NM_001034853.2(RPGR):c.2606_2620del (p.Glu869_Glu873del) AND Primary ciliary dyskinesia

Germline classification:: Likely benign (1 submission)
Last evaluated:: Jan 31, 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:: RCV000228907.9

Allele description [Variation Report for NM_001034853.2(RPGR):c.2606_2620del (p.Glu869_Glu873del)]

NM_001034853.2(RPGR):c.2606_2620del (p.Glu869_Glu873del)

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.2606_2620del (p.Glu869_Glu873del)

HGVS:

NC_000023.11:g.38286380_38286394del
NG_009553.1:g.46143_46157del
NM_000328.3:c.1905+701_1905+715del
NM_001034853.2:c.2606_2620delMANE SELECT
NM_001367245.1:c.1902+701_1902+715del
NM_001367246.1:c.1719+701_1719+715del
NM_001367247.1:c.1572+4566_1572+4580del
NM_001367248.1:c.1602+4566_1602+4580del
NM_001367249.1:c.1569+4566_1569+4580del
NM_001367250.1:c.1569+4566_1569+4580del
NM_001367251.1:c.1386+4566_1386+4580del
NP_001030025.1:p.Glu869_Glu873del
NC_000023.10:g.38145632_38145646del
NC_000023.10:g.38145633_38145647del
NM_000328.2:c.1905+701_1905+715del
NM_000328.2:c.1905+701_1905+715delAAGAAGGGGAGGAAG
NM_001034853.1:c.2606_2620del

Links:

dbSNP: rs200824587

NCBI 1000 Genomes Browser:

rs200824587

Molecular consequence:

NM_001034853.2:c.2606_2620del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_000328.3:c.1905+701_1905+715del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367245.1:c.1902+701_1902+715del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367246.1:c.1719+701_1719+715del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367247.1:c.1572+4566_1572+4580del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367248.1:c.1602+4566_1602+4580del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367249.1:c.1569+4566_1569+4580del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367250.1:c.1569+4566_1569+4580del - intron variant - [Sequence Ontology: SO:0001627]
NM_001367251.1:c.1386+4566_1386+4580del - 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
SCV001001131	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 31, 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

SCV001001131

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jan 31, 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, SCV001001131.4

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

#	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 20, 2024

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