RRH

protein-coding

retinal pigment epithelium-derived rhodopsin homolog, the group of Opsin receptors

Gene summary

Opsins are members of the guanine nucleotide-binding protein (G protein)-coupled receptor superfamily. This gene belongs to the seven-exon subfamily of mammalian opsin genes that includes opsin 5 and retinal G protein coupled receptor. [provided by RefSeq, Jul 2008]

MANE transcript

NM_006583.5

Inheritance

—

ClinVar variants

U:56B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.93

Max pathogenic AF

—

Genomic locus

chr4:109,827,972-109,849,123

External References & Databases

Ensembl (ENSG00000180245)

Transcript & Mutation Effects

hg38 • Region Span ~21.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RRH variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 56

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006583.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			55 clinvar	3 clinvar		58
nonsense				1 clinvar		1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	56	4	0	60

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006583.5	RefSeq	NP_006574.1	7	MANE Select
ENST00000317735.7	Ensembl	ENSP00000314992.4	7	MANE Select
ENST00000652276.1	Ensembl	ENSP00000498977.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

GPCRs, Class A Rhodopsin-like
Signaling by GPCR
Signal Transduction
Opsins
Class A/1 (Rhodopsin-like receptors)

Biological Process

G protein-coupled receptor signaling pathway
visual perception
phototransduction
detection of visible light
protein-chromophore linkage

Molecular Function

G protein-coupled receptor activity
G protein-coupled photoreceptor activity

Cellular Component

photoreceptor outer segment
integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000317735
Coding exons: 7
Length: 16611
Individuals with no LoFs: 125516
Homozygous LoFs: 1
Heterozygous LoFs: 231
Defined: 125748
p: 0.000923

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.103	193	189	1.02	0.00000936	2227
Missense (PolyPhen)		68	68.18	0.99736		815
Synonymous	0.431	61	65.4	0.932	0.00000357	648
Loss of Function	0.268	14	15.1	0.926	7.27e-7	178

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0065	0.0065	notable
Latino/Admixed American	0.0011	0.0011	notable
Ashkenazi Jewish	0.00069	0.00069	rare
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00055	0.00055	rare
South Asian	0.00043	0.00042	rare
Other	0.00098	0.00098	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in rpe physiology either by detecting light directly or by monitoring the concentration of retinoids or other photoreceptor-derived compounds.;

Recessive Scores

pRec: 0.129

Intolerance Scores

LoFtool: 0.731
RVIS EVS: 0.51
RVIS percentile EVS: 80.1

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.415

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium