RDH13

Summary

RDH13 (retinol dehydrogenase 13, HGNC:19978) is a protein-coding gene on chromosome 19q13.42, encoding Retinol dehydrogenase 13 (Q8NBN7). Retinol dehydrogenase with a clear preference for NADP.

This gene encodes a mitochondrial short-chain dehydrogenase/reductase, which catalyzes the reduction and oxidation of retinoids. The encoded enzyme may function in retinoic acid production and may also protect the mitochondria against oxidative stress. Alternatively spliced transcript variants have been described.

Source: NCBI Gene 112724 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 90 total
• MANE Select transcript: NM_001145971

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19978
Approved symbol	RDH13
Name	retinol dehydrogenase 13
Location	19q13.42
Locus type	gene with protein product
Status	Approved
Aliases	SDR7C3
Ensembl gene	ENSG00000160439
Ensembl biotype	protein_coding
Entrez	112724

Gene structure

Transcript identifiers

Ensembl transcripts: 23 — 14 protein_coding_CDS_not_defined, 5 protein_coding, 4 nonsense_mediated_decay

ENST00000291892, ENST00000396247, ENST00000415061, ENST00000586331, ENST00000586945, ENST00000587026, ENST00000587046, ENST00000587373, ENST00000587721, ENST00000588306, ENST00000588941, ENST00000589197, ENST00000589305, ENST00000589605, ENST00000590349, ENST00000591023, ENST00000591603, ENST00000591868, ENST00000591960, ENST00000592423, ENST00000592573, ENST00000593134, ENST00000610356

RefSeq mRNA: 2 — MANE Select: NM_001145971 NM_001145971, NM_138412

CCDS: CCDS42627, CCDS54320

Canonical transcript exons

ENST00000415061 — 7 exons

Exon	Start	End
ENSE00002799885	55062968	55063148
ENSE00003539539	55059157	55059275
ENSE00003563668	55048329	55048541
ENSE00003574699	55048659	55048763
ENSE00003658962	55047387	55047488
ENSE00003670873	55056653	55056808
ENSE00003850062	55044316	55045309

Expression profiles

Bgee: expression breadth ubiquitous, 140 present calls, max score 95.79.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.3737 / max 297.9161, expressed in 1692 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
182677	13.8343	1679
182679	1.4397	400
182676	0.6445	375
182678	0.3424	144
182680	0.0991	48
182681	0.0137	5

Top tissues by expression

140 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
lower esophagus mucosa	UBERON:0035834	95.79	gold quality
skin of leg	UBERON:0001511	94.42	gold quality
zone of skin	UBERON:0000014	94.26	gold quality
skin of abdomen	UBERON:0001416	94.00	gold quality
esophagus mucosa	UBERON:0002469	92.76	gold quality
mucosa of transverse colon	UBERON:0004991	90.02	gold quality
apex of heart	UBERON:0002098	89.64	gold quality
placenta	UBERON:0001987	89.14	gold quality
minor salivary gland	UBERON:0001830	88.77	gold quality
saliva-secreting gland	UBERON:0001044	88.68	gold quality
heart left ventricle	UBERON:0002084	88.46	gold quality
vagina	UBERON:0000996	88.44	gold quality
body of stomach	UBERON:0001161	87.89	gold quality
right lobe of thyroid gland	UBERON:0001119	87.59	gold quality
transverse colon	UBERON:0001157	87.45	gold quality
left lobe of thyroid gland	UBERON:0001120	87.08	gold quality
esophagus	UBERON:0001043	86.87	gold quality
thyroid gland	UBERON:0002046	86.87	gold quality
stomach	UBERON:0000945	86.66	gold quality
metanephros cortex	UBERON:0010533	86.51	gold quality
duodenum	UBERON:0002114	86.41	gold quality
heart	UBERON:0000948	86.06	gold quality
body of pancreas	UBERON:0001150	85.51	gold quality
right atrium auricular region	UBERON:0006631	85.46	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.20	gold quality
pituitary gland	UBERON:0000007	85.05	gold quality
cortex of kidney	UBERON:0001225	84.88	gold quality
rectum	UBERON:0001052	84.59	gold quality
fundus of stomach	UBERON:0001160	84.24	gold quality
ectocervix	UBERON:0012249	84.20	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-GEOD-124858	no	30.37
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting RDH13, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-4760-5P	99.80	69.88	1619
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-24-3P	99.59	69.97	1934
HSA-MIR-1915-3P	99.58	66.79	1988
HSA-MIR-17-3P	99.55	66.77	1311
HSA-MIR-1252-3P	99.55	67.71	2862
HSA-MIR-4293	99.22	65.46	1263
HSA-MIR-4726-3P	98.49	63.89	1385
HSA-MIR-376A-5P	97.70	65.61	863

