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NM_001134407.3(GRIN2A):c.3174C>A (p.His1058Gln) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Mar 20, 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:
RCV000484465.1

Allele description [Variation Report for NM_001134407.3(GRIN2A):c.3174C>A (p.His1058Gln)]

NM_001134407.3(GRIN2A):c.3174C>A (p.His1058Gln)

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.3174C>A (p.His1058Gln)
HGVS:
  • NC_000016.10:g.9764370G>T
  • NG_011812.2:g.423385C>A
  • NM_000833.5:c.3174C>A
  • NM_001134407.3:c.3174C>AMANE SELECT
  • NM_001134408.2:c.3174C>A
  • NP_000824.1:p.His1058Gln
  • NP_001127879.1:p.His1058Gln
  • NP_001127880.1:p.His1058Gln
  • NC_000016.9:g.9858227G>T
  • NG_011812.1:g.423385C>A
  • NM_000833.3:c.3174C>A
  • NM_000833.4:c.[3174C>A]
Protein change:
H1058Q
Links:
dbSNP: rs1064796658
NCBI 1000 Genomes Browser:
rs1064796658
Molecular consequence:
  • NM_000833.5:c.3174C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001134407.3:c.3174C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001134408.2:c.3174C>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
SCV000573598GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Likely pathogenic
(Mar 20, 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, SCV000573598.3

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

Description

The H1058Q variant in the GRIN2A gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The H1058Q variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The H1058Q 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 is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. The H1058Q variant is a strong candidate for a pathogenic variant.

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

Last Updated: Apr 6, 2024