ClinVar Miner

Submissions for variant NM_000202.8(IDS):c.514C>T (p.Arg172Ter)

dbSNP: rs104894860
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000011236 SCV000628123 pathogenic Mucopolysaccharidosis, MPS-II 2023-04-01 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 10490). This premature translational stop signal has been observed in individuals with mucopolysaccharidosis type II (PMID: 1639384, 7887413, 21829674, 24780617). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Arg172*) in the IDS gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in IDS are known to be pathogenic (PMID: 8940265, 9875019).
Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences RCV000011236 SCV001480205 pathogenic Mucopolysaccharidosis, MPS-II criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000011236 SCV002014478 pathogenic Mucopolysaccharidosis, MPS-II 2021-09-05 criteria provided, single submitter clinical testing
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein RCV000011236 SCV002512754 pathogenic Mucopolysaccharidosis, MPS-II 2021-07-13 criteria provided, single submitter clinical testing ACMG classification criteria: PVS1 very strong, PS3 supporting, PS4 moderate, PM2 moderate
Ambry Genetics RCV002336081 SCV002644813 pathogenic Inborn genetic diseases 2014-07-18 criteria provided, single submitter clinical testing The p.R172* pathogenic mutation (also known as c.514C>T and 638C>T), located in coding exon 5 of the IDS gene, results from a C to T substitution at nucleotide position 514. This changes the amino acid from an arginine to a stop codon within coding exon 5. This mutation was originally reported in a patient with a clinical diagnosis Hunter syndrome (Flomen RH et al. Genomics. 1992;13(3):543-550). In addition to the clinical data presented in the literature, since premature stop codons are typically deleterious in nature, this alteration is interpreted as a disease-causing mutation (ACMG Recommendations for Standards for Interpretation and Reporting of Sequence Variations. Revision 2007. Genet Med. 2008;10:294).
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics RCV000011236 SCV002822851 pathogenic Mucopolysaccharidosis, MPS-II 2023-01-16 criteria provided, single submitter clinical testing A Hemizygous missense variation in exon 5 of the IDS gene that results in the termination of amino acid chain at codon 172 was detected. The observed variant c.514C>T (p.Arg172Ter) has not been reported in the 1000 genomes and gnomAD databases. The in silico prediction of the variant are possibly damaging by CADD and MutationTaster2. In summary, the variant meets our criteria to be classified as pathogenic.
GeneDx RCV002512967 SCV003194806 pathogenic not provided 2023-01-18 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: 35144014, 25525159, 33676511, 21829674, 7887413, 9875019, 1639384, 30639582, 28077157)
OMIM RCV000011236 SCV000031463 pathogenic Mucopolysaccharidosis, MPS-II 1992-07-01 no assertion criteria provided literature only
Pediatrics, All India Institute of Medical Sciences, New Delhi RCV000011236 SCV001573781 affects Mucopolysaccharidosis, MPS-II 2014-04-04 no assertion criteria provided research The change c.514C>T (p.R172*) was found to be a nonsense variant, where the basic polar amino acid Arginine at 172 position was substituted by stop codon leading to early truncation of the peptide. It was found in the hemizygous condition in two non-familial patients with sever MPS-II phenotype. The patients hails from the Delhi and Bihar, India.

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