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NM_002168.4(IDH2):c.640G>A (p.Ala214Thr) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 14, 2023
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:
RCV003490892.1

Allele description [Variation Report for NM_002168.4(IDH2):c.640G>A (p.Ala214Thr)]

NM_002168.4(IDH2):c.640G>A (p.Ala214Thr)

Gene:
IDH2:isocitrate dehydrogenase (NADP(+)) 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
15q26.1
Genomic location:
Preferred name:
NM_002168.4(IDH2):c.640G>A (p.Ala214Thr)
HGVS:
  • NC_000015.10:g.90088397C>T
  • NG_023302.1:g.19080G>A
  • NM_001289910.1:c.484G>A
  • NM_001290114.2:c.250G>A
  • NM_002168.4:c.640G>AMANE SELECT
  • NP_001276839.1:p.Ala162Thr
  • NP_001277043.1:p.Ala84Thr
  • NP_002159.2:p.Ala214Thr
  • NP_002159.2:p.Ala214Thr
  • LRG_611t1:c.484G>A
  • LRG_611t2:c.640G>A
  • LRG_611:g.19080G>A
  • LRG_611p1:p.Ala162Thr
  • LRG_611p2:p.Ala214Thr
  • NC_000015.9:g.90631629C>T
  • NM_002168.3:c.640G>A
Protein change:
A162T
Molecular consequence:
  • NM_001289910.1:c.484G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001290114.2:c.250G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002168.4:c.640G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004241474Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Uncertain significance
(Dec 14, 2023) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004241474.1

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

Description

Variant summary: IDH2 c.640G>A (p.Ala214Thr) results in a non-conservative amino acid change located in the Isopropylmalate dehydrogenase-like domain (IPR024084) of the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 5.6e-05 in 251348 control chromosomes in the gnomAD database, including 1 homozygote. To our knowledge, no occurrence of c.640G>A in individuals affected with D-2-hydroxyglutaric aciduria 2 and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance.

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

Last Updated: Feb 14, 2024