NM_001034853.2(RPGR):c.905G>C (p.Cys302Ser) AND Primary ciliary dyskinesia

Germline classification:: Benign (2 submissions)
Last evaluated:: Jan 25, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001079787.9

Allele description [Variation Report for NM_001034853.2(RPGR):c.905G>C (p.Cys302Ser)]

NM_001034853.2(RPGR):c.905G>C (p.Cys302Ser)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

Xp11.4

Genomic location:

Preferred name:

NM_001034853.2(RPGR):c.905G>C (p.Cys302Ser)

HGVS:

NC_000023.11:g.38304664C>G
NG_009553.1:g.27872G>C
NM_000328.3:c.905G>C
NM_001034853.2:c.905G>CMANE SELECT
NM_001367245.1:c.902G>C
NM_001367246.1:c.905G>C
NM_001367247.1:c.905G>C
NM_001367248.1:c.935G>C
NM_001367249.1:c.902G>C
NM_001367250.1:c.902G>C
NM_001367251.1:c.905G>C
NP_000319.1:p.Cys302Ser
NP_001030025.1:p.Cys302Ser
NP_001354174.1:p.Cys301Ser
NP_001354175.1:p.Cys302Ser
NP_001354176.1:p.Cys302Ser
NP_001354177.1:p.Cys312Ser
NP_001354178.1:p.Cys301Ser
NP_001354179.1:p.Cys301Ser
NP_001354180.1:p.Cys302Ser
NC_000023.10:g.38163917C>G
NM_000328.2:c.905G>C
NR_159803.1:n.1047G>C
NR_159804.1:n.956G>C
NR_159805.1:n.1047G>C
NR_159806.1:n.1047G>C
NR_159807.1:n.1047G>C

Protein change:

C301S

Links:

dbSNP: rs62640590

NCBI 1000 Genomes Browser:

rs62640590

Molecular consequence:

NM_000328.3:c.905G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001034853.2:c.905G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001367245.1:c.902G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001367246.1:c.905G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001367247.1:c.905G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001367248.1:c.935G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001367249.1:c.902G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001367250.1:c.902G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001367251.1:c.905G>C - missense variant - [Sequence Ontology: SO:0001583]
NR_159803.1:n.1047G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_159804.1:n.956G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_159805.1:n.1047G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_159806.1:n.1047G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_159807.1:n.1047G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

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
SCV001003962	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 25, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002687686	Ambry Genetics	criteria provided, single submitter (Ambry General Variant Classification Scheme_2022)	Benign (Sep 10, 2015)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001003962

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Jan 25, 2024)

germline

clinical testing

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

SCV002687686

Ambry Genetics

criteria provided, single submitter

(Ambry General Variant Classification Scheme_2022)

Benign
(Sep 10, 2015)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	1	not provided	not provided	1	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, SCV001003962.6

#	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

From Ambry Genetics, SCV002687686.1

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

Description

This alteration is classified as benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	1	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Apr 15, 2024

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