ClinVar Miner

Submissions for variant NM_016032.4(ZDHHC9):c.286C>T (p.Arg96Trp)

dbSNP: rs1131690786
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001575552 SCV001802572 likely pathogenic not provided 2019-08-30 criteria provided, single submitter clinical testing Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 32695065, 30631761, 30402882, 28687527, 25649377)
Centogene AG - the Rare Disease Company RCV000493569 SCV002059670 pathogenic Syndromic X-linked intellectual disability Raymond type 2019-12-03 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000493569 SCV002119537 pathogenic Syndromic X-linked intellectual disability Raymond type 2021-08-09 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 429192). This variant has been observed in individual(s) with clinical features of X-linked intellectual disability (XLID) (PMID: 25649377, 28687527; Invitae). In at least one individual the variant was observed to be de novo. It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (ExAC no frequency). This sequence change replaces arginine with tryptophan at codon 96 of the ZDHHC9 protein (p.Arg96Trp). The arginine residue is highly conserved and there is a moderate physicochemical difference between arginine and tryptophan.
Department of Laboratory Medicine, Daejeon St. Mary’s Hospital RCV000493569 SCV000574703 pathogenic Syndromic X-linked intellectual disability Raymond type 2017-04-04 no assertion criteria provided clinical testing The first sporadic X-linked intellectual disability with de novo ZDHHC9 mutation identified by targeted next-generation sequencing.
OMIM RCV000493569 SCV001250831 pathogenic Syndromic X-linked intellectual disability Raymond type 2020-05-15 no assertion criteria provided literature only

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