Total submissions: 12
| Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
|---|---|---|---|---|---|---|---|---|
| Myriad Genetics, |
RCV000177016 | SCV006323085 | pathogenic | Mucopolysaccharidosis, MPS-II | 2025-02-06 | criteria provided, single submitter | clinical testing | NM_000202.5(IDS):c.253G>A(A85T) is a missense variant classified as pathogenic in the context of mucopolysaccharidosis type II. A85T has been observed in cases with relevant disease (PMID: 33676511, 27146977, 27246110). Relevant functional assessments of this variant are available in the literature (PMID: 17091340). A85T has not been observed in referenced population frequency databases. In summary, NM_000202.5(IDS):c.253G>A(A85T) is a missense variant that has functional support for pathogenicity and has been observed more frequently in cases with the relevant disease than in healthy populations. Please note: this variant was assessed in the context of healthy population screening. |
| Laboratory of Diagnosis and Therapy of Lysosomal Disorders, |
RCV000177016 | SCV005088932 | pathogenic | Mucopolysaccharidosis, MPS-II | 2024-06-07 | criteria provided, single submitter | literature only | In vitro or in vivo functional studies supportive of a damaging effect (PS3_Moderate), Prevalence of the variant significantly increased in affected individuals compared with controls (PS4_Strong), Absent from controls (or at low frequency) in gnomAD database (PM2_Moderate), Missense variant in a gene with a low rate of benign missense variation (PP2_Supporting), Multiple lines of computational evidence support a deleterious effect (PP3_Supporting), Patient’s phenotype or family history highly specific for the disease (PP4_Moderate) |
| Revvity Omics, |
RCV000177016 | SCV003829533 | likely pathogenic | Mucopolysaccharidosis, MPS-II | 2022-11-10 | criteria provided, single submitter | clinical testing | |
| Laboratorio de Genetica e Diagnostico Molecular, |
RCV000177016 | SCV003807057 | pathogenic | Mucopolysaccharidosis, MPS-II | 2023-01-29 | criteria provided, single submitter | clinical testing | ACMG classification criteria: PS3 supporting, PS4 strong, PM2 moderated, PP1 supporting, PP3 supporting, PP4 |
| Labcorp Genetics |
RCV000177016 | SCV003445854 | pathogenic | Mucopolysaccharidosis, MPS-II | 2022-06-24 | criteria provided, single submitter | clinical testing | ClinVar contains an entry for this variant (Variation ID: 92617). This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 85 of the IDS protein (p.Ala85Thr). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with mucopolysaccharidosis II (PMID: 8940265, 25976201, 26762690, 31877959). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt IDS protein function. Experimental studies have shown that this missense change affects IDS function (PMID: 17091340). For these reasons, this variant has been classified as Pathogenic. |
| Kasturba Medical College, |
RCV000177016 | SCV002053783 | pathogenic | Mucopolysaccharidosis, MPS-II | criteria provided, single submitter | clinical testing | ||
| Genome- |
RCV000177016 | SCV002014484 | pathogenic | Mucopolysaccharidosis, MPS-II | 2021-09-05 | criteria provided, single submitter | clinical testing | |
| Department of Medical Genetics, |
RCV000177016 | SCV001479333 | pathogenic | Mucopolysaccharidosis, MPS-II | criteria provided, single submitter | clinical testing | ||
| Women's Health and Genetics/Laboratory Corporation of America, |
RCV000177016 | SCV000919530 | pathogenic | Mucopolysaccharidosis, MPS-II | 2018-08-17 | criteria provided, single submitter | clinical testing | Variant summary: IDS c.253G>A (p.Ala85Thr) results in a non-conservative amino acid change located in the Sulfatase, N-terminal domain of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 169233 control chromosomes (gnomAD). c.253G>A has been reported in the literature in multiple individuals affected with Mucopolysaccharidosis Type II (Hunter Syndrome)(Alkhzouz_2016, Amartino_2014, Dvorakova_2017, Kosuga_2016). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in <10% of normal activity (Alkhzouz_2016). No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as pathogenic. |
| IIFP, |
RCV000177016 | SCV000262519 | pathogenic | Mucopolysaccharidosis, MPS-II | 2007-05-16 | criteria provided, single submitter | research | |
| Eurofins Ntd Llc |
RCV000790731 | SCV000228820 | pathogenic | not provided | 2012-09-05 | criteria provided, single submitter | clinical testing | |
| Division of Medical Genetics, |
RCV000177016 | SCV001573770 | affects | Mucopolysaccharidosis, MPS-II | 2014-04-01 | no assertion criteria provided | research | The change c.253G>A, (p.A85T) was found to be a known missense variant, where the non-polar amino acid Alanine at 85 position was substituted with another polar amino acid Threonine. Uttarilli et al., described it in MPS II patients with attenuated phenotype from Kerala and Karnataka (Uttarilli et al.,2016). Rathmann et al., described A85T initially in one European MPS-II patients with attenuated phenotype (Rathmann et al.,1982). In our study, it was detected in the hemizygous condition in patients with MPS-II attenuated phenotype, hails from from the state of UP and Bihar, India. |