NM_001034853.2(RPGR):c.3317dup (p.Ser1107fs) AND Primary ciliary dyskinesia

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 29, 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:: RCV002518809.4

Allele description [Variation Report for NM_001034853.2(RPGR):c.3317dup (p.Ser1107fs)]

NM_001034853.2(RPGR):c.3317dup (p.Ser1107fs)

Gene:

RPGR:retinitis pigmentosa GTPase regulator [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

Xp11.4

Genomic location:

Preferred name:

NM_001034853.2(RPGR):c.3317dup (p.Ser1107fs)

HGVS:

NC_000023.11:g.38285688dup
NG_009553.1:g.46854dup
NM_000328.3:c.1905+1406dup
NM_001034853.2:c.3317dupMANE SELECT
NM_001367245.1:c.1902+1406dup
NM_001367246.1:c.1719+1406dup
NM_001367247.1:c.1572+5271dup
NM_001367248.1:c.1602+5271dup
NM_001367249.1:c.1569+5271dup
NM_001367250.1:c.1569+5271dup
NM_001367251.1:c.1386+5271dup
NP_001030025.1:p.Ser1107fs
NC_000023.10:g.38144934_38144935insT
NC_000023.10:g.38144941dup
NM_001034853.1:c.3317dup
NM_001034853.1:c.3317dupA

Protein change:

S1107fs

Links:

dbSNP: rs886041376

NCBI 1000 Genomes Browser:

rs886041376

Molecular consequence:

NM_001034853.2:c.3317dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_000328.3:c.1905+1406dup - intron variant - [Sequence Ontology: SO:0001627]
NM_001367245.1:c.1902+1406dup - intron variant - [Sequence Ontology: SO:0001627]
NM_001367246.1:c.1719+1406dup - intron variant - [Sequence Ontology: SO:0001627]
NM_001367247.1:c.1572+5271dup - intron variant - [Sequence Ontology: SO:0001627]
NM_001367248.1:c.1602+5271dup - intron variant - [Sequence Ontology: SO:0001627]
NM_001367249.1:c.1569+5271dup - intron variant - [Sequence Ontology: SO:0001627]
NM_001367250.1:c.1569+5271dup - intron variant - [Sequence Ontology: SO:0001627]
NM_001367251.1:c.1386+5271dup - 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
SCV003445109	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 29, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 15734019, 21866333, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003445109

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 29, 2022)

germline

clinical testing

PubMed (3)
[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

Histopathologic study of X-linked cone-rod dystrophy (CORDX1) caused by a mutation in the RPGR exon ORF15.

Demirci FY, Gupta N, Radak AL, Rigatti BW, Mah TS, Milam AH, Gorin MB.

Am J Ophthalmol. 2005 Feb;139(2):386-8.

PubMed [citation]

PMID:: 15734019

Clinical course of cone dystrophy caused by mutations in the RPGR gene.

Thiadens AA, Soerjoesing GG, Florijn RJ, Tjiam AG, den Hollander AI, van den Born LI, Riemslag FC, Bergen AA, Klaver CC.

Graefes Arch Clin Exp Ophthalmol. 2011 Oct;249(10):1527-35. doi: 10.1007/s00417-011-1789-3. Epub 2011 Aug 25.

PubMed [citation]

PMID:: 21866333
PMCID:: PMC3178018

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003445109.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

ClinVar contains an entry for this variant (Variation ID: 280089). This variant is also known as 1564_1565insA. This premature translational stop signal has been observed in individuals with clinical features of inherited retinal dystrophy (PMID: 15734019, 21866333). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Ser1107Valfs*4) in the RPGR (ORF15) gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 46 amino acid(s) of the RPGR (ORF15) protein. For these reasons, this variant has been classified as Pathogenic.

#	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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