NM_020366.4(RPGRIP1):c.1949C>G (p.Pro650Arg) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 11, 2021
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:: RCV001877787.4

Allele description [Variation Report for NM_020366.4(RPGRIP1):c.1949C>G (p.Pro650Arg)]

NM_020366.4(RPGRIP1):c.1949C>G (p.Pro650Arg)

Gene:

RPGRIP1:RPGR interacting protein 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

14q11.2

Genomic location:

Preferred name:

NM_020366.4(RPGRIP1):c.1949C>G (p.Pro650Arg)

HGVS:

NC_000014.9:g.21324804C>G
NG_008933.1:g.41828C>G
NM_001377523.1:c.688+2800C>G
NM_001377948.1:c.875C>G
NM_001377949.1:c.796+79C>G
NM_001377950.1:c.688+2800C>G
NM_001377951.1:c.190+2800C>G
NM_020366.4:c.1949C>GMANE SELECT
NP_001364877.1:p.Pro292Arg
NP_065099.3:p.Pro650Arg
NC_000014.8:g.21792963C>G

Protein change:

P292R

Links:

dbSNP: rs769167245

NCBI 1000 Genomes Browser:

rs769167245

Molecular consequence:

NM_001377523.1:c.688+2800C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001377949.1:c.796+79C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001377950.1:c.688+2800C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001377951.1:c.190+2800C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001377948.1:c.875C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_020366.4:c.1949C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Cone-rod dystrophy 13 (CORD13)
Identifiers:: MONDO: MONDO:0011987; MedGen: C2750720; Orphanet: 1872; OMIM: 608194

Name:: Leber congenital amaurosis 6 (LCA6)
Identifiers:: MONDO: MONDO:0013446; MedGen: C1854260; Orphanet: 65; OMIM: 613826

Recent activity

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prostate and testis expressed C precursor [Mus musculus]
prostate and testis expressed C precursor [Mus musculus]
gi|13386080|ref|NP_080869.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002142960	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 11, 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

SCV002142960

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 11, 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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002142960.3

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

Description

This sequence change replaces proline with arginine at codon 650 of the RPGRIP1 protein (p.Pro650Arg). The proline residue is highly conserved and there is a moderate physicochemical difference between proline and arginine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals affected with RPGRIP1-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C15"). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Sep 29, 2024

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