ClinVar Miner

Submissions for variant NM_033305.3(VPS13A):c.3146T>C (p.Ile1049Thr)

gnomAD frequency: 0.00003  dbSNP: rs1437731472
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000520881 SCV000621295 uncertain significance not provided 2017-10-06 criteria provided, single submitter clinical testing The I1049T variant in the VPS13A gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The I1049T variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016). The I1049T variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is not conserved. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret I1049T as a variant of uncertain significance.
Illumina Laboratory Services, Illumina RCV001167732 SCV001330262 uncertain significance Chorea-acanthocytosis 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.
Natera, Inc. RCV001167732 SCV001452758 uncertain significance Chorea-acanthocytosis 2020-01-24 no assertion criteria provided clinical testing

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