SDR16C5 short chain dehydrogenase/reductase family 16C member 5 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SDR16C5provided by HGNC
Official Full Name: short chain dehydrogenase/reductase family 16C member 5provided by HGNC
Primary source: HGNC:HGNC:30311
See related: Ensembl:ENSG00000170786 MIM:608989; AllianceGenome:HGNC:30311
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: RDH#2; RDHE2; EPHD-2; RDH-E2; retSDR2
Summary: This gene encodes a member of the short-chain alcohol dehydrogenase/reductase superfamily of proteins and is involved in the oxidation of retinol to retinaldehyde. The encoded protein is associated with the endoplasmic reticulum and is predicted to contain three transmembrane helices, suggesting that it is an integral membrane protein. It recognizes all-trans-retinol and all-trans-retinaldehyde as substrates and exhibits a strong preference for NAD(+)/NADH as cofactors. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]
Expression: Biased expression in skin (RPKM 15.8), esophagus (RPKM 9.7) and 7 other tissues See more
Orthologs: all
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Genomic context

Location:: 8q12.1

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	8	NC_000008.11 (56300005..56320175, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	8	NC_060932.1 (56677119..56697312, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	8	NC_000008.10 (57212564..57232734, complement)

Chromosome 8 - NC_000008.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Observational study of gene-disease association. (HuGE Navigator)
Title: The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature.
mapped to chromosome 8; may be involved in the pathogenesis of psoriasis through its critical role in retinol metabolism in keratinocyte proliferation
Title: Identification of the hRDH-E2 gene, a novel member of the SDR family, and its increased expression in psoriatic lesion.

Submit: New GeneRIF Correction

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

EBI GWAS Catalog

Description
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. EBI GWAS Catalog EBI GWAS CatalogPubMed
Hundreds of variants clustered in genomic loci and biological pathways affect human height. EBI GWAS Catalog EBI GWAS CatalogPubMed
Identification of ten loci associated with height highlights new biological pathways in human growth. EBI GWAS Catalog EBI GWAS CatalogPubMed
Many sequence variants affecting diversity of adult human height. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables RNA polymerase II-specific DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
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 protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription corepressor activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in keratinocyte proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of gene expression, epigenetic	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in retinal metabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in retinal metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in retinol metabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in retinol metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in retinol metabolic process	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of chromatin	IDA Inferred from Direct Assay more info	PubMed
colocalizes_with endoplasmic reticulum	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 lipid droplet	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
colocalizes_with plasma membrane	IDA Inferred from Direct Assay more info	PubMed
part_of transcription repressor complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: epidermal retinol dehydrogenase 2

Names: epidermal retinal dehydrogenase 2; retinal short chain dehydrogenase reductase; retinal short-chain dehydrogenase reductase 2

NP_001304978.1

EC 1.1.1.105

NP_001304979.1

EC 1.1.1.105

NP_620419.2

EC 1.1.1.105

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.

mRNA and Protein(s)

NM_001318049.2 → NP_001304978.1 epidermal retinol dehydrogenase 2 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AC103849

Consensus CDS

CCDS83296.1

UniProtKB/TrEMBL

G3V145

Related

ENSP00000431010.1, ENST00000522671.1

Conserved Domains (2) summary

cd05339
Location:42 → 280

17beta-HSDXI-like_SDR_c; human 17-beta-hydroxysteroid dehydrogenase XI-like, classical (c) SDRs

pfam00106
Location:41 → 231

adh_short; short chain dehydrogenase
NM_001318050.2 → NP_001304979.1 epidermal retinol dehydrogenase 2 isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region and an alternate exon in the 3' coding region compared to variant 1. It encodes isoform 3, which is shorter than and has a distinct C-terminus compared to isoform 1.

Source sequence(s)

AC103849

Consensus CDS

CCDS83295.1

UniProtKB/Swiss-Prot

Q8N3Y7

UniProtKB/TrEMBL

B3KT84

Related

ENSP00000379947.2, ENST00000396721.6

Conserved Domains (2) summary

cd05339
Location:42 → 240

17beta-HSDXI-like_SDR_c; human 17-beta-hydroxysteroid dehydrogenase XI-like, classical (c) SDRs

PRK05650
Location:43 → 240

PRK05650; short chain dehydrogenase; Provisional
NM_138969.4 → NP_620419.2 epidermal retinol dehydrogenase 2 isoform 2

See identical proteins and their annotated locations for NP_620419.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate exon in the 3' coding region compared to variant 1. It encodes isoform 2, which is shorter than and has a distinct C-terminus compared to isoform 1.

Source sequence(s)

AC103849

Consensus CDS

CCDS6167.1

UniProtKB/Swiss-Prot

B4DGK2, Q330K3, Q8N3Y7, Q8TDV9, Q96LX1

Related

ENSP00000307607.3, ENST00000303749.8

Conserved Domains (1) summary

cd05339
Location:42 → 284

17beta-HSDXI-like_SDR_c; human 17-beta-hydroxysteroid dehydrogenase XI-like, classical (c) SDRs