ClinVar Miner

Submissions for variant NM_002778.4(PSAP):c.1192+6C>T

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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 RCV002942770 SCV003271960 uncertain significance Sphingolipid activator protein 1 deficiency 2024-01-15 criteria provided, single submitter clinical testing This sequence change falls in intron 10 of the PSAP gene. It does not directly change the encoded amino acid sequence of the PSAP protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs374560502, gnomAD 0.04%). 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: 2061492). 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 is not likely to affect RNA splicing. 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.
Ambry Genetics RCV002939057 SCV003553021 uncertain significance Inborn genetic diseases 2020-12-08 criteria provided, single submitter clinical testing The c.1192+6C>T intronic alteration consists of a C to T substitution 6 nucleotides after exon 10 (coding exon 10) in the PSAP gene. In silico splice site analysis predicts that this alteration will not have any significant effect on splicing. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
PreventionGenetics, part of Exact Sciences RCV004741354 SCV005349750 likely benign PSAP-related disorder 2024-04-25 no assertion criteria provided 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).

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