Submissions for variant NM_000202.8(IDS):c.641C>T (p.Thr214Met)

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Total submissions: 15

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Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Mayo Clinic Laboratories, Mayo Clinic	RCV000078368	SCV007321936	benign	not specified	2020-02-13	criteria provided, single submitter	clinical testing
Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova	RCV000205107	SCV005089156	likely pathogenic	Mucopolysaccharidosis, MPS-II	2024-06-07	criteria provided, single submitter	literature only	Absent from controls (or at low frequency) in gnomAD database (PM2_Moderate), Missense change at the same amino acid residue as a pathogenic variant (PM5_Supporting), Missense variant in a gene with a low rate of benign missense variation (PP2_Supporting), Patient’s phenotype or family history highly specific for the disease (PP4_Moderate), Multiple lines of computational evidence suggest no impact on gene or gene product (BP4_Supporting)
Genome-Nilou Lab	RCV000205107	SCV002014457	likely benign	Mucopolysaccharidosis, MPS-II	2021-09-05	criteria provided, single submitter	clinical testing
Dubai Health Genomic Medicine Center, Dubai Health	RCV000205107	SCV001984322	benign	Mucopolysaccharidosis, MPS-II	2020-01-02	criteria provided, single submitter	clinical testing
GeneDx	RCV000587097	SCV001949054	benign	not provided	2021-05-05	criteria provided, single submitter	clinical testing	This variant is associated with the following publications: (PMID: 21605424, 27884173, 27695081, 27896113, 31019283, 32448126)
Labcorp Genetics (formerly Invitae), Labcorp	RCV000205107	SCV001005466	benign	Mucopolysaccharidosis, MPS-II	2026-02-02	criteria provided, single submitter	clinical testing
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne	RCV000205107	SCV000883117	likely benign	Mucopolysaccharidosis, MPS-II	2018-11-21	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV002311549	SCV000846798	benign	Inborn genetic diseases	2014-06-27	criteria provided, single submitter	clinical testing	This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000587097	SCV000695964	benign	not provided	2017-06-26	criteria provided, single submitter	clinical testing	Variant summary: The IDS c.641C>T (p.Thr214Met) variant involves the alteration of a non-conserved nucleotide and 2/4 in silico tools predict a benign outcome for this variant. This variant was found in 444/87744 control chromosomes (12 homozygotes, 100 hemizygotes) at a frequency of 0.0050602, which is approximately 2 times the estimated maximal expected allele frequency of a pathogenic IDS variant (0.0028868), suggesting this variant is likely a benign polymorphism. A publication, Chkioua_2011, cites the variant in an affected individual, who was homozygous for the pathogenic R88P variant. This variant also co-occurred with a pathogenic variant, c.1402C>T (p.R468W) in a sample tested at our laboratory. In addition, multiple clinical diagnostic laboratories classified this variant as benign. Taken together, this variant is classified as benign.
IIFP, CONICET-UNLP	RCV000205107	SCV000262525	pathogenic	Mucopolysaccharidosis, MPS-II	2010-12-07	criteria provided, single submitter	research	The patient with this genetic variant is hemizygous for the variant in IDS gene: c.641C>T It is an X-linked disorder The disorder is Hunter disease or mucopolysaccharidosis type II The patient has a deficient activity of Iduronate 2 sulfatase in dried blood filter paper test. And normal activity of another sulfatase ruling out multiple sulfatase deficiency. He had two other family members affected from the same disorder, from the maternal side: a maternal uncle and maternal grand uncle. Both have died because of Hunter disease. Clinical manifestations are: Cifosis, short neck, disostosis multiplex, coarse face, hernia, macroglosia, claw hand, hepatosplenomegaly
Eurofins Ntd Llc (ga)	RCV000078368	SCV000110214	benign	not specified	2014-07-08	criteria provided, single submitter	clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV000078368	SCV001930394	benign	not specified		no assertion criteria provided	clinical testing
Clinical Genetics, Academic Medical Center	RCV000078368	SCV001920849	benign	not specified		no assertion criteria provided	clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	RCV000587097	SCV001800280	likely benign	not provided		no assertion criteria provided	clinical testing
Natera, Inc.	RCV000205107	SCV001462904	benign	Mucopolysaccharidosis, MPS-II	2020-09-16	no assertion criteria provided	clinical testing

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