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| Likely inborn error of metabolism - targeted testing not possible v4.125 | GSTZ1 |
Achchuthan Shanmugasundram Added comment: Comment on list classification: As reported in PMID:27876694 and reviewed by Saikat Santra, there are three boys and three girls with maleylacetoacetate isomerase deficiency (MAAID), identified by newborn screening with mildly elevated succinylacetone (SA) by mass spectrometry on dried blood spot. Four of them were identified with homozygous GSTZ1 variants, one with compound heterozygous variants and one with heterozygous variant. Hence, there is sufficient evidence available for the association of biallelic GSTZ1 variants with MAAID and this gene can be promoted to green rating in the next GMS review. |
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| Likely inborn error of metabolism - targeted testing not possible v4.124 | GSTZ1 | Achchuthan Shanmugasundram Added comment: Comment on phenotypes: This gene has been associated with maleylacetoacetate isomerase deficiency in OMIM (MIM #617596), but not with any phenotypes in Gene2Phenotype. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v4.124 | GSTZ1 | Achchuthan Shanmugasundram Phenotypes for gene: GSTZ1 were changed from Biochemical to [Maleylacetoacetate isomerase deficiency], OMIM:617596 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v4.123 | GSTZ1 | Achchuthan Shanmugasundram reviewed gene: GSTZ1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: [Maleylacetoacetate isomerase deficiency], OMIM:617596; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v4.122 | GSTZ1 |
Saikat Santra gene: GSTZ1 was added gene: GSTZ1 was added to Likely inborn error of metabolism - targeted testing not possible. Sources: Literature,Expert Review,Eligibility statement prior genetic testing Mode of inheritance for gene: GSTZ1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: GSTZ1 were set to 27876694 Phenotypes for gene: GSTZ1 were set to Biochemical Penetrance for gene: GSTZ1 were set to unknown Review for gene: GSTZ1 was set to GREEN Added comment: GSTZ1 is established as the molecular cause for maleylacetoacetate isomerase deficiency which is an established inherited metabolic disorder and associated with succinylacetone excretion so may be detected on newborn screening programmes for hereditary tyrosinaemia type1 (FAH). The committee established for developing the pathways for rolling this out recommended that genetic testing for GSTZ1 be made available via the R98 panel to help evaluate patients with mild hypersuccinylacetonaemia - but patients with elevated succinylacetone on routine metabolic testing would also benefit from this being available. Sources: Literature, Expert Review, Eligibility statement prior genetic testing |
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| Likely inborn error of metabolism - targeted testing not possible v4.122 | COX5A | Sarah Leigh edited their review of gene: COX5A: Added comment: To date, two COX5A variants have been associated with Mitochondrial complex IV deficiency, nuclear type 20 (OMIM:619064) in two unrelated cases (PMID: 28247525;35246835). Analysis of patient fibroblasts has revealed a reduced enzymatic activity and protein levels of complex IV and several of its subunits, plus, lentiviral complementation rescues the complex IV deficiency (PMID: 28247525;35246835).; Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v4.114 | VPS16 |
Sarah Leigh gene: VPS16 was added gene: VPS16 was added to Likely inborn error of metabolism - targeted testing not possible. Sources: Other Q4_23_promote_green tags were added to gene: VPS16. Mode of inheritance for gene: VPS16 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: VPS16 were set to 33938619; 34013567 Phenotypes for gene: VPS16 were set to Mucopolysaccharidosis-like syndrome (biallelic); Dystonia Associated with Lysosomal Abnormalities (monoallelic); Dystonia 30, OMIM:619291 Review for gene: VPS16 was set to GREEN Added comment: Copied from Lysosomal storage disorder panel: Four individuals from three families were identified (PMIDs: 33938619; 34013567) exhibiting a mucopolysaccharidosis (MPS)-like lysosomal storage phenotype with short stature, coarse facies, DD or regression, peripheral neuropathy, skeletal dysplasia, neutropenia, and high-normal glycosaminoglycan excretion. All harboured homozygous variants in VPS16 which segregated with disease, including a missense variant in a sib pair (c.540G>T; p.Trp180Cys) and a recurrent intronic variant (c.2272‐18C>A) in two supposedly unrelated patients (although both of Middle Eastern descent). Fibroblasts of the two patients with the intronic variant showed accumulation of lysosomal compartments and autophagosomes with significantly decreased VPS16 mRNA and protein levels, as well as HOPS/CORVET complexes. Cellular phenotypes were rescued upon re-expression of wild-type VPS16. ----- Heterozygous variants, as well as a homozygous missense variant (c.156C>A) found in a consanguineous Chinese family (PMID:27174565), have been found to cause dystonia with variable onset (OMIM:619291). It has been suggested that the discrepancies in patient phenotypes are due to different mechanisms of pathogenicity, where variants causing dystonia do not affect the levels of endolysosomal tethering (HOPS/CORVET) complexes. More research is needed to clarify the mechanisms underlying VPS16-related dystonia as only limited functional data is currently available - Steel et al. 2020 (PMID:32808683) did perform electron microscopic studies of lymphocytes and fibroblasts derived from 2 unrelated patients, which showed vacuolar abnormalities suggestive of impaired lysosomal function. Sources: Literature Arina Puzriakova (Genomics England Curator), 14 Jun 2021 Sources: Other |
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| Likely inborn error of metabolism - targeted testing not possible v4.113 | CLCN7 |
Sarah Leigh gene: CLCN7 was added gene: CLCN7 was added to Likely inborn error of metabolism - targeted testing not possible. Sources: Expert Review Amber,Literature watchlist tags were added to gene: CLCN7. Mode of inheritance for gene: CLCN7 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: CLCN7 were set to 31155284 Phenotypes for gene: CLCN7 were set to Hypopigmentation, organomegaly, and delayed myelination and development, OMIM:618541 Mode of pathogenicity for gene: CLCN7 was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments |
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| Likely inborn error of metabolism - targeted testing not possible v4.108 | CLCN6 |
Sarah Leigh gene: CLCN6 was added gene: CLCN6 was added to Likely inborn error of metabolism - targeted testing not possible. Sources: Other Mode of inheritance for gene: CLCN6 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: CLCN6 were set to 29667327; 26658788; 25794116; 21107136; 33217309; 16950870 Phenotypes for gene: CLCN6 were set to Neurodegeneration, childhood-onset, hypotonia, respiratory insufficiency and brain imaging abnormalities OMIM:619173 Review for gene: CLCN6 was set to RED Added comment: Sources: Other |
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| Likely inborn error of metabolism - targeted testing not possible v4.77 | ACACA |
Hannah Knight gene: ACACA was added gene: ACACA was added to Likely inborn error of metabolism - targeted testing not possible. Sources: Literature Mode of inheritance for gene: ACACA was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: ACACA were set to 34552920 Phenotypes for gene: ACACA were set to Acetyl-CoA carboxylase deficiency Review for gene: ACACA was set to AMBER Added comment: PMID: 34552920 (2021) reported a baby who presented in her first two years of life with global developmental delay, microcephaly, hypotonia, and dysmorphic facial features. Two VUS's in ACACA were identified, and a decreased level of ACC1 and ACC1 enzyme activity was detected in patient-derived lymphocytes. In vitro studies revealed a disruption of lipid homeostasis in patient-derived lymphocytes, further inducing the deficit of cell motility capacity and that the deficiency could be partly attenuated by palmitate. Sources: Literature |
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| Likely inborn error of metabolism - targeted testing not possible v4.51 | SPG7 | Arina Puzriakova reviewed gene: SPG7: Rating: ; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v4.50 | SPG7 | Achchuthan Shanmugasundram 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v4.44 | 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. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v4.44 | SLC22A5 | Sarah Leigh changed review comment from: 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: 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). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v4.12 | GFM2 | Arina Puzriakova Phenotypes for gene: GFM2 were changed from Multiple respiratory chain complex deficiencies (disorders of protein synthesis); Early-onset neurological presentations of mitochondrial disease to Combined oxidative phosphorylation deficiency 39, OMIM:618397 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v4.2 | 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 mode of inheritance: BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v3.5 | APOA5 | Achchuthan Shanmugasundram 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v3.2 | SLC26A6 |
Arina Puzriakova gene: SLC26A6 was added gene: SLC26A6 was added to Inborn errors of metabolism. Sources: Literature watchlist tags were added to gene: SLC26A6. Mode of inheritance for gene: SLC26A6 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: SLC26A6 were set to 35115415 Phenotypes for gene: SLC26A6 were set to Enteric hyperoxaluria and nephrolithiasis Added comment: Cornière et al. 2022 (PMID: 35115415) identified a single family with a heterozygous missense VUS (c.1519C>T/p.R507W) in the SLC26A6 gene. However, the variant was found in 5 out of 280 674 alleles reported in gnomAD (Europeans and South Asians). In vitro studies showed that the variant affects both SLC26A6 transport activity and membrane surface expression, in turn reducing Cl− dependant oxalate transport. Cotransfection studies indicated a dominant-negative effect on WT. Slc26a6 null mice similarly displayed hyperoxalemia and hyperoxaluria which were caused by defective intestinal back-secretion of dietary oxalate (PMID: 21170874; 32660969) SLC26A6 is currently not associated with any human phenotype in OMIM or G2P. Sources: Literature |
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| Likely inborn error of metabolism - targeted testing not possible v2.328 | ARSK |
