ClinVar Miner

Submissions for variant NM_002778.4(PSAP):c.1192G>A (p.Val398Ile)

gnomAD frequency: 0.00001  dbSNP: rs759178813
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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 RCV001871601 SCV002197025 uncertain significance Sphingolipid activator protein 1 deficiency 2022-07-12 criteria provided, single submitter clinical testing This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 398 of the PSAP protein (p.Val398Ile). This variant also falls at the last nucleotide of exon 10, which is part of the consensus splice site for this exon. This variant is present in population databases (rs759178813, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with PSAP-related conditions. ClinVar contains an entry for this variant (Variation ID: 991964). 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"). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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.
Fulgent Genetics, Fulgent Genetics RCV002480920 SCV002789292 uncertain significance Gaucher disease due to saposin C deficiency; Krabbe disease due to saposin A deficiency; Combined PSAP deficiency; Sphingolipid activator protein 1 deficiency; Parkinson disease 24, autosomal dominant, susceptibility to 2021-12-03 criteria provided, single submitter clinical testing
Natera, Inc. RCV001280268 SCV001467433 uncertain significance Metachromatic leukodystrophy 2020-04-11 no assertion criteria provided clinical testing

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