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NM_014249.4(NR2E3):c.932G>A (p.Arg311Gln)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
11 (Most recent: Mar 28, 2019)
Last evaluated:
Dec 26, 2018
Accession:
VCV000005532.6
Variation ID:
5532
Description:
single nucleotide variant
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NM_014249.4(NR2E3):c.932G>A (p.Arg311Gln)

Allele ID
20571
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
15q23
Genomic location
15: 71813573 (GRCh38) GRCh38 UCSC
15: 72105913 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000015.9:g.72105913G>A
NC_000015.10:g.71813573G>A
NM_014249.4:c.932G>A NP_055064.1:p.Arg311Gln missense
... more HGVS
Protein change
R311Q
Other names
-
Functional consequence
-
Global minor allele frequency (GMAF)
0.00080 (A)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00034
Trans-Omics for Precision Medicine (TOPMed) 0.00016
The Genome Aggregation Database (gnomAD) 0.00073
The Genome Aggregation Database (gnomAD), exomes 0.00040
1000 Genomes Project 0.00080
Links
ClinGen: CA117575
UniProtKB: Q9Y5X4#VAR_010034
OMIM: 604485.0005
dbSNP: rs28937873
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 3 criteria provided, multiple submitters, no conflicts Dec 26, 2018 RCV000171240.6
Pathogenic 2 criteria provided, multiple submitters, no conflicts Oct 31, 2018 RCV000668086.2
Pathogenic 1 criteria provided, single submitter Sep 8, 2017 RCV000393548.2
Pathogenic 2 criteria provided, single submitter Jun 18, 2018 RCV000005870.5
Pathogenic/Likely pathogenic 2 no assertion criteria provided Dec 30, 2017 RCV000005869.5
Likely pathogenic 1 no assertion criteria provided Apr 1, 2018 RCV000787633.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
NR2E3 - - GRCh38
GRCh37
94 107

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Jul 05, 2017)
criteria provided, single submitter
Method: clinical testing
Retinitis pigmentosa 37
Enhanced s-cone syndrome
Allele origin: unknown
Counsyl
Accession: SCV000792632.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (9)
Pathogenic
(Oct 31, 2018)
criteria provided, single submitter
Method: clinical testing
Enhanced s-cone syndrome
Retinitis pigmentosa 37
Allele origin: unknown
Fulgent Genetics,Fulgent Genetics
Accession: SCV000894055.1
Submitted: (Nov 14, 2018)
Evidence details
Publications
PubMed (1)
DOI: 10.1038/gim.2015.30
Pathogenic
(Dec 26, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV000935246.1
Submitted: (Mar 28, 2019)
Evidence details
Publications
PubMed (10)
Comment:
This sequence change replaces arginine with glutamine at codon 311 of the NR2E3 protein (p.Arg311Gln). The arginine residue is weakly conserved and there is a ... (more)
Pathogenic
(Jun 18, 2018)
criteria provided, single submitter
Method: clinical testing
Goldmann-Favre syndrome
(Autosomal recessive inheritance)
Allele origin: germline
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine
Accession: SCV000966899.1
Submitted: (Mar 21, 2019)
Evidence details
Publications
PubMed (15)
Comment:
The p.Arg311Gln variant in NR2E3 has been reported in the homozygous or compound heterozygous state in more than 15 individuals with Enhanced S-cone syndrome an ... (more)
Likely pathogenic
(-)
criteria provided, single submitter
Method: research
Not provided
Allele origin: germline
Developmental Genetics Unit,King Faisal Specialist Hospital & Research Centre
Accession: SCV000221437.1
Submitted: (Apr 14, 2015)
Evidence details
Pathogenic
(Jun 27, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000618198.2
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The c.932 G>A variant in the NR2E3 gene has been reported previously in association with enhanced S-cone syndrome (ESCS) when present in the heterozygous state, ... (more)
Pathogenic
(Sep 08, 2017)
criteria provided, single submitter
Method: clinical testing
NR2E3-Related Disorders
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000393797.3
Submitted: (Feb 01, 2019)
Evidence details
Publications
PubMed (4)
Comment:
The NR2E3 c.932G>A (p.Arg311Gln) variant has been reported in three studies in which it is found in a homozygous state in a total of 12 ... (more)
Likely pathogenic
(Dec 30, 2017)
no assertion criteria provided
Method: curation
Enhanced s-cone syndrome
Allele origin: unknown
Department of Genetics,Sultan Qaboos University Hospital, Oman
Accession: SCV000891646.1
Submitted: (Oct 25, 2018)
Evidence details
Publications
PubMed (2)
Likely pathogenic
(Apr 01, 2018)
no assertion criteria provided
Method: research
Retinitis pigmentosa
Allele origin: unknown
Medical Genetics Laboratory, Kennedy Center,Juliane Marie Center, Rigshospitalet
Study: VeluxRD
Accession: SCV000926618.1
Submitted: (Dec 05, 2018)
Evidence details
Publications
PubMed (1)
Pathogenic
(Apr 01, 2008)
no assertion criteria provided
Method: literature only
ENHANCED S-CONE SYNDROME
Allele origin: germline
OMIM
Accession: SCV000026051.4
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (3)
Pathogenic
(Apr 01, 2008)
no assertion criteria provided
Method: literature only
GOLDMANN-FAVRE SYNDROME
Allele origin: germline
OMIM
Accession: SCV000026052.4
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (3)

