NM_001034853.2(RPGR):c.2594_2596del (p.Gly865del) AND Primary ciliary dyskinesia

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 26, 2024
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:: RCV001986568.5

Allele description [Variation Report for NM_001034853.2(RPGR):c.2594_2596del (p.Gly865del)]

NM_001034853.2(RPGR):c.2594_2596del (p.Gly865del)

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.2594_2596del (p.Gly865del)

HGVS:

NC_000023.11:g.38286405_38286407del
NG_009553.1:g.46131_46133del
NM_000328.3:c.1905+689_1905+691del
NM_001034853.2:c.2594_2596delMANE SELECT
NM_001367245.1:c.1902+689_1902+691del
NM_001367246.1:c.1719+689_1719+691del
NM_001367247.1:c.1572+4554_1572+4556del
NM_001367248.1:c.1602+4554_1602+4556del
NM_001367249.1:c.1569+4554_1569+4556del
NM_001367250.1:c.1569+4554_1569+4556del
NM_001367251.1:c.1386+4554_1386+4556del
NP_001030025.1:p.Gly865del
NC_000023.10:g.38145656_38145658del
NC_000023.10:g.38145658_38145660del
NM_001034853.1:c.2594_2596del
NM_001034853.1:c.2594_2596delGAG

Protein change:

G865del

Links:

dbSNP: rs771584745

NCBI 1000 Genomes Browser:

rs771584745

Molecular consequence:

NM_001034853.2:c.2594_2596del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_000328.3:c.1905+689_1905+691del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367245.1:c.1902+689_1902+691del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367246.1:c.1719+689_1719+691del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367247.1:c.1572+4554_1572+4556del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367248.1:c.1602+4554_1602+4556del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367249.1:c.1569+4554_1569+4556del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367250.1:c.1569+4554_1569+4556del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367251.1:c.1386+4554_1386+4556del - 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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Chromosome neighbors for GEO Profiles (Select 25687439) (20)
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Chromosome neighbors for GEO Profiles (Select 7055439) (17)
GEO Profiles
DNAH6 dynein axonemal heavy chain 6 [Homo sapiens]
DNAH6 dynein axonemal heavy chain 6 [Homo sapiens]
Gene ID:1768

Gene
Gene Links for GEO Profiles (Select 125824445) (1)
Gene
CCND3 cyclin D3 [Homo sapiens]
CCND3 cyclin D3 [Homo sapiens]
Gene ID:896

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002285767	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 26, 2024)	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

SCV002285767

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 26, 2024)

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, SCV002285767.3

#	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.2594_2596del, results in the deletion of 1 amino acid(s) of the RPGR (ORF15) protein (p.Gly865del), but otherwise preserves the integrity of the reading frame. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with RPGR (ORF15)-related conditions. ClinVar contains an entry for this variant (Variation ID: 1491495). 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: Oct 26, 2024

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