ClinVar Miner

Submissions for variant NM_005476.7(GNE):c.1267A>G (p.Ile423Val)

gnomAD frequency: 0.00066  dbSNP: rs35638832
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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000343980 SCV000337083 uncertain significance not provided 2017-02-28 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000298514 SCV000480101 likely benign Inclusion Body Myopathy, Recessive 2016-06-14 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000353363 SCV000480102 likely benign GNE myopathy 2016-06-14 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000277347 SCV000480103 benign Sialuria 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Invitae RCV000533442 SCV000632640 likely benign GNE myopathy; Sialuria 2024-01-13 criteria provided, single submitter clinical testing
GeneDx RCV000343980 SCV002817667 uncertain significance not provided 2023-02-09 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Revvity Omics, Revvity RCV000343980 SCV003815055 uncertain significance not provided 2019-10-15 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003387823 SCV004099599 likely benign not specified 2023-09-07 criteria provided, single submitter clinical testing Variant summary: GNE c.1360A>G (p.Ile454Val) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00019 in 282854 control chromosomes (gnomAD), predominantly at a frequency of 0.0017 within the African or African-American subpopulation in the gnomAD database. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 1.5 fold of the estimated maximal expected allele frequency for a pathogenic variant in GNE causing Inclusion Body Myopathy 2 (0.0011), suggesting that the variant is a benign polymorphism found primarily in populations of African or African-American origin. To our knowledge, no occurrence of c.1360A>G in individuals affected with Inclusion Body Myopathy 2 and no experimental evidence demonstrating its impact on protein function have been reported. Seven ClinVar submitters have assessed the variant since 2014: four classified the variant as uncertain significance, two as likely benign, and one as benign. Based on the evidence outlined above, the variant was classified as likely benign.
Mayo Clinic Laboratories, Mayo Clinic RCV000343980 SCV004225029 uncertain significance not provided 2023-04-27 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003977768 SCV004790433 likely benign GNE-related condition 2022-11-13 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).
Natera, Inc. RCV000353363 SCV001457582 uncertain significance GNE myopathy 2020-01-08 no assertion criteria provided clinical testing

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