ClinVar Miner

Submissions for variant NM_018297.4(NGLY1):c.1201A>T (p.Arg401Ter) (rs201337954)

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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine RCV000043663 SCV000258427 pathogenic Congenital disorder of deglycosylation 2015-09-09 criteria provided, single submitter research This study shows that diverse genetic causes underlie CVI.
GeneDx RCV000309063 SCV000329581 pathogenic not provided 2018-07-19 criteria provided, single submitter clinical testing The R401X nonsense variant in the NGLY1 gene has previously been reported in association with NGLY1-CDDG in multiple unrelated individuals (Enns et al. 2014; Lam et al., 2017). This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The R401X variant is observed in 55/126604 (0.043%) alleles from individuals of non-Finnish European background, and 59/276946 (0.021%) total alleles in the gnomAD dataset (Lek et al., 2016). We interpret R401X as a pathogenic variant.
Invitae RCV000043663 SCV000654066 pathogenic Congenital disorder of deglycosylation 2020-10-28 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg401*) in the NGLY1 gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs201337954, ExAC 0.03%). This particular variant has been reported in the literature in several homozygous or compound heterozygous individuals with NGLY1 deficiency (PMID: 24651605, 26350515, 27388694). ClinVar contains an entry for this variant (Variation ID: 50962). Loss-of-function variants in NGLY1 are known to be pathogenic (PMID: 24651605). For these reasons, this variant has been classified as Pathogenic.
Fulgent Genetics,Fulgent Genetics RCV000043663 SCV000894311 pathogenic Congenital disorder of deglycosylation 2018-10-31 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000309063 SCV001334701 pathogenic not provided 2020-03-01 criteria provided, single submitter clinical testing
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen RCV000309063 SCV001447023 pathogenic not provided 2020-10-23 criteria provided, single submitter clinical testing
Baylor Genetics RCV000043663 SCV001526742 pathogenic Congenital disorder of deglycosylation 2018-01-22 criteria provided, single submitter clinical testing This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. This variant has been previously reported in patients with NGLY1 deficiency [PMID 22581936, 26350515, 24651605, 27388694]
OMIM RCV000043663 SCV000071685 pathogenic Congenital disorder of deglycosylation 2014-03-20 no assertion criteria provided literature only
GeneReviews RCV000043663 SCV000891725 pathogenic Congenital disorder of deglycosylation 2017-08-25 no assertion criteria provided literature only
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000309063 SCV001740562 pathogenic not provided no assertion criteria provided clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV000309063 SCV001800049 pathogenic not provided no assertion criteria provided clinical testing

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