ClinVar Miner

Submissions for variant NM_002778.4(PSAP):c.875T>G (p.Val292Gly)

gnomAD frequency: 0.00001  dbSNP: rs758866050
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001921495 SCV002204385 uncertain significance Sphingolipid activator protein 1 deficiency 2022-04-13 criteria provided, single submitter clinical testing This sequence change replaces valine, which is neutral and non-polar, with glycine, which is neutral and non-polar, at codon 292 of the PSAP protein (p.Val292Gly). This variant is present in population databases (rs758866050, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with PSAP-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics RCV002291509 SCV002583302 uncertain significance Combined PSAP deficiency 2022-08-26 criteria provided, single submitter clinical testing The homozygous variant for c.881T>G in exon 8 of PSAP gene was detected. This variant has not been reported in the 1000 genomes and has a MAF of 0.001% in the gnomAD database. The insilico predition is disease causing by FATHMM and Mut-Pred.
Neuberg Centre For Genomic Medicine, NCGM RCV003339831 SCV004048302 uncertain significance Parkinson disease 24, autosomal dominant, susceptibility to criteria provided, single submitter clinical testing The missense variant in c.884T>G (p.Val295Gly) in PSAP gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.Val295Gly variant is novel (not in any individuals) in 1000 Genomes and has allele frequency (0.001193%) in gnomAD database. The amino acid Val at position 295 is changed to a Gly changing protein sequence and it might alter its composition and physico-chemical properties. The variant is predicted to be damaging by both SIFT and PolyPhen2. The amino acid change p.Val295Gly in PSAP is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Uncertain Significance

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