; 34954817).
Undiagnosed metabolic disorders v1.535 ACO2 Sarah Leigh Added comment: Comment on mode of inheritance: PMID: 34056600 reports 61 cases of genetically unsolved inherited optic neuropathies who were harbouring variants in ACO2, of which 50 carried dominant variants (the remaining 11 cases were biallelic). The authors state that this is the first report of monoallelic pathogenic ACO2 variants resulting in dominant optic atrophy.
Undiagnosed metabolic disorders v1.531 SLC16A1 Sarah Leigh edited their review of gene: SLC16A1: Changed phenotypes to: Erythrocyte lactate transporter defect, OMIM:245340, Hyperinsulinemic hypoglycemia, familial, 7, OMIM:610021, Monocarboxylate transporter 1 deficiency, OMIM:616095; Changed mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Undiagnosed metabolic disorders v1.531 SLC16A1 Sarah Leigh Phenotypes for gene: SLC16A1 were changed from mainly ketosis with borderline reduction in glucose; Hyperinsulinemic hypoglycemia, familial, 7 to Erythrocyte lactate transporter defect, OMIM:245340; Hyperinsulinemic hypoglycemia, familial, 7, OMIM:610021; Monocarboxylate transporter 1 deficiency, OMIM:616095
Undiagnosed metabolic disorders v1.525 C19orf12 Sarah Leigh Added comment: Comment on mode of inheritance: Monfrini et al (PMID: 29295770) and Gregory et al (PMID: 31087512) have reported heterozygous pathogenic C19ORF12 variants in patients with neurodegeneration with brain iron accumulation 4 (OMIM: 614298). Therefore, the mode of inheritance for this gene should be BOTH monoallelic and biallelic, autosomal or pseudoautosomal.
Undiagnosed metabolic disorders v1.517 PNPT1 Arina Puzriakova Phenotypes for gene: PNPT1 were changed from Disorders of mitochondrial protein import (Mitochondrial respiratory chain disorders (caused by nuclear variants only)); Multiple respiratory chain complex deficiencies (disorders of protein synthesis); Combined oxidative phosphorylation deficiency 13, 614932; Deafness, autosomal recessive 70, 614934; respiratory chain disorder; hearing loss to Combined oxidative phosphorylation deficiency 13, OMIM:614932; Deafness, autosomal recessive 70, OMIM:614934; Disorders of mitochondrial protein import (Mitochondrial respiratory chain disorders (caused by nuclear variants only)); Multiple respiratory chain complex deficiencies (disorders of protein synthesis)
Undiagnosed metabolic disorders v1.506 CPT2 Arina Puzriakova Phenotypes for gene: CPT2 were changed from Carnitine palmitoyltransferase II (CPTII) deficiency (Disorders of carnitine transport and the carnitine cycle); CPT deficiency, hepatic, type II 600649; CPT II deficiency, lethal neonatal 608836 to CPT II deficiency, infantile, OMIM:600649; CPT II deficiency, lethal neonatal, OMIM:608836; CPT II deficiency, myopathic, stress-induced, OMIM:255110; Carnitine palmitoyltransferase II (CPTII) deficiency (Disorders of carnitine transport and the carnitine cycle)
Undiagnosed metabolic disorders v1.504 MVK Arina Puzriakova Phenotypes for gene: MVK were changed from Hyper-IgD syndrome 260920; Mevalonic aciduria 610377; Porokeratosis 3, multiple types 175900 to Hyper-IgD syndrome, OMIM:260920; Mevalonic aciduria, OMIM:610377; Porokeratosis 3, multiple types, OMIM:175900
Undiagnosed metabolic disorders v1.501 HIBADH Zornitza Stark gene: HIBADH was added
gene: HIBADH was added to Undiagnosed metabolic disorders. Sources: Literature
Mode of inheritance for gene: HIBADH was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: HIBADH were set to 34176136
Phenotypes for gene: HIBADH were set to organic aciduria
Review for gene: HIBADH was set to RED
Added comment: Single family reported with two siblings presenting with 3-Hydroxyisobutyric aciduria. Male sib with neurodevelopmental symptoms, female sibling asymptomatic. No functional studies
Sources: Literature
Undiagnosed metabolic disorders v1.497 CLPB Arina Puzriakova Added comment: Comment on mode of inheritance: Updated MOI from 'Biallelic' to 'Both mono- and biallelic'.

Association between biallelic variants and disease is well established, with more than 35 affected individuals reported. Recently, six unrelated individuals with de novo monoallelic missense variants in CLPB were identified (PMID: 34140661). The phenotype strongly overlapped with that observed in the recessive disease, including 3-MGA-uria in all cases.
Undiagnosed metabolic disorders v1.493 GLS Arina Puzriakova commented on gene: GLS: Added 'watchlist_MOI' tag to highlight monoallelic phenotype (MIM# 618339) which is also relevant to this panel, but as there is only a single case reported to date this is not yet sufficient to update the MOI.
Undiagnosed metabolic disorders v1.444 NDUFC2 Sarah Leigh commented on gene: NDUFC2: Associated with relevant phenotype in OMIM, but not Gen2Phen. At least 2 variants have been reported in two unrelated cases, together with supportive functional evidence (PMID 32969598). There are also 2 families with complex I deficiency with reported by Carl Fratter (10 May 2019, Oxford University Hospitals NHS Trust).
Undiagnosed metabolic disorders v1.440 GLS Arina Puzriakova Added comment: Comment on list classification: Upgraded from Red to Amber. There are sufficient cases, supported by functional data, to rate this gene Green - however, detection of the 5' UTR triplet expansion (PMID:30970188) must first be validated within the Genomics England pipeline.

When excluding cases with the STR, the remaining evidence is not sufficient for inclusion as diagnostic-grade and therefore keeping Amber until the STR is validated or additional cases arise.
Undiagnosed metabolic disorders v1.437 GLS Arina Puzriakova Added comment: Comment on mode of inheritance: As evidence for pathogenicity of monoallelic variants is limited (currently only 1 case), MOI will remain as 'Biallelic' until further cases emerge that support an association between monoallelic variants and disease.
