NM_001034853.2(RPGR):c.2747_2749del (p.Glu916del) AND Primary ciliary dyskinesia

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 16, 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:: RCV002616704.4

Allele description [Variation Report for NM_001034853.2(RPGR):c.2747_2749del (p.Glu916del)]

NM_001034853.2(RPGR):c.2747_2749del (p.Glu916del)

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.2747_2749del (p.Glu916del)

HGVS:

NC_000023.11:g.38286251_38286253del
NG_009553.1:g.46284_46286del
NM_000328.3:c.1905+842_1905+844del
NM_001034853.2:c.2747_2749delMANE SELECT
NM_001367245.1:c.1902+842_1902+844del
NM_001367246.1:c.1719+842_1719+844del
NM_001367247.1:c.1572+4707_1572+4709del
NM_001367248.1:c.1602+4707_1602+4709del
NM_001367249.1:c.1569+4707_1569+4709del
NM_001367250.1:c.1569+4707_1569+4709del
NM_001367251.1:c.1386+4707_1386+4709del
NP_001030025.1:p.Glu916del
NC_000023.10:g.38145503_38145505del
NC_000023.10:g.38145504_38145506del

Protein change:

E916del

Molecular consequence:

NM_001034853.2:c.2747_2749del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_000328.3:c.1905+842_1905+844del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367245.1:c.1902+842_1902+844del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367246.1:c.1719+842_1719+844del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367247.1:c.1572+4707_1572+4709del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367248.1:c.1602+4707_1602+4709del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367249.1:c.1569+4707_1569+4709del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367250.1:c.1569+4707_1569+4709del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367251.1:c.1386+4707_1386+4709del - 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
SCV003508566	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 16, 2022)	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

SCV003508566

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 16, 2022)

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003508566.2

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

Description

This variant, c.2747_2749del, results in the deletion of 1 amino acid(s) of the RPGR (ORF15) protein (p.Glu916del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with RPGR (ORF15)-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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.

#	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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