ClinVar Miner

Submissions for variant NM_152419.3(HGSNAT):c.1323C>A (p.Tyr441Ter)

dbSNP: rs1804568176
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001877710 SCV002139097 pathogenic Mucopolysaccharidosis, MPS-III-C; Retinitis pigmentosa 73 2022-10-17 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 1374201). This variant has not been reported in the literature in individuals affected with HGSNAT-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Tyr441*) in the HGSNAT gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in HGSNAT are known to be pathogenic (PMID: 17033958, 19479962).
Lifecell International Pvt. Ltd RCV003228806 SCV003925680 likely pathogenic Mucopolysaccharidosis, MPS-III-C criteria provided, single submitter clinical testing A Heterozygous Nonsense variant c.1323C>A in Exon 13 of the HGSNAT gene that results in the amino acid substitution p.Tyr441* was identified. The observed variant is novel in gnomAD exomes and genomes. The severity of the impact of this variant on the protein is high, based on the effect of the protein and REVEL score . Rare Exome Variant Ensemble Learner (REVEL) is an ensembl method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen- 2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons. The REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing. ClinVar has also classified this variant as Pathogenic [Variation ID:1374201]. For these reasons, this variant has been classified as Likely Pathogenic.

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