Undiagnosed metabolic disorders v1.433 HS2ST1 Ivone Leong gene: HS2ST1 was added
gene: HS2ST1 was added to Undiagnosed metabolic disorders. Sources: Literature
Mode of inheritance for gene: HS2ST1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: HS2ST1 were set to 33159882
Phenotypes for gene: HS2ST1 were set to Intellectual disability; dysmorphic features; congenital anomalies
Review for gene: HS2ST1 was set to GREEN
Added comment: This gene is not associated with a relevant phenotype in OMIM or Gene2Phenotype. Only 2 of 3 unrelated families with affected individuals described in PMID: 33159882 were reported to have ID. The affected individuals in the third family could not be assessed for ID. Other features affected individuals had were muscular hypotonia, hypoplasia/agenesis of corpus callosum, skeletal abnormalities, uni/bilateral renal agenesis (2/3) and craniofacial dysmorphism.

There is enough evidence to support a gene-disease association, so this gene has been rated Green.
Sources: Literature
Undiagnosed metabolic disorders v1.417 ALG14 Sarah Leigh Added comment: Comment on list classification: Associated with Myasthenic syndrome, congenital, 15, without tubular aggregates 616227 in OMIM, but not associated with phenotype in Gen2Phen. At least 6 variants reported in at least 5 cases with varying phenotypes. PMID 23404334 reports compound heterozygous (p.P65L, P.R104*) sibs, who manifested with myasthenic syndromes, but did not have intellectural disability nor seizures and were 62 and 51 years old when reported. PMID 28733338 reports two compound heterozygous (p.D74N, pV141G), (p.D74N, p.R109Q) cases and a homozygous (p.D74N), with early and lethal neurodegeneration with myasthenic and myopathic features, but the cases died before intellectual disability was manifiest. However, seizures were evident in two compound heterozygous families. PMID 30221345 reports a homozygous splicing variant in a case with intellectual disability and seizures. Functional studies were presented showing that this variant resulting in exon skipping, however, this was not completely prenetrant as wild type protein was detected at a low level in the patient.
Undiagnosed metabolic disorders v1.415 ISCU Sarah Leigh changed review comment from: Comment on mode of inheritance: PMID 29079705 reports a novel de novo dominant variant in ISCU associated with mitochondrial myopathy, which justifies the mode of inheritance recorded.; to: Comment on mode of inheritance: PMID 29079705 reports a novel de novo dominant variant missense p.G97V variant has been reported and therefore this may represent a specific mechanism of action. Further evidence is needed to determine which (if any) other monoallelic variants will cause disease beyond mitochondrial myopathy, which justifies the mode of inheritance recorded.
Undiagnosed metabolic disorders v1.415 ISCU Sarah Leigh Added comment: Comment on mode of inheritance: PMID 29079705 reports a novel de novo dominant variant in ISCU associated with mitochondrial myopathy, which justifies the mode of inheritance recorded.
Undiagnosed metabolic disorders v1.405 SLC6A3 Catherine Snow Phenotypes for gene: SLC6A3 were changed from Dopamine transporter deficiency syndrome (Other disorders of neurotransmitter metabolism) ; Early onset dystonia; Intellectual disability; Parkinson Disease and Complex Parkinsonism to Parkinsonism-dystonia, infantile, 1, 613135; Dopamine transporter deficiency syndrome (Other disorders of neurotransmitter metabolism); Early onset dystonia; Intellectual disability; Parkinson Disease and Complex Parkinsonism
Undiagnosed metabolic disorders v1.396 TRAP1 Catherine Snow gene: TRAP1 was added
gene: TRAP1 was added to Undiagnosed metabolic disorders. Sources: Expert list
Mode of inheritance for gene: TRAP1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TRAP1 were set to 24152966
Phenotypes for gene: TRAP1 were set to VACTERL; CAKUT
Review for gene: TRAP1 was set to GREEN
Added comment: Not in OMIM or Gene2Phenotype. Recessive mutations reported in 2 families with CAKUT, and 3 families with VACTERL. Metabolism phenotype as the encoded protein has ATPase activity and interacts with tumor necrosis factor type I.
Sources: Expert list
Undiagnosed metabolic disorders v1.395 MRPL12 Catherine Snow gene: MRPL12 was added
gene: MRPL12 was added to Undiagnosed metabolic disorders. Sources: Expert list
Mode of inheritance for gene: MRPL12 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MRPL12 were set to 23603806
Phenotypes for gene: MRPL12 were set to Multiple respiratory chain complex deficiencies (disorders of protein synthesis)
Review for gene: MRPL12 was set to RED
Added comment: A single reported family in the literature therefore classified as Red.
Sources: Expert list
Undiagnosed metabolic disorders v1.392 LARS Catherine Snow changed review comment from: LARS1 has a relevant phenotype and is in OMIM, but not in Gene2Phenotype. PMID: 30349989 describes a premature girl who was identified to have compound hetrozygous variants in LARS1, this has caused infantile liver failure syndrome, type 1 (ILFS1). The paper also summarised the clinical features of reported patients with infantile liver failure syndrome type 1 caused by cytosolic leucine-tRNA synthetase deficiency, in total 6 compound hetrozygous variants identified in 14 patients in 7 families. Sufficient variants and relevant phenotype to upgrade LARS1 from Red to Green.
Sources: Expert Review; to: LARS1 has a relevant phenotype and is in OMIM, but not in Gene2Phenotype. PMID: 30349989 describes a premature girl who was identified to have compound hetrozygous variants in LARS1, this has caused infantile liver failure syndrome, type 1 (ILFS1). The paper also summarised the clinical features of reported patients with infantile liver failure syndrome type 1 caused by cytosolic leucine-tRNA synthetase deficiency, in total 6 compound hetrozygous variants identified in 14 patients in 7 families. Sufficient variants and relevant phenotype to classify LARS1 as Green.
Sources: Expert Review
Undiagnosed metabolic disorders v1.392 LARS Catherine Snow gene: LARS was added
gene: LARS was added to Undiagnosed metabolic disorders. Sources: Expert Review
Mode of inheritance for gene: LARS was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: LARS were set to 28774368; 30349989; 22607940
Phenotypes for gene: LARS were set to ?Infantile liver failure syndrome 1, 615438
Review for gene: LARS was set to GREEN
Added comment: LARS1 has a relevant phenotype and is in OMIM, but not in Gene2Phenotype. PMID: 30349989 describes a premature girl who was identified to have compound hetrozygous variants in LARS1, this has caused infantile liver failure syndrome, type 1 (ILFS1). The paper also summarised the clinical features of reported patients with infantile liver failure syndrome type 1 caused by cytosolic leucine-tRNA synthetase deficiency, in total 6 compound hetrozygous variants identified in 14 patients in 7 families. Sufficient variants and relevant phenotype to upgrade LARS1 from Red to Green.
