RDH5
protein-codingretinol 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]
- RDH1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~4.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0007639
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0007639
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0007639
Submitter: PanelApp Australia
Inheritance Pattern: SD
Disease ID:MONDO:0007639
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0007639
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0007639
Submitter: PanelApp Australia
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)
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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to RDH5 variants in ClinVar
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.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 4 | 61 | 65 | |||
| missense | 3 | 24 | 139 | 10 | 176 | |
| nonsense | 11 | 8 | 19 | |||
| start loss | 0 | |||||
| frameshift | 13 | 16 | 1 | 30 | ||
| splice donor/acceptor (+/-2bp) | 1 | 3 | 4 | |||
| Total | 28 | 51 | 144 | 71 | 0 | 294 |
Highest pathogenic variant AF is 0.00028111783
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002896.2 | 4 | MANE Select | |
| Ensembl | ENSP00000257895.6 | 4 | MANE Select | |
| RefSeq | NP_001186700.1 | 4 | Standard | |
| Ensembl | ENSP00000449927.1 | 4 | Standard |
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:
- 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-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.394 | 171 | 186 | 0.919 | 0.0000112 | 2004 |
| Missense (PolyPhen) | 49 | 55.098 | 0.88933 | 588 | ||
| Synonymous | 0.101 | 78 | 79.1 | 0.986 | 0.00000425 | 728 |
| Loss of Function | -0.195 | 15 | 14.2 | 1.06 | 0.00000112 | 107 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.00058 | 0.00058 | rare |
| Ashkenazi Jewish | 0.0013 | 0.0013 | notable |
| East Asian | 0.00065 | 0.00065 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00044 | 0.00044 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- 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
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |