ClinVar Miner

Submissions for variant NM_000512.5(GALNS):c.477G>A (p.Trp159Ter)

gnomAD frequency: 0.00001  dbSNP: rs398123439
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000790674 SCV000230937 pathogenic not provided 2013-05-14 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000178782 SCV000825972 pathogenic Mucopolysaccharidosis, MPS-IV-A 2025-01-01 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Trp159*) in the GALNS gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in GALNS are known to be pathogenic (PMID: 12442278). This variant is present in population databases (rs398123439, gnomAD 0.003%). This premature translational stop signal has been observed in individual(s) with mucopolysaccharidosis IVA (PMID: 23876334). ClinVar contains an entry for this variant (Variation ID: 93179). 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.
Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova RCV000178782 SCV001547710 pathogenic Mucopolysaccharidosis, MPS-IV-A 2021-02-01 criteria provided, single submitter research Nonsense variant (PVS1_very strong); in vivo functional studies supportive of a damaging effect on the gene product (low to null enzymatic activity in homozygotes; PS3_supporting); the prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls (PS4_strong); very low frequency in gnomAD v2.1.1 (PM2_moderate)
Revvity Omics, Revvity RCV000178782 SCV002024148 pathogenic Mucopolysaccharidosis, MPS-IV-A 2022-06-10 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000178782 SCV002045024 pathogenic Mucopolysaccharidosis, MPS-IV-A 2021-11-07 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000178782 SCV002814701 pathogenic Mucopolysaccharidosis, MPS-IV-A 2021-08-06 criteria provided, single submitter clinical testing
GeneDx RCV000790674 SCV005389508 pathogenic not provided 2024-05-01 criteria provided, single submitter clinical testing Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 23876334, 27694994)

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