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RDH5 retinol dehydrogenase 5 [ Homo sapiens (human) ]

Gene ID: 5959, updated on 11-Apr-2024

Summary

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Official Symbol
RDH5provided by HGNC
Official Full Name
retinol dehydrogenase 5provided by HGNC
Primary source
HGNC:HGNC:9940
See related
Ensembl:ENSG00000135437 MIM:601617; AllianceGenome:HGNC:9940
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
RDH1; 9cRDH; SDR9C5; HSD17B9
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]
Expression
Biased expression in fat (RPKM 73.0), liver (RPKM 14.5) and 5 other tissues See more
Orthologs
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Genomic context

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Location:
12q13.2
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (55720393..55724705)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (55687027..55691339)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (56114177..56118489)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:56075179-56075854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:56078881-56079380 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:56087579-56088778 Neighboring gene thiol methyltransferase 1B Neighboring gene integrin subunit alpha 7 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4534 Neighboring gene BLOC1S1-RDH5 readthrough Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6454 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6455 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6456 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6457 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6458 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:56114612-56115240 Neighboring gene biogenesis of lysosomal organelles complex 1 subunit 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4535 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:56122619-56123225 Neighboring gene CD63 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6459 Neighboring gene CD63 molecule Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4537 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:56140299-56140802 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr12:56140803-56141306 Neighboring gene growth differentiation factor 11 Neighboring gene SAP domain containing ribonucleoprotein

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Novel variants in the RDH5 Gene in a Chinese Han family with fundus albipunctatus. Qian T, et al. BMC Ophthalmol, 2022 Feb 11. PMID 35148716, Free PMC Article
  2. RDH5-Related Fundus Albipunctatus in a Large Japanese Cohort. Katagiri S, et al. Invest Ophthalmol Vis Sci, 2020 Mar 9. PMID 32232344, Free PMC Article
  3. A founder RDH5 splice site mutation leads to retinitis punctata albescens in two inbred Pakistani kindreds. Khan R, et al. Ophthalmic Genet, 2020 Feb. PMID 31933420
  4. A novel mutation in RDH5 gene causes retinitis pigmentosa in consanguineous Pakistani family. Sultan N, et al. Genes Genomics, 2018 May. PMID 29892959
  5. RDH5 retinopathy (fundus albipunctatus) with preserved rod function. Liu X, et al. Retina, 2015 Mar. PMID 25170858

See all (60) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Novel variants in the RDH5 Gene in a Chinese Han family with fundus albipunctatus.
    Title: Novel variants in the RDH5 Gene in a Chinese Han family with fundus albipunctatus.
  2. Shared Features in Retinal Disorders With Involvement of Retinal Pigment Epithelium.
    Title: Shared Features in Retinal Disorders With Involvement of Retinal Pigment Epithelium.
  3. Retinal dehydrogenase 5 (RHD5) attenuates metastasis via regulating HIPPO/YAP signaling pathway in Hepatocellular Carcinoma.
    Title: Retinal dehydrogenase 5 (RHD5) attenuates metastasis via regulating HIPPO/YAP signaling pathway in Hepatocellular Carcinoma.
  4. A founder RDH5 splice site mutation leads to retinitis punctata albescens in two inbred Pakistani kindreds.
    Title: A founder RDH5 splice site mutation leads to retinitis punctata albescens in two inbred Pakistani kindreds.
  5. Multimodal imaging and electroretinography of RDH5-related fundus albipunctatus (FAP) revealed high frequencies of macular involvement in older patients and decreased cone responses.
    Title: RDH5-Related Fundus Albipunctatus in a Large Japanese Cohort.
  6. a novel homozygous missense mutation, (c.602 C > T) in exon 4 of the RDH5 gene (MIM: 601617) was identified. This mutation resulted in substitution of phenyl alanine for serine at amino acid 201 (p.Ser201Phe) of the RDH5 gene. Identification of this mutation reveals the allelic heterogeneity of RDH5 in patients with retinitis pigmentosa phenotype.
    Title: A novel mutation in RDH5 gene causes retinitis pigmentosa in consanguineous Pakistani family.
  7. We conclude that the expression of Rlbp1 and Rdh5 critically depends on functional Mitf in the RPE and suggest that MITF has an important role in controlling retinoid processing in the RPE.
    Title: Microphthalmia-associated transcription factor regulates the visual cycle genes Rlbp1 and Rdh5 in the retinal pigment epithelium.
  8. A novel c.832C>T (p.Arg278Ter) nonsense mutation in RDH5 was identified. Preserved rod function was observed in one young subject in this study.
    Title: RDH5 retinopathy (fundus albipunctatus) with preserved rod function.
  9. Macular cone density is lower and the regularity of the macular cone mosaic spatial arrangement is disrupted in eyes with fundus albipunctatus.
    Title: Cone abnormalities in fundus albipunctatus associated with RDH5 mutations assessed using adaptive optics scanning laser ophthalmoscopy.
  10. RDH5 sequence analysis revealed a novel five base pair deletion, c.913_917delGTGCT (p.Val305Hisfs*29), in family A, and a novel missense mutation, c.758T>G (p.Met253Arg), in family B with fundus albipunctatus.
    Title: Novel mutations in RDH5 cause fundus albipunctatus in two consanguineous Pakistani families.
Submit: New GeneRIF Correction See all GeneRIFs (26)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Pigmentary retinal dystrophy
MedGen: C0311338 OMIM: 136880 GeneReviews: Not available
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EBI GWAS Catalog

