ClinVar Miner

Submissions for variant NM_000593.6(TAP1):c.1564C>T (p.Gln522Ter)

gnomAD frequency: 0.00004  dbSNP: rs967210854
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001041667 SCV001205293 pathogenic MHC class I deficiency 2023-12-17 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Gln582*) in the TAP1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in TAP1 are known to be pathogenic (PMID: 10074494, 10074495). This variant is present in population databases (no rsID available, gnomAD 0.006%). This premature translational stop signal has been observed in individual(s) with hereditary major histocompatibility complex (MHC) class I deficiency (PMID: 16299152). It has also been observed to segregate with disease in related individuals. This variant is also known as Q522X. ClinVar contains an entry for this variant (Variation ID: 839821). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV004720047 SCV005325140 pathogenic not provided 2023-08-31 criteria provided, single submitter clinical testing Reported as heterozygous, without a second pathogenic variant identified, in an individual with recurrent respiratory tract infections and decreased major histocompatibility complex expression (Van den Berg et al., 2019); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 25525159, 10074495, 10074494, 16299152, Berg2016[case report])
GenomeConnect, ClinGen RCV001041667 SCV002818425 not provided MHC class I deficiency no assertion provided phenotyping only Variant classified as Pathogenic and reported on 10-12-2021 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.

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