ClinVar Miner

Submissions for variant NM_002778.4(PSAP):c.623T>G (p.Ile208Ser)

gnomAD frequency: 0.00008  dbSNP: rs200319381
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics RCV000514444 SCV000610142 uncertain significance not provided 2017-03-09 criteria provided, single submitter clinical testing
GeneDx RCV000514444 SCV000621587 uncertain significance not provided 2017-10-10 criteria provided, single submitter clinical testing The I208S variant in the PSAP gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The I208S variant is observed in 160/34420 (0.46%) alleles from individuals of Latino background, in the ExAC dataset, an individuals were reported to be homozygous (Lek et al., 2016). The I208S variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is not conserved. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret I208S as a variant of uncertain significance.
Invitae RCV001081218 SCV001049205 likely benign Sphingolipid activator protein 1 deficiency 2024-01-24 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003962415 SCV004784854 likely benign PSAP-related condition 2022-08-05 criteria provided, single submitter clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
Natera, Inc. RCV001272678 SCV001454917 likely benign Metachromatic leukodystrophy 2019-11-11 no assertion criteria provided clinical testing

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