ClinVar Miner

Submissions for variant NM_033305.3(VPS13A):c.6404dup (p.Ser2136fs)

gnomAD frequency: 0.00003  dbSNP: rs951347128
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001236468 SCV001409192 pathogenic not provided 2024-01-05 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Ser2136Lysfs*2) in the VPS13A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in VPS13A are known to be pathogenic (PMID: 12404112, 21598378). This variant is present in population databases (no rsID available, gnomAD 0.008%). This premature translational stop signal has been observed in individual(s) with choreo-acanthocytosis (PMID: 11381253, 21598378). This variant is also known as 6404-6405insT, 2135Lfsx1. ClinVar contains an entry for this variant (Variation ID: 4683). For these reasons, this variant has been classified as Pathogenic.
Centogene AG - the Rare Disease Company RCV000004947 SCV002059769 pathogenic Chorea-acanthocytosis 2020-12-15 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000004947 SCV002801662 likely pathogenic Chorea-acanthocytosis 2022-03-03 criteria provided, single submitter clinical testing
Neuberg Supratech Reference Laboratories Pvt Ltd, Neuberg Centre for Genomic Medicine RCV000004947 SCV004048166 likely pathogenic Chorea-acanthocytosis criteria provided, single submitter clinical testing The frameshift variant c.6404dup (p.Ser2136LysfsTer2) in VPS13A gene has been observed in combination with another VPS13A variant in individuals affected with choreo-acanthocytosis (Tomiyasu A et.al.,2011). This variant has been reported to the ClinVar database as Pathogenic. The p.Ser2136LysfsTer2 variant is novel (not in any individuals) in 1000 Genomes and allele frequency of 0.00003733% is reported in gnomAD. This variant causes a frameshift starting with codon Serine 2136, changes this amino acid to Lysine residue, and creates a premature Stop codon at position 2 of the new reading frame, denoted p.Ser2136LysfsTer2. For these reasons, this variant has been classified as Likely Pathogenic.
OMIM RCV000004947 SCV000025123 pathogenic Chorea-acanthocytosis 2001-06-01 no assertion criteria provided literature only
Natera, Inc. RCV000004947 SCV002078271 pathogenic Chorea-acanthocytosis 2021-03-02 no assertion criteria provided clinical testing

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