Literature-anchored findings (GeneRIF, showing 1)

• RDH13 exhibits a wide tissue distribution and, by contrast with other members of the RDH11-like group of short-chain dehydrogenases/reductases, is a mitochondrial rather than a microsomal protein. (PMID:18039331)

Cross-species orthologs

8 orthologs

Organism	Symbol	Gene ID
mus_musculus	Rdh13	ENSMUSG00000008435
rattus_norvegicus	Rdh13	ENSRNOG00000027919
caenorhabditis_elegans		WBGENE00000971
caenorhabditis_elegans		WBGENE00000972
caenorhabditis_elegans		WBGENE00010762
caenorhabditis_elegans		WBGENE00017082
caenorhabditis_elegans		WBGENE00017131
caenorhabditis_elegans		WBGENE00017971

Paralogs (4): KDSR (ENSG00000119537), DHRS13 (ENSG00000167536), DHRSX (ENSG00000169084), RDH14 (ENSG00000240857)

Protein

Protein identifiers

Retinol dehydrogenase 13 — Q8NBN7 (reviewed: Q8NBN7)

Alternative names: Short chain dehydrogenase/reductase family 7C member 3

All UniProt accessions (5): Q8NBN7, G8JLA1, K7EMY5, K7EQB5, K7ERV1

UniProt curated annotations — full annotation on UniProt →

Function. Retinol dehydrogenase with a clear preference for NADP. Oxidizes all-trans-retinol, but seems to reduce all-trans-retinal with much higher efficiency. Has no activity toward steroids.

Subcellular location. Mitochondrion inner membrane.

Tissue specificity. Widely expressed. In the retina, detected in the inner segment of the photoreceptor cells. Weak signals are observed in a small population of inner nuclear neurons and the inner plexiform layer.

Pathway. Cofactor metabolism; retinol metabolism.

Similarity. Belongs to the short-chain dehydrogenases/reductases (SDR) family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8NBN7-1	1	yes
Q8NBN7-2	2

RefSeq proteins (2): NP_001139443, NP_612421 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002347	SDR_fam	Family
IPR020904	Sc_DH/Rdtase_CS	Conserved_site
IPR036291	NAD(P)-bd_dom_sf	Homologous_superfamily

Pfam: PF00106

Enzyme classification (BRENDA):

• EC 1.1.1.300 — NADP-retinol dehydrogenase (BRENDA: 11 organisms, 101 substrates, 7 inhibitors, 67 Km, 12 kcat entries)

Substrate kinetics (BRENDA)

14 substrates with measured Km, best-characterized 14. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
ALL-TRANS-RETINAL	0.0001–0.5	19
NADPH	0.0005–0.23	10
NADP+	0.0004–0.8	9
ALL-TRANS-RETINOL	0.0006–1.3	6
NADH	2.22–1300	4
ALL-TRANS-3-HYDROXYRETINAL	0.0032–0.0044	3
ESTRONE	0.0096–0.0307	3
NAD+	0.004–680	3
9-CIS-RETINAL	0.0001–0.19	2
RETINAL	0.007–0.13	2
11-CIS-RETINAL	0.0001	1
11-CIS-RETINOL	0.0016	1
13-CIS-RETINAL	0.62	1
9-CIS-RETINOL	0.0016	1

Catalyzed reactions (Rhea), 1 shown:

• all-trans-retinol + NADP(+) = all-trans-retinal + NADPH + H(+) (RHEA:25033)

UniProt features (9 total): binding site 2, modified residue 2, initiator methionine 1, chain 1, active site 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NBN7-F1	89.42	0.75

