ClinVar Miner

Submissions for variant NM_001367721.1(CASK):c.1186C>T (p.Pro396Ser)

gnomAD frequency: 0.00026  dbSNP: rs137852820
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001086366 SCV000831734 likely benign Intellectual disability, CASK-related, X-linked 2023-12-12 criteria provided, single submitter clinical testing
Eurofins Ntd Llc (ga) RCV000733420 SCV000861488 uncertain significance not provided 2018-06-07 criteria provided, single submitter clinical testing
Mendelics RCV000990800 SCV001141839 likely benign Syndromic X-linked intellectual disability Najm type 2020-05-06 criteria provided, single submitter clinical testing This variant, that leads to the substitution of proline in codon 396 for serine, has been previously reported in medical literature to segregate with the phenotype of X-linked intellectual deficiency in one family (PMID: 19377476). However, functional studies demonstrate that it results in a structurally stable protein and interactions with liprin-α, Mint-1 and Veli are preserved (PMID: 24505460). In addition, it is observed at a higher than expected frequency in population databases, including 5 hemizygous individuals (gnomAD v2.1.1). Therefore, this variant was considered to be likely benign.
GeneDx RCV000733420 SCV001793621 likely benign not provided 2020-02-14 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 19377476, 23871722, 33090494, 24505460, 21954287, 22452838, 19847910, 21735175, 29426960, 25886057, 20029458)
Ambry Genetics RCV002326675 SCV002634078 likely benign Inborn genetic diseases 2018-01-24 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
CeGaT Center for Human Genetics Tuebingen RCV000733420 SCV004702339 likely benign not provided 2024-01-01 criteria provided, single submitter clinical testing CASK: BS2
OMIM RCV000012292 SCV000032526 pathogenic FG syndrome 4 2009-05-01 no assertion criteria provided literature only

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