U.S. flag

An official website of the United States government

NM_001034853.2(RPGR):c.2630del (p.Glu877fs) AND Primary ciliary dyskinesia

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 31, 2022
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:
RCV003111567.5

Allele description [Variation Report for NM_001034853.2(RPGR):c.2630del (p.Glu877fs)]

NM_001034853.2(RPGR):c.2630del (p.Glu877fs)

Gene:
RPGR:retinitis pigmentosa GTPase regulator [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
Xp11.4
Genomic location:
Preferred name:
NM_001034853.2(RPGR):c.2630del (p.Glu877fs)
HGVS:
  • NC_000023.11:g.38286369del
  • NG_009553.1:g.46167del
  • NM_000328.3:c.1905+725del
  • NM_001034853.2:c.2630delMANE SELECT
  • NM_001367245.1:c.1902+725del
  • NM_001367246.1:c.1719+725del
  • NM_001367247.1:c.1572+4590del
  • NM_001367248.1:c.1602+4590del
  • NM_001367249.1:c.1569+4590del
  • NM_001367250.1:c.1569+4590del
  • NM_001367251.1:c.1386+4590del
  • NP_001030025.1:p.Glu877fs
  • NC_000023.10:g.38145622del
  • NM_001034853.1:c.2630del
Protein change:
E877fs
Molecular consequence:
  • NM_001034853.2:c.2630del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000328.3:c.1905+725del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001367245.1:c.1902+725del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001367246.1:c.1719+725del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001367247.1:c.1572+4590del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001367248.1:c.1602+4590del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001367249.1:c.1569+4590del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001367250.1:c.1569+4590del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001367251.1:c.1386+4590del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Primary ciliary dyskinesia
Synonyms:
Ciliary dyskinesia
Identifiers:
MONDO: MONDO:0016575; MedGen: C0008780; OMIM: PS244400; Human Phenotype Ontology: HP:0012265

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003787211Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Dec 31, 2022) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Next-generation sequencing identifies unexpected genotype-phenotype correlations in patients with retinitis pigmentosa.

Birtel J, Gliem M, Mangold E, Müller PL, Holz FG, Neuhaus C, Lenzner S, Zahnleiter D, Betz C, Eisenberger T, Bolz HJ, Charbel Issa P.

PLoS One. 2018;13(12):e0207958. doi: 10.1371/journal.pone.0207958.

PubMed [citation]
PMID:
30543658
PMCID:
PMC6292620

Clinical course, genetic etiology, and visual outcome in cone and cone-rod dystrophy.

Thiadens AA, Phan TM, Zekveld-Vroon RC, Leroy BP, van den Born LI, Hoyng CB, Klaver CC; Writing Committee for the Cone Disorders Study Group Consortium., Roosing S, Pott JW, van Schooneveld MJ, van Moll-Ramirez N, van Genderen MM, Boon CJ, den Hollander AI, Bergen AA, De Baere E, Cremers FP, Lotery AJ.

Ophthalmology. 2012 Apr;119(4):819-26. doi: 10.1016/j.ophtha.2011.10.011. Epub 2012 Jan 20.

PubMed [citation]
PMID:
22264887
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV003787211.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the gnomAD database. This sequence change creates a premature translational stop signal (p.Glu877Glyfs*212) in the RPGR (ORF15) gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 276 amino acid(s) of the RPGR (ORF15) protein. This premature translational stop signal has been observed in individual(s) with retinitis pigmentosa (PMID: 30543658). For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the RPGR (ORF15) protein in which other variant(s) (p.Leu1130Lysfs*13) have been determined to be pathogenic (PMID: 22264887; Invitae). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. ClinVar contains an entry for this variant (Variation ID: 1802366).

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

Last Updated: Sep 16, 2024