Arina Puzriakova gene: ARSK was added gene: ARSK was added to Inborn errors of metabolism. Sources: Literature Mode of inheritance for gene: ARSK was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: ARSK were set to 34916232 Phenotypes for gene: ARSK were set to Mucopolysaccharidoses with short stature, coarse facial features and dysostosis multiplex Review for gene: ARSK was set to AMBER Added comment: Verheyen et al. 2022 (PMID: 34916232) reported four affected individuals of two unrelated consanguineous families with homozygous variants c.250C>T, p.(Arg84Cys) and c.560T>A, p.(Leu187Ter) in ARSK, respectively. Patients were affected with skeletal dysplasia, resembling spondyloepiphysial dysplasia. Reverse phenotyping in two individuals from one family revealed additional cardiac and ophthalmological abnormalities. Sources: Literature |
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| Likely inborn error of metabolism - targeted testing not possible v2.325 | GPHN | Arina Puzriakova Phenotypes for gene: GPHN were changed from Molybdenum cofactor deficiency C 615501; Mo cofactor deficiency, complementation group C (Disorders of molybdenum cofactor metabolism); epileptic encephalopathy to Molybdenum cofactor deficiency C, OMIM:615501; Mo cofactor deficiency, complementation group C (Disorders of molybdenum cofactor metabolism) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v2.249 | 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v2.249 | SLC16A1 | Sarah Leigh Phenotypes for gene: SLC16A1 were changed from Hyperinsulinemic hypoglycemia, familial, 7; mainly ketosis with borderline reduction in glucose to Erythrocyte lactate transporter defect, OMIM:245340; Hyperinsulinemic hypoglycemia, familial, 7, OMIM:610021; Monocarboxylate transporter 1 deficiency, OMIM:616095 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v2.224 | EXT1 | Arina Puzriakova Mode of inheritance for gene EXT1 was changed from BIALLELIC, autosomal or pseudoautosomal to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v2.212 | PDK3 | Arina Puzriakova reviewed gene: PDK3: Rating: ; Mode of pathogenicity: None; Publications: 23297365, 26801680, 27388934, 28902413, 32504000, 34387338; Phenotypes: Charcot-Marie-Tooth disease, X-linked dominant, 6, OMIM:300905; Mode of inheritance: X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v2.206 | TARS2 | Sarah Leigh Added comment: Comment on publications: PMID: 24827421 - Compound heterozygous variants in TARS2 were reported in the proband and his affected sister - a missense mutation (c.845C>T, p.Pro282Leu) and a nucleotide change in position +3 of intron 6 (g.4255A>G, c.695+3A>G). The parents carrying one of the variants, one unaffected sister carried one variant, and the other unaffected sibling carried neither. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v2.206 | TARS2 | Sarah Leigh Publications for gene: TARS2 were set to PMID: 24827421 - Compound heterozygous variants in TARS2 were reported in the proband and his affected sister - a missense mutation (c.845C>T, p.Pro282Leu) and a nucleotide change in position +3 of intron 6 (g.4255A>G, c.695+3A>G). The parents carrying one of the variants, one unaffected sister carried one variant, and the other unaffected sibling carried neither. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v2.184 | EHHADH | Arina Puzriakova Mode of inheritance for gene: EHHADH was changed from BIALLELIC, autosomal or pseudoautosomal to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v2.183 | EHHADH | Arina Puzriakova reviewed gene: EHHADH: Rating: ; Mode of pathogenicity: None; Publications: 24401050, 27160910; Phenotypes: ?Fanconi renotubular syndrome 3, OMIM:615605; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v2.182 | ACAT2 | Arina Puzriakova Phenotypes for gene: ACAT2 were changed from Developmental delay to ?ACAT2 deficiency, OMIM:614055; Increased serum lactate and pyruvate; High levels of ketones; Low levels of cytosolic acetoacetyl-CoA thiolase; Hypotonia; Severe developmental delay | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v2.171 | 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. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v2.171 | 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v2.41 | NUS1 | Eleanor Williams edited their review of gene: NUS1: Added comment: Provisionally associated with ?Congenital disorder of glycosylation, type 1aa #617082 (AR) in OMIM based on family reported in Park et al 2014 (PMID: 25066056). They describe a family of Roma origin in which 2 out of 4 siblings presented with congenital scoliosis, severe neurological impairment, refractory epilepsy, hearing deficit and visual impairment with discrete bilateral macular lesions. A homozgyous missense mutation, R290H, was found in NUS1 (called NGBR in the paper) by exome sequencing. It segregated with the disease in the family. Patient fibroblasts showed reduced dolichol profiles and enhanced accumulation of free cholesterol as do fibroblasts from mice lacking NgBR.; Changed publications: 25066056; Changed phenotypes: ?Congenital disorder of glycosylation, type 1aa OMIM:617082, congenital disorder of glycosylation, type IAA MONDO:0014904 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v2.35 | HS2ST1 |
Ivone Leong gene: HS2ST1 was added gene: HS2ST1 was added to Inborn errors of metabolism. Sources: Literature for-review tags were added to gene: HS2ST1. 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 AMBER 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. This gene should be considered for Green gene rating status at the next review. Sources: Literature |
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| Likely inborn error of metabolism - targeted testing not possible v2.18 | 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) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v2.16 | TKFC |
Arina Puzriakova gene: TKFC was added gene: TKFC was added to Inborn errors of metabolism. Sources: Literature watchlist tags were added to gene: TKFC. Mode of inheritance for gene: TKFC was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: TKFC were set to 32004446 Phenotypes for gene: TKFC were set to Triokinase and FMN cyclase deficiency syndrome, 618805 Review for gene: TKFC was set to AMBER Added comment: Associated with phenotype in OMIM, and a possible gene for TKFC-related Cataracts and Multisystem Disease in G2P. PMID: 32004446 (2020) - Two sib pairs from two unrelated consanguineous families with an inborn error of metabolism caused by distinct homozygous variants in TKFC. In Family 1, both sibs had congenital cataracts but otherwise presented disparate phenotypes. The older sister had DD (motor and speech) and cerebellar hypoplasia; while the younger sister had liver dysfunction and fatal cardiomyopathy at 11 weeks with severe lactic acidosis following a febrile illness. In Family 2, the brother exhibited global DD as well as bilateral cataracts at 22 months. He developed progressive non-cholestatic liver failure, and at 3yrs-10months he could not walk independently and had no words. His older sister, had delayed speech development and learning difficulties, but is otherwise well and did not have cataracts. Both variants segregated with disease in each family, and some functional data of the variants using yeast cells. Sources: Literature |
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| Likely inborn error of metabolism - targeted testing not possible v2.9 | SLC5A6 |
Sarah Leigh gene: SLC5A6 was added gene: SLC5A6 was added to Inborn errors of metabolism. Sources: Literature Mode of inheritance for gene: SLC5A6 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SLC5A6 were set to 27904971; 31392107; 31754459; 23104561; 29669219 Phenotypes for gene: SLC5A6 were set to SLC5A6-related Neurodevelopmental Disorder Review for gene: SLC5A6 was set to GREEN Added comment: Not associated with phenotype in OMIM and as possible Gen2Phen gene for SLC5A6-related Neurodevelopmental Disorder. At least 5 variants published in three unrelated famililies (4 cases total) with SLC5A6-related Neurodevelopmental Disorder, together with supportive functional studies (PMID 29669219; 23104561). One of the cases had mixed semiology seizures including focal dyscognitive, absence, tonic spasms and generalised convulsive seizures with electrographic features of encephalopathy with generalised and independent multifocal spike-wave discharges (PMID 31754459), another case had brain, immune, bone and intestinal dysfunction (PMID 27904971) and the third had metabolic dysfunction mimicking biotinidase deficiency (PMID 31392107). This condition could be treated with biotin supplementation and introduction of pantothenic acid supplementation (PMID 31392107). Sources: Literature |
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| Likely inborn error of metabolism - targeted testing not possible v2.1 | PCYT2 |
Sarah Leigh edited their review of gene: PCYT2: Added comment: Vaz et al. (2019 - PMID: 31637422 - DDD study among the co-authors) report on 5 individuals - from 4 families - with biallelic PCYT2 mutations. The phenotype corresponded to a complex hererditary paraplegia with global DD, regression (4/5), ID (mild in 3/5, severe in 2/5), spastic para-/tetraparesis, epilepsy (5/5 - variable onset 2-16 yrs - focal or tonic-clonic seizures) and progressive cerebral and cerebellar atrophy. Exome sequencing in all revealed biallelic PCYT2 variants, confirmed with Sanger s. in probands and their parents (NM_001184917.2 - corresponding to the canonical transcript used as Ref below): - P1 (Fam1) : 2 missense SNVs in trans configuration, c.730C>T or p.His244Tyr and c.920C>T or p.Pro307Leu - P2 (Fam2 - consanguineous of White British origin), P3 (Fam3 - Consanguineous of Turkish origin), P4,5 (Fam4 - consanguineous, unspecified origin) : homozygosity for c.1129C>T or p.Arg377Ter) affecting the last exon of 8/12 transcripts, including the canonical one. Individuals with the same genotype displayed variable degrees of ID (eg P3 - severe / P2, P4,5 - mild ID). For sibs in Fam4, homozygosity for a missense SACS variant led to consideration of the respective disorder (AR spastic ataxia of Charlevoix-Saguenay) though the variant was predicted to be tolerated in silico and notably the MRI images not suggestive. All variants were absent from / had extremely low AF in public databases, with no homozygotes. Posphatidylethanolamine (PE) is a membrane lipid, particularly enriched in human brain (45% of phospholypid fraction). PE is synthesized either via the CDP-ethanolamine pathway or by decarboxylation of phosphatidylserine in mitochondria. PCYT2 encodes CTP:phosophoethanolamine cytidyltransferase (ET) which is an ubiquitously expressed rate-limiting