rs62642057
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1PM2PM5PP3_StrongPP5_Very_Strong
The NM_001034853.2(RPGR):c.823G>C(p.Gly275Arg) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G275C) has been classified as Pathogenic.
Frequency
Genomes: not found (cov: 23)
Consequence
RPGR
NM_001034853.2 missense
NM_001034853.2 missense
Scores
13
1
1
Clinical Significance
Conservation
PhyloP100: 5.74
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 Pathogenic. Variant got 18 ACMG points.
PM1
?
In a repeat RCC1 5 (size 51) in uniprot entity RPGR_HUMAN there are 22 pathogenic changes around while only 4 benign (85%) in NM_001034853.2
PM2
?
Very rare variant in population databases, with high coverage;
PM5
?
Other missense variant is known to change same aminoacid residue: Variant chrX-38304746-C-A is described in ClinVar as [Pathogenic]. Clinvar id is 2118600.Status of the report is criteria_provided_single_submitter, 1 stars.
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.994
PP5
?
Variant X-38304746-C-G is Pathogenic according to our data. Variant chrX-38304746-C-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 866638.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPGR | NM_001034853.2 | c.823G>C | p.Gly275Arg | missense_variant | 8/15 | ENST00000645032.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPGR | ENST00000645032.1 | c.823G>C | p.Gly275Arg | missense_variant | 8/15 | NM_001034853.2 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD3 genomes
?
Cov.:
23
GnomAD4 exome Cov.: 29
GnomAD4 exome
Cov.:
29
GnomAD4 genome ? Cov.: 23
GnomAD4 genome
?
Cov.:
23
ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Aug 11, 2023 | For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Gly275 amino acid residue in RPGR. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 8817343, 16969763, 17724181, 23213406, 30622176, 31456290). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt RPGR protein function. ClinVar contains an entry for this variant (Variation ID: 866638). This missense change has been observed in individuals with retinitis pigmentosa (PMID: 32702353; external communication). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 275 of the RPGR protein (p.Gly275Arg). - |
Retinal dystrophy Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Blueprint Genetics | Jul 10, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Pathogenic
FATHMM_MKL
Pathogenic
D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D;D;D;D;D;D;D
MetaSVM
Pathogenic
D
MutationAssessor
Pathogenic
H;H;H;.;H;H;H;.;.
MutationTaster
Benign
D;D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;.;D;.;.;.;D;.;.
REVEL
Pathogenic
Sift
Pathogenic
D;.;D;.;.;.;.;.;.
Sift4G
Pathogenic
D;.;D;.;.;.;D;.;.
Polyphen
D;D;.;.;.;.;.;.;.
Vest4
MutPred
Loss of catalytic residue at L280 (P = 0.1215);Loss of catalytic residue at L280 (P = 0.1215);Loss of catalytic residue at L280 (P = 0.1215);Loss of catalytic residue at L280 (P = 0.1215);Loss of catalytic residue at L280 (P = 0.1215);Loss of catalytic residue at L280 (P = 0.1215);Loss of catalytic residue at L280 (P = 0.1215);.;Loss of catalytic residue at L280 (P = 0.1215);
MVP
MPC
1.9
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
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