ClinVar Miner

Submissions for variant NM_000380.4(XPA):c.389+1G>A

dbSNP: rs1554701931
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000673551 SCV000798765 likely pathogenic Xeroderma pigmentosum group A 2018-03-30 criteria provided, single submitter clinical testing
3billion RCV000673551 SCV004013691 pathogenic Xeroderma pigmentosum group A criteria provided, single submitter clinical testing The variant is not observed in the gnomAD v2.1.1 dataset. The variant is predicted to alter splicing and result in a loss or disruption of normal protein function. Multiple pathogenic loss-of-function variants are reported downstream of the variant. The variant has been reported to be associated with XPA related disorder (ClinVar ID: VCV000557410). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.
Labcorp Genetics (formerly Invitae), Labcorp RCV003688877 SCV004434747 pathogenic not provided 2023-02-14 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 557410). Disruption of this splice site has been observed in individuals with xeroderma pigmentosum (PMID: 27607234). This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 3 of the XPA gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in XPA are known to be pathogenic (PMID: 27607234).

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