enzyme for PE biosynthesis in the former pathway. In silico, the 2 missense variants - localizing in the CTP catalytic domain 2 - were predicted to be damaging, as well as to affect protein stability. Fibroblasts of 3 patients (P1, P2, P3) representing all variants were studied: - Enzymatic activity was shown to be significantly reduced (though not absent) compared to controls. Abnormalities were noted upon Western Blot incl. absence in all 3 patients studied of one of the 2 bands normally found in controls (probably representing the longer isoform), reduced intensity in all 3 of another band probably corresponding to a shorter isoform, and presence of an additional band of intermediate molec. mass in patients with the truncating variant. - RT-PCR on mRNA from patient fibroblasts did not reveal (significant) reduction compared to controls. - Lipidomic profile of patient fibroblasts was compatible with the location of the block in the phospholipid biosynthesis pathway and different from controls. The lipidomic profile had similarities with what has been reported for EPT1 deficiency, the enzyme directly downstream of ET. The SELENO1-related phenotype (/EPT1 deficiency) is also highly overlapping. CRISPR-Cas9 was used to generate pcyt2 partial or complete knockout (ko) zebrafish, targeting either the final (ex13) or another exon (ex3) respectively. mRNA expression was shown to be moderately reduced in the first case and severely reduced/absent in the second, compared to wt. Similarly, complete-ko (ex3) led to significantly lower survival, with impaired though somewhat better survival of partial-ko (ex13) zebrafish. Complete knockout of Pcyt2 in mice is embryonically lethal (PMID cited: 17325045) while heterozygous mice develop features of metabolic syndrome (PMID cited: 22764088). Given lethality in knockout zebrafish / mice and the residual activity (15-20%) in patient fibroblasts, the variants reported were thought to be hypomorphic and complete loss of function possibly incompatible with life. PCYT2 is not associated with any phenotype in OMIM/G2P/SysID and not commonly included in gene panels for ID. As a result this gene could included in the ID / epilepsy panels with green (~/>3 indiv/fam/variants with the nonsense found in different populations, consistent phenotype, lipidomics, in silico/in vitro/in vivo evidence) or amber rating. [Please consider inclusion in other possibly relevant panels eg. for metabolic disorders, etc]. Sources: Literature Konstantinos Varvagiannis (Other), 11 Nov 2019; Changed rating: GREEN |
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| Likely inborn error of metabolism - targeted testing not possible v1.422 | UPB1 | Ellen McDonagh changed review comment from: Additional comments were provided by Dr Clare Beesley and colleagues (Great Ormond Street Hospital for Children NHS Foundation Trust) as part of the GMS Metabolic Specialist disease test group: 16 mutations reported in HGMD & several families have been reported in the literature. Heterologous expression of A85E mutant enzyme in E. coli yielded no residual activity (Van Kuilenburg et al., 2004, PMID: 15385443].; to: Additional comments were provided by Dr Clare Beesley and colleagues (Great Ormond Street Hospital for Children NHS Foundation Trust) as part of the GMS Metabolic Specialist disease test group: 16 mutations reported in HGMD & several families have been reported in the literature. Heterologous expression of A85E mutant enzyme in E. coli yielded no residual activity (Van Kuilenburg et al., 2004, PMID: 15385443). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.422 | UPB1 | Ellen McDonagh commented on gene: UPB1: Additional comments were provided by Dr Clare Beesley and colleagues (Great Ormond Street Hospital for Children NHS Foundation Trust) as part of the GMS Metabolic Specialist disease test group: 16 mutations reported in HGMD & several families have been reported in the literature. Heterologous expression of A85E mutant enzyme in E. coli yielded no residual activity (Van Kuilenburg et al., 2004, PMID: 15385443]. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.421 | ALG2 | Ellen McDonagh Added comment: Comment on list classification: Promoted from Red to Amber due to feedback from the GMS Metabolic Specialist disease test group. Information provided: 1 patient described with functional studies carried out: Expression of wildtype but not of mutant ALG2 cDNA restored the mannosyltransferase activity and the biosynthesis of dolichol-linked oligosaccharides both in patient fibroblasts and in yeast cells with an ALG2 mutation (PMID: 12684507). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.420 | BCAT2 | Ellen McDonagh Added comment: Comment on list classification: Promoted from Red to Green due to expert review from representation of the GMS Metabolic disease specialist test group; multiple cases reported and this is a treatable. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.406 | NSUN3 | Catherine Snow changed review comment from: PMID: 27356879 - reports on a loss-of-function mutation in NSUN3 in a patient presenting with combined mitochondrial respiratory chain complex deficiency.; to: PMID: 27356879 - reports on a compound heterozygous variant resulting in a loss-of-function mutation in NSUN3 in a patient presenting with combined mitochondrial respiratory chain complex deficiency. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.396 | SLC25A4 | Catherine Snow Mode of inheritance for gene: SLC25A4 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.395 | ABCB7 | Catherine Snow Mode of inheritance for gene: ABCB7 was changed from X-LINKED: hemizygous mutation in males, biallelic mutations in females to X-LINKED: hemizygous mutation in males, biallelic mutations in females | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.395 | ABCB7 | Catherine Snow 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.384 | 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.384 | SLC6A3 |
Catherine Snow changed review comment from: 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. Promoted from Amber to Green. SLC7A9 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.; 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. Promoted 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. |
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| Likely inborn error of metabolism - targeted testing not possible v1.383 | 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. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.382 | SLC6A8 |
Catherine Snow changed review comment from: 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. Comment on list classification: Promoted from Amber to Green. SLC6A8 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.; 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. Promoted from Amber to Green. SLC6A8 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. |
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| Likely inborn error of metabolism - targeted testing not possible v1.381 | 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.379 | 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.360 | WFS1 | Catherine Snow reviewed gene: WFS1: Rating: GREEN; Mode of pathogenicity: None; Publications: 30171196; Phenotypes: Wolfram syndrome 1, 222300, Wolfram-like syndrome, autosomal dominant, 614296, Diabetes mellitus, noninsulin-dependent, association with, 125853; Mode of inheritance: BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.359 | 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.359 | VIPAS39 |
Catherine Snow changed review comment from: 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. Promoted from Amber to Green. VIPAS39 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: 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. Promoted from Amber to Green. VIPAS39 is associated with an appropriate phenotype on OMIM and Gene2Phenotype. There are >23 cases in literature. Therefore, enough evidence for this gene to be promoted to Green status. |
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| Likely inborn error of metabolism - targeted testing not possible v1.353 | UMOD |
Catherine Snow changed review comment from: 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. Promoted from Amber to Green. UMOD 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: 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. 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. |
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| Likely inborn error of metabolism - targeted testing not possible v1.353 | 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.345 | TAT |
Catherine Snow Added comment: Comment on publications: PMID: 28255985 Reports on 106 families, represented by 143 individuals, carrying a total of 36 genetic variants. Variants include large deletions, non‐synonymous and nonsense amino‐acid changes, frameshifts and splice variants. |
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| Likely inborn error of metabolism - targeted testing not possible v1.345 | TAT | Catherine Snow Publications for gene: TAT were set to 27604308; 28255985 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.344 | TAT | Catherine Snow Publications for gene: TAT were set to 27604308; 28255985 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.344 | TAT | Catherine Snow Publications for gene: TAT were set to 27604308 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.343 | TAT | Catherine Snow Classified gene: TAT as Green List (high evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.343 | TAT | Catherine Snow Gene: tat has been classified as Green List (High Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.342 | TAT | Catherine Snow reviewed gene: TAT: Rating: GREEN; Mode of pathogenicity: None; Publications: 28255985; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.339 | STS | Catherine Snow edited their review of gene: STS: Changed mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.331 | SLC2A1 |
Ivone Leong 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. 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. |
