ClinVar Miner

Submissions for variant NM_000512.5(GALNS):c.463G>A (p.Gly155Arg)

gnomAD frequency: 0.00001  dbSNP: rs398123438
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000178783 SCV000230938 pathogenic not provided 2013-06-13 criteria provided, single submitter clinical testing
Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova RCV001578563 SCV001547703 pathogenic Mucopolysaccharidosis, MPS-IV-A 2021-02-01 criteria provided, single submitter research In vitro and in vivo functional studies supportive of a damaging effect on the gene product (low to null enzymatic activity in homozygotes; low to null in vitro enzymatic activity; PS3_strong); 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); multiple lines of computational evidence support a deleterious effect on the gene (PP3_supporting)
CeGaT Center for Human Genetics Tuebingen RCV000178783 SCV001747169 pathogenic not provided 2021-04-01 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001578563 SCV002045025 pathogenic Mucopolysaccharidosis, MPS-IV-A 2021-11-07 criteria provided, single submitter clinical testing
Genetics and Molecular Pathology, SA Pathology RCV002272058 SCV002556967 pathogenic Skeletal dysplasia 2021-10-21 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV001578563 SCV003832540 likely pathogenic Mucopolysaccharidosis, MPS-IV-A 2022-04-04 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000178783 SCV004226684 pathogenic not provided 2023-02-15 criteria provided, single submitter clinical testing PP3, PP4, PM2, PM3_strong, PS4_moderate
Labcorp Genetics (formerly Invitae), Labcorp RCV001578563 SCV004296416 pathogenic Mucopolysaccharidosis, MPS-IV-A 2023-12-17 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 155 of the GALNS protein (p.Gly155Arg). This variant is present in population databases (rs398123438, gnomAD 0.006%). This missense change has been observed in individual(s) with mucopolysaccharidosis type IVA (PMID: 24120057, 32024277). ClinVar contains an entry for this variant (Variation ID: 93178). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt GALNS protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic.
Fulgent Genetics, Fulgent Genetics RCV001578563 SCV005641498 pathogenic Mucopolysaccharidosis, MPS-IV-A 2024-05-16 criteria provided, single submitter clinical testing

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