ClinVar Miner

Submissions for variant NM_004320.6(ATP2A1):c.428G>A (p.Arg143Gln)

gnomAD frequency: 0.00005  dbSNP: rs750195772
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000547197 SCV000638297 uncertain significance Brody myopathy 2022-09-06 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 143 of the ATP2A1 protein (p.Arg143Gln). This variant is present in population databases (rs750195772, gnomAD 0.07%). This missense change has been observed in individual(s) with Brody myopathy (PMID: 32040565). ClinVar contains an entry for this variant (Variation ID: 464089). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Illumina Laboratory Services, Illumina RCV000547197 SCV001277722 uncertain significance Brody myopathy 2018-01-13 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Revvity Omics, Revvity RCV000547197 SCV003834427 uncertain significance Brody myopathy 2022-06-24 criteria provided, single submitter clinical testing
Suna and Inan Kirac Foundation Neurodegeneration Research Laboratory, Koc University RCV000547197 SCV004023391 pathogenic Brody myopathy 2023-08-07 criteria provided, single submitter research
Breakthrough Genomics, Breakthrough Genomics RCV004691871 SCV005194299 uncertain significance not provided criteria provided, single submitter not provided

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