RDH10

protein-coding

retinol dehydrogenase 10, the group of Short chain dehydrogenase/reductase superfamily

Gene summary

This gene encodes a retinol dehydrogenase, which converts all-trans-retinol to all-trans-retinal, with preference for NADP as a cofactor. Studies in mice suggest that this protein is essential for synthesis of embryonic retinoic acid and is required for limb, craniofacial, and organ development. [provided by RefSeq, Dec 2011]

MANE transcript

NM_172037.5

Inheritance

—

ClinVar variants

U:30

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr8:73,294,602-73,325,281

External References & Databases

Ensembl (ENSG00000121039)

Transcript & Mutation Effects

hg38 • Region Span ~30.7 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 RDH10 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 26

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_172037.5. 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						0
missense			30 clinvar			30
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	30	0	0	30

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_172037.5	RefSeq	NP_742034.1	6	MANE Select
ENST00000240285.10	Ensembl	ENSP00000240285.5	6	MANE Select
ENST00000519380.1	Ensembl	ENSP00000428132.1	5	Standard
ENST00000519380.2	Ensembl	ENSP00000428132.1	5	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
rdh10a	Danio rerio	Structure: cardiac muscle cell Quality: increased amount abnormal

Gene / Model

Organism

Observed Phenotype

rdh10a

Danio rerio

Structure: cardiac muscle cell

Quality: increased amount

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Retinol metabolism - Homo sapiens (human)
miR-targeted genes in epithelium - TarBase
miR-targeted genes in leukocytes - TarBase
miR-targeted genes in lymphocytes - TarBase
miR-targeted genes in muscle cell - TarBase

Biological Process

retinoid metabolic process
metanephros development
in utero embryonic development
retinoic acid biosynthetic process
visual perception

Molecular Function

retinol dehydrogenase activity
NADP-retinol dehydrogenase activity

Cellular Component

nucleus
cytoplasm
endoplasmic reticulum membrane
lipid droplet
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000240285
Coding exons: 6
Length: 30670
Individuals with no LoFs: 125646
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 125647
p: 0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.03	71	188	0.378	0.00000952	2220
Missense (PolyPhen)		8	65.428	0.12227		766
Synonymous	1.47	57	72.9	0.781	0.00000392	671
Loss of Function	3.33	0	12.9	0.00	6.31e-7	162

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Retinol dehydrogenase with a clear preference for NADP. Converts all-trans-retinol to all-trans-retinal. Has no detectable activity towards 11-cis-retinol, 9-cis-retinol and 13-cis-retinol. {ECO:0000269|PubMed:12407145}.;

Recessive Scores

pRec: 0.142

Intolerance Scores

RVIS EVS: 0.39
RVIS percentile EVS: 75.75

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.427

Gene Damage Prediction

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