ClinVar Miner

Submissions for variant NM_000512.5(GALNS):c.898+1G>C

gnomAD frequency: 0.00001  dbSNP: rs761850746
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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 RCV000210353 SCV001547827 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)
Labcorp Genetics (formerly Invitae), Labcorp RCV000210353 SCV004297066 pathogenic Mucopolysaccharidosis, MPS-IV-A 2023-06-10 criteria provided, single submitter clinical testing ClinVar contains an entry for this variant (Variation ID: 224783). Disruption of this splice site has been observed in individuals with mucopolysaccharidosis type IVA (PMID: 9298823, 15235041). This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 8 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). 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.
GeneReviews RCV000210353 SCV000266396 not provided Mucopolysaccharidosis, MPS-IV-A no assertion provided literature only

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