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 200 (proton acceptor)

Ligand- & substrate-binding residues (2): 45–51; 174

Post-translational modifications (2): 2, 323

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-5365859	RA biosynthesis pathway

MSigDB gene sets: 128 (showing top): GOBP_REGULATION_OF_HORMONE_LEVELS, GOBP_NEUROGENESIS, GOBP_RETINOL_METABOLIC_PROCESS, GOBP_NEURAL_RETINA_DEVELOPMENT, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, GOBP_EYE_PHOTORECEPTOR_CELL_DIFFERENTIATION, BILD_E2F3_ONCOGENIC_SIGNATURE, GOBP_PHOTORECEPTOR_CELL_DEVELOPMENT, GOBP_RESPONSE_TO_RADIATION, GOCC_MITOCHONDRIAL_ENVELOPE, GOBP_RETINAL_METABOLIC_PROCESS, GARY_CD5_TARGETS_DN, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, GOBP_RETINA_LAYER_FORMATION, GOBP_LIPID_METABOLIC_PROCESS

GO Biological Process (6): response to high light intensity (GO:0009644), retina layer formation (GO:0010842), eye photoreceptor cell development (GO:0042462), retinal metabolic process (GO:0042574), lipid metabolic process (GO:0006629), retinol metabolic process (GO:0042572)

GO Molecular Function (2): all-trans-retinol dehydrogenase (NADP+) activity (GO:0052650), oxidoreductase activity (GO:0016491)

GO Cellular Component (3): mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Signaling by Retinoic Acid	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
retinoid metabolic process	2
olefinic compound metabolic process	2
response to light intensity	1
neural retina development	1
anatomical structure formation involved in morphogenesis	1
retina morphogenesis in camera-type eye	1
eye photoreceptor cell differentiation	1
photoreceptor cell development	1
aldehyde metabolic process	1
primary metabolic process	1
primary alcohol metabolic process	1
hormone metabolic process	1
alcohol dehydrogenase (NADP+) activity	1
retinol metabolic process	1
catalytic activity	1
cytoplasm	1
intracellular membrane-bounded organelle	1
organelle inner membrane	1
mitochondrial membrane	1
cellular anatomical structure	1

Protein interactions and networks

STRING

3349 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RDH13	BCO2	Q9BYV7	500
RDH13	CYP3A5	P20815	492
RDH13	LRAT	O95237	440
RDH13	PPP1R12C	Q9BZL4	427
RDH13	SYT5	O00445	417
RDH13	SORD	Q00796	416
RDH13	BCO1	Q9HAY6	401
RDH13	TFPT	P0C1Z6	401
RDH13	ZNF579	Q8NAF0	398
RDH13	OR5M11	Q96RB7	395
RDH13	THNSL1	Q8IYQ7	373
RDH13	ZNF584	Q8IVC4	371
RDH13	UQCC5	Q8WVI0	362
RDH13	CYP26A1	O43174	359
RDH13	LINC02914	Q52M58	355

IntAct

94 interactions, top by confidence:

A	B	Type	Score
CCM2	KRIT1	psi-mi:“MI:0914”(association)	0.960
GBA2	ILVBL	psi-mi:“MI:0914”(association)	0.640
LSM5	LSM1	psi-mi:“MI:0914”(association)	0.640
NRAS	RGL2	psi-mi:“MI:0914”(association)	0.550
SLC15A1	METTL15	psi-mi:“MI:0914”(association)	0.530
EMILIN1	METTL15	psi-mi:“MI:0914”(association)	0.530
DEFA5	NUDT19	psi-mi:“MI:0914”(association)	0.530
NT5E	SCAMP1	psi-mi:“MI:0914”(association)	0.530
ALPI	ALPP	psi-mi:“MI:0914”(association)	0.530
PCDHB5	RPL23	psi-mi:“MI:0914”(association)	0.530
ZSCAN18	ZNF24	psi-mi:“MI:0914”(association)	0.530
PON1	PON3	psi-mi:“MI:0914”(association)	0.530
CUEDC1	TOM1	psi-mi:“MI:0914”(association)	0.530
ZNF44	RDH13	psi-mi:“MI:0915”(physical association)	0.400
CYP3A5	RDH13	psi-mi:“MI:0915”(physical association)	0.370
PSKH1	RDH13	psi-mi:“MI:0915”(physical association)	0.370
CFTR	RDH13	psi-mi:“MI:0915”(physical association)	0.370
GADD45G	RDH13	psi-mi:“MI:0915”(physical association)	0.370
SAMHD1	B2M	psi-mi:“MI:0914”(association)	0.350
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350
ATP6V0D1		psi-mi:“MI:0914”(association)	0.350
PROSER2	VWA8	psi-mi:“MI:0914”(association)	0.350
SLC39A12	POM121C	psi-mi:“MI:0914”(association)	0.350

