NM_207122.2(EXT2):c.124A>G (p.Met42Val) AND Exostoses, multiple, type 2

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: Jan 28, 2024
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:: RCV001086119.12

Allele description [Variation Report for NM_207122.2(EXT2):c.124A>G (p.Met42Val)]

NM_207122.2(EXT2):c.124A>G (p.Met42Val)

Gene:

EXT2:exostosin glycosyltransferase 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11p11.2

Genomic location:

Preferred name:

NM_207122.2(EXT2):c.124A>G (p.Met42Val)

HGVS:

NC_000011.10:g.44107836A>G
NG_007560.1:g.17288A>G
NM_000401.3:c.223A>G
NM_001178083.3:c.124A>G
NM_001389628.1:c.124A>G
NM_001389630.1:c.124A>G
NM_207122.2:c.124A>GMANE SELECT
NP_000392.3:p.Met75Val
NP_001171554.1:p.Met42Val
NP_001376557.1:p.Met42Val
NP_001376559.1:p.Met42Val
NP_997005.1: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
NM_207122.1:c.124A>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_001178083.3:c.124A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001389628.1:c.124A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001389630.1:c.124A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_207122.2:c.124A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000371826	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Apr 27, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV001001047	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 28, 2024)	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

SCV000371826

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Likely benign
(Apr 27, 2017)

germline

clinical testing

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

Citation Link,

SCV001001047

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Jan 28, 2024)

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

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000371826.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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.

#	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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001001047.6

#	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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