rs137852551
Positions:
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PVS1PP5
The NM_001034853.2(RPGR):c.2929G>T(p.Gly977Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 9)
Consequence
RPGR
NM_001034853.2 stop_gained
NM_001034853.2 stop_gained
Scores
2
3
Clinical Significance
Conservation
PhyloP100: 0.299
Genes affected
RPGR (HGNC:10295): (retinitis pigmentosa GTPase regulator) This gene encodes a protein with a series of six RCC1-like domains (RLDs), characteristic of the highly conserved guanine nucleotide exchange factors. The encoded protein is found in the Golgi body and interacts with RPGRIP1. This protein localizes to the outer segment of rod photoreceptors and is essential for their viability. Mutations in this gene have been associated with X-linked retinitis pigmentosa (XLRP). Multiple alternatively spliced transcript variants that encode different isoforms of this gene have been reported, but the full-length natures of only some have been determined. [provided by RefSeq, Dec 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. There are 28 pathogenic variants in the truncated region.
PP5
?
Variant X-38286070-C-A is Pathogenic according to our data. Variant chrX-38286070-C-A is described in ClinVar as [Pathogenic]. Clinvar id is 9918.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-38286070-C-A is described in Lovd as [Pathogenic]. Variant chrX-38286070-C-A is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPGR | NM_001034853.2 | c.2929G>T | p.Gly977Ter | stop_gained | 15/15 | ENST00000645032.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPGR | ENST00000645032.1 | c.2929G>T | p.Gly977Ter | stop_gained | 15/15 | NM_001034853.2 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 9
GnomAD3 genomes
?
Cov.:
9
GnomAD4 exome Cov.: 11
GnomAD4 exome
Cov.:
11
GnomAD4 genome ? Cov.: 9
GnomAD4 genome
?
Cov.:
9
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
X-linked cone-rod dystrophy 1 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 01, 2005 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Benign
FATHMM_MKL
Benign
N
MutationTaster
Benign
A;A;A;A;A;A
Vest4
0.83
GERP RS
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at