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| Undiagnosed metabolic disorders v1.640 | CPOX | Ida Ertmanska Mode of inheritance for gene: CPOX was changed from BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.637 | CPOX |
Ida Ertmanska changed review comment from: Comment on mode of inheritance: As reviewed by Sharon Whatley, variants in CPOX may cause autosomal dominant or autosomal recessive porphyria. Biallelic variants tend to cause earlier onset and more severe symptoms. Hence, the MOI should be changed from 'BOTH monoallelic and biallelic, autosomal or pseudoautosomal' to 'BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal'. CPOX is associated with Coproporphyria 121300 (AR and AD) and Harderoporphyria 618892 (AR) in OMIM (accessed 20th Oct 2025).; to: Comment on mode of inheritance: As reviewed by Sharon Whatley, variants in CPOX may cause autosomal dominant or autosomal recessive porphyria. Monoallelic variants in CPOX have very low clinical penetrance (<1%) and may be challenging to report as diagnostic. Hence, BIALLELIC, autosomal or pseudoautosomal MOI would be more appropriate. CPOX is associated with Coproporphyria 121300 (AR and AD) and Harderoporphyria 618892 (AR) in OMIM (accessed 20th Oct 2025). |
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| Undiagnosed metabolic disorders v1.637 | CPOX | Ida Ertmanska Mode of inheritance for gene CPOX was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.634 | CPOX | Ida Ertmanska reviewed gene: CPOX: Rating: GREEN; Mode of pathogenicity: None; Publications: 6886003, 7757079, 8012360, 9454777, 10505225, 11074238, 11309681, 16159891, 21103937, 23236641, 23605133, 30828546, 33008663, 37540847, 38940544, 40296768; Phenotypes: Coproporphyria, OMIM:121300, Harderoporphyria, OMIM:618892; Mode of inheritance: BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.632 | CPOX | Sharon Whatley reviewed gene: CPOX: Rating: GREEN; Mode of pathogenicity: None; Publications: 38940544, 11309681, 37540847, 23236641, 11074238, 23605133, 16159891, 40296768, 33008663, 30828546, 21103937, 16159891, 10505225, 9454777, 7757079, 8012360, 6886003; Phenotypes: 121300, 618892; Mode of inheritance: BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.631 | PPOX |
Sharon Whatley changed review comment from: Relevant metabolic investigation: urine porphobilinogen and plasma porphyrin fluorescence emission PMID: 38940544 Aarsand reports that the acute porphyrias are a group of rare inborn errors of metabolism caused by abnormal functioning of haem biosynthesis enzymes and are associated with acute neurovisceral attacks characterized by severe abdominal pain and neuropsychiatric symptoms that may require highly specialized intensive care. The acute porphyrias, acute intermittent porphyria (AIP), variegate porphyria (VP) and hereditary coproporphyria (HCP), usually become symptomatic in early adulthood. PMID: 10486317 Whatley found that skin lesions were the only manifestation of VP in 59% of patients whereas 21% of patients had acute attacks and skin lesions. The remainder having only acute attacks. PMID: 8290408 Hift reports that the cutaneous VP presents with photosensitivity which may result in blistering, erosions, a fragile skin with chronic scarring and pigmentary changes PMID: 38940544 Aarsand reports that VP is an autosomal dominant disorder and estimates that individuals with a predisposition for VP in the general population is 1/3,000 (except where founder effects occur e.g. South Africa). A rough estimate of the penetrance of pathogenic variants in this gene is given as 1%. Due to this low penetrance, genetic testing alone may be misleading and cause misdiagnosis. IPNET advises that VP is diagnosed using biochemical tests (urine porphobilinogen during an acute attack followed by plasma porphyrin fluorescence emission or if the patient only has cutaneous symptoms plasma porphyrin fluorescence emission) as the penetrance of variegate porphyria is so low PMID: 37879139 Assaleh reports that biallelic VP is rare. To the best of our knowledge there are 25 patients (in 21 families) reported with homozygous VP (PMID: 40114189 Kaiser, 37879139 Assaleh, 33159949 Cho and references therein). It usually presents in infancy with severe cutaneous manifestations. In some cases, patients may have hand deformities, nystagmus, growth delay and intellectual disability. Careful consideration should be given to the reporting of a single pathogenic variant as an incidental finding in the PPOX gene, due to its low clinical penetrance.; to: Relevant metabolic investigation: urine porphobilinogen and plasma porphyrin fluorescence emission PMID: 38940544 Aarsand reports that the acute porphyrias are a group of rare inborn errors of metabolism caused by abnormal functioning of haem biosynthesis enzymes and are associated with acute neurovisceral attacks characterized by severe abdominal pain and neuropsychiatric symptoms that may require highly specialized intensive care. The acute porphyrias, acute intermittent porphyria (AIP), variegate porphyria (VP) and hereditary coproporphyria (HCP), usually become symptomatic in early adulthood. PMID: 10486317 Whatley found that skin lesions were the only manifestation of VP in 59% of patients whereas 21% of patients had acute attacks and skin lesions. The remainder having only acute attacks. PMID: 8290408 Hift reports that the cutaneous VP presents with photosensitivity which may result in blistering, erosions, a fragile skin with chronic scarring and pigmentary changes PMID: 38940544 Aarsand reports that VP is an autosomal dominant disorder and estimates that individuals with a predisposition for VP in the general population is 1/3,000 (except where founder effects occur e.g. South Africa). A rough estimate of the penetrance of pathogenic variants in this gene is given as 1%. Due to this low penetrance, genetic testing alone may be misleading and cause misdiagnosis. IPNET advises that VP is diagnosed using biochemical tests (urine porphobilinogen during an acute attack followed by plasma porphyrin fluorescence emission or if the patient only has cutaneous symptoms plasma porphyrin fluorescence emission) as the penetrance of VP is so low PMID: 37879139 Assaleh reports that biallelic VP is rare. To the best of our knowledge there are 25 patients (in 21 families) reported with homozygous VP (PMID: 40114189 Kaiser, 37879139 Assaleh, 33159949 Cho and references therein). It usually presents in infancy with severe cutaneous manifestations. In some cases, patients may have hand deformities, nystagmus, growth delay and intellectual disability. Careful consideration should be given to the reporting of a single pathogenic variant as an incidental finding in the PPOX gene, due to its low clinical penetrance. |
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| Undiagnosed metabolic disorders v1.631 | PPOX | Sharon Whatley reviewed gene: PPOX: Rating: GREEN; Mode of pathogenicity: None; Publications: 38940544, 10486317, 8290408, 38940544, 37879139, 40114189, 33159949; Phenotypes: 176200, 620483; Mode of inheritance: BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.627 | HMBS | Sharon Whatley reviewed gene: HMBS: Rating: GREEN; Mode of pathogenicity: None; Publications: 38940544, 27539938, 14262853, 1577472, 15534187, 14970743, 27558376, 31153822, 34089223; Phenotypes: 176000, 620711, 620704; Mode of inheritance: BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.596 | SLC12A3 | Sarah Leigh commented on gene: SLC12A3: Heterozygous digenic SLC12A3 and CLCNKB variants have been associated with a variant of Gitelman syndrome (PMID: 26770037;30999883). However, the current GMS rare disease bioinformatic pipeline does not allow for interpretation of digenic events. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.595 | SLC22A5 | Sarah Leigh changed review comment from: Comment on mode of inheritance: The mode of inheritance for SLC22A5 variants should be BOTH Monoallelic and Biallelic. Although, most of the evidence for symptoms associated SLC22A5 are seen in a patients with biallelic variants (HGNC:10969, OMIM:603377, Gen2Phen, Orphanet:118781, ClinGen), a few individuals heterozygous for SLC22A5 variants have been seen with a milder phenotype (PMID: 10545605; 11261427).; to: Comment on mode of inheritance: The mode of inheritance for SLC22A5 variants should be BIALLELIC, autosomal or pseudoautosomal. Although, heterozygous SLC22A5 variants have been seen in a few cases, these are detectable biochemically and are not associated with clear clinical presentation (PMID: 10545605; 11261427). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.574 | SPG7 | Sarah Leigh Mode of inheritance for gene: SPG7 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 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 v1.567 | GPHN | Arina Puzriakova Phenotypes for gene: GPHN were changed from Mo cofactor deficiency, complementation group C (Disorders of molybdenum cofactor metabolism); epileptic encephalopathy; Molybdenum cofactor deficiency C 615501 to Molybdenum cofactor deficiency C, OMIM:615501; Mo cofactor deficiency, complementation group C (Disorders of molybdenum cofactor metabolism) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.541 | APOA5 | Arina Puzriakova Mode of inheritance for gene: APOA5 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 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 v1.510 | EXT1 | Arina Puzriakova Mode of inheritance for gene: EXT1 was changed from BIALLELIC, autosomal or pseudoautosomal to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.509 | DNM2 | Arina Puzriakova Mode of inheritance for gene: DNM2 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.477 | APOA5 | Sarah Leigh commented on gene: APOA5: The Q3_21_MOI tag has been added to this gene as the MOI should be changed to - BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.477 | APOA5 | Sarah Leigh edited their review of gene: APOA5: Added comment: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene for familial hypertriglycidaemia. Both risk polymorphisms (PMID 12417525; 12915450) and rarer APOA5 variants have been identified in hyperchylomicronemia, late-onset (OMIM:144650) and susceptibility to hypertriglyceridemia (OMIM:145750)(PMID: 23307945; 27678447; 16200213). In general, cases carrying biallelic variants (both polymorphisms and rarer variants) have a severer phenotype than monoallelic carriers (PMID: 12417525; 23307945; 27678447; 16200213).; Changed mode of inheritance: BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.469 | ABCB7 | Ivone Leong Added comment: Comment on mode of inheritance: MOI changed from "X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)" to "X-LINKED: hemizygous mutation in males, biallelic mutations in females" as there is no evidence that carrier females have ataxia. