NM_006915.3(RP2):c.844C>T (p.Arg282Trp) AND not specified

Germline classification:: Benign/Likely benign (3 submissions)
Last evaluated:: Mar 8, 2022
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:: RCV000177264.9

Allele description [Variation Report for NM_006915.3(RP2):c.844C>T (p.Arg282Trp)]

NM_006915.3(RP2):c.844C>T (p.Arg282Trp)

Gene:

RP2:RP2 activator of ARL3 GTPase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xp11.3

Genomic location:

Preferred name:

NM_006915.3(RP2):c.844C>T (p.Arg282Trp)

HGVS:

NC_000023.11:g.46860063C>T
NG_009107.1:g.28152C>T
NM_006915.3:c.844C>TMANE SELECT
NP_008846.2:p.Arg282Trp
NC_000023.10:g.46719498C>T
NM_006915.2:c.844C>T
O75695:p.Arg282Trp

Protein change:

R282W

Links:

UniProtKB: O75695#VAR_014535; dbSNP: rs1805147

Molecular consequence:

NM_006915.3:c.844C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000229108	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Benign (Oct 23, 2014)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 10862093, 10937588, 11992260, 22334370 Citation Link,
SCV000540207	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Likely benign (Mar 29, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002500231	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (Mar 8, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000229108

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Benign
(Oct 23, 2014)

germline

clinical testing

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

Citation Link,

SCV000540207

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Likely benign
(Mar 29, 2016)

germline

clinical testing

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

SCV002500231

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Benign
(Mar 8, 2022)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Novel frameshift mutations in the RP2 gene and polymorphic variants.

Thiselton DL, Zito I, Plant C, Jay M, Hodgson SV, Bird AC, Bhattacharya SS, Hardcastle AJ.

Hum Mutat. 2000 Jun;15(6):580.

PubMed [citation]

PMID:: 10862093

X-linked retinitis pigmentosa: mutation spectrum of the RPGR and RP2 genes and correlation with visual function.

Sharon D, Bruns GA, McGee TL, Sandberg MA, Berson EL, Dryja TP.

Invest Ophthalmol Vis Sci. 2000 Aug;41(9):2712-21.

PubMed [citation]

PMID:: 10937588

See all PubMed Citations (5)

Details of each submission

From Eurofins Ntd Llc (ga), SCV000229108.6

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

#	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		1	not provided	not provided	not provided

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000540207.1

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

Description

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency in ESP (all): 235/10563=2.23%

#	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 Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002500231.1

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

Description

Variant summary: RP2 c.844C>T (p.Arg282Trp) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.018 in 182850 control chromosomes, predominantly at a frequency of 0.03 within the Non-Finnish European subpopulation in the gnomAD database, including 25 homozygotes. The observed variant frequency within Non-Finnish European control individuals in the gnomAD database is approximately 13.86 fold of the estimated maximal expected allele frequency for a pathogenic variant in RP2 causing Retinitis Pigmentosa, X-Linked phenotype (0.0022), strongly suggesting that the variant is a benign polymorphism found primarily in populations of Non-Finnish European origin. Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as benign.

#	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: Jun 20, 2026

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