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| Likely inborn error of metabolism - targeted testing not possible v1.320 | COQ7 | Sarah Leigh Added comment: Comment on phenotypes: complex multisystem presentation;primary coenzyme Q10 deficiency | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.320 | COQ7 | Sarah Leigh Phenotypes for gene: COQ7 were changed from complex multisystem presentation; primary coenzyme Q10 deficiency to ?Coenzyme Q10 deficiency, primary, 8 616733 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.311 | ATP5A1 | Sarah Leigh changed review comment from: Comment on list classification: 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: 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 mentioned in this article have inherited a heterozygous variant from their father while not expressing the maternal allele due to unknown variant affecting expression. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.287 | STAT2 | Sarah Leigh Classified gene: STAT2 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.287 | 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. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.287 | STAT2 | Sarah Leigh Gene: stat2 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.286 | SPTLC1 |
Catherine Snow changed review comment from: Promoted from Amber to Green. This gene is associated with a relevant disease in OMIM and there is enough evidence to support a gene-disease association. SPTLC1, encodes one of the two subunits of serine palmitoyltransferase (SPT), the enzyme catalyzing the first and rate-limiting step in the de novo synthesis of sphingolipids. PMID 20097765 reports that mutations in SPTLC1 cause a gain of function mechanism, which results in the formation of two atypical and neurotoxic sphingolipid metabolites. Confirmed cases in Bristol (see review on Hereditary Neuropathy panel https://panelapp.genomicsengland.co.uk/panels/85/) and in sufficient publications.; to: Promoted from Amber to Green. This gene is associated with a relevant disease in OMIM and there is enough evidence to support a gene-disease association. SPTLC1, encodes one of the two subunits of serine palmitoyltransferase (SPT), the enzyme catalyzing the first and rate-limiting step in the de novo synthesis of sphingolipids. PMID 20097765 reports that mutations in SPTLC1 cause a gain of function mechanism, which results in the formation of two atypical and neurotoxic sphingolipid metabolites. Confirmed cases in Bristol (see review on Hereditary Neuropathy panel https://panelapp.genomicsengland.co.uk/panels/85/) and in sufficient publications. 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. |
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| Likely inborn error of metabolism - targeted testing not possible v1.283 | 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.281 | SPTLC2 |
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. SPTLC2, encodes one of the two subunits of serine palmitoyltransferase (SPT), the enzyme catalyzing the first and rate-limiting step in the de novo synthesis of sphingolipids. PMID: 20920666 reports on three heterozygous missense mutations in the SPTLC2 subunit of SPT in four families and also confirmed cases in Bristol (see review on Hereditary Neuropathy panel https://panelapp.genomicsengland.co.uk/panels/85/). 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: 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. SPTLC2, encodes one of the two subunits of serine palmitoyltransferase (SPT), the enzyme catalyzing the first and rate-limiting step in the de novo synthesis of sphingolipids. PMID: 20920666 reports on three heterozygous missense mutations in the SPTLC2 subunit of SPT in four families and also confirmed cases in Bristol (see review on Hereditary Neuropathy panel https://panelapp.genomicsengland.co.uk/panels/85/). 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. |
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| Likely inborn error of metabolism - targeted testing not possible v1.281 | SPTLC2 | Catherine Snow reviewed gene: SPTLC2: Rating: GREEN; Mode of pathogenicity: None; Publications: 20920666; Phenotypes: Neuropathy, hereditary sensory and autonomic, type IC, 613640; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.278 | IER3IP1 | Sarah Leigh changed review comment from: Comment on list classification: IER3IP1 has been demoted to Red on the Mitochondrial disorders panel on the recommendation of the GMS mitochondrial specialist test group, including by Carl Fratter (Oxford University Hospitals NHS Trust). It is associated with Microcephaly, epilepsy, and diabetes syndrome 614231, which is not technically a mitochondrial disorder, as the phenotype is quite different to other mitochondrial conditions, thus in the opinion of Helen Britain the phenotypes reported, the condition could initially present as a mimic of a mitochondrial presentation e.g. abnormal liver enzymes, diabetes, neurological dysfunction and therefore a green rating on metabolic panels would seem appropriate.; to: Comment on list classification: IER3IP1 has been demoted to Red on the Mitochondrial disorders panel on the recommendation of the GMS mitochondrial specialist test group, including by Carl Fratter (Oxford University Hospitals NHS Trust). It is associated with Microcephaly, epilepsy, and diabetes syndrome 614231, which is not technically a mitochondrial disorder, as the phenotype is quite different to other mitochondrial conditions. Thus in the opinion of Helen Britain (Genomics England Clinical Fellow) the phenotypes reported could initially present as a mimic of a mitochondrial presentation e.g. abnormal liver enzymes, diabetes, neurological dysfunction and therefore a green rating on metabolic panels would seem appropriate. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.278 | IER3IP1 | Sarah Leigh changed review comment from: Comment on list classification: IER3IP1 is being demoted to Red on this panel on the recommendation of the GMS mitochondrial specialist test group, including by Carl Fratter (Oxford University Hospitals NHS Trust). As it is associated with Microcephaly, epilepsy, and diabetes syndrome 614231, which is not technically a mitochondrial disorder, as the phenotype is quite different to other mitochondrial conditions.; to: Comment on list classification: IER3IP1 has been demoted to Red on the Mitochondrial disorders panel on the recommendation of the GMS mitochondrial specialist test group, including by Carl Fratter (Oxford University Hospitals NHS Trust). It is associated with Microcephaly, epilepsy, and diabetes syndrome 614231, which is not technically a mitochondrial disorder, as the phenotype is quite different to other mitochondrial conditions, thus in the opinion of Helen Britain the phenotypes reported, the condition could initially present as a mimic of a mitochondrial presentation e.g. abnormal liver enzymes, diabetes, neurological dysfunction and therefore a green rating on metabolic panels would seem appropriate. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.270 | PEX5 | Sarah Leigh Added comment: Comment on phenotypes: Peroxisome biogenesis disorder 2A (Zellweger) 214110;Peroxisome biogenesis disorder 2B 202370;Rhizomelic chondrodysplasia punctata, type 5 616716 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.264 | 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. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.254 | ALAS2 | Sarah Leigh edited their review of gene: ALAS2: Added comment: 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 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 mode of inheritance: X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.247 | 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.243 | ATP5A1 | Sarah Leigh Added comment: Comment on list classification: 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. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.182 | MOCS2 | Sarah Leigh Added comment: Comment on phenotypes: Intellectual disability;Mo cofactor deficiency, complementation group B (Disorders of molybdenum cofactor metabolism) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.182 | MOCS2 | Sarah Leigh Phenotypes for gene: MOCS2 were changed from Intellectual disability; Mo cofactor deficiency, complementation group B (Disorders of molybdenum cofactor metabolism) to Molybdenum cofactor deficiency B 252160 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.179 | MOCS1 | Sarah Leigh Added comment: Comment on phenotypes: Intellectual disability;Mo cofactor deficiency, complementation group A (Disorders of molybdenum cofactor metabolism) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.179 | MOCS1 | Sarah Leigh Phenotypes for gene: MOCS1 were changed from Intellectual disability; Mo cofactor deficiency, complementation group A (Disorders of molybdenum cofactor metabolism) to Molybdenum cofactor deficiency A 252150 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.137 | 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.134 | 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.134 | 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.133 | 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.129 | GAMT | Sarah Leigh Added comment: Comment on phenotypes: Intellectual disability;Guanidinoacetate methyltransferase deficiency (Mitochondrial respiratory chain disorders (caused by nuclear variants only), disorders of creatinine metabolism) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.129 | GAMT | Sarah Leigh Phenotypes for gene: GAMT were changed from Intellectual disability; Guanidinoacetate methyltransferase deficiency (Mitochondrial respiratory chain disorders (caused by nuclear variants only), disorders of creatinine metabolism) to Cerebral creatine deficiency syndrome 2 612736 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.121 | 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.111 | DHODH | Sarah Leigh Added comment: Comment on phenotypes: Unexplained skeletal dysplasia;Bilateral microtia;Deafness and congenital structural abnormalities;Dihydroorotate dehydrogenase deficiency (Disorders of pyrimidine metabolism) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.111 | DHODH | Sarah Leigh Phenotypes for gene: DHODH were changed from Unexplained skeletal dysplasia; Bilateral microtia; Deafness and congenital structural abnormalities; Dihydroorotate dehydrogenase deficiency (Disorders of pyrimidine metabolism) to Miller syndrome 263750 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.78 | 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.76 | GFM2 |
Sarah Leigh Source Expert Review Green was added to GFM2. Mode of inheritance for gene GFM2 was changed from Unknown to BIALLELIC, autosomal or pseudoautosomal Added phenotypes Multiple respiratory chain complex deficiencies (disorders of protein synthesis); Early-onset neurological presentations of mitochondrial disease for gene: GFM2 Publications for gene GFM2 were changed from to 22700954; 26016410; 29075935 Rating Changed from Red List (low evidence) to Green List (high evidence) |
