ClinVar Miner

Submissions for variant NM_002351.5(SH2D1A):c.138-1G>A

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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 RCV003509078 SCV004298981 pathogenic X-linked lymphoproliferative disease due to SH2D1A deficiency 2023-09-14 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. Disruption of this splice site has been observed in individual(s) with EBV-associated lymphoproliferation (PMID: 24616127). This variant is not present in population databases (gnomAD no frequency). This sequence change affects an acceptor splice site in intron 1 of the SH2D1A 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 SH2D1A are known to be pathogenic (PMID: 9771704, 11049992, 15711562).
GeneDx RCV004701744 SCV005201692 pathogenic not provided 2024-01-17 criteria provided, single submitter clinical testing Canonical splice site variant predicted to result in a null allele in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 24616127)

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