NM_001034853.2(RPGR):c.3423G>A (p.Trp1141Ter) AND Primary ciliary dyskinesia

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 29, 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:: RCV002571387.3

Allele description

NM_001034853.2(RPGR):c.3423G>A (p.Trp1141Ter)

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.3423G>A (p.Trp1141Ter)

HGVS:

NC_000023.11:g.38285576C>T
NG_009553.1:g.46960G>A
NM_000328.3:c.1905+1518G>A
NM_001034853.2:c.3423G>AMANE SELECT
NM_001367245.1:c.1902+1518G>A
NM_001367246.1:c.1719+1518G>A
NM_001367247.1:c.1572+5383G>A
NM_001367248.1:c.1602+5383G>A
NM_001367249.1:c.1569+5383G>A
NM_001367250.1:c.1569+5383G>A
NM_001367251.1:c.1386+5383G>A
NP_001030025.1:p.Trp1141Ter
NC_000023.10:g.38144829C>T
NM_001034853.1:c.3423G>A

Protein change:

W1141*

Molecular consequence:

NM_000328.3:c.1905+1518G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001367245.1:c.1902+1518G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001367246.1:c.1719+1518G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001367247.1:c.1572+5383G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001367248.1:c.1602+5383G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001367249.1:c.1569+5383G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001367250.1:c.1569+5383G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001367251.1:c.1386+5383G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001034853.2:c.3423G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Primary ciliary dyskinesia
Synonyms:: Ciliary dyskinesia
Identifiers:: MONDO: MONDO:0016575; MedGen: C0008780; OMIM: PS244400; Human Phenotype Ontology: HP:0012265

Recent activity

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ras-related GTP binding protein, partial [Pseudalmenus chlorinda]
ras-related GTP binding protein, partial [Pseudalmenus chlorinda]
gi|2569165849|gb|WMI10846.1|

Protein
Homo sapiens chromosome 5 open reading frame 13, mRNA (cDNA clone MGC:88723 IMAG...
Homo sapiens chromosome 5 open reading frame 13, mRNA (cDNA clone MGC:88723 IMAGE:5922876), complete cds
gi|47939646|gb|BC072013.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003224775	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 29, 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

SCV003224775

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 29, 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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV003224775.2

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

Description

This sequence change creates a premature translational stop signal (p.Trp1141*) in the RPGR (ORF15) gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 12 amino acid(s) of the RPGR (ORF15) protein. 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. ClinVar contains an entry for this variant (Variation ID: 1802316). 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 16, 2024

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