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| Likely inborn error of metabolism - targeted testing not possible v1.75 | STAT2 | Sarah Leigh Classified gene: STAT2 as Red List (low evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.75 | STAT2 | Sarah Leigh Added comment: Comment on list classification: STAT2 is rated as Red on this panel on the recommendation of the GMS mitochondrial specialist test group, including by Carl Fratter (Oxford University Hospitals NHS Trust). Although it is associated with elongated mitochondria, the Immunodeficiency 44 616636 phenotype is not appropriate for this panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.75 | STAT2 | Sarah Leigh Gene: stat2 has been classified as Red List (Low Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.74 | STAT2 | Sarah Leigh Phenotypes for gene: STAT2 were changed from elongated mitochondria; severe neurological deterioration following viral infection to Immunodeficiency 44 616636; elongated mitochondria; severe neurological deterioration following viral infection | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.53 | 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) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v1.47 | TAT |
Ivone Leong Source NHS GMS was added to TAT. Source London North GLH was added to TAT. |
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| Likely inborn error of metabolism - targeted testing not possible v1.25 | CTH | Louise Daugherty Phenotypes for gene: CTH were changed from to Cystathioninuria, 219500 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v0.25 | GLUD1 | Ellen McDonagh Added comment: Comment on mode of pathogenicity: Mutation consequence summary from G2P = activating. OMIM reports several missense variants. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism - targeted testing not possible v0.4 | TRAP1 |
Ellen McDonagh gene: TRAP1 was added gene: TRAP1 was added to Inborn errors of metabolism. Sources: Expert Review Red Mode of inheritance for gene: TRAP1 was set to Unknown Publications for gene: TRAP1 were set to PMID: 24152966 - recessive mutations reported in 2 families with CAKUT, and 3 families with VACTERL. |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | WDR45 |
Ellen McDonagh gene: WDR45 was added gene: WDR45 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: WDR45 was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Publications for gene: WDR45 were set to 27604308 Phenotypes for gene: WDR45 were set to Neurodegeneration with brain iron accumulation 5 |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | STS |
Ellen McDonagh gene: STS was added gene: STS was added to Inborn errors of metabolism. Sources: Expert Review Amber Mode of inheritance for gene: STS was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Publications for gene: STS were set to 27604308 Phenotypes for gene: STS were set to X-linked ichthyosis (Other disorders in the metabolism of sterols); Autosomal recessive congenital ichthyosis |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | SLC35A2 |
Ellen McDonagh gene: SLC35A2 was added gene: SLC35A2 was added to Inborn errors of metabolism. Sources: Expert Review Amber Mode of inheritance for gene: SLC35A2 was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Publications for gene: SLC35A2 were set to 27604308 Phenotypes for gene: SLC35A2 were set to Intellectual disability; SLC35A2-CDG (other congenital disorders of glycosylation) |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | PRPS1 |
Ellen McDonagh gene: PRPS1 was added gene: PRPS1 was added to Inborn errors of metabolism. Sources: Expert Review Amber Mode of inheritance for gene: PRPS1 was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Publications for gene: PRPS1 were set to 27604308 Phenotypes for gene: PRPS1 were set to Intellectual disability; Charcot-Marie-Tooth disease; Phosphoribosyl pyrophosphate synthetase 1 defects (Disorders of purine metabolism); Congenital hearing impairment (profound/severe); Intellectual_disability |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | PDK3 |
Ellen McDonagh gene: PDK3 was added gene: PDK3 was added to Inborn errors of metabolism. Sources: Expert Review Red Mode of inheritance for gene: PDK3 was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Phenotypes for gene: PDK3 were set to ?Charcot-Marie-Tooth disease, X-linked dominant, 6, 300905 |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | PDHA1 |
Ellen McDonagh gene: PDHA1 was added gene: PDHA1 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: PDHA1 was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Phenotypes for gene: PDHA1 were set to Leigh syndrome, X-linked, 308930; Pyruvate dehydrogenase E1-alpha deficiency, 312170 |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | OTC |
Ellen McDonagh gene: OTC was added gene: OTC was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: OTC was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Publications for gene: OTC were set to 27604308 Phenotypes for gene: OTC were set to Ornithine transcarbamylase deficiency, 311250; Ornithine transcarbamylase deficiency (Urea cycle disorders and inherited hyperammonaemias) |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | NSDHL |
Ellen McDonagh gene: NSDHL was added gene: NSDHL was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: NSDHL was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Publications for gene: NSDHL were set to 27604308 Phenotypes for gene: NSDHL were set to Congenital hemidysplasia with ichtyosiform erythroderma and limb defects (Disorders of sterol biosynthesis); CHILD syndrome 308050 XLD; CK syndrome 300831 XLR |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | NDUFB11 |
Ellen McDonagh gene: NDUFB11 was added gene: NDUFB11 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: NDUFB11 was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Phenotypes for gene: NDUFB11 were set to histiocytoid cardiomyopathy; microphthalmia with linear skin defects syndrome; Linear skin defects with multiple congenital anomalies 3; Isolated complex I deficiency |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | LAMP2 |
Ellen McDonagh gene: LAMP2 was added gene: LAMP2 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: LAMP2 was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Publications for gene: LAMP2 were set to 27604308 Phenotypes for gene: LAMP2 were set to Danon disease |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | HSD17B10 |
Ellen McDonagh gene: HSD17B10 was added gene: HSD17B10 was added to Inborn errors of metabolism. Sources: Expert Review Amber Mode of inheritance for gene: HSD17B10 was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Publications for gene: HSD17B10 were set to 27604308 Phenotypes for gene: HSD17B10 were set to Intellectual disability; 2-Methyl-3-hydroxybutyric aciduria, HSD10 disease (Organic acidurias); Intellectual_disability |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | HCCS |
Ellen McDonagh gene: HCCS was added gene: HCCS was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: HCCS was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Phenotypes for gene: HCCS were set to Linear skin defects with multiple congenital anomalies 1; Microphthalmia, syndromic 7, 309801 |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | GLA |
Ellen McDonagh gene: GLA was added gene: GLA was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: GLA was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Publications for gene: GLA were set to 27604308 Phenotypes for gene: GLA were set to Fabry disease, cardiac variant, 301500; Fabry Disease; Fabry disease (Sphingolipidoses); Fabry disease, 301500 |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | GK |
Ellen McDonagh gene: GK was added gene: GK was added to Inborn errors of metabolism. Sources: Expert Review Amber Mode of inheritance for gene: GK was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Publications for gene: GK were set to 27604308 Phenotypes for gene: GK were set to Glycerol kinase deficiency (Disorders of glycerol metabolism); Intellectual disability; Intellectual_disability |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | EBP |
Ellen McDonagh gene: EBP was added gene: EBP was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: EBP was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Publications for gene: EBP were set to 27604308 Phenotypes for gene: EBP were set to MEND syndrome 300960 XLR; Chondrodysplasia punctata, X-linked dominant 302960 XLD; X-linked dominant chondrodysplasia punctata 2 (Disorders of sterol biosynthesis) |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | COX7B |
Ellen McDonagh gene: COX7B was added gene: COX7B was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: COX7B was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Phenotypes for gene: COX7B were set to Linear skin defects with multiple congenital anomalies; Isolated complex IV deficiency; Aplasia cutis congenita, reticulolinear, with microcephaly, facial dysmorphism and other congenital anomalies, 300887; MICROPHTHALMIA WITH LINEAR SKIN LESIONS |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | ALG13 |
Ellen McDonagh gene: ALG13 was added gene: ALG13 was added to Inborn errors of metabolism. Sources: Expert Review Amber Mode of inheritance for gene: ALG13 was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Publications for gene: ALG13 were set to 27604308 Phenotypes for gene: ALG13 were set to Intellectual disability; Epileptic encephalopathy; ALG13-CDG (Disorders of protein N-glycosylation) |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | ALAS2 |
Ellen McDonagh gene: ALAS2 was added gene: ALAS2 was added to Inborn errors of metabolism. Sources: Expert Review Amber Mode of inheritance for gene: ALAS2 was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Publications for gene: ALAS2 were set to 27604308 Phenotypes for gene: ALAS2 were set to Erythropoietic protoporphyria, mild variant; X-linked sideroblastic anaemia (XLSA) (Porphyrias with acute painful photosensitivity); X-linked dominant protoporphyria (Porphyrias with acute painful photosensitivity) |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | ABCD1 |
Ellen McDonagh gene: ABCD1 was added gene: ABCD1 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: ABCD1 was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Publications for gene: ABCD1 were set to 27604308 Phenotypes for gene: ABCD1 were set to X-linked adrenoleukodystrophy (Disorders of peroxisomal alpha-, beta and omega-oxidation); Adrenoleukodystrophy 300100 |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | ABCB7 |