Citations for this variant

Title Author Journal Year Link
Molecular genetic analysis using targeted NGS analysis of 677 individuals with retinal dystrophy. Jespersgaard C Scientific reports 2019 PMID: 30718709
Next-generation sequencing reveals the mutational landscape of clinically diagnosed Usher syndrome: copy number variations, phenocopies, a predominant target for translational read-through, and <i>PEX26</i> mutated in Heimler syndrome. Neuhaus C Molecular genetics & genomic medicine 2017 PMID: 28944237
Identifying mutations in Tunisian families with retinal dystrophy. Habibi I Scientific reports 2016 PMID: 27874104
Macular cystoid spaces in patients with retinal dystrophy. Lingao MD Ophthalmic genetics 2016 PMID: 26894784
Expanding the clinical, allelic, and locus heterogeneity of retinal dystrophies. Patel N Genetics in medicine : official journal of the American College of Medical Genetics 2016 PMID: 26355662
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S Genetics in medicine : official journal of the American College of Medical Genetics 2015 PMID: 25741868
Differential dimerization of variants linked to enhanced S-cone sensitivity syndrome (ESCS) located in the NR2E3 ligand-binding domain. von Alpen D Human mutation 2015 PMID: 25703721
Dependable and efficient clinical utility of target capture-based deep sequencing in molecular diagnosis of retinitis pigmentosa. Wang J Investigative ophthalmology & visual science 2014 PMID: 25097241
The crystal structure of the orphan nuclear receptor NR2E3/PNR ligand binding domain reveals a dimeric auto-repressed conformation. Tan MH PloS one 2013 PMID: 24069298
A comprehensive analysis of sequence variants and putative disease-causing mutations in photoreceptor-specific nuclear receptor NR2E3. Kanda A Molecular vision 2009 PMID: 19898638
Mutations in the DNA-binding domain of NR2E3 affect in vivo dimerization and interaction with CRX. Roduit R PloS one 2009 PMID: 19823680
The spectrum of retinal diseases caused by NR2E3 mutations in Israeli and Palestinian patients. Bandah D Archives of ophthalmology (Chicago, Ill. : 1960) 2009 PMID: 19273793
Phenotypic features of patients with NR2E3 mutations. Pachydaki SI Archives of ophthalmology (Chicago, Ill. : 1960) 2009 PMID: 19139342
Mutations in NR2E3 can cause dominant or recessive retinal degenerations in the same family. Escher P Human mutation 2009 PMID: 19006237
Treatment of adult-onset acute macular retinoschisis in enhanced s-cone syndrome with oral acetazolamide. Iannaccone A American journal of ophthalmology 2009 PMID: 18835469
Analysis of the involvement of the NR2E3 gene in autosomal recessive retinal dystrophies. Bernal S Clinical genetics 2008 PMID: 18294254
The loss of transcriptional inhibition by the photoreceptor-cell specific nuclear receptor (NR2E3) is not a necessary cause of enhanced S-cone syndrome. Fradot M Molecular vision 2007 PMID: 17438525
An Arg311Gln NR2E3 mutation in a family with classic Goldmann-Favre syndrome. Chavala SH The British journal of ophthalmology 2005 PMID: 16024868
The photoreceptor-specific nuclear receptor Nr2e3 interacts with Crx and exerts opposing effects on the transcription of rod versus cone genes. Peng GH Human molecular genetics 2005 PMID: 15689355
The nuclear receptor NR2E3 plays a role in human retinal photoreceptor differentiation and degeneration. Milam AH Proceedings of the National Academy of Sciences of the United States of America 2002 PMID: 11773633
The photoreceptor cell-specific nuclear receptor gene (PNR) accounts for retinitis pigmentosa in the Crypto-Jews from Portugal (Marranos), survivors from the Spanish Inquisition. Gerber S Human genetics 2000 PMID: 11071390
Mutation of a nuclear receptor gene, NR2E3, causes enhanced S cone syndrome, a disorder of retinal cell fate. Haider NB Nature genetics 2000 PMID: 10655056

Record last updated Oct 27, 2019