NM_014249.4(NR2E3):c.119-1G>A AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 25, 2022
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:: RCV001230648.5

Allele description

NM_014249.4(NR2E3):c.119-1G>A

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.119-1G>A

HGVS:

NC_000015.10:g.71811482G>A
NG_009113.2:g.5928G>A
NM_014249.4:c.119-1G>AMANE SELECT
NM_016346.4:c.119-1G>A
NC_000015.9:g.72103822G>A
NM_014249.3:c.119-1G>A

Links:

dbSNP: rs2054179222

NCBI 1000 Genomes Browser:

rs2054179222

Molecular consequence:

NM_014249.4:c.119-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_016346.4:c.119-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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translation elongation factor 1-alpha, partial [Lepidoderma neoperforatum]
translation elongation factor 1-alpha, partial [Lepidoderma neoperforatum]
gi|2312626664|gb|UXQ89377.1|

Protein
Waegelea antarctica isolate P115 cytochrome oxidase subunit 1 gene, partial cds;...
Waegelea antarctica isolate P115 cytochrome oxidase subunit 1 gene, partial cds; mitochondrial
gi|1858369404|gb|MN486299.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001403133	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 25, 2022)	germline	clinical testing	PubMed (8) [See all records that cite these PMIDs] 10655056, 24474277, 25079116, 31306293, 16199547, 15459973, 27522502, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001403133

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 25, 2022)

germline

clinical testing

PubMed (8)
[See all records that cite these PMIDs]

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

Citations

PubMed

Mutation of a nuclear receptor gene, NR2E3, causes enhanced S cone syndrome, a disorder of retinal cell fate.

Haider NB, Jacobson SG, Cideciyan AV, Swiderski R, Streb LM, Searby C, Beck G, Hockey R, Hanna DB, Gorman S, Duhl D, Carmi R, Bennett J, Weleber RG, Fishman GA, Wright AF, Stone EM, Sheffield VC.

Nat Genet. 2000 Feb;24(2):127-31.

PubMed [citation]

PMID:: 10655056

Identification of mutations causing inherited retinal degenerations in the israeli and palestinian populations using homozygosity mapping.

Beryozkin A, Zelinger L, Bandah-Rozenfeld D, Shevach E, Harel A, Storm T, Sagi M, Eli D, Merin S, Banin E, Sharon D.

Invest Ophthalmol Vis Sci. 2014 Feb 24;55(2):1149-60. doi: 10.1167/iovs.13-13625.

PubMed [citation]

PMID:: 24474277

See all PubMed Citations (8)

Details of each submission

From Invitae, SCV001403133.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (8)

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 957640). Disruption of this splice site has been observed in individual(s) with autosomal recessive enhanced S-cone syndrome (PMID: 10655056, 24474277, 25079116, 31306293). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change affects an acceptor splice site in intron 1 of the NR2E3 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in NR2E3 are known to be pathogenic (PMID: 15459973, 27522502).

#	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: Feb 20, 2024

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