Ellen McDonagh gene: ABCB7 was added gene: ABCB7 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: ABCB7 was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Publications for gene: ABCB7 were set to PMID: 26242992; 17192398; 22398176 Phenotypes for gene: ABCB7 were set to congenital cerebellar hypoplasia/atrophy (PMID: 26242992).; Anemia, sideroblastic, with ataxia; Disorders of iron homeostasis |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | TIMM8A |
Ellen McDonagh gene: TIMM8A was added gene: TIMM8A was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: TIMM8A was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Phenotypes for gene: TIMM8A were set to Mohr-Tranebjaerg syndrome, 304700; Jensen syndrome, 311150; Disorders of the mitochondrial import system; Deafness, X-linked 1, progressive |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | TAZ |
Ellen McDonagh gene: TAZ was added gene: TAZ was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: TAZ was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Phenotypes for gene: TAZ were set to Barth syndrome, 302060; Disorders of mitochondrial lipid metabolism |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | SSR4 |
Ellen McDonagh gene: SSR4 was added gene: SSR4 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: SSR4 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Publications for gene: SSR4 were set to 26264460 Phenotypes for gene: SSR4 were set to ?Congenital disorder of glycosylation, type Iy 300934 |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | SLC6A8 |
Ellen McDonagh gene: SLC6A8 was added gene: SLC6A8 was added to Inborn errors of metabolism. Sources: Expert Review Amber Mode of inheritance for gene: SLC6A8 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Publications for gene: SLC6A8 were set to 27604308 Phenotypes for gene: SLC6A8 were set to Intellectual disability; Creatine transporter deficiency (Mitochondrial respiratory chain disorders (caused by nuclear variants only), disorders of creatinine metabolism) |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | RPL10 |
Ellen McDonagh gene: RPL10 was added gene: RPL10 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: RPL10 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Publications for gene: RPL10 were set to 25316788 Phenotypes for gene: RPL10 were set to Mental retardation, X-linked, syndromic, 35 |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | PIGA |
Ellen McDonagh gene: PIGA was added gene: PIGA was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: PIGA was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Publications for gene: PIGA were set to 25885527 Phenotypes for gene: PIGA were set to Multiple congenital anomalies-hypotonia-seizures syndrome 2 300868; PIGA-CDG (Disorders of glycosphingolipid and glycosylphosphatidylinositol anchor glycosylation) |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | PHKA2 |
Ellen McDonagh gene: PHKA2 was added gene: PHKA2 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: PHKA2 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Publications for gene: PHKA2 were set to 27604308 Phenotypes for gene: PHKA2 were set to Glycogen Storage Disease; Glycogen Storage Disorders- Liver; Glycogen storage disease, type IXa2, 306000; Glycogen storage disease, type IXa1, 306000; hepatomegaly and mild hypoglycaemia; Glycogen storage disease type IX Hepatic phosphorylase kinase deficiency (Glycogen storage disorders) |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | PHKA1 |
Ellen McDonagh gene: PHKA1 was added gene: PHKA1 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: PHKA1 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Publications for gene: PHKA1 were set to 27604308 |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | PGK1 |
Ellen McDonagh gene: PGK1 was added gene: PGK1 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: PGK1 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Publications for gene: PGK1 were set to 27604308 Phenotypes for gene: PGK1 were set to Phosphoglycerate kinase 1 deficiency |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | OCRL |
Ellen McDonagh gene: OCRL was added gene: OCRL was added to Inborn errors of metabolism. Sources: Expert Review Amber Mode of inheritance for gene: OCRL was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Publications for gene: OCRL were set to 27604308 Phenotypes for gene: OCRL were set to Lowe syndrome (Disorders of amino acid transport); Renal tract calcification (or Nephrolithiasis/nephrocalcinosis); Intellectual disability; Intellectual_disability; Cataracts |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | MAOA |
Ellen McDonagh gene: MAOA was added gene: MAOA was added to Inborn errors of metabolism. Sources: Expert Review Amber Mode of inheritance for gene: MAOA was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Publications for gene: MAOA were set to 27604308 Phenotypes for gene: MAOA were set to Brunner syndrome |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | MAGT1 |
Ellen McDonagh gene: MAGT1 was added gene: MAGT1 was added to Inborn errors of metabolism. Sources: Expert Review Amber Mode of inheritance for gene: MAGT1 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Publications for gene: MAGT1 were set to 27604308 Phenotypes for gene: MAGT1 were set to Combined B and T cell defect; IAP-CDG (Disorders of protein N-glycosylation) |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | IDS |
Ellen McDonagh gene: IDS was added gene: IDS was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: IDS was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Publications for gene: IDS were set to 27604308 Phenotypes for gene: IDS were set to MUCOPOLYSACCHARIDOSIS TYPE 2; MPS II, Hunter disease (Mucopolysaccharidoses); Mucopolysaccharidosis II, 309900; Mucopolysaccharidosis Type II |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | HPRT1 |
Ellen McDonagh gene: HPRT1 was added gene: HPRT1 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: HPRT1 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Publications for gene: HPRT1 were set to 27604308 Phenotypes for gene: HPRT1 were set to HPRT-related gout |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | HCFC1 |
Ellen McDonagh gene: HCFC1 was added gene: HCFC1 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: HCFC1 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Phenotypes for gene: HCFC1 were set to Mental retardation, X-linked 3 (methylmalonic acidemia and homocysteinemia, cblX type ) 309541 |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | ATP7A |
Ellen McDonagh gene: ATP7A was added gene: ATP7A was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: ATP7A was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Phenotypes for gene: ATP7A were set to Menkes disease |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | ATP6AP1 |
Ellen McDonagh gene: ATP6AP1 was added gene: ATP6AP1 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: ATP6AP1 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Phenotypes for gene: ATP6AP1 were set to Immunodeficiency 47 |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | ARSE |
Ellen McDonagh gene: ARSE was added gene: ARSE was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: ARSE was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Phenotypes for gene: ARSE were set to Chondrodysplasia punctata, X-linked recessive 302950 |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | AIFM1 |
Ellen McDonagh gene: AIFM1 was added gene: AIFM1 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: AIFM1 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Publications for gene: AIFM1 were set to PMID: 20362274 (two related males); PMID: 23217327 Phenotypes for gene: AIFM1 were set to Disorders of mitochondrial apoptosis; Cowchock syndrome, 310490; Combined oxidative phosphorylation deficiency 6, 300816 |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | TARS2 |
Ellen McDonagh gene: TARS2 was added gene: TARS2 was added to Inborn errors of metabolism. Sources: Expert Review Amber Mode of inheritance for gene: TARS2 was set to Unknown Publications for gene: TARS2 were set to PMID: 24827421 - Compound heterozygous variants in TARS2 were reported in the proband and his affected sister - a missense mutation (c.845C>T, p.Pro282Leu) and a nucleotide change in position +3 of intron 6 (g.4255A>G, c.695+3A>G). The parents carrying one of the variants, one unaffected sister carried one variant, and the other unaffected sibling carried neither. Phenotypes for gene: TARS2 were set to Multiple respiratory chain complex deficiencies (disorders of protein synthesis); ?Combined oxidative phosphorylation deficiency 21, 615918 |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | GGT1 |
Ellen McDonagh gene: GGT1 was added gene: GGT1 was added to Inborn errors of metabolism. Sources: Expert Review Red Mode of inheritance for gene: GGT1 was set to Unknown Publications for gene: GGT1 were set to 27604308; 24816252 Phenotypes for gene: GGT1 were set to Gamma-glutamyl transpeptidase deficiency; Glutathionuria (Disorders of the gamma-glutamyl cycle) |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | UROD |
Ellen McDonagh gene: UROD was added gene: UROD was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: UROD was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: UROD were set to 27604308 Phenotypes for gene: UROD were set to Porphyria cutanea tarda (Porphyrias with erosive photodermatosis) |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | TM6SF2 |
Ellen McDonagh gene: TM6SF2 was added gene: TM6SF2 was added to Inborn errors of metabolism. Sources: Expert Review Red Mode of inheritance for gene: TM6SF2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: TM6SF2 were set to 28235613 Phenotypes for gene: TM6SF2 were set to non-alcoholic fatty liver disease |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | SLC25A4 |
Ellen McDonagh gene: SLC25A4 was added gene: SLC25A4 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: SLC25A4 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: SLC25A4 were set to 27604308 Phenotypes for gene: SLC25A4 were set to Progressive External Ophthalmoplegia with Mitochondrial DNADeletions; Disorders of mitochondrial protein transport; Disorders of mitochondrial DNA maintenance and integrity; Required for mtDNA maintenance (Mitochondrial respiratory chain disorders (caused by nuclear variants only)); Progressive external ophthalmoplegia with mitochondrial DNA deletions 3, 609283Mitochondrial DNA depletion syndrome 12 (cardiomyopathic type), 615418 |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | SDHAF2 |
Ellen McDonagh gene: SDHAF2 was added gene: SDHAF2 was added to Inborn errors of metabolism. Sources: Expert Review Amber Mode of inheritance for gene: SDHAF2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: SDHAF2 were set to 27604308 Phenotypes for gene: SDHAF2 were set to Neuro-endocrine Tumours- PCC and PGL; Multiple endocrine tumours; Multiple Tumours; Complex II (Mitochondrial respiratory chain disorders (caused by nuclear variants only), OXPHOS assembly factors) |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | RANBP2 |
Ellen McDonagh gene: RANBP2 was added gene: RANBP2 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: RANBP2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: RANBP2 were set to 27604308 Phenotypes for gene: RANBP2 were set to Acute necrotizing encephalopathy (Other metabolic disorders) |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | POLG2 |
Ellen McDonagh gene: POLG2 was added gene: POLG2 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: POLG2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Phenotypes for gene: POLG2 were set to Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 4,610131; Disorders of mitochondrial DNA maintenance and integrity; Progressive External Ophthalmoplegia with Mitochondrial DNA Deletions |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | IDH2 |
Ellen McDonagh gene: IDH2 was added gene: IDH2 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: IDH2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: IDH2 were set to 24049096; 20847235 Phenotypes for gene: IDH2 were set to Mitochondrial isocitrate dehydrogenase deficiency (Organic acidurias); D-2-hydroxyglutaric aciduria 2, 613657 |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | FXYD2 |
Ellen McDonagh gene: FXYD2 was added gene: FXYD2 was added to Inborn errors of metabolism. Sources: Expert Review Red Mode of inheritance for gene: FXYD2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: FXYD2 were set to 27604308 Phenotypes for gene: FXYD2 were set to Hypomagnesemia 2, renal 154020; Hypomagnesaemia type 2, renal (Disorder of magnesium metabolism) |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | GPHN |
Ellen McDonagh gene: GPHN was added gene: GPHN was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: GPHN was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal Publications for gene: GPHN were set to 27604308 Phenotypes for gene: GPHN were set to Molybdenum cofactor deficiency C 615501; Mo cofactor deficiency, complementation group C (Disorders of molybdenum cofactor metabolism); epileptic encephalopathy |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | VKORC1 |
Ellen McDonagh gene: VKORC1 was added gene: VKORC1 was added to Inborn errors of metabolism. Sources: Expert Review Amber Mode of inheritance for gene: VKORC1 was set to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal Publications for gene: VKORC1 were set to 27604308 Phenotypes for gene: VKORC1 were set to Vitamin K epoxide reductase deficiency (Other disorders of vitamins and cofactors); Inherited bleeding disorders |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | SLC7A9 |
Ellen McDonagh gene: SLC7A9 was added gene: SLC7A9 was added to Inborn errors of metabolism. Sources: Expert Review Amber Mode of inheritance for gene: SLC7A9 was set to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal Publications for gene: SLC7A9 were set to 27604308; 24816252 Phenotypes for gene: SLC7A9 were set to Renal tract calcification (or Nephrolithiasis/nephrocalcinosis); Cystinuria (Disorders of amino acid transport) |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | SLC3A1 |
Ellen McDonagh gene: SLC3A1 was added gene: SLC3A1 was added to Inborn errors of metabolism. Sources: Expert Review Amber Mode of inheritance for gene: SLC3A1 was set to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal Publications for gene: SLC3A1 were set to 27604308 Phenotypes for gene: SLC3A1 were set to Renal tract calcification (or Nephrolithiasis/nephrocalcinosis); Cystinuria (Disorders of amino acid transport); Hypotonia-cystinuria syndrome (Disorders of amino acid transport) |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | OPA1 |
Ellen McDonagh gene: OPA1 was added gene: OPA1 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: OPA1 was set to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal Phenotypes for gene: OPA1 were set to Optic atrophy plus syndrome, 125250; {Glaucoma, normal tension, susceptibility to}, 606657; Disorders of mitochondrial DNA maintenance and integrity; Progressive External Ophthalmoplegia with Mitochondrial DNA Deletions; Optic atrophy 1, 165500; Mitochondrial DNA Depletion Syndrome |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | NDUFA1 |
Ellen McDonagh gene: NDUFA1 was added gene: NDUFA1 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: NDUFA1 was set to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal Phenotypes for gene: NDUFA1 were set to Mitochondrial complex I deficiency, 252010; Mitochondrial Diseases; Isolated complex I deficiency |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | HSPD1 |
Ellen McDonagh gene: HSPD1 was added gene: HSPD1 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: HSPD1 was set to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal Phenotypes for gene: HSPD1 were set to Leukodystrophy, hypomyelinating, 4, 612233; Spastic paraplegia 13, autosomal dominant, 605280 |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | GDAP1 |
Ellen McDonagh gene: GDAP1 was added gene: GDAP1 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: GDAP1 was set to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal Publications for gene: GDAP1 were set to 11743579 Phenotypes for gene: GDAP1 were set to Charcot Marie Tooth disease (CMT4A); Charcot-Marie-Tooth disease, type 4A; Charcot-Marie-Tooth disease, recessive intermediate, A; Charcot-Marie-Tooth disease, axonal, with vocal cord paresis; Charcot-Marie-Tooth disease, axonal, type 2K |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | ALPL |
Ellen McDonagh gene: ALPL was added gene: ALPL was added to Inborn errors of metabolism. Sources: Expert Review Amber Mode of inheritance for gene: ALPL was set to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal Publications for gene: ALPL were set to 27604308 Phenotypes for gene: ALPL were set to Unexplained skeletal dysplasia; Osteogenesis Imperfecta; Craniosynostosis syndromes phenotypes; Hypophosphatasia (Disorders of pyridoxine metabolism) |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | AFG3L2 |
Ellen McDonagh gene: AFG3L2 was added gene: AFG3L2 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: AFG3L2 was set to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal Phenotypes for gene: AFG3L2 were set to Ataxia, spastic, 5, autosomal recessive, 614487; Spinocerebellar ataxia 28, 610246; Disorders of mitochondrial DNA maintenance and integrity |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | TAT |
Ellen McDonagh gene: TAT was added gene: TAT was added to Inborn errors of metabolism. Sources: Expert Review Amber Mode of inheritance for gene: TAT was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: TAT were set to 27604308 Phenotypes for gene: TAT were set to Intellectual disability; Tyrosinaemia type II (Disorders of phenylalanine or tyrosine metabolism) |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | STAT2 |
Ellen McDonagh gene: STAT2 was added gene: STAT2 was added to Inborn errors of metabolism. Sources: Expert Review Red Mode of inheritance for gene: STAT2 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: STAT2 were set to PMID: 26122121 Phenotypes for gene: STAT2 were set to elongated mitochondria; severe neurological deterioration following viral infection |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | SLC39A8 |
Ellen McDonagh gene: SLC39A8 was added gene: SLC39A8 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: SLC39A8 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SLC39A8 were set to 27604308 Phenotypes for gene: SLC39A8 were set to Congenital disorder of glycosylation, type IIn 616721; Hypomagnesaemia with cerebellar atrophy, hypotonia, strabismus, developmental delay, short stature, mild skeletal dysplasia, and connective tissue abnormalities (Disorder of magnesium metabolism) |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | SLC2A2 |
Ellen McDonagh gene: SLC2A2 was added gene: SLC2A2 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: SLC2A2 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SLC2A2 were set to 27604308 Phenotypes for gene: SLC2A2 were set to Glycogen storage disease type XI (Glycogen storage disorders); Glycogen Storage Disorders- Liver; Glucose transporter 2 deficiency (Disorders of glucose transport); Fanconi-Bickel Syndrome; renal falcon syndrome, aminoaciduria phosphaturia, small stature, malabsorption, hepatomegaly and nephromegaly. |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | SLC25A38 |
Ellen McDonagh Added phenotypes severe, non-syndromic, microcytic/hypochromic sideroblastic anemia; nonsyndromic autosomal recessive congenital sideroblastic anemia; congenital sideroblastic anemias for gene: SLC25A38 Publications for gene SLC25A38 were changed from 27604308 to PMID: 26821380 (potential novel treatment using glycine and folate).; PMID: 19731322 (12 probands with mutations in this gene); PMID: 25985931 (mutations detected in 3 patients in this gene); PMID: 21393332 (11 patients); PMID: 19412178 |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | PEX7 |
Ellen McDonagh gene: PEX7 was added gene: PEX7 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: PEX7 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: PEX7 were set to 27604308 Phenotypes for gene: PEX7 were set to Peroxisome biogenesis disorder 9B 614879; Rhizomelic chondrodysplasia punctata, type 1; Rhizomelic chondrodysplasia punctata type 1 (Peroxisomal disorders) |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | OXCT1 |
Ellen McDonagh gene: OXCT1 was added gene: OXCT1 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: OXCT1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: OXCT1 were set to 27604308 Phenotypes for gene: OXCT1 were set to Succinyl CoA:3-oxoacid CoA transferase deficiency; severe ketosis on fasting often ketotic in fed state no hepatomegaly; Succinyl-CoA:3-Oxoacid-CoA transferase (SCOT) deficiency (Disorders of ketone body metabolism); Succinyl CoA:3-oxoacid CoA transferase deficiency (Mitochondrial respiratory chain disorders (caused by nuclear variants only)) |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | NAT8L |
Ellen McDonagh gene: NAT8L was added gene: NAT8L was added to Inborn errors of metabolism. Sources: Expert Review Red Mode of inheritance for gene: NAT8L was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: NAT8L were set to 19807691 Phenotypes for gene: NAT8L were set to ?N-acetylaspartate deficiency 614063 |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | MTR |
