ClinVar Miner

Submissions for variant NM_001290043.2(TAP2):c.1733C>T (p.Ala578Val)

gnomAD frequency: 0.00068  dbSNP: rs78328107
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001037927 SCV001201364 uncertain significance MHC class I deficiency 2022-06-24 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 578 of the TAP2 protein (p.Ala578Val). This variant is present in population databases (rs78328107, gnomAD 0.2%). This variant has not been reported in the literature in individuals affected with TAP2-related conditions. ClinVar contains an entry for this variant (Variation ID: 836733). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Not Available"; Align-GVGD: "Class C0"). 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.
Baylor Genetics RCV001037927 SCV001527399 uncertain significance MHC class I deficiency 2018-04-17 criteria provided, single submitter clinical testing This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
Neuberg Centre For Genomic Medicine, NCGM RCV005225212 SCV005870917 uncertain significance MHC class I deficiency 1 criteria provided, single submitter clinical testing The missense c.1733C>T(p.Ala578Val) variant in TAP2 gene has not been reported previously as a pathogenic variant nor a benign variant, to our knowledge. The p.Ala578Val variant has been reported with allele frequency of 0.03% in gnomAD Exomes. This variant has been reported to the ClinVar database as Uncertain Significance. The amino acid change p.Ala578Val in TAP2 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Ala at position 578 is changed to a Val changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as a Variant of Uncertain Significance (VUS).
Ambry Genetics RCV005286271 SCV005952227 uncertain significance Inborn genetic diseases 2025-01-23 criteria provided, single submitter clinical testing The c.1733C>T (p.A578V) alteration is located in exon 10 (coding exon 9) of the TAP2 gene. This alteration results from a C to T substitution at nucleotide position 1733, causing the alanine (A) at amino acid position 578 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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