NM_001034853.2(RPGR):c.2964_2965del (p.Glu989fs) AND Primary ciliary dyskinesia

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 13, 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:: RCV002549201.4

Allele description [Variation Report for NM_001034853.2(RPGR):c.2964_2965del (p.Glu989fs)]

NM_001034853.2(RPGR):c.2964_2965del (p.Glu989fs)

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.2964_2965del (p.Glu989fs)

HGVS:

NC_000023.11:g.38286036_38286037del
NG_009553.1:g.46501_46502del
NM_000328.3:c.1905+1059_1905+1060del
NM_001034853.2:c.2964_2965delMANE SELECT
NM_001367245.1:c.1902+1059_1902+1060del
NM_001367246.1:c.1719+1059_1719+1060del
NM_001367247.1:c.1572+4924_1572+4925del
NM_001367248.1:c.1602+4924_1602+4925del
NM_001367249.1:c.1569+4924_1569+4925del
NM_001367250.1:c.1569+4924_1569+4925del
NM_001367251.1:c.1386+4924_1386+4925del
NP_001030025.1:p.Glu989fs
NC_000023.10:g.38145287_38145288del
NC_000023.10:g.38145289_38145290del
NM_001034853.1:c.2964_2965del
NM_001034853.1:c.2964_2965delGG

Protein change:

E989fs

Links:

dbSNP: rs1555961440

NCBI 1000 Genomes Browser:

rs1555961440

Molecular consequence:

NM_001034853.2:c.2964_2965del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_000328.3:c.1905+1059_1905+1060del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367245.1:c.1902+1059_1902+1060del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367246.1:c.1719+1059_1719+1060del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367247.1:c.1572+4924_1572+4925del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367248.1:c.1602+4924_1602+4925del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367249.1:c.1569+4924_1569+4925del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367250.1:c.1569+4924_1569+4925del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367251.1:c.1386+4924_1386+4925del - 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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003445111	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 13, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 16936086, 30029497, 32679846, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003445111

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 13, 2023)

germline

clinical testing

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

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

Mutational screening of the RP2 and RPGR genes in Spanish families with X-linked retinitis pigmentosa.

García-Hoyos M, Garcia-Sandoval B, Cantalapiedra D, Riveiro R, Lorda-Sánchez I, Trujillo-Tiebas MJ, Rodriguez de Alba M, Millan JM, Baiget M, Ramos C, Ayuso C.

Invest Ophthalmol Vis Sci. 2006 Sep;47(9):3777-82.

PubMed [citation]

PMID:: 16936086

Application of Whole Exome and Targeted Panel Sequencing in the Clinical Molecular Diagnosis of 319 Chinese Families with Inherited Retinal Dystrophy and Comparison Study.

Wang L, Zhang J, Chen N, Wang L, Zhang F, Ma Z, Li G, Yang L.

Genes (Basel). 2018 Jul 19;9(7). doi:pii: E360. 10.3390/genes9070360.

PubMed [citation]

PMID:: 30029497
PMCID:: PMC6071067

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003445111.2

#	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.Glu989Glyfs*89) in the RPGR (ORF15) gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 164 amino acid(s) of the RPGR (ORF15) protein. For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 812409). This variant is also known as g.ORF15 1211_1212delGG. This premature translational stop signal has been observed in individuals with retinitis pigmentosa (PMID: 16936086, 30029497, 32679846). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency).

#	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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