rs62640587
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 4P and 8B. PS1_ModeratePM1BP4_StrongBS2
The NM_001034853.2(RPGR):āc.865A>Gā(p.Ile289Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000121 in 1,201,878 control chromosomes in the GnomAD database, including 1 homozygotes. There are 51 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin UniProt.
Frequency
Consequence
NM_001034853.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RPGR | NM_001034853.2 | c.865A>G | p.Ile289Val | missense_variant | 8/15 | ENST00000645032.1 | NP_001030025.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RPGR | ENST00000645032.1 | c.865A>G | p.Ile289Val | missense_variant | 8/15 | NM_001034853.2 | ENSP00000495537.1 | |||
ENSG00000250349 | ENST00000465127.1 | c.172-361417T>C | intron_variant | 5 | ENSP00000417050.1 |
Frequencies
GnomAD3 genomes AF: 0.0000983 AC: 11AN: 111869Hom.: 0 Cov.: 23 AF XY: 0.000206 AC XY: 7AN XY: 34013
GnomAD3 exomes AF: 0.000137 AC: 25AN: 181885Hom.: 0 AF XY: 0.000120 AC XY: 8AN XY: 66565
GnomAD4 exome AF: 0.000124 AC: 135AN: 1089955Hom.: 1 Cov.: 28 AF XY: 0.000124 AC XY: 44AN XY: 355755
GnomAD4 genome AF: 0.0000983 AC: 11AN: 111923Hom.: 0 Cov.: 23 AF XY: 0.000205 AC XY: 7AN XY: 34077
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Feb 03, 2022 | Variant summary: RPGR c.865A>G (p.Ile289Val) results in a conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00014 in 181885 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in RPGR causing Retinitis Pigmentosa, X-Linked (0.00014 vs 0.005), however 8 hemizygotes are present in the gnomad population database, suggesting the variant may benign. c.865A>G has been reported in the literature in individuals affected with Retinitis Pigmentosa, X-Linked including in a family with 2 affected males and 3 female carriers, where only the RPGR gene was tested (Miano_1999, Churchill_2013, Weisschuh_2020). These reports do not provide unequivocal conclusions about association of the variant with Retinitis Pigmentosa, X-Linked. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as uncertain significance. - |
RPGR-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 23, 2021 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Primary ciliary dyskinesia Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 13, 2024 | - - |
Retinitis pigmentosa Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
not provided Other:1
not provided, no classification provided | literature only | Retina International | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at