ClinVar Miner

Submissions for variant NM_000512.5(GALNS):c.319+2T>C

dbSNP: rs2143005067
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova RCV001578291 SCV001547659 likely pathogenic Mucopolysaccharidosis, MPS-IV-A 2021-02-01 criteria provided, single submitter curation Splicing variant in canonical site (PVS1_very strong); absent from gnomAD v2.1.1 (PM2_moderate)
Fulgent Genetics, Fulgent Genetics RCV001578291 SCV002811748 likely pathogenic Mucopolysaccharidosis, MPS-IV-A 2021-10-19 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001578291 SCV003461743 pathogenic Mucopolysaccharidosis, MPS-IV-A 2025-02-02 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 3 of the GALNS 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 GALNS are known to be pathogenic (PMID: 12442278). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individuals with mucopolysaccharidosis type IVA (PMID: 34387910; internal data). ClinVar contains an entry for this variant (Variation ID: 1048188). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.

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