ClinVar Miner

Submissions for variant NM_005609.4(PYGM):c.1237A>T (p.Asn413Tyr)

gnomAD frequency: 0.00157  dbSNP: rs142054672
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000675637 SCV000224967 uncertain significance not provided 2014-05-15 criteria provided, single submitter clinical testing
GeneDx RCV000675637 SCV000582943 uncertain significance not provided 2018-06-22 criteria provided, single submitter clinical testing The N413Y variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The N413Y variant is observed in 116/18,784 (0.62%) alleles from individuals of African background in large population cohorts (Lek et al., 2016). The N413Y variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. In-silico analyses, including protein predictors and evolutionary conservation, support a deleterious effect.In summary, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Invitae RCV001079321 SCV001115122 benign Glycogen storage disease, type V 2024-01-31 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001079321 SCV004562981 uncertain significance Glycogen storage disease, type V 2023-08-17 criteria provided, single submitter clinical testing The PYGM c.1237A>T; p.Asn413Tyr variant (rs142054672), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 193681). This variant is found in the African/African-American population with an allele frequency of 0.6% (125/19,752 alleles) in the Genome Aggregation Database. Computational analyses predict that this variant is deleterious (REVEL: 0711). While the relatively high population frequency suggests that this is likely a benign variant, given the lack of clinical and functional data, the significance of the p.Asn413Tyr variant is uncertain at this time.
PreventionGenetics, part of Exact Sciences RCV003937552 SCV004756346 likely benign PYGM-related condition 2019-06-05 criteria provided, single submitter clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
Mayo Clinic Laboratories, Mayo Clinic RCV000675637 SCV000801338 uncertain significance not provided 2017-05-24 no assertion criteria provided clinical testing
Natera, Inc. RCV001079321 SCV001452660 uncertain significance Glycogen storage disease, type V 2020-04-14 no assertion criteria provided clinical testing

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