RDH13

protein-coding

retinol dehydrogenase 13, the group of Short chain dehydrogenase/reductase superfamily

Gene summary

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. [provided by RefSeq, Mar 2009]

MANE transcript

NM_001145971.2

Inheritance

—

ClinVar variants

U:76B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.27

Max pathogenic AF

—

Genomic locus

chr19:55,039,108-55,071,291

External References & Databases

Ensembl (ENSG00000160439)

Transcript & Mutation Effects

hg38 • Region Span ~32.2 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 RDH13 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 73

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001145971.2. 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				3 clinvar	1 clinvar	4
missense			75 clinvar	2 clinvar		77
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	76	5	1	82

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001145971.2	RefSeq	NP_001139443.1	7	MANE Select
ENST00000415061.8	Ensembl	ENSP00000391121.2	7	MANE Select
NM_138412.4	RefSeq	NP_612421.1	5	Standard
ENST00000291892.10	Ensembl	ENSP00000291892.6	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Signal Transduction
RA biosynthesis pathway
Signaling by Retinoic Acid
Signaling by Nuclear Receptors

Biological Process

response to high light intensity
retina layer formation
eye photoreceptor cell development
retinol metabolic process
oxidation-reduction process

Molecular Function

NADP-retinol dehydrogenase activity

Cellular Component

mitochondrial inner membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000415061
Coding exons: 7
Length: 32184
Individuals with no LoFs: 124684
Homozygous LoFs: 0
Heterozygous LoFs: 114
Defined: 124798
p: 0.000457

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.586	232	208	1.11	0.0000135	2094
Missense (PolyPhen)		78	79.462	0.98161		751
Synonymous	-0.455	101	95.3	1.06	0.00000689	688
Loss of Function	-0.956	18	14.1	1.27	8.55e-7	149

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000066	0.000065	rare
Latino/Admixed American	0.00061	0.00061	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0018	0.0018	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.00034	0.00033	rare
South Asian	0.00066	0.00065	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Does not exhibit retinol dehydrogenase (RDH) activity in vitro.;

Intolerance Scores

LoFtool: 0.318
RVIS EVS: -0.04
RVIS percentile EVS: 50.45

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.973

Gene Damage Prediction

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