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NM_207122.2(EXT2):c.429C>A (p.Tyr143Ter) AND Exostoses, multiple, type 2

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Mar 4, 2017
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV000553165.4

Allele description [Variation Report for NM_207122.2(EXT2):c.429C>A (p.Tyr143Ter)]

NM_207122.2(EXT2):c.429C>A (p.Tyr143Ter)

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.429C>A (p.Tyr143Ter)
HGVS:
  • NC_000011.10:g.44108141C>A
  • NG_007560.1:g.17593C>A
  • NM_000401.3:c.528C>A
  • NM_001178083.3:c.429C>A
  • NM_001389628.1:c.429C>A
  • NM_001389630.1:c.429C>A
  • NM_207122.2:c.429C>AMANE SELECT
  • NP_000392.3:p.Tyr176Ter
  • NP_001171554.1:p.Tyr143Ter
  • NP_001376557.1:p.Tyr143Ter
  • NP_001376559.1:p.Tyr143Ter
  • NP_997005.1:p.Tyr143Ter
  • NP_997005.1:p.Tyr143Ter
  • LRG_494t1:c.528C>A
  • LRG_494t2:c.429C>A
  • LRG_494:g.17593C>A
  • LRG_494p1:p.Tyr176Ter
  • LRG_494p2:p.Tyr143Ter
  • NC_000011.9:g.44129691C>A
  • NM_207122.1:c.429C>A
Protein change:
Y143*
Links:
dbSNP: rs1555002543
NCBI 1000 Genomes Browser:
rs1555002543
Molecular consequence:
  • NM_000401.3:c.528C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001178083.3:c.429C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001389628.1:c.429C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001389630.1:c.429C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_207122.2:c.429C>A - nonsense - [Sequence Ontology: SO:0001587]

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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000640989Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Mar 4, 2017) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Multiple osteochondromas: mutation update and description of the multiple osteochondromas mutation database (MOdb).

Jennes I, Pedrini E, Zuntini M, Mordenti M, Balkassmi S, Asteggiano CG, Casey B, Bakker B, Sangiorgi L, Wuyts W.

Hum Mutat. 2009 Dec;30(12):1620-7. doi: 10.1002/humu.21123. Review.

PubMed [citation]
PMID:
19810120

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 Invitae, SCV000640989.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

While this particular variant has not been reported in the literature, loss-of-function variants in EXT2 are known to be pathogenic (PMID: 19810120). This sequence change creates a premature translational stop signal at codon 143 (p.Tyr143*) of the EXT2 gene. It is expected to result in an absent or disrupted protein product. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Feb 20, 2024