NM_207122.2(EXT2):c.482del (p.Asn161fs) AND Exostoses, multiple, type 2

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 28, 2019
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:: RCV001223589.6

Allele description [Variation Report for NM_207122.2(EXT2):c.482del (p.Asn161fs)]

NM_207122.2(EXT2):c.482del (p.Asn161fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

11p11.2

Genomic location:

Preferred name:

NM_207122.2(EXT2):c.482del (p.Asn161fs)

HGVS:

NC_000011.10:g.44108194del
NG_007560.1:g.17646del
NM_000401.3:c.581del
NM_001178083.3:c.482del
NM_001389628.1:c.482del
NM_001389630.1:c.482del
NM_207122.2:c.482delMANE SELECT
NP_000392.3:p.Asn194fs
NP_001171554.1:p.Asn161fs
NP_001376557.1:p.Asn161fs
NP_001376559.1:p.Asn161fs
NP_997005.1:p.Asn161fs
LRG_494t1:c.581del
LRG_494t2:c.482del
LRG_494:g.17646del
LRG_494p1:p.Asn194fs
NC_000011.9:g.44129743del
NC_000011.9:g.44129744del
NM_207122.1:c.482del

Protein change:

N161fs

Links:

dbSNP: rs1590548336

NCBI 1000 Genomes Browser:

rs1590548336

Molecular consequence:

NM_000401.3:c.581del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001178083.3:c.482del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001389628.1:c.482del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001389630.1:c.482del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_207122.2:c.482del - frameshift variant - [Sequence Ontology: SO:0001589]

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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fc56d09.x1 Zebrafish WashU MPIMG EST Danio rerio cDNA clone IMAGE:3725393 3', mR...
fc56d09.x1 Zebrafish WashU MPIMG EST Danio rerio cDNA clone IMAGE:3725393 3', mRNA sequence
gi|5341659|gnl|dbEST|2833914|gb|AI7 .1|

Nucleotide
fbxl4 F-box and leucine-rich repeat protein 4 [Danio rerio]
fbxl4 F-box and leucine-rich repeat protein 4 [Danio rerio]
Gene ID:492349

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001395745	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 28, 2019)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 10679937, 19810120, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001395745

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 28, 2019)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

Molecular basis of multiple exostoses: mutations in the EXT1 and EXT2 genes.

Wuyts W, Van Hul W.

Hum Mutat. 2000;15(3):220-7. Review.

PubMed [citation]

PMID:: 10679937

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

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001395745.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Asn161Thrfs*109) in 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. Loss-of-function variants in EXT2 are known to be pathogenic (PMID: 10679937, 19810120). This variant has not been reported in the literature in individuals with EXT2-related conditions. This variant is not present in population databases (ExAC no frequency).

#	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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