ClinVar Miner

Submissions for variant NM_002778.4(PSAP):c.650C>T (p.Thr217Ile) (rs121918103)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000624006 SCV000742960 pathogenic Inborn genetic diseases 2017-09-25 criteria provided, single submitter clinical testing
Invitae RCV000014289 SCV000828384 likely pathogenic Sphingolipid activator protein 1 deficiency 2018-03-15 criteria provided, single submitter clinical testing This sequence change replaces threonine with isoleucine at codon 217 of the PSAP protein (p.Thr217Ile). The threonine residue is weakly conserved and there is a moderate physicochemical difference between threonine and isoleucine. This variant is present in population databases (rs121918103, ExAC 0.05%). This variant has been reported to segregate with saposin B deficiency in two families (PMID: 2320574, 2302219). ClinVar contains an entry for this variant (Variation ID: 13361). Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Deleterous"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000732106 SCV000860012 likely pathogenic not provided 2018-02-26 criteria provided, single submitter clinical testing
OMIM RCV000014289 SCV000034538 pathogenic Sphingolipid activator protein 1 deficiency 1990-04-01 no assertion criteria provided literature only

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