ClinVar Miner

Submissions for variant NM_000046.5(ARSB):c.1197C>G (p.Phe399Leu) (rs200793396)

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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 RCV000677462 SCV000802969 likely pathogenic Mucopolysaccharidosis type 6 2018-01-01 criteria provided, single submitter curation In vitro functional studies supportive of a damaging effect on the gene product (low to no ARSB activity in homozygotes; PS3); Very low frequency in ExAC (PM2)
Illumina Clinical Services Laboratory,Illumina RCV000677462 SCV000915136 pathogenic Mucopolysaccharidosis type 6 2018-09-10 criteria provided, single submitter clinical testing The ARSB c.1197C>G (p.Phe399Leu) missense variant has been reported in five studies and is found in a total of seven individuals with mucopolysaccharidosis, type VI, including in one in a homozygous state and in six in a compound heterozygous state, including one sibling pair (Yang et al. 2001; Ching-Wan et al. 2004; Lin et al. 2008; But et al. 2011; Zheng et al. 2014). The p.Phe399Leu variant was also found in a heterozygous state in two unaffected parents (Ching-Wan et al. 2004). The p.Phe399Leu variant was absent from 150 control subjects and is reported at a frequency of 0.000174 in the East Asian population of the Genome Aggregation Database. Based on the evidence, the p.Phe399Leu variant is classified as pathogenic for mucopolysaccharidosis. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Invitae RCV000677462 SCV001221173 pathogenic Mucopolysaccharidosis type 6 2020-01-13 criteria provided, single submitter clinical testing This sequence change replaces phenylalanine with leucine at codon 399 of the ARSB protein (p.Phe399Leu). The phenylalanine residue is moderately conserved and there is a small physicochemical difference between phenylalanine and leucine. This variant is present in population databases (rs200793396, ExAC 0.02%). This variant has been observed in individual(s) with mucopolysaccharidosis type VI (PMID: 18486607, 25190157, 11802522). ClinVar contains an entry for this variant (Variation ID: 559688). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. For these reasons, this variant has been classified as Pathogenic.

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