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NM_020442.6(VARS2):c.2228G>A (p.Arg743Gln) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 15, 2016
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:
RCV000414668.1

Allele description [Variation Report for NM_020442.6(VARS2):c.2228G>A (p.Arg743Gln)]

NM_020442.6(VARS2):c.2228G>A (p.Arg743Gln)

Genes:
LOC126859646:MED14-independent group 3 enhancer GRCh37_chr6:30889690-30890889 [Gene]
VARS2:valyl-tRNA synthetase 2, mitochondrial [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
6p21.33
Genomic location:
Preferred name:
NM_020442.6(VARS2):c.2228G>A (p.Arg743Gln)
HGVS:
  • NC_000006.12:g.30923146G>A
  • NG_034224.1:g.13939G>A
  • NM_001167733.3:c.1808G>A
  • NM_001167734.2:c.2318G>A
  • NM_020442.6:c.2228G>AMANE SELECT
  • NP_001161205.1:p.Arg603Gln
  • NP_001161206.1:p.Arg773Gln
  • NP_001161206.1:p.Arg773Gln
  • NP_065175.4:p.Arg743Gln
  • NC_000006.11:g.30890923G>A
  • NM_001167734.1:c.2318G>A
Protein change:
R603Q
Links:
dbSNP: rs1057518559
NCBI 1000 Genomes Browser:
rs1057518559
Molecular consequence:
  • NM_001167733.3:c.1808G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001167734.2:c.2318G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020442.6:c.2228G>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
SCV000492321GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Dec 15, 2016) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000492321.1

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

Description

The R773Q variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The R773Q variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The R773Q variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. 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: Mar 26, 2023