NM_014249.4(NR2E3):c.309C>A (p.Cys103Ter) AND not provided

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

Germline classification:: Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:: Jan 8, 2024
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:: RCV001390830.28

Allele description

NM_014249.4(NR2E3):c.309C>A (p.Cys103Ter)

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.309C>A (p.Cys103Ter)

HGVS:

NC_000015.10:g.71811829C>A
NG_009113.2:g.6275C>A
NM_014249.4:c.309C>AMANE SELECT
NM_016346.4:c.309C>A
NP_055064.1:p.Cys103Ter
NP_057430.1:p.Cys103Ter
NC_000015.9:g.72104169C>A
NM_014249.3:c.309C>A
NM_014249.4:c.309C>A

Protein change:

C103*

Links:

dbSNP: rs955766374

NCBI 1000 Genomes Browser:

rs955766374

Molecular consequence:

NM_014249.4:c.309C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_016346.4:c.309C>A - nonsense - [Sequence Ontology: SO:0001587]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Training course content for phlebotomists - WHO Guidelines on Drawing Blood
Training course content for phlebotomists - WHO Guidelines on Drawing Blood
PREDICTED: Homo sapiens ADP ribosylation factor like GTPase 6 (ARL6), transcript...
PREDICTED: Homo sapiens ADP ribosylation factor like GTPase 6 (ARL6), transcript variant X6, misc_RNA
gi|2462593067|ref|XR_008486837.1|

Nucleotide
Escherichia coli 103385_TEPEC_DMEM_0.52_BR2
Escherichia coli 103385_TEPEC_DMEM_0.52_BR2

biosample
Rattus norvegicus regulatory factor X5 (Rfx5), transcript variant 2, mRNA
Rattus norvegicus regulatory factor X5 (Rfx5), transcript variant 2, mRNA
gi|2475243377|ref|NM_001419499.1|

Nucleotide
PREDICTED: Homo sapiens ADP ribosylation factor like GTPase 6 (ARL6), transcript...
PREDICTED: Homo sapiens ADP ribosylation factor like GTPase 6 (ARL6), transcript variant X1, misc_RNA
gi|2217346425|ref|XR_924185.4|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001592691	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 8, 2024)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 15459973, 27522502, 30543658, 28492532
SCV001961519	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Aug 1, 2021)	germline	clinical testing	Citation Link,
SCV003817505	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Nov 16, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001592691

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 8, 2024)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

SCV001961519

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Pathogenic
(Aug 1, 2021)

germline

clinical testing

Citation Link,

SCV003817505

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Nov 16, 2021)

germline

clinical testing

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

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	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mutation analysis of NR2E3 and NRL genes in Enhanced S Cone Syndrome.

Wright AF, Reddick AC, Schwartz SB, Ferguson JS, Aleman TS, Kellner U, Jurklies B, Schuster A, Zrenner E, Wissinger B, Lennon A, Shu X, Cideciyan AV, Stone EM, Jacobson SG, Swaroop A.

Hum Mutat. 2004 Nov;24(5):439.

PubMed [citation]

PMID:: 15459973

New truncation mutation of the NR2E3 gene in a Japanese patient with enhanced S-cone syndrome.

Kuniyoshi K, Hayashi T, Sakuramoto H, Mishima H, Tsuneoka H, Tsunoda K, Iwata T, Shimomura Y.

Jpn J Ophthalmol. 2016 Nov;60(6):476-485. Epub 2016 Aug 13.

PubMed [citation]

PMID:: 27522502

See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001592691.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Cys103*) in the NR2E3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in NR2E3 are known to be pathogenic (PMID: 15459973, 27522502). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This premature translational stop signal has been observed in individual(s) with autosomal recessive retinitis pigmentosa (PMID: 30543658). ClinVar contains an entry for this variant (Variation ID: 867206). For these reasons, this variant has been classified 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

From CeGaT Center for Human Genetics Tuebingen, SCV001961519.19

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	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	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

From Revvity Omics, Revvity, SCV003817505.2

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

#	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 13, 2024

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