ClinVar Miner

Submissions for variant NM_000512.5(GALNS):c.1177G>T (p.Ala393Ser)

gnomAD frequency: 0.05170  dbSNP: rs2303269
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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000079023 SCV000110892 benign not specified 2017-10-24 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV000079023 SCV000304607 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000378709 SCV000399633 benign Mucopolysaccharidosis, MPS-IV-A 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000079023 SCV001361770 benign not specified 2019-02-15 criteria provided, single submitter clinical testing Variant summary: GALNS c.1177G>T (p.Ala393Ser) results in a conservative amino acid change located in the Sulfatase, N-terminal domain of the encoded protein sequence. Five of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.06 in 275882 control chromosomes in the gnomAD database, including 553 homozygotes. The observed variant frequency is approximately 29-folds higher than the estimated maximal expected allele frequency for a pathogenic variant in GALNS causing Mucopolysaccharidosis Type IVA (Morquio Syndrome A) phenotype (0.002), strongly suggesting that the variant is benign. Three ClinVar submissions from clinical diagnostic laboratories (evaluation after 2014) cite the variant as likely benign/benign. Based on the evidence outlined above, the variant was classified as benign.
Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova RCV000378709 SCV001547917 benign Mucopolysaccharidosis, MPS-IV-A 2021-02-01 criteria provided, single submitter curation Allele frequency is >5% in gnomAD v2.1.1 (BA1_stand-alone); allele frequency is greater than expected for disorder (BS1_strong); multiple lines of computational evidence suggest no impact on gene or gene product (BP4_supporting)
Labcorp Genetics (formerly Invitae), Labcorp RCV000378709 SCV001718520 benign Mucopolysaccharidosis, MPS-IV-A 2024-02-01 criteria provided, single submitter clinical testing
GeneDx RCV000675532 SCV001873283 benign not provided 2018-06-25 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 25252036, 24035930, 16837223, 21251309, 15235041, 15241807, 9452036)
Genome-Nilou Lab RCV000378709 SCV002045052 benign Mucopolysaccharidosis, MPS-IV-A 2021-11-07 criteria provided, single submitter clinical testing
Breakthrough Genomics, Breakthrough Genomics RCV000675532 SCV005252580 benign not provided criteria provided, single submitter not provided
Mayo Clinic Laboratories, Mayo Clinic RCV000675532 SCV000801223 benign not provided 2015-10-22 no assertion criteria provided clinical testing

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