NM_000202.8(IDS):c.785T>A (p.Val262Glu) AND Mucopolysaccharidosis, MPS-II

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Sep 1, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001981569.8

Allele description [Variation Report for NM_000202.8(IDS):c.785T>A (p.Val262Glu)]

NM_000202.8(IDS):c.785T>A (p.Val262Glu)

Genes:

LOC106050102:IDS recombination region [Gene]
IDS:iduronate 2-sulfatase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xq28

Genomic location:

Preferred name:

NM_000202.8(IDS):c.785T>A (p.Val262Glu)

HGVS:

NC_000023.11:g.149496440A>T
NG_011900.3:g.13895T>A
NG_042264.2:g.9796A>T
NM_000202.8:c.785T>AMANE SELECT
NM_001166550.4:c.515T>A
NM_006123.5:c.785T>A
NP_000193.1:p.Val262Glu
NP_001160022.1:p.Val172Glu
NP_006114.1:p.Val262Glu
NC_000023.10:g.148577971A>T
NG_042264.1:g.9795A>T
NR_104128.2:n.954T>A

Protein change:

V172E

Links:

dbSNP: rs782053689

NCBI 1000 Genomes Browser:

rs782053689

Molecular consequence:

NM_000202.8:c.785T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001166550.4:c.515T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_006123.5:c.785T>A - missense variant - [Sequence Ontology: SO:0001583]
NR_104128.2:n.954T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Mucopolysaccharidosis, MPS-II (MPS2)
Synonyms:: Mucopolysaccharidosis type II; Attenuated MPS (subtype; formerly known as mild MPS II); Severe MPS II; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0010674; MedGen: C0026705; Orphanet: 580; OMIM: 309900

Recent activity

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Oreortyx pictus large subunit ribosomal RNA gene, partial sequence; mitochondria...
Oreortyx pictus large subunit ribosomal RNA gene, partial sequence; mitochondrial
gi|1883898075|gb|MT588067.1|

Nucleotide
proteasome subunit beta type-2 isoform 1 [Mus musculus]
proteasome subunit beta type-2 isoform 1 [Mus musculus]
gi|227116345|ref|NP_036100.3|

Protein
Chain A, PROTEIN SERINE/THREONINE PHOSPHATASE-1 (ALPHA ISOFORM, TYPE 1)
Chain A, PROTEIN SERINE/THREONINE PHOSPHATASE-1 (ALPHA ISOFORM, TYPE 1)
gi|1633403|pdb|1FJM|A

Protein
PREDICTED: Belonocnema kinseyi zinc finger protein 431-like (LOC117182373), mRNA
PREDICTED: Belonocnema kinseyi zinc finger protein 431-like (LOC117182373), mRNA
gi|1830578462|ref|XM_033375573.1|

Nucleotide
thioredoxin reductase 3 isoform 1 [Mus musculus]
thioredoxin reductase 3 isoform 1 [Mus musculus]
gi|296010803|ref|NP_001171529.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002222558	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 1, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004235544	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jul 13, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002222558

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 1, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004235544

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jul 13, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002222558.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on IDS protein function. ClinVar contains an entry for this variant (Variation ID: 1443998). This variant has not been reported in the literature in individuals affected with IDS-related conditions. This variant is present in population databases (rs782053689, gnomAD 0.001%), including at least one homozygous and/or hemizygous individual. This sequence change replaces valine, which is neutral and non-polar, with glutamic acid, which is acidic and polar, at codon 262 of the IDS protein (p.Val262Glu).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Revvity Omics, Revvity, SCV004235544.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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