NM_207122.2(EXT2):c.896G>A (p.Arg299His) AND Exostoses, multiple, type 2

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: Jan 10, 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:: RCV000945936.13

Allele description [Variation Report for NM_207122.2(EXT2):c.896G>A (p.Arg299His)]

NM_207122.2(EXT2):c.896G>A (p.Arg299His)

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.896G>A (p.Arg299His)

HGVS:

NC_000011.10:g.44124941G>A
NG_007560.1:g.34393G>A
NM_000401.3:c.995G>A
NM_001178083.3:c.896G>A
NM_001389628.1:c.896G>A
NM_001389630.1:c.896G>A
NM_207122.2:c.896G>AMANE SELECT
NP_000392.3:p.Arg332His
NP_001171554.1:p.Arg299His
NP_001376557.1:p.Arg299His
NP_001376559.1:p.Arg299His
NP_997005.1:p.Arg299His
NP_997005.1:p.Arg299His
LRG_494t1:c.995G>A
LRG_494t2:c.896G>A
LRG_494:g.34393G>A
LRG_494p1:p.Arg332His
LRG_494p2:p.Arg299His
NC_000011.9:g.44146491G>A
NM_207122.1:c.896G>A

Protein change:

R299H

Links:

dbSNP: rs76901081

NCBI 1000 Genomes Browser:

rs76901081

Molecular consequence:

NM_000401.3:c.995G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001178083.3:c.896G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001389628.1:c.896G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001389630.1:c.896G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_207122.2:c.896G>A - 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
SCV000371839	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,
SCV001092011	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 10, 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

SCV000371839

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,

SCV001092011

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Jan 10, 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

Methylation status of EXT1 and EXT2 promoters and two mutations of EXT2 in chondrosarcoma.

Tsuchiya T, Osanai T, Ogose A, Tamura G, Chano T, Kaneko Y, Ishikawa A, Orui H, Wada T, Ikeda T, Namba M, Takigawa M, Kawashima H, Hotta T, Tsuchiya A, Ogino T, Motoyama T.

Cancer Genet Cytogenet. 2005 Apr 15;158(2):148-55.

PubMed [citation]

PMID:: 15796962

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, SCV000371839.3

#	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, SCV001092011.6

#	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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