NM_001034853.2(RPGR):c.2481AGAGGA[1] (p.Glu831_Glu832del) AND Primary ciliary dyskinesia

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 27, 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:: RCV003538239.1

Allele description [Variation Report for NM_001034853.2(RPGR):c.2481AGAGGA[1] (p.Glu831_Glu832del)]

NM_001034853.2(RPGR):c.2481AGAGGA[1] (p.Glu831_Glu832del)

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.2481AGAGGA[1] (p.Glu831_Glu832del)

HGVS:

NC_000023.11:g.38286510TCTTCC[1]
NG_009553.1:g.46018AGAGGA[1]
NM_000328.3:c.1905+582_1905+587del
NM_001034853.2:c.2481AGAGGA[1]MANE SELECT
NM_001367245.1:c.1902+582_1902+587del
NM_001367246.1:c.1719+582_1719+587del
NM_001367247.1:c.1572+4447_1572+4452del
NM_001367248.1:c.1602+4447_1602+4452del
NM_001367249.1:c.1569+4447_1569+4452del
NM_001367250.1:c.1569+4447_1569+4452del
NM_001367251.1:c.1386+4447_1386+4452del
NP_001030025.1:p.Glu831_Glu832del
NC_000023.10:g.38145760_38145765del
NC_000023.10:g.38145763TCTTCC[1]
NM_001034853.2:c.2487_2492delMANE SELECT

Molecular consequence:

NM_001034853.2:c.2481AGAGGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_000328.3:c.1905+582_1905+587del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367245.1:c.1902+582_1902+587del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367246.1:c.1719+582_1719+587del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367247.1:c.1572+4447_1572+4452del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367248.1:c.1602+4447_1602+4452del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367249.1:c.1569+4447_1569+4452del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367250.1:c.1569+4447_1569+4452del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367251.1:c.1386+4447_1386+4452del - 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
SCV004336369	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 27, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004336369

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 27, 2023)

germline

clinical testing

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

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV004336369.1

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with RPGR (ORF15)-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant, c.2487_2492del, results in the deletion of 2 amino acid(s) of the RPGR (ORF15) protein (p.Glu831_Glu832del), but otherwise preserves the integrity of the reading frame.

#	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: May 12, 2024

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