Sources: Expert Review
Undiagnosed metabolic disorders v1.373 TCN2 Catherine Snow Added comment: Comment on publications: There are >3 unrelated cases reported in the literature.
Undiagnosed metabolic disorders v1.368 STS Catherine Snow changed review comment from: Comment on list classification: Promoted from Amber to Green. This gene is associated with a relevant disease on OMIM and Gene2Phenotype and there is enough evidence to support a gene-disease association.

This gene was part of an initial gene list collated by Emma Ashton on behalf of the London North GLH, for GMS Metabolic Consensus Specialist Test Group. Additional information was not provided, such as mode of inheritance and phenotype.; to: Comment on list classification: Promoted from Amber to Green. This gene is associated with a relevant disease on OMIM and Gene2Phenotype and there is enough evidence to support a gene-disease association.
Undiagnosed metabolic disorders v1.365 ISCA2 Sarah Leigh gene: ISCA2 was added
gene: ISCA2 was added to Undiagnosed metabolic disorders. Sources: Literature
Mode of inheritance for gene: ISCA2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ISCA2 were set to 25539947; 29359243
Phenotypes for gene: ISCA2 were set to Multiple mitochondrial dysfunctions syndrome 4 616370
Review for gene: ISCA2 was set to GREEN
Added comment: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 3 variants reported in two different ethinicities. Rated green based on review of Anna de Burca (Clinical Fellow, Genomic England).
Sources: Literature
Undiagnosed metabolic disorders v1.361 SLC2A1 Ivone Leong Added comment: Comment on list classification: Promoted from Amber to Green. SLC2A1 is associated with GLUT1 deficiency syndrome 1 and GLUT1 deficiency syndrome 2 on OMIM and Gene2Phenotype. There are >3 unrelated cases reported on OMIM. Therefore, there is enough evidence for this gene to be promoted to Green status.
Undiagnosed metabolic disorders v1.359 HSPA9 Sarah Leigh Added comment: Comment on phenotypes: Monoallelic variants reported in Anemia, sideroblastic, 4 182170.
Undiagnosed metabolic disorders v1.358 HSPA9 Sarah Leigh gene: HSPA9 was added
gene: HSPA9 was added to Undiagnosed metabolic disorders. Sources: Literature
Mode of inheritance for gene: HSPA9 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: HSPA9 were set to 26598328
Phenotypes for gene: HSPA9 were set to Even-plus syndrome 616854
Review for gene: HSPA9 was set to AMBER
Added comment: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 3 variants reported in two unrelated cases.
Sources: Literature
Undiagnosed metabolic disorders v1.357 FDX2 Sarah Leigh Added comment: Comment on list classification: Based on reviews from Carl Fratter and Zornitza Stark (below).
This gene was added as Green due to the overall review and evidence assessment from the GMS mitochondrial specialist test group, submitted by Carl Fratter (May 2019) on behalf of GMS mitochondrial specialist test group: 3 unrelated familties; iron sulfur pathway. From panel: Possible mitochondrial disorder - nuclear genes (Version 0.187).
Promoted from red to amber, based on the expert review by Zornitza Stark (Australian Genomics) and the literature. FDX2 is associated with a phenotype in OMIM and not Gene2Phenotype. PMID: 24281368 describes a patient born of consanguineous Jewish Moroccan patents with episodic mitochondrial myopathy without optic atrophy or reversible leukoencephalopathy. The authors identified a homozygous missense variant in this gene (M1L). PMID: 30010796 describes 6 patients from 2 apparently unrelated Brazilian familes from the same geographical region with episodic mitochondrial myopathy. All affected individuals had the same homozygous variant (P144L). No haplotype analysis was performed. As there are only 2 different variants reported in this gene and no haplotype analysis was performed in PMID: 30010796 it was decided that there is currently not enough evidence to promote this gene to green status.
Undiagnosed metabolic disorders v1.350 COX8A Sarah Leigh gene: COX8A was added
gene: COX8A was added to Undiagnosed metabolic disorders. Sources: Literature
Mode of inheritance for gene: COX8A was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: COX8A were set to 26685157
Phenotypes for gene: COX8A were set to ?Mitochondrial complex IV deficiency 220110
Review for gene: COX8A was set to RED
Added comment: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 1 variant reported in a 12.5-year old girl, born of Turkish parents who were likely distantly related, with mitochondrial complex I deficiency. The proband died from cardiorespiratory failure associated with infection and metabolic crisis at 12.5 years. No further variants reported to date (30/09/2019).
Sources: Literature
Undiagnosed metabolic disorders v1.349 COQ7 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 in unrelated cases, together with supportive functional studies.
Undiagnosed metabolic disorders v1.347 TMEM126A Sarah Leigh Added comment: Comment on list classification: This gene was part of an initial gene list collated by Emma Ashton on behalf of the London North GLH, for GMS Metabolic Consensus Specialist Test Group. Additional information was not provided, such as mode of inheritance and phenotype.
Associated with the phenotype Optic atrophy 7 612989 in OMIM, but not associated with phenotype in Gen2Phen. At least 2 variants reported in unrelated cases.
The red rating is based on Helen Britain's opinion that, the phenotype of Optic atrophy 7 612989 will not present via a metabolic team. TMEM126A is green on the Optic neuropathy panel.
Undiagnosed metabolic disorders v1.344 PDK3 Sarah Leigh Added comment: Comment on list classification: This gene was part of an initial gene list collated by Emma Ashton on behalf of the London North GLH, for GMS Metabolic Consensus Specialist Test Group. Additional information was not provided, such as mode of inheritance and phenotype.
Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 2 variants reported in at least three unrelated cases, together with functional studies.
Undiagnosed metabolic disorders v1.343 PDK3 Sarah Leigh Added comment: Comment on mode of pathogenicity: A gain of function mechanism has been reported for the p.R158H variant, resulting in a more activity than the wild-type kinase (PMID: 23297365).
Undiagnosed metabolic disorders v1.342 COX4I2 Sarah Leigh changed review comment from: Comment on list classification: This gene should remain Amber due to the overall review and evidence assessment from the GMS mitochondrial specialist test group, submitted by Carl Fratter.