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.469 | ABCB7 | Ivone Leong Mode of inheritance for gene: ABCB7 was changed from X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) to X-LINKED: hemizygous mutation in males, biallelic mutations in females | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.465 | ATAD3A |
Arina Puzriakova Added comment: Comment on mode of inheritance: Changed MOI from 'Biallelic' to 'Both mono- and biallelic'. At least 6 families with heterozygous variants (PMID: 27640307; 28158749) and 7 unrelated families with biallelic SNVs in this gene (PMID: 27640307; 29053797; 31727539; 32607449; 33845882). Metabolic evaluation often show elevated 3-methylglutaconate and lactate in patients with variants in this gene. |
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| Undiagnosed metabolic disorders v1.419 | AHCY | Arina Puzriakova commented on gene: AHCY: Added 'treatable' tag as some patients have shown improvement following dietary management (particularly methionine restriction and supplementation with creatine and phosphatidylcholine) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.416 | SLC25A4 | Sarah Leigh Mode of inheritance for gene: SLC25A4 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.406 | SLC35A2 | Catherine Snow reviewed gene: SLC35A2: Rating: GREEN; Mode of pathogenicity: None; Publications: 30746764; Phenotypes: Congenital disorder of glycosylation, type IIm, 300896; Mode of inheritance: X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.405 | SLC3A1 | Catherine Snow reviewed gene: SLC3A1: Rating: GREEN; Mode of pathogenicity: None; Publications: 12239244; Phenotypes: Cystinuria, 220100; Mode of inheritance: BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.403 | SLC6A3 | Catherine Snow Added comment: Comment on list classification: ted from Amber to Green. SLC6A3 is associated with an appropriate phenotype on OMIM. There are >3 unrelated cases listed on OMIM. Therefore, enough evidence for this gene to be promoted to Green status. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.402 | RBP4 | Ivone Leong Added comment: Comment on list classification: Promoted from Amber to Green. RBP4 is associated with retinoid metabolism on OMIM, but not on Gene2Phenotype. There are >3 unrelated cases listed on OMIM. Therefore, enough evidence for this gene to be promoted to Green status. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.400 | SLC6A8 | Catherine Snow reviewed gene: SLC6A8: Rating: GREEN; Mode of pathogenicity: None; Publications: 21660517; Phenotypes: Cerebral creatine deficiency syndrome 1, 300352; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.399 | SLC7A9 | Catherine Snow reviewed gene: SLC7A9: Rating: GREEN; Mode of pathogenicity: None; Publications: 12239244; Phenotypes: Cystinuria, 220100; Mode of inheritance: BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 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 |
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| Undiagnosed metabolic disorders v1.386 | WFS1 | Catherine Snow Added comment: Comment on list classification: Promoted from Amber to Green. WFS1 is associated with an appropriate phenotype on OMIM and Gene2Phenotype. There are >3 unrelated cases listed on OMIM. Therefore, enough evidence for this gene to be promoted to Green status. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.385 | VKORC1 | Catherine Snow changed review comment from: Comment on list classification: Promoted from Amber to Green. PTS is associated with an appropriate phenotype on OMIM and Gene2Phenotype. There are >3 unrelated cases listed on OMIM. Therefore, enough evidence for this gene to be promoted to Green status.; to: Comment on list classification: Promoted from Amber to Green. VKORC1 is associated with an appropriate phenotype on OMIM and Gene2Phenotype. There are >3 unrelated cases listed on OMIM. Therefore, enough evidence for this gene to be promoted to Green status. