ClinVar Miner

Submissions for variant NM_000202.8(IDS):c.1402C>T (p.Arg468Trp) (rs199422231)

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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000723439 SCV000232921 pathogenic not provided 2014-07-28 criteria provided, single submitter clinical testing
LISIN Facultad de Ciencias Exactas, Universidad Nacional de La Plata RCV000180471 SCV000262540 pathogenic Mucopolysaccharidosis, MPS-II 2014-06-10 criteria provided, single submitter research
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000180471 SCV000695962 pathogenic Mucopolysaccharidosis, MPS-II 2017-06-26 criteria provided, single submitter clinical testing Variant summary: The IDS c.1402C>T (p.Arg468Trp) variant involves the alteration of a non-conserved nucleotide. 4/4 in silico tools predict a damaging outcome for this variant (SNPsandGO not captured due to low reliability index). This variant is absent in 159432 control chromosomes. This variant has been reported in multiple affected individuals mostly presented with severe form of the disease. Functional studies showed variant with <5% of WTs enzyme activity. Variant affecting the same codon R468Q has also been reported in multiple affected males presenting with Mucopolysaccharidosis type II (Hunter syndrome), suggesting the functional importance of this residue. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant is classified as pathogenic.
Invitae RCV000180471 SCV001376052 pathogenic Mucopolysaccharidosis, MPS-II 2019-08-30 criteria provided, single submitter clinical testing This sequence change replaces arginine with tryptophan at codon 468 of the IDS protein (p.Arg468Trp). The arginine residue is highly conserved and there is a moderate physicochemical difference between arginine and tryptophan. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individuals affected with mucopolysaccharidosis type II (PMID: 28077157, 30639582, 1284597, 15614569). ClinVar contains an entry for this variant (Variation ID: 10497). This variant has been reported to affect IDS protein function (PMID: 1284597, 15614569). For these reasons, this variant has been classified as Pathogenic.
Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences RCV000180471 SCV001480197 pathogenic Mucopolysaccharidosis, MPS-II criteria provided, single submitter clinical testing
OMIM RCV000011243 SCV000031470 pathogenic Mucopolysaccharidosis, type II, mild form 1992-12-01 no assertion criteria provided literature only
GeneReviews RCV000180471 SCV000999928 pathogenic Mucopolysaccharidosis, MPS-II 2018-10-04 no assertion criteria provided literature only
Counsyl RCV000180471 SCV001132228 pathogenic Mucopolysaccharidosis, MPS-II 2017-06-26 no assertion criteria provided clinical testing
Pediatrics,All India Institute of Medical Sciences, New Delhi RCV000180471 SCV001573783 affects Mucopolysaccharidosis, MPS-II 2014-04-05 no assertion criteria provided research The change c.1402C>T (p.R468W) was found to be a missense variant, where the basic polar positive amino acid Arginine at 468 position is substituted by aromatic nonpolar neutral amino acid Tryptophan. It was detected in a hemizygous state in three patients from two families. All three with attenuated phenotypes from UP (2 sibs) Jharkhand (single patient) India.

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