NM_001034853.2(RPGR):c.1216_1217del (p.Leu406fs) AND Primary ciliary dyskinesia

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 8, 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:: RCV003538637.2

Allele description [Variation Report for NM_001034853.2(RPGR):c.1216_1217del (p.Leu406fs)]

NM_001034853.2(RPGR):c.1216_1217del (p.Leu406fs)

Gene:

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

Variant type:

Microsatellite

Cytogenetic location:

Xp11.4

Genomic location:

Preferred name:

NM_001034853.2(RPGR):c.1216_1217del (p.Leu406fs)

HGVS:

NC_000023.11:g.38298984AG[1]
NG_009553.1:g.33549CT[1]
NM_000328.3:c.1216_1217del
NM_001034853.2:c.1216_1217delMANE SELECT
NM_001367245.1:c.1213_1214del
NM_001367246.1:c.1060-1533_1060-1532del
NM_001367247.1:c.1216_1217del
NM_001367248.1:c.1246_1247del
NM_001367249.1:c.1213_1214del
NM_001367250.1:c.1213_1214del
NM_001367251.1:c.1060-1533_1060-1532del
NP_000319.1:p.Leu406fs
NP_001030025.1:p.Leu406fs
NP_001354174.1:p.Leu405fs
NP_001354176.1:p.Leu406fs
NP_001354177.1:p.Leu416fs
NP_001354178.1:p.Leu405fs
NP_001354179.1:p.Leu405fs
NC_000023.10:g.38158237AG[1]
NC_000023.10:g.38158237_38158238del
NM_001034853.1:c.1216_1217del
NR_159803.1:n.1416CT[1]
NR_159804.1:n.1265CT[1]
NR_159805.1:n.1356CT[1]
NR_159806.1:n.1356CT[1]
NR_159807.1:n.1356CT[1]
NR_159808.1:n.1468CT[1]

Protein change:

L405fs

Links:

dbSNP: rs2067448565

NCBI 1000 Genomes Browser:

rs2067448565

Molecular consequence:

NM_000328.3:c.1216_1217del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001034853.2:c.1216_1217del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001367245.1:c.1213_1214del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001367247.1:c.1216_1217del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001367248.1:c.1246_1247del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001367249.1:c.1213_1214del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001367250.1:c.1213_1214del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001367246.1:c.1060-1533_1060-1532del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367251.1:c.1060-1533_1060-1532del - intron variant - [Sequence Ontology: SO:0001627]
NR_159803.1:n.1416CT[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_159804.1:n.1265CT[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_159805.1:n.1356CT[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_159806.1:n.1356CT[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_159807.1:n.1356CT[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_159808.1:n.1468CT[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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

cytochrome oxidase subunit 1, partial (mitochondrion) [Telamonia dimidiata]
cytochrome oxidase subunit 1, partial (mitochondrion) [Telamonia dimidiata]
gi|1675201036|gb|QCW08551.1|

Protein

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004299799	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 8, 2023)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 12657579, 34985506, 16055928, 16969763, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004299799

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 8, 2023)

germline

clinical testing

PubMed (5)
[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

X-linked retinitis pigmentosa: RPGR mutations in most families with definite X linkage and clustering of mutations in a short sequence stretch of exon ORF15.

Bader I, Brandau O, Achatz H, Apfelstedt-Sylla E, Hergersberg M, Lorenz B, Wissinger B, Wittwer B, Rudolph G, Meindl A, Meitinger T.

Invest Ophthalmol Vis Sci. 2003 Apr;44(4):1458-63.

PubMed [citation]

PMID:: 12657579

Prevalence of RPGR-Mediated Retinal Dystrophy in an Unselected Cohort of Over 5000 Patients.

Tuupanen S, Gall K, Sistonen J, Saarinen I, Kämpjärvi K, Wells K, Merkkiniemi K, von Nandelstadh P, Sarantaus L, Känsäkoski J, Mårtenson E, Västinsalo H, Schleit J, Sankila EM, Kere A, Junnila H, Siivonen P, Andreevskaya M, Kytölä V, Muona M, Salmenperä P, Myllykangas S, et al.

Transl Vis Sci Technol. 2022 Jan 3;11(1):6. doi: 10.1167/tvst.11.1.6.

PubMed [citation]

PMID:: 34985506
PMCID:: PMC8742508

See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004299799.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

For these reasons, this variant has been classified as Pathogenic. This variant is also known as 1275_1276delCT (L406fsX451). This premature translational stop signal has been observed in individual(s) with clinical features of RPGR-related conditions (PMID: 12657579, 34985506). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Leu406Ilefs*46) in the RPGR gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in RPGR are known to be pathogenic (PMID: 16055928, 16969763).

#	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

ClinVar

Relating variation to medicine