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NM_014249.3(NR2E3):c.166G>A (p.Gly56Arg) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 22, 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:
RCV000286602.1

Allele description

NM_014249.3(NR2E3):c.166G>A (p.Gly56Arg)

Gene:
NR2E3:nuclear receptor subfamily 2 group E member 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
15q23
Genomic location:
Preferred name:
NM_014249.3(NR2E3):c.166G>A (p.Gly56Arg)
HGVS:
  • NC_000015.10:g.71811530G>A
  • NG_009113.2:g.5976G>A
  • NM_014249.3:c.166G>A
  • NM_016346.3:c.166G>A
  • NP_055064.1:p.Gly56Arg
  • NP_057430.1:p.Gly56Arg
  • NC_000015.9:g.72103870G>A
  • NG_009113.1:g.5977G>A
  • NM_014249.2:c.166G>A
  • Q9Y5X4:p.Gly56Arg
Protein change:
G56R; GLY56ARG
Links:
UniProtKB: Q9Y5X4#VAR_037026; OMIM: 604485.0006; dbSNP: rs121912631
NCBI 1000 Genomes Browser:
rs121912631
Molecular consequence:
  • NM_014249.3:c.166G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000330651GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Pathogenic
(Jul 22, 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, SCV000330651.5

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

Description

The G56R pathogenic variant in the NR2E3 gene has been reported previously in several families with autosomal dominant retinitis pigmentosa (adRP), with one study reporting this variant in 7/201 (3.5%) of families with adRP who were tested (Coppieters et al., 2007; Blanco-Kelly et al., 2016). This variant was not observed in approximately 6300 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 G56R variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved, and in silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret G56R as a pathogenic variant.

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

Last Updated: Dec 9, 2018