One homozygous variant (c.412G>A, p.E138K) reported in 5 Arab Muslim patients with exocrine pancreatic insufficiency, dyserythropoietic anemia, and calvarial hyperostosis (612714) (PMID 19268275) and heterozygous variant (c.253C>T, p.R85W) found together with a heterozygous COX10 variant (c.1096G>T, p.V366L)(PMID 22592081).; to: Comment on list classification: This gene was part of an initial gene list collated by Emma Ashton on behalf of the London North GLH, for GMS Metabolic Consensus Specialist Test Group. Additional information was not provided, such as mode of inheritance and phenotype.
This gene should remain Amber due to the overall review and evidence assessment from the GMS mitochondrial specialist test group, submitted by Carl Fratter.
One homozygous variant (c.412G>A, p.E138K) reported in 5 Arab Muslim patients with exocrine pancreatic insufficiency, dyserythropoietic anemia, and calvarial hyperostosis (612714) (PMID 19268275) and heterozygous variant (c.253C>T, p.R85W) found together with a heterozygous COX10 variant (c.1096G>T, p.V366L)(PMID 22592081).
Undiagnosed metabolic disorders v1.342 COA5 Sarah Leigh changed review comment from: Associated with phenotype in OMIM and as a possible G2P. At least 1 variant reported.; to: This gene was part of an initial gene list collated by Emma Ashton on behalf of the London North GLH, for GMS Metabolic Consensus Specialist Test Group. Additional information was not provided, such as mode of inheritance and phenotype. Associated with phenotype in OMIM and as a possible G2P. At least 1 variant reported.
Undiagnosed metabolic disorders v1.342 ATP5E Sarah Leigh changed review comment from: Comment on list classification: Updated information and Amber review collated by Carl Fratter May 2019 on behalf of GMS mitochondrial specialist test group: 1 reported case with functional studies.; to: Comment on list classification: This gene was part of an initial gene list collated by Emma Ashton on behalf of the London North GLH, for GMS Metabolic Consensus Specialist Test Group. Additional information was not provided, such as mode of inheritance and phenotype. Updated information and Amber review collated by Carl Fratter May 2019 on behalf of GMS mitochondrial specialist test group: 1 reported case with functional studies.
Undiagnosed metabolic disorders v1.328 COX4I2 Sarah Leigh Added comment: Comment on list classification: This gene should remain Amber due to the overall review and evidence assessment from the GMS mitochondrial specialist test group, submitted by Carl Fratter.
One homozygous variant (c.412G>A, p.E138K) reported in 5 Arab Muslim patients with exocrine pancreatic insufficiency, dyserythropoietic anemia, and calvarial hyperostosis (612714) (PMID 19268275) and heterozygous variant (c.253C>T, p.R85W) found together with a heterozygous COX10 variant (c.1096G>T, p.V366L)(PMID 22592081).
Undiagnosed metabolic disorders v1.320 ATP5E Sarah Leigh Added comment: Comment on list classification: Updated information and Amber review collated by Carl Fratter May 2019 on behalf of GMS mitochondrial specialist test group: 1 reported case with functional studies.
Undiagnosed metabolic disorders v1.312 SPR Catherine Snow changed review comment from: Promoted from Amber to Green. This gene is associated with a relevant disease on OMIM and Gene2Phenotype and there is enough evidence to support a gene-disease association. Sepiapterin reductase (SR) deficiency leads to altered tetrahydrobiopterin (BH4) biosynthesis and abnormal biogenic amine metabolism. Most individuals improve with L-dopa administration, therefore treatable tag has been added.; to: Promoted from Amber to Green. This gene is associated with a relevant disease in OMIM and Gene2Phenotype and there is enough evidence to support a gene-disease association. Sepiapterin reductase (SR) deficiency leads to altered tetrahydrobiopterin (BH4) biosynthesis and abnormal biogenic amine metabolism. Most individuals improve with L-dopa administration, therefore treatable tag has been added.
Undiagnosed metabolic disorders v1.310 SLC25A12 Ivone Leong Added comment: Comment on list classification: Promoted from Amber to Green. Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 3 biallelic variants reported in unrelated cases.
Undiagnosed metabolic disorders v1.309 SLC25A12 Ivone Leong Phenotypes for gene: SLC25A12 were changed from Disorders of mitochondrial solute import (Mitochondrial respiratory chain disorders (caused by nuclear variants only)); Inherited white matter disorders to Disorders of mitochondrial solute import (Mitochondrial respiratory chain disorders (caused by nuclear variants only)); Inherited white matter disorders; Epileptic encephalopathy, early infantile, 39 612949; Hypomyelination, global cerebral, 612949
Undiagnosed metabolic disorders v1.306 SC5D Ivone Leong Added comment: Comment on list classification: Promoted from Amber to Green. This gene is associated with a relevant disease on OMIM and Gene2Phenotype and there is enough evidence to support a gene-disease association.
Undiagnosed metabolic disorders v1.305 RNASEH2B Ivone Leong changed review comment from: Comment on list classification: Demoted from Amber to Red. RNASEH2B is associated with Aicardi-Goutieres syndrome 2 on OMIM and Gene2Phenotype. There are 2 unrelated cases on OMIM supporting the gene-disease link between RNASEH2B with Aicardi-Goutieres syndrome; however, RNASEH2B does not appear to be associated with a metabolic phenotype. Therefore this gene has been demoted to red.; to: Comment on list classification: Demoted from Amber to Red. RNASEH2B is associated with Aicardi-Goutieres syndrome 2 on OMIM and Gene2Phenotype. There are 2 unrelated cases on OMIM about RNASEH2B causing Aicardi-Goutieres syndrome; however, RNASEH2B does not appear to be associated with a metabolic phenotype. Therefore this gene has been demoted to red.
Undiagnosed metabolic disorders v1.304 RNASEH2B Ivone Leong Added comment: Comment on list classification: Demoted from Amber to Red. RNASEH2B is associated with Aicardi-Goutieres syndrome 2 on OMIM and Gene2Phenotype. There are 2 unrelated cases on OMIM supporting the gene-disease link between RNASEH2B with Aicardi-Goutieres syndrome; however, RNASEH2B does not appear to be associated with a metabolic phenotype. Therefore this gene has been demoted to red.
Undiagnosed metabolic disorders v1.302 RNASEH2A Ivone Leong changed review comment from: RNASEH2A is associated with Aicardi-Goutieres syndrome 4 on OMIM and Gene2Phenotype. RNASEH2A does not appear to be associated with a metabolic phenotype. Therefore this gene will remain Amber.; to: RNASEH2A is associated with Aicardi-Goutieres syndrome 4 on OMIM and Gene2Phenotype. There are >3 unrelated cases on OMIM supporting the gene-disease link between RNASEH2A with Aicardi-Goutieres syndrome; however, RNASEH2A does not appear to be associated with a metabolic phenotype. Therefore this gene has been demoted to red.
