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NM_001134407.3(GRIN2A):c.2696G>A (p.Arg899Gln) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Nov 2, 2017
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:
RCV000479065.2

Allele description [Variation Report for NM_001134407.3(GRIN2A):c.2696G>A (p.Arg899Gln)]

NM_001134407.3(GRIN2A):c.2696G>A (p.Arg899Gln)

Gene:
GRIN2A:glutamate ionotropic receptor NMDA type subunit 2A [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p13.2
Genomic location:
Preferred name:
NM_001134407.3(GRIN2A):c.2696G>A (p.Arg899Gln)
HGVS:
  • NC_000016.10:g.9764848C>T
  • NG_011812.2:g.422907G>A
  • NM_000833.5:c.2696G>A
  • NM_001134407.3:c.2696G>AMANE SELECT
  • NM_001134408.2:c.2696G>A
  • NP_000824.1:p.Arg899Gln
  • NP_001127879.1:p.Arg899Gln
  • NP_001127880.1:p.Arg899Gln
  • NC_000016.9:g.9858705C>T
  • NG_011812.1:g.422907G>A
  • NM_000833.3:c.2696G>A
Protein change:
R899Q
Links:
dbSNP: rs759145938
NCBI 1000 Genomes Browser:
rs759145938
Molecular consequence:
  • NM_000833.5:c.2696G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001134407.3:c.2696G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001134408.2:c.2696G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000573470GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Nov 2, 2017) 		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, SCV000573470.3

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

Description

A variant of uncertain significance has been identified in the GRIN2A gene. The R899Q variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The R899Q variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The R899Q 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 where amino acids with similar properties to Arginine are tolerated across species. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. 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: May 1, 2024