ClinVar Miner

Submissions for variant NM_003896.4(ST3GAL5):c.82+1G>C

gnomAD frequency: 0.00001  dbSNP: rs878854615
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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 RCV000229539 SCV000288016 likely pathogenic GM3 synthase deficiency 2024-12-15 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 1 of the ST3GAL5 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in ST3GAL5 are known to be pathogenic (PMID: 15502825, 22990144, 27232954). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with ST3GAL5-related conditions (PMID: 31440721). ClinVar contains an entry for this variant (Variation ID: 239583). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Baylor Genetics RCV000229539 SCV001520496 likely pathogenic GM3 synthase deficiency 2019-11-15 criteria provided, single submitter clinical testing This variant was determined to be likely pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].
Ambry Genetics RCV004020809 SCV004958474 uncertain significance Inborn genetic diseases 2023-11-01 criteria provided, single submitter clinical testing The c.82+1G>C intronic variant results from a G to C substitution one nucleotide after coding exon 1 of the ST3GAL5 gene. This region of the ST3GAL5 gene is excluded from other biologically relevant ST3GAL5 transcripts. This allele was reported in one heterozygous individual in population-based cohorts in the Genome Aggregation Database (gnomAD). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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