Undiagnosed metabolic disorders v1.301 HARS2 Sarah Leigh Added comment: Comment on publications: PMID: 21464306: One family reported, with five affected siblings who were compound heterozygous for variants L200V and V368L. Functional evidence in c.elegans was provided. PMID: 27650058: patients with sporadic Perrault syndrome IV-1 and VI-I were homozygous for the c.1010A>G (p.Tyr337Cys) variant. The patients were claimed not to be related, but originated from the same region in Morocco and the variant was characterised as being in the same haplotype, suggesting a founder effect. Found at a frequency of 1/121332 in Exac.
Undiagnosed metabolic disorders v1.299 FECH Sarah Leigh Added comment: Comment on phenotypes: Erythropoietic protoporphyria (Porphyrias with acute painful photosensitivity);Erythropoietic protoporphyria, mild variant
Undiagnosed metabolic disorders v1.299 FECH Sarah Leigh Phenotypes for gene: FECH were changed from Erythropoietic protoporphyria (Porphyrias with acute painful photosensitivity); Erythropoietic protoporphyria, mild variant to Protoporphyria, erythropoietic, 1 177000
Undiagnosed metabolic disorders v1.295 DHODH Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene. At least 11 variants reported in 6 families (PMID 19915526), together with a knockout mouse model (PMID 27626380).
Undiagnosed metabolic disorders v1.292 DHCR24 Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene. At least 7 variants reported in at least cases, two of the variants were in cis in a case which was compound heterozygous with another variant (PMID 11519011). Supportive functional studies were also presented.
Undiagnosed metabolic disorders v1.276 CLDN19 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 at least 6 unrelated cases.
Undiagnosed metabolic disorders v1.271 CISD2 Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as both RD and IF Gen2Phen gene. At least 3 variants reported in unrelated cases, together with segration and functional studies.
Undiagnosed metabolic disorders v1.266 ALPL Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene. At least 16 variants reported in hypophosphatasia, infantile 241500, some of these variants and others were found in childhood and adult Hypophosphatasia and two addtional variants were reported in a case of perinatal lethal hypophosphatasia (PMID 11745997).
Undiagnosed metabolic disorders v1.256 ALDH3A2 Sarah Leigh edited their review of gene: ALDH3A2: Added comment: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene. At least 9 variants reported.; Changed rating: GREEN; Changed publications: 27604308, 10792573, 10577908; Changed phenotypes: Sjogren-Larsson syndrome 270200
Undiagnosed metabolic disorders v1.256 ALAS2 Sarah Leigh edited their review of gene: ALAS2: Added comment: Associated with phenotype in OMIM and not in Gen2Phen. At least 18 variants identified in Anemia, sideroblastic, 1 300751 and two variants in Protoporphyria, erythropoietic, X-linked 300752 in six unrelated families, together with functional studies.; Changed rating: GREEN; Changed publications: 27604308, 1570328, 7560104, 12663458, 18760763; Changed phenotypes: Anemia, sideroblastic, 1 300751, Protoporphyria, erythropoietic, X-linked 300752
Undiagnosed metabolic disorders v1.256 ADSL Sarah Leigh edited their review of gene: ADSL: Added comment: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene. At least 8 variants reported associated with adenylosuccinase deficiency in at least 10 unrelated cases.; Changed rating: GREEN; Changed publications: 27604308, 18830228, 12016589, 10090474; Changed phenotypes: Adenylosuccinase deficiency 103050, Intellectual disability, Epileptic encephalopathy
Undiagnosed metabolic disorders v1.256 ADA Sarah Leigh edited their review of gene: ADA: Added comment: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene. At least 30 variants reported associated with Adenosine deaminase deficiency.; Changed rating: GREEN; Changed publications: 27604308, 3684597, 2783588, 1680289; Changed phenotypes: Adenosine deaminase deficiency, partial 102700, Severe combined immunodeficiency due to ADA deficiency 102700, Combined B and T cell defect, SCID, Infantile enterocolitis & monogenic inflammatory bowel disease
Undiagnosed metabolic disorders v1.256 ACY1 Sarah Leigh edited their review of gene: ACY1: Added comment: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene. At least 7 variants reported in at least 9 unrelated cases.; Changed rating: GREEN; Changed publications: 27604308, 24117009, 17562838, 16465618; Changed phenotypes: Aminoacylase 1 deficiency 609924, Intellectual disability
Undiagnosed metabolic disorders v1.254 PSAT1 Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as probable Gen2Phen gene for ?Phosphoserine aminotransferase deficiency 610992; Neu-Laxova syndrome 2 616038. At least 5 variants reported in 6 cases of Neu-Laxova syndrome 2 616038 and 2 variants in a case of ?Phosphoserine aminotransferase deficiency 610992.
Undiagnosed metabolic disorders v1.251 PRPS1 Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene for Arts syndrome 301835, Charcot-Marie-Tooth disease, X-linked recessive, 5 311070, Deafness, X-linked 1 304500 and Phosphoribosylpyrophosphate synthetase superactivity 300661. At least 22 variants have been reported across the phenotypes.
Undiagnosed metabolic disorders v1.246 POR Sarah Leigh Publications for gene: POR were set to 27604308
Undiagnosed metabolic disorders v1.245 POR Sarah Leigh Classified gene: POR as Green List (high evidence)
Undiagnosed metabolic disorders v1.245 POR Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 10 variants associated with Antley-Bixler syndrome with genital anomalies and disordered steroidogenesis 201750 and 6 variants associated with Disordered steroidogenesis due to cytochrome P450 oxidoreductase 613571.
Undiagnosed metabolic disorders v1.245 POR Sarah Leigh Gene: por has been classified as Green List (High Evidence).
Undiagnosed metabolic disorders v1.244 POR Sarah Leigh Phenotypes for gene: POR were changed from Antley-Bixler syndrome with disordered steroidogenesis; Craniosynostosis syndromes phenotypes; Disorders of sex development; Unexplained skeletal dysplasia to Antley-Bixler syndrome with genital anomalies and disordered steroidogenesis 201750; Disordered steroidogenesis due to cytochrome P450 oxidoreductase 613571
Undiagnosed metabolic disorders v1.243 POR Sarah Leigh Deleted their comment
Undiagnosed metabolic disorders v1.243 POR Sarah Leigh Deleted their comment
Undiagnosed metabolic disorders v1.243 POR Sarah Leigh Deleted their comment
Undiagnosed metabolic disorders v1.243 POR Sarah Leigh Deleted their comment
Undiagnosed metabolic disorders v1.243 POR Sarah Leigh Deleted their comment
Undiagnosed metabolic disorders v1.242 PNP Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 10 variants reported.
