RDH16

protein-coding

retinol dehydrogenase 16, the group of Short chain dehydrogenase/reductase superfamily

Gene summary

Enables all-trans-retinol dehydrogenase (NAD+) activity; androstan-3-alpha,17-beta-diol dehydrogenase (NAD+) activity; and androsterone dehydrogenase [NAD(P)+] activity. Involved in steroid metabolic process. Predicted to be located in endoplasmic reticulum lumen and endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_003708.5

Inheritance

—

ClinVar variants

U:63B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.95

Max pathogenic AF

—

Genomic locus

chr12:56,951,431-56,959,374

External References & Databases

Ensembl (ENSG00000139547)

Transcript & Mutation Effects

hg38 • Region Span ~7.9 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 RDH16 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 61

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003708.5. 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			1 clinvar			1
missense			57 clinvar	4 clinvar	1 clinvar	62
nonsense			1 clinvar			1
start loss						0
frameshift					1 clinvar	1
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	63	4	2	69

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003708.5	RefSeq	NP_003699.3	4	MANE Select
ENST00000398138.5	Ensembl	ENSP00000381206.3	4	MANE Select
NM_001320108.2	RefSeq	NP_001307037.1	3	Standard
ENST00000869320.1	Ensembl	ENSP00000539379.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Retinol metabolism - Homo sapiens (human)
Vitamin A Deficiency
Retinol Metabolism
Signaling by GPCR
Signal Transduction

Biological Process

lipid metabolic process
electron transport chain

Molecular Function

retinol dehydrogenase activity
electron transfer activity

Cellular Component

endoplasmic reticulum membrane
integral component of membrane
organelle membrane
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000398138
Coding exons: 4
Length: 7940
Individuals with no LoFs: 124936
Homozygous LoFs: 10
Heterozygous LoFs: 800
Defined: 125746
p: 0.00323

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0955	189	185	1.02	0.0000111	2037
Missense (PolyPhen)		56	54.851	1.0209		653
Synonymous	0.837	71	80.6	0.881	0.00000508	662
Loss of Function	0.142	10	10.5	0.953	5.43e-7	122

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00044	0.00043	rare
Latino/Admixed American	0.0072	0.0072	notable
Ashkenazi Jewish	0.0048	0.0048	notable
East Asian	0.026	0.025	notable
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00016	0.00015	rare
South Asian	0.00089	0.00085	rare
Other	0.0012	0.0011	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Oxidoreductase with a preference for NAD. Oxidizes all- trans-retinol and 13-cis-retinol to the corresponding aldehydes. Has higher activity towards CRBP-bound retinol than with free retinol. Oxidizes 3-alpha-hydroxysteroids. Oxidizes androstanediol and androsterone to dihydrotestosterone and androstanedione. Can also catalyze the reverse reaction. {ECO:0000269|PubMed:10329026, ECO:0000269|PubMed:12534290, ECO:0000269|PubMed:9677409}.;

Intolerance Scores

LoFtool: 0.281
RVIS EVS: -0.36
RVIS percentile EVS: 29.16

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.180

Gene Damage Prediction

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