ClinVar Miner

Submissions for variant NM_000593.6(TAP1):c.1203C>G (p.Asn401Lys)

gnomAD frequency: 0.00003  dbSNP: rs756823000
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000642355 SCV000764024 uncertain significance MHC class I deficiency 2021-09-26 criteria provided, single submitter clinical testing 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. 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: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with TAP1-related conditions. This variant is present in population databases (rs756823000, ExAC 0.001%). This sequence change replaces asparagine with lysine at codon 461 of the TAP1 protein (p.Asn461Lys). The asparagine residue is moderately conserved and there is a moderate physicochemical difference between asparagine and lysine.
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV000642355 SCV001190469 uncertain significance MHC class I deficiency 2021-03-30 criteria provided, single submitter clinical testing TAP1 NM_000593.5 exon 5 p.Asn461Lys (c.1383C>G): This variant has not been reported in the literature but is present in 0.001% (2/113768) of European alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/6-32818142-G-C). This variant is present in ClinVar (Variation ID:534703). Evolutionary conservation suggests that this variant may not impact the protein; computational predictive tools suggest that this variant may impact the protein. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.

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