Undiagnosed metabolic disorders v1.240 PINK1 Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 12 variants were reported.
Undiagnosed metabolic disorders v1.237 PIGM Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as possible Gen2Phen gene. At least 1 variant was reported in 2 unrelated families (PMID 16767100), together with supportive functional studies (PMID 17442906 & 25293775).
Undiagnosed metabolic disorders v1.233 PHGDH Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene for both phenotypes. At least 6 variants reported in 6 unrelated cases of Phosphoglycerate dehydrogenase deficiency 601815 and 4 variants reported in 4 unrelated cases of Neu-Laxova syndrome 1 256520.
Undiagnosed metabolic disorders v1.230 PEPD Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene. At least 11 variants reported.
Undiagnosed metabolic disorders v1.228 PDPR Sarah Leigh Added comment: Comment on list classification: Not associated with a phenotype in OMIM or in Gen2Phen. At least 1 variant reported in a case of global developmental delay, typical Joubert syndrome, according to PMID 25558065.
Undiagnosed metabolic disorders v1.226 PCSK9 Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 3 gain of function variants reported in unrelated cases of Hypercholesterolemia, familial, 3 603776 and at least 5 loss of function variants have been reported in unrelated cases of {Low density lipoprotein cholesterol level QTL 1} 603776.
Undiagnosed metabolic disorders v1.223 PCK1 Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 3 variants reported in unrelated cases.
Undiagnosed metabolic disorders v1.218 PANK2 Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 13 variants reported for Neurodegeneration with brain iron accumulation 234200 and 3 variants in 2 unrelated cases of HARP syndrome 607236.
Undiagnosed metabolic disorders v1.216 OPLAH Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 3 variants have been reported. It is not clear whether the mode of inheritance is biallelic or monoallelic as homozygous and heterozygote cases have been seen. The PMID 21651516 reports two sibs who are homozygous for a terminating variant, the younger brother is 5-oxoprolinase deficiency, however, his clinically unaffected sister just has increased 5-oxoproline excretion.
Undiagnosed metabolic disorders v1.213 OCRL Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene for both Dent disease 2 300555 and Lowe syndrome 309000. At least 5variants reported in Dent disease 2 300555 and 4 variants in Lowe syndrome 309000.
Undiagnosed metabolic disorders v1.212 OCRL Sarah Leigh Added comment: Comment on phenotypes: Lowe syndrome (Disorders of amino acid transport);Cataracts;Intellectual disability;Intellectual_disability;Renal tract calcification (or Nephrolithiasis/nephrocalcinosis)
Undiagnosed metabolic disorders v1.212 OCRL Sarah Leigh Phenotypes for gene: OCRL were changed from Lowe syndrome (Disorders of amino acid transport); Cataracts; Intellectual disability; Intellectual_disability; Renal tract calcification (or Nephrolithiasis/nephrocalcinosis) to Dent disease 2 300555; Lowe syndrome 309000
Undiagnosed metabolic disorders v1.210 NDUFB9 Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 1 variant reported, together with supportive functional studies.
Undiagnosed metabolic disorders v1.209 NDUFB9 Sarah Leigh Added comment: Comment on publications: PMID: 22200994 Reports one probound heterozygous for a variant (c.140G>T, p.Arg47Leu) within NDUFB9 with parents not available for genetic testing, and in vitro complement studies in patient fibroblasts showed wildtype NDUFB9 did not rescue complex I activity, therefore was deemed not pathogenic. Reports two brothers homozygous for a variant in the gene, with parents who are heterozygous carriers (c.191T>C, p.Leu64Pro). In vitro, fibroblasts from the proband showed low complex I activity, and wildtype NDUFB9 rescued complex I activity.
Undiagnosed metabolic disorders v1.206 MVK Sarah Leigh changed review comment from: Comment on list classification: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 8 variants reported in Hyper-IgD syndrome 260920, 9 variants reported in Mevalonic aciduria 610377 and 8 variants reported in Porokeratosis 3, multiple types 175900.; to: Comment on list classification: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. Numerous variants reported for each phenotype.
Undiagnosed metabolic disorders v1.205 MVK Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 8 variants reported in Hyper-IgD syndrome 260920, 9 variants reported in Mevalonic aciduria 610377 and 8 variants reported in Porokeratosis 3, multiple types 175900.
Undiagnosed metabolic disorders v1.204 MVK Sarah Leigh Phenotypes for gene: MVK were changed from Mevalonate kinase deficiency (Disorders of sterol biosynthesis); Infantile enterocolitis & monogenic inflammatory bowel disease to Hyper-IgD syndrome 260920; Mevalonic aciduria 610377; Porokeratosis 3, multiple types 175900
Undiagnosed metabolic disorders v1.201 MTPAP Sarah Leigh Added comment: Comment on list classification: Associated with phenotype in OMIM and not in Gen2Phen. At least 2 variants identified in unrelated cases, and supportive functional studies.
Undiagnosed metabolic disorders v1.200 MTFMT Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 8 variants reported.
Undiagnosed metabolic disorders v1.194 MOCS2 Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene. At least 9 variants reported in at least 8 unrelated cases, together with supportive functional studies.
Undiagnosed metabolic disorders v1.191 MOCS1 Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene. At least 5 variants reported unrelated cases.
Undiagnosed metabolic disorders v1.187 MAOA Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene. At least 4 variants reported in unrelated cases.
Undiagnosed metabolic disorders v1.185 MAGT1 Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as possible Gen2Phen gene. At least 3 variants reported in unrelated cases, together with mouse knock-out model (PMID 29581357).
Undiagnosed metabolic disorders v1.183 LIPC Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 3 variants reported in two unrelated families with Hepatic lipase deficiency, 614025.
Undiagnosed metabolic disorders v1.182 LIPC Sarah Leigh Added comment: Comment on list classification: This gene was part of an initial gene list collated by Emma Ashton on behalf of the London North GLH, for GMS Metabolic Consensus Specialist Test Group. Additional information was not provided, such as mode of inheritance and phenotype.
Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 3 variants reported in two unrelated families with Hepatic lipase deficiency, 614025.
Undiagnosed metabolic disorders v1.177 LDLRAP1 Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 11 variants reported.
Undiagnosed metabolic disorders v1.173 LDLR Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. Over 2000 variants reported.
Undiagnosed metabolic disorders v1.169 LBR Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene for Greenberg skeletal dysplasia 215140. At least 15 variants have been reported, in 5 unrelated cases of Pelger-Huet anomaly 169400, 3 unrelated cases of Pelger-Huet anomaly with mild skeletal anomalies 618019, 5 unrelated cases of Greenberg skeletal dysplasia 215140 and in a single case of ?Reynolds syndrome 613471.
Undiagnosed metabolic disorders v1.167 ISCU Sarah Leigh Added comment: Comment on list classification: Sufficient published reported biallelic cases, with supportive functional studies. The most frequent reported variant c.343+382G>C g.108567650G>C is deep in intron five of the gene and strengthens a weak splicing acceptor site, with consequent retention of a 100-bp intronic sequence upstream of the known terminal exon, introduction of a stop codon and decreased levels of ISCU mRNA and protein (PMID 18304497). This may be missed by standard sequencing.
Undiagnosed metabolic disorders v1.165 HSD17B10 Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene for 2-methyl-3-hydroxybutyrylL-coA dehydrogenase deficiency and for mental retardation syndromic X-linked type 10 . At least 8 variants reported.
Undiagnosed metabolic disorders v1.161 HPS1 Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene. At least 7 variants reported in at least 5 unrelated cases.
Undiagnosed metabolic disorders v1.158 HPD Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as probable Gen2Phen gene for both phenotypes. At least 4 variants reported in unrelated cases of Tyrosinemia, type III 276710 and 4 variants in 6 unrelated cases of Hawkinsinuria 140350 (at least 2 of these cases were compound heterozygotes).
Undiagnosed metabolic disorders v1.155 HADH Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene. Numerous variants reported in unrelated cases of Hyperinsulinemic hypoglycemia, familial, 4 609975.
Undiagnosed metabolic disorders v1.152 GNMT Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 3 variants reported in 2 unrelated cases, with supportive functional data.
Undiagnosed metabolic disorders v1.150 GLUL Sarah Leigh Added comment: Comment on list classification: This gene was part of an initial gene list collated by Emma Ashton on behalf of the London North GLH, for GMS Metabolic Consensus Specialist Test Group. Additional information was not provided, such as mode of inheritance and phenotype.
Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene. At least 3 variants reported in unrelated cases.
Undiagnosed metabolic disorders v1.147 GK Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene. At least 8 variants reported.
Undiagnosed metabolic disorders v1.145 GK Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene. At least 8 variants reported.
Undiagnosed metabolic disorders v1.140 GAMT 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 4 unrelated cases.
Undiagnosed metabolic disorders v1.138 FTCD Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene. At least 15 variants reported.
Undiagnosed metabolic disorders v1.136 FGFR2 Sarah Leigh Added comment: Comment on list classification: Associated with 14 phenotypes in OMIM and as confirmed Gen2Phen gene for acrocephalosyndactyly type V, Antley-Bixler syndrome, Apert syndrome, Beare-Stevenson cutis gyrata syndrome, Crouzon syndrome, familial scaphocephaly syndrome, Jackson-Weiss syndrome, lacrimo-auriculo-dento-digital syndrome. At least 44 variants reported.
Undiagnosed metabolic disorders v1.132 DPM3 Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as probable Gen2Phen gene. At least 2 variants reported as homozygotes in two unrelated cases, together with segregation and supportive functional studies.
Undiagnosed metabolic disorders v1.124 POLG2 Sarah Leigh Added comment: Comment on mode of inheritance: Reporting and characterization of a homozygous POLG2 variant in mitochondrial DNA depletion syndrome and in an autosomal recessive epilepsy family without ophthalmoplegia (PMID 27592148; 30157269; 31286721).
Undiagnosed metabolic disorders v1.121 RANBP2 Sarah Leigh Added comment: Comment on list classification: Demoted RANBP2 from Green to Amber following review by Zornitza Stark and agreement from Helen Brittain (Genomics England clinical team). Recent papers report patients with symptoms (including seizures) after a viral illness (PMID:30796099, PMID:28336122, PMID:25128471). However, listed as a susceptibility locus in OMIM, and papers report incomplete penetrance: variant present in asymptomatic maternal grandmother in PMID:30796099 and in the father in PMID:28336122. Therefore further information (e.g. on penetrance) is required for a clear gene:disease association.
Undiagnosed metabolic disorders v1.120 DHCR7 Sarah Leigh Added comment: Comment on list classification: Associated with phenotype in OMIM and as confirmed Gen2Phen gene. At least 21 variants reported.
Undiagnosed metabolic disorders v1.117 FUT8 Louise Daugherty gene: FUT8 was added
gene: FUT8 was added to Undiagnosed metabolic disorders. Sources: Expert Review
Mode of inheritance for gene: FUT8 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: FUT8 were set to 29304374
Phenotypes for gene: FUT8 were set to Congenital disorder of glycosylation with defective fucosylation, 618005
Review for gene: FUT8 was set to GREEN
Added comment: Adding to Undiagnosed metabolic disorders panel after reviewing panels for GMS, as recommended by the Genomics England clinical team, to benefit the 100K participants. Enough evidence to support gene-disease association and relevance to this panel to rate this gene Green.
Sources: Expert Review
Undiagnosed metabolic disorders v1.114 ARSG Sarah Leigh changed review comment from: Candidate gene for neuronal ceroid lipofuscinosis as reported in dogs and mice models (PubMed: 20679209, 22689975, 25452429, 26975023) and in a ; to: Candidate gene for neuronal ceroid lipofuscinosis as reported in dogs and mice models (PubMed: 20679209, 22689975, 25452429, 26975023) and in 5 affected members of 3 consanguineous Yemenite Jewish families (PMID 29300381).
Undiagnosed metabolic disorders v1.112 ARSG Sarah Leigh changed review comment from: Candidate gene for neuronal ceroid lipofuscinosis as reported in dogs and mice; to: Candidate gene for neuronal ceroid lipofuscinosis as reported in dogs and mice models (PubMed: 20679209, 22689975, 25452429, 26975023) and in a
Undiagnosed metabolic disorders v1.106 UQCRQ Sarah Leigh Added comment: Comment on list classification: Amber review collated by Carl Fratter (May 2019) on behalf of GMS mitochondrial specialist test group: One variant reported in a consanguineous Israeli Bedouin kindred with Mitochondrial complex III deficiency, nuclear type 4 (615159)(PMID: 18439546).
