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NM_001034853.2(RPGR):c.3238C>T (p.Gln1080Ter) AND multiple conditions

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jan 24, 2023
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:
RCV003447702.1

Allele description [Variation Report for NM_001034853.2(RPGR):c.3238C>T (p.Gln1080Ter)]

NM_001034853.2(RPGR):c.3238C>T (p.Gln1080Ter)

Gene:
RPGR:retinitis pigmentosa GTPase regulator [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xp11.4
Genomic location:
Preferred name:
NM_001034853.2(RPGR):c.3238C>T (p.Gln1080Ter)
HGVS:
  • NC_000023.11:g.38285761G>A
  • NG_009553.1:g.46775C>T
  • NM_000328.3:c.1905+1333C>T
  • NM_001034853.2:c.3238C>TMANE SELECT
  • NM_001367245.1:c.1902+1333C>T
  • NM_001367246.1:c.1719+1333C>T
  • NM_001367247.1:c.1572+5198C>T
  • NM_001367248.1:c.1602+5198C>T
  • NM_001367249.1:c.1569+5198C>T
  • NM_001367250.1:c.1569+5198C>T
  • NM_001367251.1:c.1386+5198C>T
  • NP_001030025.1:p.Gln1080Ter
  • NC_000023.10:g.38145014G>A
Protein change:
Q1080*
Molecular consequence:
  • NM_000328.3:c.1905+1333C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001367245.1:c.1902+1333C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001367246.1:c.1719+1333C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001367247.1:c.1572+5198C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001367248.1:c.1602+5198C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001367249.1:c.1569+5198C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001367250.1:c.1569+5198C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001367251.1:c.1386+5198C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001034853.2:c.3238C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
X-linked cone-rod dystrophy 1 (CORDX1)
Identifiers:
MONDO: MONDO:0010566; MedGen: C1844776; Orphanet: 1872; OMIM: 304020
Name:
Retinitis pigmentosa 3
Synonyms:
Cone-rod degeneration X-linked; Choroidoretinal degeneration with retinal reflex in heterozygous women; Retinitis pigmentosa 15
Identifiers:
MONDO: MONDO:0010227; MedGen: C1845667; Orphanet: 791; OMIM: 300029
Name:
Retinitis pigmentosa, X-linked, and sinorespiratory infections, with or without deafness (RPSRDF)
Identifiers:
MedGen: C2749137; Orphanet: 247522; OMIM: 300455
Name:
Macular degeneration, X-linked atrophic (RPGR)
Identifiers:
MONDO: MONDO:0010443; MedGen: C3151784; Orphanet: 1872; OMIM: 300834

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004175318Genetics and Molecular Pathology, SA Pathology

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Jan 24, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Genetics and Molecular Pathology, SA Pathology, SCV004175318.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The RPGR c.3238C>T variant is classified as LIKELY PATHOGENIC (PVS1, PM2) The RPGR c.3238C>T variant is a single nucleotide change which is predicted to result in premature termination of the protein product at codon 1080 (PVS1). This variant is absent from population databases (PM2). This variant has not been reported in dbSNP, ClinVar or HGMD. Whilst this variant is within the repetitive purine-rich region of the exon ORF15, it is at the 3' end of the repeat, whilst the majority of pathogenic variants are located at the 5' end.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Dec 17, 2023