Description
Genome-wide meta-analyses of multiancestry cohorts identify multiple new susceptibility loci for refractive error and myopia.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of retinol dehydrogenase 5 (11-cis/9-cis) (RDH5) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Readthrough BLOC1S1-RDH5

Readthrough gene: BLOC1S1-RDH5, Included gene: BLOC1S1

Homology

Clone Names

  • FLJ39337, FLJ97089

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 11-cis-retinol dehydrogenase IEA
Inferred from Electronic Annotation
more info
  
enables all-trans-retinol dehydrogenase (NAD+) activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables all-trans-retinol dehydrogenase (NAD+) activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables all-trans-retinol dehydrogenase (NAD+) activity TAS
Traceable Author Statement
more info
  
enables androstan-3-alpha,17-beta-diol dehydrogenase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables androsterone dehydrogenase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein homodimerization activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in response to stimulus IEA
Inferred from Electronic Annotation
more info
  
involved_in retinoid metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in retinoid metabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in retinoid metabolic process TAS
Traceable Author Statement
more info
  
involved_in retinol metabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in steroid metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in steroid metabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in visual perception IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cell body IEA
Inferred from Electronic Annotation
more info
  
located_in endoplasmic reticulum lumen IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  
is_active_in intracellular membrane-bounded organelle IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
retinol dehydrogenase 5
Names
11-cis RDH
11-cis RoDH
9-cis retinol dehydrogenase
9-cis-retinol specific dehydrogenase
retinol dehydrogenase 1
retinol dehydrogenase 5 (11-cis and 9-cis)
retinol dehydrogenase 5 (11-cis/9-cis)
short chain dehydrogenase/reductase family 9C member 5
NP_001186700.1
NP_002896.2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_008606.1 RefSeqGene

    Range
    5027..9339
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001199771.3 → NP_001186700.1  retinol dehydrogenase 5

    See identical proteins and their annotated locations for NP_001186700.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    BC028298, BI765016, BP381700
    Consensus CDS
    CCDS31829.1
    UniProtKB/Swiss-Prot
    O00179, Q8TAI2, Q92781
    Related
    ENSP00000447128.1, ENST00000548082.1
    Conserved Domains (2) summary
    PRK08017
    Location:31 → 308
    PRK08017; oxidoreductase; Provisional
    cd09805
    Location:30 → 306
    type2_17beta_HSD-like_SDR_c; human 17beta-hydroxysteroid dehydrogenase type 2 (type 2 17beta-HSD)-like, classical (c) SDRs

  2. NM_002905.5 → NP_002896.2  retinol dehydrogenase 5

    See identical proteins and their annotated locations for NP_002896.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 5' UTR, compared to variant 1. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    BP381700, BU617433, U43559
    Consensus CDS
    CCDS31829.1
    UniProtKB/Swiss-Prot
    O00179, Q8TAI2, Q92781
    Related
    ENSP00000257895.6, ENST00000257895.10
    Conserved Domains (2) summary
    PRK08017
    Location:31 → 308
    PRK08017; oxidoreductase; Provisional
    cd09805
    Location:30 → 306
    type2_17beta_HSD-like_SDR_c; human 17beta-hydroxysteroid dehydrogenase type 2 (type 2 17beta-HSD)-like, classical (c) SDRs

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    55720393..55724705
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    55687027..55691339
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q92781.1 GenPept UniProtKB/Swiss-Prot:Q92781

Gene LinkOut

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