Ellen McDonagh gene: MTR was added gene: MTR was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: MTR was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: MTR were set to 27604308 Phenotypes for gene: MTR were set to Homocystinuria-megaloblastic anemia, cblG complementation type |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | MOCS2 |
Ellen McDonagh gene: MOCS2 was added gene: MOCS2 was added to Inborn errors of metabolism. Sources: Expert Review Amber Mode of inheritance for gene: MOCS2 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: MOCS2 were set to 27604308 Phenotypes for gene: MOCS2 were set to Intellectual disability; Mo cofactor deficiency, complementation group B (Disorders of molybdenum cofactor metabolism) |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | MOCS1 |
Ellen McDonagh gene: MOCS1 was added gene: MOCS1 was added to Inborn errors of metabolism. Sources: Expert Review Amber Mode of inheritance for gene: MOCS1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: MOCS1 were set to 27604308 Phenotypes for gene: MOCS1 were set to Intellectual disability; Mo cofactor deficiency, complementation group A (Disorders of molybdenum cofactor metabolism) |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | MMAB |
Ellen McDonagh gene: MMAB was added gene: MMAB was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: MMAB was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: MMAB were set to 27604308 Phenotypes for gene: MMAB were set to Defect in adenosylcobalamin synthesis-cbl B (Disorders of cobalamin absorption, transport and metabolism); Methylmalonic aciduria, vitamin B12-responsive, due to defect in synthesis of adenosylcobalamin, cblB complementation type 251110 |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | KARS |
Ellen McDonagh Added phenotypes Deafness, autosomal recessive 89, 613916; Multiple respiratory chain complex deficiencies (disorders of protein synthesis); Charcot-Marie-Tooth disease, recessive intermediate, B (Lysyl-tRNA synthetase mutations) (Mitochondrial respiratory chain disorders (caused by nuclear variants only)); Charcot-Marie-Tooth disease, recessive intermediate, B, 613641 for gene: KARS Publications for gene KARS were changed from to 27604308 |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | GSS |
Ellen McDonagh gene: GSS was added gene: GSS was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: GSS was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: GSS were set to 27604308 Phenotypes for gene: GSS were set to Glutathione synthetase (GSS) deficiency; Glutathione synthetase deficiency 266130; Glutathione synthetase deficiency with 5-oxoprolinuria; Glutathione synthetase deficiency without 5-oxoprolinuria; Pyroglutamic aciduria; 5-oxoprolinuria; Hemolytic anemia due to glutathione synthetase deficiency 231900; Glutathione synthetase deficiency (Disorders of the gamma-glutamyl cycle); Fanconi nephropathy |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | GNPTG |
Ellen McDonagh gene: GNPTG was added gene: GNPTG was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: GNPTG was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: GNPTG were set to 27604308 Phenotypes for gene: GNPTG were set to Mucolipidosis III, Pseudo-Hurler polydystrophy (Other lysosomal disorders); mucolipidpsis type III complementation group C; Mucolipidosis, Type III Gamma; Mucolipidosis III gamma |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | GNPAT |
Ellen McDonagh gene: GNPAT was added gene: GNPAT was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: GNPAT was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: GNPAT were set to 27604308 Phenotypes for gene: GNPAT were set to Rhizomelic chondrodysplasia punctata type 2 (Peroxisomal disorders); Rhizomelic chondrodysplasia punctata, type 2 222765 |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | GAMT |
Ellen McDonagh gene: GAMT was added gene: GAMT was added to Inborn errors of metabolism. Sources: Expert Review Amber Mode of inheritance for gene: GAMT was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: GAMT were set to 27604308 Phenotypes for gene: GAMT were set to Intellectual disability; Guanidinoacetate methyltransferase deficiency (Mitochondrial respiratory chain disorders (caused by nuclear variants only), disorders of creatinine metabolism) |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | EPG5 |
Ellen McDonagh gene: EPG5 was added gene: EPG5 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: EPG5 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: EPG5 were set to 28624465; 23222957; 26917586; 23674064; 25331754; 23838600; 26395118 Phenotypes for gene: EPG5 were set to Vici syndrome, 242840; IMMUNODEFICIENCY WITH CLEFT LIP/PALATE, CATARACT, HYPOPIGMENTATION, AND ABSENT CORPUS CALLOSUM |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | DHODH |
Ellen McDonagh gene: DHODH was added gene: DHODH was added to Inborn errors of metabolism. Sources: Expert Review Amber Mode of inheritance for gene: DHODH was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: DHODH were set to 27604308 Phenotypes for gene: DHODH were set to Unexplained skeletal dysplasia; Bilateral microtia; Deafness and congenital structural abnormalities; Dihydroorotate dehydrogenase deficiency (Disorders of pyrimidine metabolism) |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | DARS2 |
Ellen McDonagh Added phenotypes Leukoencephalopathy with brain stem and spinal cord involvement and lactate elevation, 611105; Multiple respiratory chain complex deficiencies (disorders of protein synthesis); Required for mitochondrial gene expression (Mitochondrial respiratory chain disorders (caused by nuclear variants only)) for gene: DARS2 Publications for gene DARS2 were changed from to 27604308 |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | DARS2 |
Ellen McDonagh gene: DARS2 was added gene: DARS2 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: DARS2 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: DARS2 were set to Leukoencephalopathy with brain stem and spinal cord involvement and lactate elevation, 611105; Multiple respiratory chain complex deficiencies (disorders of protein synthesis) |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | CUBN |
Ellen McDonagh gene: CUBN was added gene: CUBN was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: CUBN was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: CUBN were set to Intrinsic factor receptor deficiency due to CUBN mutations (Disorders of cobalamin absorption, transport and metabolism); Megaloblastic anemia-1, Finnish type; Proteinuric renal disease; Unexplained kidney failure in young people |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | COQ7 |
Ellen McDonagh gene: COQ7 was added gene: COQ7 was added to Inborn errors of metabolism. Sources: Expert Review Red Mode of inheritance for gene: COQ7 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: COQ7 were set to PMID: 26084283 Phenotypes for gene: COQ7 were set to complex multisystem presentation; primary coenzyme Q10 deficiency |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | B4GALT7 |
Ellen McDonagh Added phenotypes Ehlers-Danlos syndrome with short stature and limb anomalies 130070; B4GALT7-CDG (Disorders of protein O-glycosylation, O-mannosylglycan synthesis deficiencies); B4GALT7-CDG (Disorders of protein O-glycosylation, O-mannosylglycan synthesis deficiencies, Disorders of protein O-glycosylation, O-xylosylglycan synthesis deficiencies); Beta-1,4-galactosyltransferase 7 deficiency (Disorders of protein O-glycosylation, O-xylosylglycan synthesis deficiencies) for gene: B4GALT7 Publications for gene B4GALT7 were changed from 27827381 to 27604308 |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | B4GALT7 |
Ellen McDonagh gene: B4GALT7 was added gene: B4GALT7 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: B4GALT7 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: B4GALT7 were set to 27827381 Phenotypes for gene: B4GALT7 were set to Ehlers-Danlos syndrome with short stature and limb anomalies 130070; B4GALT7-CDG (Disorders of protein O-glycosylation, O-mannosylglycan synthesis deficiencies, Disorders of protein O-glycosylation, O-xylosylglycan synthesis deficiencies) |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | B3GAT3 |
Ellen McDonagh Added phenotypes Multiple joint dislocations, short stature, craniofacial dysmorphism, with or without congenital heart defects 245600; B3GAT3-CDG (Disorders of protein O-glycosylation, O-mannosylglycan synthesis deficiencies) for gene: B3GAT3 Publications for gene B3GAT3 were changed from 27871226; 26086840; 21763480 to 27604308 |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | B3GAT3 |
Ellen McDonagh gene: B3GAT3 was added gene: B3GAT3 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: B3GAT3 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: B3GAT3 were set to 27871226; 26086840; 21763480 Phenotypes for gene: B3GAT3 were set to Multiple joint dislocations, short stature, craniofacial dysmorphism, with or without congenital heart defects 245600; B3GAT3-CDG (Disorders of protein O-glycosylation, O-mannosylglycan synthesis deficiencies) |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | AMN |
Ellen McDonagh gene: AMN was added gene: AMN was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: AMN was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: AMN were set to 27604308 Phenotypes for gene: AMN were set to Intrinsic factor receptor deficiency due to AMN mutations (Disorders of cobalamin absorption, transport and metabolism); Proteinuric renal disease; Unexplained kidney failure in young people |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | ALDOB |
Ellen McDonagh gene: ALDOB was added gene: ALDOB was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: ALDOB was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: ALDOB were set to 27604308 Phenotypes for gene: ALDOB were set to hereditary fructose intolerance; Hereditary fructose intolerance (Disorders of fructose metabolism); acidosis with ketototic hypoglycaemia often hepatomegaly in acute presentation |
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| Likely inborn error of metabolism - targeted testing not possible v0.4 | AGPS |
Ellen McDonagh gene: AGPS was added gene: AGPS was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: AGPS was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: AGPS were set to 27604308 Phenotypes for gene: AGPS were set to Rhizomelic chondrodysplasia punctata, type 3 600121; Rhizomelic chondrodysplasia punctata type 3 (Peroxisomal disorders) |
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