NM_014249.4(NR2E3):c.119-2A>C AND Retinitis pigmentosa

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

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Jul 24, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000787627.6

Allele description

NM_014249.4(NR2E3):c.119-2A>C

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.119-2A>C

Other names:

NP_055064.1:p.?

HGVS:

NC_000015.10:g.71811481A>C
NG_009113.2:g.5927A>C
NM_014249.4:c.119-2A>CMANE SELECT
NM_016346.4:c.119-2A>C
NC_000015.9:g.72103821A>C
NM_014249.2:c.119-2A>C
NM_014249.3:c.119-2A>C
NM_016346.2:c.119-2A>C
NM_016346.3:c.119-2A>C

Nucleotide change:

IVS1AS, A-C

Links:

OMIM: 604485.0001; dbSNP: rs2723341

NCBI 1000 Genomes Browser:

rs2723341

Molecular consequence:

NM_014249.4:c.119-2A>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_016346.4:c.119-2A>C - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:: Retinitis pigmentosa (RP)
Synonyms:: Tapetoretinal degeneration
Identifiers:: MONDO: MONDO:0019200; MeSH: D012174; MedGen: C0035334; Orphanet: 791; OMIM: 268000; OMIM: PS268000

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000926612	Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet - VeluxRD	no assertion criteria provided	Pathogenic (Apr 1, 2018)	unknown	research	PubMed (1) [See all records that cite this PMID]
SCV001950299	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Apr 1, 2021)	germline	curation	PubMed (23) [See all records that cite these PMIDs] 25703721, 25097241, 23989059, 21217109, 19718767, 19273793, 18294254, 15459973, 10655056, 24474277, 23591405, 25079116, 26894784, 27573156, 28224992, 29193891, 28559085, 29343940, 28771251, 29431110, 30324420, 25741868, 34906470
SCV004030428	Ophthalmic Genetics Group, Institute of Molecular and Clinical Ophthalmology Basel	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jul 24, 2023)	germline	research	PubMed (2) [See all records that cite these PMIDs] 36909829, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000926612

Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet - VeluxRD

no assertion criteria provided

Pathogenic
(Apr 1, 2018)

unknown

research

PubMed (1)
[See all records that cite this PMID]

SCV001950299

Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Apr 1, 2021)

germline

curation

PubMed (23)
[See all records that cite these PMIDs]

SCV004030428

Ophthalmic Genetics Group, Institute of Molecular and Clinical Ophthalmology Basel

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jul 24, 2023)

germline

research

PubMed (2)
[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	yes	1	not provided	not provided	not provided	not provided	research, curation
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	research

Citations

PubMed

Molecular genetic analysis using targeted NGS analysis of 677 individuals with retinal dystrophy.

Jespersgaard C, Fang M, Bertelsen M, Dang X, Jensen H, Chen Y, Bech N, Dai L, Rosenberg T, Zhang J, Møller LB, Tümer Z, Brøndum-Nielsen K, Grønskov K.

Sci Rep. 2019 Feb 4;9(1):1219. doi: 10.1038/s41598-018-38007-2.

PubMed [citation]

PMID:: 30718709
PMCID:: PMC6362094

Differential dimerization of variants linked to enhanced S-cone sensitivity syndrome (ESCS) located in the NR2E3 ligand-binding domain.

von Alpen D, Tran HV, Guex N, Venturini G, Munier FL, Schorderet DF, Haider NB, Escher P.

Hum Mutat. 2015 Jun;36(6):599-610. doi: 10.1002/humu.22775. Epub 2015 Apr 27.

PubMed [citation]

PMID:: 25703721
PMCID:: PMC5014385

See all PubMed Citations (25)

Details of each submission

From Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet - VeluxRD, SCV000926612.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	research	PubMed (1)
2	not provided	not provided	not provided	not provided	research	PubMed (1)

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

From Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, SCV001950299.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	PubMed (23)

Description

The c.119-2A>C variant in NR2E3 was identified in an individual with Retinitis pigmentosa, via a collaborative study between the Broad Institute's Center for Mendelian Genomics and the Pierce lab (https://oculargenomics.meei.harvard.edu/labs/pierce-lab/lab-members/). Through a review of available evidence we were able to apply the following criteria: PVS1, PM2, PM3. Based on this evidence we have classified this variant as Pathogenic. If you have any questions about the classification please reach out to the Pierce Lab.

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

From Ophthalmic Genetics Group, Institute of Molecular and Clinical Ophthalmology Basel, SCV004030428.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	research	PubMed (2)

Description

Clinical significance based on ACMG v2.0

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

Last Updated: May 1, 2024

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