BioGRID (102): RDH13 (Affinity Capture-MS), RDH13 (Affinity Capture-MS), RDH13 (Affinity Capture-MS), RDH13 (Affinity Capture-MS), RDH13 (Affinity Capture-MS), RDH13 (Affinity Capture-MS), DDOST (Co-fractionation), KDSR (Co-fractionation), RDH13 (Co-fractionation), RDH13 (Co-fractionation), RDH13 (Co-fractionation), RPN1 (Co-fractionation), RPN2 (Co-fractionation), RDH13 (Affinity Capture-MS), RDH13 (Affinity Capture-MS)

ESM2 similar proteins: A0A078IS66, A0A078ISJ6, A0A0B6VQ48, A0A1V0QS34, A0A2H3CZZ2, A0AAW1NHX6, A2RVM0, A4UHT7, A5PJJ7, B2X050, B8A5W4, G9N4A9, O17795, O74959, P16232, P40579, P40580, P59837, P70385, Q05A13, Q071N0, Q08651, Q17703, Q17704, Q4JK73, Q5F389, Q5NVG2, Q5R9W5, Q5ZJG8, Q6AYS8, Q6P3L6, Q6QA32, Q6RVV4, Q7SHI2, Q7TQA3, Q7Z5P4, Q8BYK4, Q8CEE7, Q8N3Y7, Q8NBN7

Diamond homologs: A0A017SEY2, A0A023I4F1, A0A078IS66, A0A078ISJ6, A0A0U1LQE2, A0A0U5CNP2, A0A1B7YCL6, A0A1V0QS34, A0A1V6PAN1, A0A223HDI5, A0A2H3CNT9, A0A2H3D905, A0A443HJZ3, A0A482ND39, A0A823A767, A0PJE2, A2RVM0, A6QP05, B2X050, B6H062, B8A5W4, C8VI80, D7UTD0, G1XTZ5, I1RL15, O32291, O74959, P0DXW2, P16152, P19871, P21218, P35320, P40747, P47727, P50163, P51657, P59837, Q01289, Q03326, Q08651

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

90 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	72
Likely benign	5
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1136 predictions. Top by Δscore:

Variant	Effect	Δscore
19:55045308:CC:C	acceptor_gain	1.0000
19:55045309:CC:C	acceptor_gain	1.0000
19:55045310:C:CC	acceptor_gain	1.0000
19:55047382:CTCA:C	donor_loss	1.0000
19:55047383:TCA:T	donor_loss	1.0000
19:55047384:CACC:C	donor_loss	1.0000
19:55047385:A:AC	donor_gain	1.0000
19:55047385:A:C	donor_loss	1.0000
19:55047386:C:CC	donor_gain	1.0000
19:55047484:AGAGC:A	acceptor_gain	1.0000
19:55047485:GAGC:G	acceptor_gain	1.0000
19:55047486:AGC:A	acceptor_gain	1.0000
19:55047486:AGCCT:A	acceptor_loss	1.0000
19:55047487:GC:G	acceptor_gain	1.0000
19:55047487:GCC:G	acceptor_loss	1.0000
19:55047488:CC:C	acceptor_gain	1.0000
19:55047489:C:CC	acceptor_gain	1.0000
19:55047489:C:T	acceptor_gain	1.0000
19:55047490:T:C	acceptor_loss	1.0000
19:55048323:CCGTA:C	donor_loss	1.0000
19:55048324:CGTA:C	donor_loss	1.0000
19:55048325:GTAC:G	donor_loss	1.0000
19:55048326:TACC:T	donor_loss	1.0000
19:55048327:A:C	donor_loss	1.0000
19:55048328:C:CT	donor_loss	1.0000
19:55048346:AGCT:A	donor_gain	1.0000
19:55048347:G:C	donor_gain	1.0000
19:55048524:T:C	acceptor_gain	1.0000
19:55048524:T:TC	acceptor_gain	1.0000
19:55048539:GACC:G	acceptor_loss	1.0000