Undiagnosed metabolic disorders v1.104 MANBA Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene. At least 9 variants reported in 6 unrelated cases.
Undiagnosed metabolic disorders v1.102 ASAH1 Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene. At least 7 variants reported in 6 cases of Farber lipogranulomatosis 228000 and 5 variants in 3 cases of Spinal muscular atrophy with progressive myoclonic epilepsy 159950.
Undiagnosed metabolic disorders v1.97 NDUFA1 Ellen McDonagh Added comment: Comment on mode of inheritance: Changed from 'Both monoallelic and biallelic' to X-linked, as encoded on the X-chromosome. One study reports a female with a heterozygous variant who developed a very mild form of complex I deficiency due to skewed X inactivation [PMID: 21596602].
Undiagnosed metabolic disorders v1.92 SLC35A1 Rebecca Foulger Added comment: Comment on list classification: Updated rating from Red to Green as agreed with Helen Brittain following review of 2018 paper (PMID:30115659) and promotion to Green on the 'Congenital disorders of glycosylation' panel. In addition to the 'leaky' polymorphism reported in PMID:15576474, there are 3 cases (PMIDs 23873973, 28856833, 30115659) to support causation of glycosylation disorder.
Undiagnosed metabolic disorders v1.90 ATAD3A Julia Baptista gene: ATAD3A was added
gene: ATAD3A was added to Undiagnosed metabolic disorders. Sources: Literature
Mode of inheritance for gene: ATAD3A was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: ATAD3A were set to 27640307
Phenotypes for gene: ATAD3A were set to Lactic acidosis; Methylglutaconic aciduria; Neurological abnormalities; Cerebellar hypoplasia; Optic atrophy; Hypertrophic cardiomyopathy; Scoliosis; Spinal muscular atrophy
Review for gene: ATAD3A was set to GREEN
gene: ATAD3A was marked as current diagnostic
Added comment: A raised plasma lactate was reported in 4/7 families and methylglutaconic aciduria in 3/7 families (PMID: 27640307). Multiple patients with a diagnosis are described as having "severe metabolic disease".
Sources: Literature
Undiagnosed metabolic disorders v1.87 SLC25A4 Rebecca Foulger Phenotypes for gene: SLC25A4 were changed from Required for mtDNA maintenance (Mitochondrial respiratory chain disorders (caused by nuclear variants only)); Disorders of mitochondrial DNA maintenance and integrity; Disorders of mitochondrial protein transport; Progressive external ophthalmoplegia with mitochondrial DNA deletions 3, 609283Mitochondrial DNA depletion syndrome 12 (cardiomyopathic type), 615418; Progressive External Ophthalmoplegia with Mitochondrial DNADeletions to Required for mtDNA maintenance (Mitochondrial respiratory chain disorders (caused by nuclear variants only)); Disorders of mitochondrial DNA maintenance and integrity; Disorders of mitochondrial protein transport; Progressive external ophthalmoplegia with mitochondrial DNA deletions 3, 609283; Mitochondrial DNA depletion syndrome 12 (cardiomyopathic type), 615418; Progressive External Ophthalmoplegia with Mitochondrial DNADeletions
Undiagnosed metabolic disorders v1.82 RPIA Sarah Leigh commented on gene: RPIA: Review by Konstantinos Varvagiannis for the Genetic Epilepsy syndromes panel. 9 Dec 2018, 1:44 a.m.
Panel version: 0.1488
Biallelic pathogenic variants in RPIA cause Ribose 5-phosphate isomerase deficiency, MIM 608611. PMID: 14988808 is the first report on the disorder with molecular (incl. genetic) confirmation of the diagnosis. A patient initially investigated for early developmental delay, leukoencephalopathy, seizures with onset at 4 years, with subsequent neurologic regression and peripheral neuropathy at the age of 7, was suspected to have a disorder of the pentose phosphate pathway on the basis of highly elevated polyols on brain MRS and body fluid analysis. Reduced ribose 5-phosphate isomerase activity was shown in fibroblasts. Genetic testing demonstrated the presence of a missense (NM_144563.2:c.404C>T or p.Ala135Val - previously referred to as A61V) as well as a frameshift variant (NM_144563.2:c.762delG or p.Asn255Ilefs). Additional extensive supportive functional studies were published a few years later (PMID: 20499043). [This patient was initially described in PMID: 10589548]. PMID: 28801340 is a report on a second patient. This individual presented with delayed early development (independent walking and speech achieved at 2 and 5 years respectively), seizures and regression at the age of 7 with MRI white matter abnormalities. Review of magnetic resonance spectroscopy (MRS) was suggestive of elevated polyols (arabitol and ribitol). In line with this, genetic testing revealed a homozygous missense variant in RPIA (NM_144563.2:c.592T>C or p.Phe198Leu). Urine analysis confirmed elevated excretion of polyols, thus confirming the diagnosis. PMID: 30088433 reports on a boy with neonatal onset leukoencephalopathy and developmental delay having undergone early metabolic testing and aCGH (the latter at the age of 16 months). Persistance of his delay motivated exome sequencing at the age of approx. 4.5 years which demonstrated 2 RPIA variants (NM_144563.2:c.253G>A or p.Ala85Thr and NM_144563.2:c.347-1G>A). Measurement of ribitol and arabitol in urine demonstrated significant elevations (>20x) consistent with this diagnosis. 2 of the 3 patients described in the literature presented seizures. As a result this gene can be considered for inclusion in this panel as amber. [This gene is also present in the Undiagnosed metabolic disorders gene panel as red. Please consider upgrade based on these further publications.]. Sources: Literature
Undiagnosed metabolic disorders v1.81 RPIA Sarah Leigh Added comment: Comment on list classification: Based on additional variants reported in PMIDs 28801340; 30088433.
Undiagnosed metabolic disorders POR Sarah Leigh edited their review of POR
Undiagnosed metabolic disorders POR Sarah Leigh edited their review of POR
Undiagnosed metabolic disorders POR Sarah Leigh edited their review of POR
Undiagnosed metabolic disorders POR Sarah Leigh edited their review of POR
Undiagnosed metabolic disorders POR Sarah Leigh edited their review of POR
Undiagnosed metabolic disorders POR Sarah Leigh reviewed POR