ClinVar Miner

Submissions for variant NM_013296.5(GPSM2):c.1062+1G>T

gnomAD frequency: 0.00006  dbSNP: rs777695770
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000507416 SCV000603857 pathogenic not specified 2016-11-02 criteria provided, single submitter clinical testing
GeneDx RCV001731315 SCV001983288 pathogenic not provided 2023-11-10 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: 22578326, 27312216, 36147510)
Division Of Personalized Genomic Medicine, Columbia University Irving Medical Center RCV000029166 SCV004190165 pathogenic Chudley-McCullough syndrome 2021-12-13 criteria provided, single submitter clinical testing The c.1062+1G>T variant in the GPSM2 gene is a heterozygous canonical splice site variant, which affects an acceptor splice site in intron 9 (14 introns total; NM_013296.5). This mutation results in loss of exon 9 in the transcript and is predicted to generate a truncated protein, p.Arg318Argfs*8 (PMID: 22578326). Homozygous or compound heterozygous loss-of-function variants in GPSM2 have been reported in patient cohorts with Chudley-McCullough syndrome (PMID: 22578326). This variant in a homozygous state has been reported in two families with autosomal recessive Chudley-McCullough syndrome (PMID: 22578326 and 27312216). This variant has not been observed in the Genome Aggregation Database (gnomAD), indicating it is not a common benign variant in the populations represented in this database. This variant has been reported in the ClinVar database as a pathogenic variant (Variant ID: 35494; last accessed 12/13/2021).
OMIM RCV000029166 SCV000051811 pathogenic Chudley-McCullough syndrome 2012-06-08 no assertion criteria provided literature only

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