NM_014249.4(NR2E3):c.227G>A (p.Arg76Gln) AND NR2E3-related disorder

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Sep 5, 2024
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:: RCV000261496.7

Allele description [Variation Report for NM_014249.4(NR2E3):c.227G>A (p.Arg76Gln)]

NM_014249.4(NR2E3):c.227G>A (p.Arg76Gln)

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_014249.4(NR2E3):c.227G>A (p.Arg76Gln)

HGVS:

NC_000015.10:g.71811591G>A
NG_009113.2:g.6037G>A
NM_014249.4:c.227G>AMANE SELECT
NM_016346.4:c.227G>A
NP_055064.1:p.Arg76Gln
NP_057430.1:p.Arg76Gln
NC_000015.9:g.72103931G>A
NM_014249.2:c.227G>A
NM_014249.3:c.227G>A
Q9Y5X4:p.Arg76Gln

Protein change:

R76Q; ARG76GLN

Links:

UniProtKB: Q9Y5X4#VAR_009266; OMIM: 604485.0003; dbSNP: rs104894493

NCBI 1000 Genomes Browser:

rs104894493

Molecular consequence:

NM_014249.4:c.227G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_016346.4:c.227G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: NR2E3-related disorder
Synonyms:: NR2E3-Related Disorders; NR2E3-related condition
Identifiers:: MedGen: CN239387

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000393760	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSLVariantClassificationCriteria RUGD 01 April 2020)	Pathogenic (Sep 5, 2024)	unknown	clinical testing	Citation Link,
SCV005355300	PreventionGenetics, part of Exact Sciences	no assertion criteria provided	Pathogenic (May 16, 2024)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000393760

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSLVariantClassificationCriteria RUGD 01 April 2020)

Pathogenic
(Sep 5, 2024)

unknown

clinical testing

Citation Link,

SCV005355300

PreventionGenetics, part of Exact Sciences

no assertion criteria provided

Pathogenic
(May 16, 2024)

germline

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000393760.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From PreventionGenetics, part of Exact Sciences, SCV005355300.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The NR2E3 c.227G>A variant is predicted to result in the amino acid substitution p.Arg76Gln. This variant has been previously reported in individuals with enhanced S-cone syndrome or autosomal recessive retinal disease (see for example Haider et al. 2000. PubMed ID: 10655056; Li et al. 2017. PubMed ID: 28418496; Stone et al. 2017. PubMed ID: 28559085, Supplementary Table 1). An alternate nucleotide change affecting the same amino acid (c.226C>T, p.Arg76Trp) has also been reported in individuals with retinal disease (Haider et al. 2000. PubMed ID: 10655056; Ge et al. 2015. PubMed ID: 26667666; Stone et al. 2017. PubMed ID: 28559085, Supplementary Table 1). This variant is reported in 0.038% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant is interpreted as pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 26, 2024

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