RDH10

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

Basic information

Region (hg38): 8:73294602-73325281

Links

ENSG00000121039 ∙ NCBI:157506 ∙ OMIM:607599 ∙ HGNC:19975 ∙ Uniprot:Q8IZV5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RDH10 gene.

• not_specified (24 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RDH10 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000172037.5. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			28			28
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	28	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RDH10	protein_coding	protein_coding	ENST00000240285	6	30670

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125646	0	1	125647	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.03	71	188	0.378	0.00000952	2220
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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}.
• Pathway: 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;Vitamin A and Carotenoid Metabolism;Signaling by GPCR;Signal Transduction;RA biosynthesis pathway;The canonical retinoid cycle in rods (twilight vision);retinol biosynthesis;Signaling by Retinoic Acid;Signaling by Nuclear Receptors;G alpha (i) signalling events;Visual phototransduction;the visual cycle I (vertebrates);GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.142

Intolerance Scores

• rvis_EVS: 0.39
• rvis_percentile_EVS: 75.75

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.427

Gene Damage Prediction

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

Zebrafish Information Network

• Gene name: rdh10a
• Affected structure: cardiac muscle cell
• Phenotype tag: abnormal
• Phenotype quality: increased amount

Gene ontology

• Biological process: retinoid metabolic process;metanephros development;in utero embryonic development;retinoic acid biosynthetic process;visual perception;gonad development;neural crest cell development;embryonic camera-type eye development;embryonic forelimb morphogenesis;retinol metabolic process;retinal metabolic process;ear development;nose development;embryonic viscerocranium morphogenesis;oxidation-reduction process;primary lung bud formation;bud elongation involved in lung branching;positive regulation of retinoic acid biosynthetic process
• Cellular component: nucleus;cytoplasm;endoplasmic reticulum membrane;lipid droplet;integral component of membrane;organelle membrane;cell body
• Molecular function: retinol dehydrogenase activity;NADP-retinol dehydrogenase activity