NM_000401.3(EXT2):c.223A>G (p.Met75Val) AND Multiple exostoses type 2

Clinical significance:Benign/Likely benign (Last evaluated: Nov 27, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV001086119.3

Allele description [Variation Report for NM_000401.3(EXT2):c.223A>G (p.Met75Val)]

NM_000401.3(EXT2):c.223A>G (p.Met75Val)

Gene:
EXT2:exostosin glycosyltransferase 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11p11.2
Genomic location:
Preferred name:
NM_000401.3(EXT2):c.223A>G (p.Met75Val)
HGVS:
  • NC_000011.10:g.44107836A>G
  • NG_007560.1:g.17288A>G
  • NM_000401.3:c.223A>G
  • NM_001178083.2:c.124A>G
  • NM_207122.1:c.124A>G
  • NP_000392.3:p.Met75Val
  • NP_001171554.1:p.Met42Val
  • NP_997005.1:p.Met42Val
  • LRG_494t1:c.223A>G
  • LRG_494t2:c.124A>G
  • LRG_494:g.17288A>G
  • LRG_494p1:p.Met75Val
  • LRG_494p2:p.Met42Val
  • NC_000011.9:g.44129386A>G
  • Q93063:p.Met42Val
Protein change:
M42V
Links:
UniProtKB: Q93063#VAR_033921; dbSNP: rs4755779
NCBI 1000 Genomes Browser:
rs4755779
Molecular consequence:
  • NM_000401.3:c.223A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001178083.2:c.124A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_207122.1:c.124A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Multiple exostoses type 2 (EXT2)
Synonyms:
EXOSTOSES, MULTIPLE, TYPE II
Identifiers:
MONDO: MONDO:0007586; MedGen: C1851413; Orphanet: 321; OMIM: 133701

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000371826Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Likely benign
(Apr 27, 2017)
germlineclinical testing

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

Citation Link,

SCV001001047Invitaecriteria provided, single submitter
Benign
(Nov 27, 2020)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

20 novel point mutations and one large deletion in EXT1 and EXT2 genes: report of diagnostic screening in a large Italian cohort of patients affected by hereditary multiple exostosis.

Ciavarella M, Coco M, Baorda F, Stanziale P, Chetta M, Bisceglia L, Palumbo P, Bengala M, Raiteri P, Silengo M, Caldarini C, Facchini R, Lala R, Cavaliere ML, De Brasi D, Pasini B, Zelante L, Guarnieri V, D'Agruma L.

Gene. 2013 Feb 25;515(2):339-48. doi: 10.1016/j.gene.2012.11.055. Epub 2012 Dec 20.

PubMed [citation]
PMID:
23262345

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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Illumina Clinical Services Laboratory,Illumina, SCV000371826.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV001001047.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 18, 2021

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