RDH5

protein-coding

retinol dehydrogenase 5, the group of Short chain dehydrogenase/reductase superfamily

Gene summary

This gene encodes an enzyme belonging to the short-chain dehydrogenases/reductases (SDR) family. This retinol dehydrogenase functions to catalyze the final step in the biosynthesis of 11-cis retinaldehyde, which is the universal chromophore of visual pigments. Mutations in this gene cause autosomal recessive fundus albipunctatus, a rare form of night blindness that is characterized by a delay in the regeneration of cone and rod photopigments. Alternative splicing results in multiple transcript variants. Read-through transcription also exists between this gene and the neighboring upstream BLOC1S1 (biogenesis of lysosomal organelles complex-1, subunit 1) gene. [provided by RefSeq, Dec 2010]

Previous symbols:
  • RDH1

MANE transcript

NM_002905.5

Inheritance

AD, AR, SD

ClinVar variants

P:79U:144B:71

Top phenotype

Fundus albipunctatus

gnomAD constraint

pLI —, LoF o/e 1.06

Max pathogenic AF

—

Genomic locus

chr12:55,720,367-55,724,705

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~4.3 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

fundus albipunctatusSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007639

Submitter: Orphanet

fundus albipunctatusSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0007639

Submitter: Labcorp Genetics (formerly Invitae)

fundus albipunctatusSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007639

Submitter: PanelApp Australia

fundus albipunctatusDEFINITIVE

Inheritance Pattern: SD

Disease ID:MONDO:0007639

Submitter: Ambry Genetics

fundus albipunctatusDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0007639

Submitter: G2P

fundus albipunctatusSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0007639

Submitter: PanelApp Australia

RDH5-related retinopathyDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0100443

Submitter: ClinGen

The RDH5 gene was first reported in relation to autosomal recessive “RDH5-related retinopathy” in 1999 (Yamamoto et al, PMID 10369264). Biallelic variants in RDH5 have been reported in individuals with various clinical features. Many individuals are reported to have fundus albipunctatus, with night blindness from childhood, stationary or slow progression of rod abnormalities, frequent and progressive cone abnormalities in older age, the presence of white dots in the retina, and cone dystrophy developing with age in some patients while others have been diagnosed with retinitis pigmentosa. Due to the variability in phenotype, for this curation, these phenotypes have been lumped together as “RDH5-related retinopathy”. To date, over 40 variants in the RDH5 gene have been reported in individuals with retinal dystrophy, and most of them are missense variants (Skorczyk-Werner et al 2015, PMID 25820994). Here, eleven unique variants in eleven probands were curated from seven publications (Yamamoto et al, 1999, PMID 10369264; Gonzalez-Fernandez et al, 1999, PMID 10617778; Nakamura et al, 2000, PMID 11053295; Wada et al, 2001, PMID 11448328; Pras et al, 2012, PMID 22815624; Almutairi et al, 2020, PMID 33369259; Katagiri et al, 2020, PMID 32232344). These variants included missense, nonsense, and frameshift variants in addition to one variant, c.928delCinsGAAG (p.Leu310GluVal), which is commonly identified in Japanese patients (Nakamura et al, 2000, PMID 11053295; Katagiri et al, 2020, PMID 32232344; Skorczyk-Werner et al 2015, PMID 25820994). More evidence is available in the literature, but the maximum score for genetic evidence (12 points) has been reached. The mechanism of pathogenicity is loss of function. Of note, in two reported patients, only a single variant was identified (Pras et al, 2012, PMID: 22815624). However, there is currently insufficient evidence to indicate that a single RDH5 variant can cause retinal disease. The gene-disease relationship is also supported by experimental evidence including the function of the RDH5 gene product in the visual cycle, which is consistent with the features noted in patients with biallelic variants (Driessen et al, 1995, PMID 7544779), the expression pattern of RDH5, specifically in the retinal pigment epithelium (Driessen et al, 1995, PMID 7544779; Swamy and McGaughey, 2019, PMID 31343654), physical interaction of RDH5 with RPE65, another gene implicated in retinal dystrophy with a role in the visual cycle (Aoun et al, 2021, PMID 34281261), and the features of an rdh5 knock-out mouse (Driessen et al, 2000, PMID 10825191). In summary, RDH5 is definitively associated with autosomal recessive RDH5-related retinopathy. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This classification was approved by the ClinGen Retina GCEP (SOP v8) on September 2, 2021.

Clinical Genomic Database (CGD)

Fundus albipunctatusAR

Manifestation: Ophthalmologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 10617778; 10369264; 11153648; 11812441; 16637847; 20829743; 21529959; 22669287; 22736946; 22815624Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RDH5 variants in ClinVar

15 Conditions Cataloged
not providedTotal: 266
Pigmentary retinal dystrophyTotal: 64
RDH5-related disorderTotal: 60
Inborn genetic diseasesTotal: 44
not specifiedTotal: 35
Fundus albipunctatus, autosomal recessiveTotal: 9
Retinal dystrophyTotal: 7
See casesTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002905.5. 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.

EffectPLPVUSLBBSum
synonymous
4
clinvar
61
clinvar
65
missense
3
clinvar
24
clinvar
139
clinvar
10
clinvar
176
nonsense
11
clinvar
8
clinvar
19
start loss
0
frameshift
13
clinvar
16
clinvar
1
clinvar
30
splice donor/acceptor (+/-2bp)
1
clinvar
3
clinvar
4
Total2851144710294

Highest pathogenic variant AF is 0.00028111783

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_002905.5RefSeqNP_002896.24MANE Select
ENST00000257895.10EnsemblENSP00000257895.64MANE Select
NM_001199771.3RefSeqNP_001186700.14Standard
ENST00000547072.5EnsemblENSP00000449927.14Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Retinol metabolism - Homo sapiens (human)
  • Vitamin A and Carotenoid Metabolism
  • Signaling by GPCR
  • Signal Transduction
  • RA biosynthesis pathway

Biological Process

  • retinoid metabolic process
  • visual perception
  • retinol metabolic process
  • response to stimulus
  • oxidation-reduction process

Molecular Function

  • retinol dehydrogenase activity

Cellular Component

  • endoplasmic reticulum lumen
  • endoplasmic reticulum membrane
  • cell body

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000257895
Coding exons
4
Length
4339
Individuals with no LoFs
125643
Homozygous LoFs
0
Heterozygous LoFs
105
Defined
125748
p
0.000418
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.3941711860.9190.00001122004
Missense (PolyPhen)4955.0980.88933588
Synonymous0.1017879.10.9860.00000425728
Loss of Function-0.1951514.21.060.00000112107

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000250.00025rare
Latino/Admixed American0.000580.00058rare
Ashkenazi Jewish0.00130.0013notable
East Asian0.000650.00065rare
Finnish00.0absent
European (Non-Finnish)0.000440.00044rare
South Asian0.000130.00013rare
Other0.000330.00033rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Stereospecific 11-cis retinol dehydrogenase, which catalyzes the final step in the biosynthesis of 11-cis retinaldehyde, the universal chromophore of visual pigments. Also able to oxidize 9-cis-retinol and 13-cis-retinol, but not all- trans-retinol. Active in the presence of NAD as cofactor but not in the presence of NADP. {ECO:0000269|PubMed:10588954, ECO:0000269|PubMed:9115228}.;

Recessive Scores

pRec
0.218

Intolerance Scores

LoFtool
0.305
RVIS EVS
0.08
RVIS percentile EVS
60.31

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
S
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.904

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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