AlphaMissense

2130 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:55048378:G:C	S203R	0.996
19:55048378:G:T	S203R	0.996
19:55048380:T:G	S203R	0.996
19:55048379:C:A	S203I	0.994
19:55048389:A:G	Y200H	0.994
19:55047443:G:A	T235I	0.992
19:55048735:G:C	N123K	0.992
19:55048735:G:T	N123K	0.992
19:55045206:G:C	F288L	0.991
19:55045206:G:T	F288L	0.991
19:55045208:A:G	F288L	0.991
19:55048534:A:C	F151L	0.991
19:55048534:A:T	F151L	0.991
19:55048536:A:G	F151L	0.991
19:55045131:A:C	S313R	0.990
19:55045131:A:T	S313R	0.990
19:55045133:T:G	S313R	0.990
19:55048373:A:G	L205P	0.990
19:55048484:C:G	R168P	0.990
19:55048666:G:C	N146K	0.990
19:55048666:G:T	N146K	0.990
19:55045267:G:T	A268D	0.989
19:55048469:G:C	S173W	0.989
19:55047461:T:C	H229R	0.988
19:55048375:C:A	K204N	0.988
19:55048375:C:G	K204N	0.988
19:55048376:T:G	K204T	0.988
19:55059189:C:T	G51E	0.988
19:55059190:C:A	G51W	0.988
19:55059219:A:T	V41D	0.987

dbSNP variants (sampled 300 via entrez): RS1000059137 (19:55044071 C>T), RS1000087297 (19:55069603 T>A), RS1000118475 (19:55069854 G>A), RS1000211189 (19:55053181 G>T), RS1000338315 (19:55044496 C>A,G), RS1000384372 (19:55067407 G>A), RS1000410375 (19:55043916 G>A), RS1000465830 (19:55047221 C>G,T), RS1000547939 (19:55040908 C>T), RS1000627854 (19:55059274 C>A), RS1000644972 (19:55051814 C>G,T), RS1000712530 (19:55052975 T>A,C), RS1000753909 (19:55047714 A>G), RS1000787703 (19:55060086 G>A), RS1000991113 (19:55066454 CCTCTCTCTTCCT>C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST90002395_422	Mean platelet volume	1.000000e-09
GCST90002401_299	Platelet distribution width	2.000000e-12

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007984	platelet component distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression, affects cotreatment	3
Benzo(a)pyrene	affects methylation	2
aristolochic acid I	increases expression	1
bisphenol F	increases expression	1
sodium arsenate	decreases expression	1
sodium arsenite	decreases expression	1
zinc chromate	increases abundance, affects expression	1
manganese chloride	increases abundance, decreases expression	1
benzo(e)pyrene	decreases methylation	1
di-n-butylphosphoric acid	affects expression	1
chromium hexavalent ion	affects expression, increases abundance	1
bisphenol S	decreases expression, affects cotreatment	1
Bortezomib	increases expression	1
Coumestrol	decreases expression	1
Dichlorodiphenyl Dichloroethylene	increases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Lead	decreases expression	1
Manganese	decreases expression, increases abundance	1
Methapyrilene	decreases methylation	1
NADP	affects binding, increases activity	1
Oxygen	increases expression	1
Plant Extracts	decreases expression	1
Smoke	decreases expression	1
Testosterone	increases expression	1
Valproic Acid	affects expression	1
1-Methyl-3-isobutylxanthine	decreases expression, affects cotreatment	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1
beta-Naphthoflavone	decreases expression	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_TI68	HAP1 RDH13 (-) 1	Cancer cell line	Male
CVCL_XS20	HAP1 RDH13 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.