ClinVar Miner

Submissions for variant NM_002778.4(PSAP):c.607C>T (p.Gln203Ter)

dbSNP: rs1554880848
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 3
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000578629 SCV000681131 pathogenic not provided 2017-11-16 criteria provided, single submitter clinical testing The Q203X variant in the PSAP gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The Q203X variant is not observed in large population cohorts (Lek et al., 2016). We interpret Q203X as a pathogenic variant.
Labcorp Genetics (formerly Invitae), Labcorp RCV002529049 SCV003216605 pathogenic Sphingolipid activator protein 1 deficiency 2023-04-19 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 489144). This variant has not been reported in the literature in individuals affected with PSAP-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gln203*) in the PSAP gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PSAP are known to be pathogenic (PMID: 8554069, 11309366, 17616409, 19267410, 30632081).
3billion RCV002529049 SCV003841900 pathogenic Sphingolipid activator protein 1 deficiency 2023-02-23 criteria provided, single submitter clinical testing The variant is not observed in the gnomAD v2.1.1 dataset. This variant was predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. The variant has been reported to be associated with PSAP related disorder (ClinVar ID: VCV000489144). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.