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.384 | VKORC1 | Catherine Snow reviewed gene: VKORC1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: Vitamin K-dependent clotting factors, combined deficiency of, 2, 607473, Warfarin resistance, 122700; Mode of inheritance: BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.379 | UMOD | Catherine Snow changed review comment from: Promoted from Amber to Green. UMOD is associated with an appropriate phenotype on OMIM but not in Gene2Phenotype. There are >3 unrelated cases listed on OMIM. Therefore, enough evidence for this gene to be promoted to Green status.; to: Promoted from Amber to Green. UMOD is associated with an appropriate phenotype on OMIM but not in Gene2Phenotype. There are >3 unrelated cases listed on OMIM. Therefore, enough evidence for this gene to be promoted to Green status. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.378 | UMOD | Catherine Snow reviewed gene: UMOD: Rating: GREEN; Mode of pathogenicity: None; Publications: 31422399, 29180396; Phenotypes: Hyperuricemic nephropathy, familial juvenile 1, 162000; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.371 | TAT | Catherine Snow Publications for gene: TAT were set to 27604308 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.370 | TAT | Catherine Snow Classified gene: TAT as Green List (high evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.370 | TAT | Catherine Snow Gene: tat has been classified as Green List (High Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.369 | TAT | Catherine Snow reviewed gene: TAT: Rating: GREEN; Mode of pathogenicity: None; Publications: 27604308, 28255985; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.366 | STS | Catherine Snow reviewed gene: STS: Rating: GREEN; Mode of pathogenicity: None; Publications: 1539590, 29672931; Phenotypes: Ichthyosis, X-linked, 308100; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 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 v1.357 | 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. |
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| Undiagnosed metabolic disorders v1.351 | DNM2 |
Sarah Leigh gene: DNM2 was added gene: DNM2 was added to Undiagnosed metabolic disorders. Sources: Other Mode of inheritance for gene: DNM2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Phenotypes for gene: DNM2 were set to Centronuclear myopathy 1 160150; -Marie-Tooth disease, axonal type 2M 606482; Charcot-Marie-Tooth disease, dominant intermediate B 606482 |
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| Undiagnosed metabolic disorders v1.351 | DNM2 |
Sarah Leigh gene: DNM2 was added gene: DNM2 was added to Undiagnosed metabolic disorders. Sources: Other Mode of inheritance for gene: DNM2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Phenotypes for gene: DNM2 were set to Centronuclear myopathy 1 160150; -Marie-Tooth disease, axonal type 2M 606482; Charcot-Marie-Tooth disease, dominant intermediate B 606482 |
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| Undiagnosed metabolic disorders v1.342 | ATP5A1 | Sarah Leigh changed review comment from: Comment on list classification: Two variants together with functional studies. The Amber rating is based on the views of Anna de Burca (Genomics England Clinical Fellow) that the interpretation of PMID 23599390 that the boys in this publication have inherited a heterozygous variant from their father while not expressing the maternal allele due to unknown variant affecting expression.; 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. The Amber rating is based on the views of Anna de Burca (Genomics England Clinical Fellow) that the interpretation of PMID 23599390 that the boys in this publication have inherited a heterozygous variant from their father while not expressing the maternal allele due to unknown variant affecting expression. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.316 | ATP5A1 | Sarah Leigh changed review comment from: Comment on list classification: Two variants together with functional studies. The Amber rating is based on the views of Anna de Burca (Genomics England Clinical Fellow) that the interpretation of PMID 23599390 that the boys have inherited a heterozygous variant from their father while not expressing the maternal allele due to unknown variant affecting expression.; to: Comment on list classification: Two variants together with functional studies. The Amber rating is based on the views of Anna de Burca (Genomics England Clinical Fellow) that the interpretation of PMID 23599390 that the boys in this publication have inherited a heterozygous variant from their father while not expressing the maternal allele due to unknown variant affecting expression. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.314 | SPTLC1 | Catherine Snow reviewed gene: SPTLC1: Rating: GREEN; Mode of pathogenicity: Other; Publications: 20097765, 21618344, 20097765, 30420926; Phenotypes: Neuropathy, hereditary sensory and autonomic, type IA, 162400; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.312 | SPTLC2 | Catherine Snow reviewed gene: SPTLC2: Rating: GREEN; Mode of pathogenicity: None; Publications: 27604308, 20920666; Phenotypes: Neuropathy, hereditary sensory and autonomic, type IC, 613640; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.297 | DHODH | Sarah Leigh Added comment: Comment on phenotypes: Dihydroorotate dehydrogenase deficiency (Disorders of pyrimidine metabolism);Bilateral microtia;Deafness and congenital structural abnormalities;Unexplained skeletal dysplasia | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.297 | DHODH | Sarah Leigh Phenotypes for gene: DHODH were changed from Dihydroorotate dehydrogenase deficiency (Disorders of pyrimidine metabolism); Bilateral microtia; Deafness and congenital structural abnormalities; Unexplained skeletal dysplasia to Miller syndrome 263750 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.284 | PTS | Ivone Leong Added comment: Comment on list classification: Promoted from Amber to Green. PTS is associated with an appropriate phenotype on OMIM and Gene2Phenotype. There are >3 unrelated cases listed on OMIM. Therefore, enough evidence for this gene to be promoted to Green status. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.249 | PRPS1 | Sarah Leigh Mode of inheritance for gene: PRPS1 was changed from X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) to X-LINKED: hemizygous mutation in males, biallelic mutations in females | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.247 | ATP5A1 | Sarah Leigh Added comment: Comment on list classification: Two variants together with functional studies. The Amber rating is based on the views of Anna de Burca (Genomics England Clinical Fellow) that the interpretation of PMID 23599390 that the boys have inherited a heterozygous variant from their father while not expressing the maternal allele due to unknown variant affecting expression. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.192 | MOCS2 | Sarah Leigh Added comment: Comment on phenotypes: Mo cofactor deficiency, complementation group B (Disorders of molybdenum cofactor metabolism);Intellectual disability | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.192 | MOCS2 | Sarah Leigh Phenotypes for gene: MOCS2 were changed from Mo cofactor deficiency, complementation group B (Disorders of molybdenum cofactor metabolism); Intellectual disability to Molybdenum cofactor deficiency B 252160 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.189 | MOCS1 | Sarah Leigh Added comment: Comment on phenotypes: Mo cofactor deficiency, complementation group A (Disorders of molybdenum cofactor metabolism);Intellectual disability | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.189 | MOCS1 | Sarah Leigh Phenotypes for gene: MOCS1 were changed from Mo cofactor deficiency, complementation group A (Disorders of molybdenum cofactor metabolism); Intellectual disability to Molybdenum cofactor deficiency A 252150 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.144 | GK | Sarah Leigh Mode of inheritance for gene: GK was changed from X-LINKED: hemizygous mutation in males, biallelic mutations in females to X-LINKED: hemizygous mutation in males, biallelic mutations in females | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.143 | GK | Sarah Leigh Mode of inheritance for gene: GK was changed from X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) to X-LINKED: hemizygous mutation in males, biallelic mutations in females | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.137 | FGFR2 | Sarah Leigh Mode of inheritance for gene: FGFR2 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.129 | STAT2 | Sarah Leigh Classified gene: STAT2 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.129 | STAT2 | Sarah Leigh Added comment: Comment on list classification: Based on recommendation of Helen Britain (Clinical Fellow, Genomics England), that the majority of cases will be presenting in the context of overwhelming infection. The raised lactate and encephalomyopathy are potentially relevant phenotypes for this panel, however more evidence is needed on how common this presentation is, and whether it is always clearly associated with a proven infection. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.129 | STAT2 | Sarah Leigh Gene: stat2 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.128 | STAT2 |
Sarah Leigh gene: STAT2 was added gene: STAT2 was added to Undiagnosed metabolic disorders. Sources: Other Mode of inheritance for gene: STAT2 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: STAT2 were set to Immunodeficiency 44 616636 Review for gene: STAT2 was set to AMBER Added comment: Sources: Other |
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| Undiagnosed metabolic disorders v1.124 | POLG2 | Sarah Leigh Mode of inheritance for gene: POLG2 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.97 | NDUFA1 | Ellen McDonagh Mode of inheritance for gene: NDUFA1 was changed from BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 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 |
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| Undiagnosed metabolic disorders | TAT | Sarah Leigh commented on TAT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders | TAT | Sarah Leigh reviewed TAT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||