NM_000401.3(EXT2):c.344A>C (p.Asp115Ala) AND not provided

Clinical significance:Uncertain significance

Review status:(0/4) 0 stars out of maximum of 4 stars

no assertion criteria provided

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001355388.1

Allele description [Variation Report for NM_000401.3(EXT2):c.344A>C (p.Asp115Ala)]

NM_000401.3(EXT2):c.344A>C (p.Asp115Ala)

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.344A>C (p.Asp115Ala)
HGVS:
  • NC_000011.10:g.44107957A>C
  • NG_007560.1:g.17409A>C
  • NM_000401.3:c.344A>C
  • NM_001178083.2:c.245A>C
  • NM_207122.1:c.245A>C
  • NP_000392.3:p.Asp115Ala
  • NP_001171554.1:p.Asp82Ala
  • NP_997005.1:p.Asp82Ala
  • LRG_494t1:c.344A>C
  • LRG_494t2:c.245A>C
  • LRG_494:g.17409A>C
  • LRG_494p1:p.Asp115Ala
  • LRG_494p2:p.Asp82Ala
  • NC_000011.9:g.44129507A>C
Protein change:
D115A
Links:
dbSNP: rs534539796
NCBI 1000 Genomes Browser:
rs534539796
Molecular consequence:
  • NM_000401.3:c.344A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001178083.2:c.245A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_207122.1:c.245A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001550262Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria providedUncertain significanceunknownclinical testing

Summary from all submissions

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

Details of each submission

From Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001550262.1

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

Description

The EXT2 p.Asp115Ala variant was not identified in the literature but was identified in dbSNP (ID: rs534539796) and ClinVar (classified as likely benign by Illumina). The variant was identified in control databases in 14 of 251264 chromosomes at a frequency of 0.00005572 (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the South Asian population in 14 of 30614 chromosomes (freq: 0.000457), but was not observed in the African, Latino, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), or Other populations. The p.Asp115 residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and three of four in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a greater than 10% difference in splicing; this is not very predictive of pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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

Last Updated: Apr 12, 2021

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