NM_000401.3(EXT2):c.1859C>T (p.Thr620Met) AND not provided

Clinical significance:Uncertain significance (Last evaluated: Nov 3, 2017)

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:
RCV000725983.4

Allele description [Variation Report for NM_000401.3(EXT2):c.1859C>T (p.Thr620Met)]

NM_000401.3(EXT2):c.1859C>T (p.Thr620Met)

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.1859C>T (p.Thr620Met)
HGVS:
  • NC_000011.10:g.44232450C>T
  • NG_007560.1:g.141902C>T
  • NM_000401.3:c.1859C>T
  • NM_001178083.2:c.1790C>T
  • NM_207122.1:c.1760C>T
  • NP_000392.3:p.Thr620Met
  • NP_001171554.1:p.Thr597Met
  • NP_997005.1:p.Thr587Met
  • LRG_494t1:c.1859C>T
  • LRG_494t2:c.1760C>T
  • LRG_494:g.141902C>T
  • LRG_494p1:p.Thr620Met
  • LRG_494p2:p.Thr587Met
  • NC_000011.9:g.44254000C>T
Protein change:
T587M
Links:
dbSNP: rs138495222
NCBI 1000 Genomes Browser:
rs138495222
Molecular consequence:
  • NM_000401.3:c.1859C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001178083.2:c.1790C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_207122.1:c.1760C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000340999EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Uncertain significance
(Apr 27, 2016)
germlineclinical testing

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

Citation Link,

SCV000617673GeneDxcriteria provided, single submitter
Uncertain significance
(Nov 3, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown1not 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

Details of each submission

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000340999.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From GeneDx, SCV000617673.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The T587M variant has been published previously in association with hereditary multiple exostoses (Jennes et al., 2009; Stavropoulos et al., 2016). However, the variant is observed in 45/30776 (0.1462%) alleles from individuals of South Asian background in large population cohorts, including one homozygote (Lek et al., 2016). T587M is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. In-silico analyses, including protein predictors and evolutionary conservation, support a deleterious effect. In summary, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

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

Last Updated: Jun 6, 2021

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