RDH10
retinol dehydrogenase 10, the group of Short chain dehydrogenase/reductase superfamily
Basic information
Region (hg38): 8:73294601-73325281
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
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.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 0 | 0 |
Variants in RDH10
This is a list of pathogenic ClinVar variants found in the RDH10 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-73295302-G-C | not specified | Uncertain significance (Feb 27, 2024) | ||
| 8-73295338-G-T | not specified | Uncertain significance (Mar 06, 2023) | ||
| 8-73295471-C-T | not specified | Uncertain significance (Dec 06, 2021) | ||
| 8-73320998-G-A | not specified | Uncertain significance (Jan 31, 2023) | ||
| 8-73321002-A-G | not specified | Uncertain significance (Feb 13, 2024) | ||
| 8-73321071-G-A | not specified | Uncertain significance (Jun 16, 2024) | ||
| 8-73322680-A-G | not specified | Uncertain significance (Dec 05, 2022) | ||
| 8-73322939-G-C | not specified | Uncertain significance (Oct 29, 2021) |
GnomAD
Source:
| 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 |
|---|---|---|---|---|---|---|
| 0.986 | 0.0141 | 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:
- 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
- loftool
- rvis_EVS
- 0.39
- rvis_percentile_EVS
- 75.75
Haploinsufficiency Scores
- pHI
- 0.294
- hipred
- Y
- hipred_score
- 0.662
- ghis
- 0.492
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 |
Mouse Genome Informatics
- Gene name
- Rdh10
- Phenotype
- vision/eye phenotype; hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; digestive/alimentary phenotype; skeleton phenotype; renal/urinary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; liver/biliary system phenotype; embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; reproductive system phenotype; growth/size/body region phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); craniofacial phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; taste/olfaction phenotype;
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