rs28933394

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM2PM5PP3_StrongPP5_Very_Strong

The NM_000539.3(RHO):ā€‹c.173C>Gā€‹(p.Thr58Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,888 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (ā˜…ā˜…). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T58M) has been classified as Likely pathogenic.

Frequency

Genomes: not found (cov: 33)
Exomes š‘“: 6.8e-7 ( 0 hom. )

Consequence

RHO
NM_000539.3 missense

Scores

15
3
1

Clinical Significance

Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:9

Conservation

PhyloP100: 6.17
Variant links:
Genes affected
RHO (HGNC:10012): (rhodopsin) The protein encoded by this gene is found in rod cells in the back of the eye and is essential for vision in low-light conditions. The encoded protein binds to 11-cis retinal and is activated when light hits the retinal molecule. Defects in this gene are a cause of congenital stationary night blindness. [provided by RefSeq, Aug 2017]

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 16 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PM5
Other missense variant is known to change same aminoacid residue: Variant chr3-129528906-C-T is described in Lovd as [Likely_pathogenic].
PP3
MetaRNN computational evidence supports a deleterious effect, 0.991
PP5
Variant 3-129528906-C-G is Pathogenic according to our data. Variant chr3-129528906-C-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 13016.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-129528906-C-G is described in Lovd as [Pathogenic]. Variant chr3-129528906-C-G is described in Lovd as [Pathogenic]. Variant chr3-129528906-C-G is described in Lovd as [Likely_pathogenic]. Variant chr3-129528906-C-G is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RHONM_000539.3 linkuse as main transcriptc.173C>G p.Thr58Arg missense_variant 1/5 ENST00000296271.4 NP_000530.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RHOENST00000296271.4 linkuse as main transcriptc.173C>G p.Thr58Arg missense_variant 1/51 NM_000539.3 ENSP00000296271 P1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461888
Hom.:
0
Cov.:
33
AF XY:
0.00000138
AC XY:
1
AN XY:
727244
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
8.99e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:9
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Retinitis pigmentosa 4 Pathogenic:4
Pathogenic, criteria provided, single submitterclinical testingMendelicsMay 28, 2019- -
Pathogenic, no assertion criteria providedliterature onlyOMIMOct 01, 1991- -
Likely pathogenic, criteria provided, single submitterclinical testingCentre for Genomic Medicine, Manchester, Central Manchester University HospitalsSep 01, 2020- -
Likely pathogenic, criteria provided, single submitterclinical testingMGZ Medical Genetics CenterFeb 04, 2022- -
not provided Pathogenic:2
Likely pathogenic, criteria provided, single submitterclinical testingGeneDxAug 24, 2023In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 2333895, 15823756, 21094163, 8486634, 1924344, 2215617, 36648560, 30977563, 32483926, 25408095, 32882181, 32795431, 31717845, 29847639, 33777460, 31908405, 1929926, 28981474, 32037395, 18385078, 1882937, 8328469) -
Pathogenic, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpDec 27, 2022For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change affects RHO function (PMID: 1924344). 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 RHO protein function. ClinVar contains an entry for this variant (Variation ID: 13016). This missense change has been observed in individuals with autosomal dominant retinitis pigmentosa (PMID: 2215617, 29847639). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces threonine, which is neutral and polar, with arginine, which is basic and polar, at codon 58 of the RHO protein (p.Thr58Arg). -
Retinal dystrophy Pathogenic:2
Likely pathogenic, criteria provided, single submitterresearchDept Of Ophthalmology, Nagoya UniversityOct 01, 2023- -
Pathogenic, criteria provided, single submitterclinical testingBlueprint GeneticsJul 29, 2019- -
RHO-related disorder Pathogenic:1
Pathogenic, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesAug 05, 2024The RHO c.173C>G variant is predicted to result in the amino acid substitution p.Thr58Arg. This variant was reported in the heterozygous state in individuals with autosomal dominant retinitis pigmentosa (see, for example, Dryja et al. 1990. PubMed ID: 2215617; Jacobson et al. 1991. PubMed ID: 1882937; supplementary data, Comander et al. 2017. PubMed ID: 28981474; Martin-Merida et al. 2018. PubMed ID: 29847639; Georgiou et al. 2020. PubMed ID: 32795431). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. This variant is interpreted as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.99
BayesDel_addAF
Pathogenic
0.41
D
BayesDel_noAF
Pathogenic
0.36
CADD
Pathogenic
29
DANN
Uncertain
1.0
DEOGEN2
Pathogenic
0.86
D
Eigen
Pathogenic
0.97
Eigen_PC
Pathogenic
0.89
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Pathogenic
0.99
D
M_CAP
Pathogenic
0.37
D
MetaRNN
Pathogenic
0.99
D
MetaSVM
Uncertain
0.62
D
MutationAssessor
Pathogenic
4.1
H
MutationTaster
Benign
1.0
D
PrimateAI
Uncertain
0.74
T
PROVEAN
Pathogenic
-4.7
D
REVEL
Pathogenic
0.82
Sift
Pathogenic
0.0
D
Sift4G
Pathogenic
0.0010
D
Polyphen
1.0
D
Vest4
0.97
MutPred
0.94
Gain of MoRF binding (P = 0.0295);
MVP
0.99
MPC
0.93
ClinPred
1.0
D
GERP RS
5.5
Varity_R
1.0
gMVP
0.99

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs28933394; hg19: chr3-129247749; API