RDH12
retinol dehydrogenase 12, the group of Short chain dehydrogenase/reductase superfamily
Basic information
Region (hg38): 14:67701886-67734451
Links
Transcripts
Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 4.
| Transcript ID | Protein ID | Coding exons | MANE Select | MANE Plus Clinical |
|---|---|---|---|---|
ENST00000267502.3 | ENSP00000267502.3 | 7 | - | - |
ENST00000551171.6 | ENSP00000449079.1 | 7 | yes | - |
NM_000152443.3 | NP_000689656.2 | 7 | yes | - |
XM_047430965.1 | XP_047286921.1 | 7 | - | - |
Phenotypes
GenCC
Source:
- RDH12-related recessive retinopathy (Definitive), mode of inheritance: AR
- RDH12-related dominant retinopathy (Moderate), mode of inheritance: AD
- Leber congenital amaurosis 13 (Strong), mode of inheritance: AR
- Leber congenital amaurosis 13 (Strong), mode of inheritance: AD
- retinitis pigmentosa (Supportive), mode of inheritance: AD
- Leber congenital amaurosis (Supportive), mode of inheritance: AD
- Leber congenital amaurosis 13 (Definitive), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Leber congenital amaurosis 13; Retinitis pigmentosa 53 | AD/AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Ophthalmologic | 15258582; 15322982; 16269441; 17197551; 18779497; 19140180; 19840725; 20736127; 22065924 |
Loading mutation effect viewer...
ClinVar
This is a list of variants' phenotypes submitted to
- Leber_congenital_amaurosis_13 (561 variants)
- Leber_congenital_amaurosis (110 variants)
- Retinal_dystrophy (63 variants)
- not_provided (45 variants)
- Retinitis_pigmentosa (32 variants)
- Inborn_genetic_diseases (29 variants)
- not_specified (18 variants)
- RDH12-related_disorder (12 variants)
- Macular_dystrophy (7 variants)
- Retinitis_Pigmentosa,_Recessive (5 variants)
- Cone-rod_dystrophy (4 variants)
- Retinitis_pigmentosa_53 (2 variants)
- Abnormality_of_the_eye (2 variants)
- Stargardt_disease (1 variants)
- Macular_dystrophy_with_or_without_cone_dysfunction (1 variants)
- Optic_atrophy (1 variants)
- See_cases (1 variants)
- Autosomal_dominant_retinitis_pigmentosa (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RDH12 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000152443.3. 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 | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 169 | 3 | 174 | ||
| missense | 13 | 62 | 181 | 3 | 259 | |
| nonsense | 14 | 7 | 21 | |||
| start loss | 2 | 2 | ||||
| frameshift | 25 | 22 | 1 | 48 | ||
| splice donor/acceptor (+/-2bp) | 10 | 12 | 22 | |||
| Total | 62 | 103 | 186 | 172 | 3 |
Highest pathogenic variant AF is 0.00018009928
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RDH12 | protein_coding | protein_coding | ENST00000551171 | 7 | 32567 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 125656 | 0 | 92 | 125748 | 0.000366 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.142 | 182 | 177 | 1.03 | 0.0000110 | 2018 |
| Missense in Polyphen | 86 | 78.487 | 1.0957 | 924 | ||
| Synonymous | -1.33 | 91 | 76.3 | 1.19 | 0.00000463 | 683 |
| Loss of Function | 0.292 | 14 | 15.2 | 0.919 | 0.00000113 | 156 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000866 | 0.000865 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000110 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000553 | 0.000545 |
| Middle Eastern | 0.000110 | 0.000109 |
| South Asian | 0.0000980 | 0.0000980 |
| Other | 0.000491 | 0.000489 |
dbNSFP
Source:
- Function
- FUNCTION: Exhibits an oxidoreductive catalytic activity towards retinoids. Most efficient as an NADPH-dependent retinal reductase. Displays high activity toward 9-cis and all-trans-retinol. Also involved in the metabolism of short-chain aldehydes. No steroid dehydrogenase activity detected. Might be the key enzyme in the formation of 11-cis-retinal from 11-cis-retinol during regeneration of the cone visual pigments. {ECO:0000269|PubMed:12226107}.;
- Disease
- DISEASE: Retinitis pigmentosa 53 (RP53) [MIM:612712]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269|PubMed:19140180, ECO:0000269|PubMed:19956407}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Retinol metabolism - Homo sapiens (human);Vitamin A Deficiency;Retinol Metabolism;Vitamin A and Carotenoid Metabolism;Signaling by GPCR;Signal Transduction;The canonical retinoid cycle in rods (twilight vision);Visual signal transduction: Rods;retinol biosynthesis;G alpha (i) signalling events;Visual phototransduction;the visual cycle I (vertebrates);GPCR downstream signalling;Visual signal transduction: Cones
(Consensus)
Recessive Scores
- pRec
- 0.182
Intolerance Scores
- loftool
- 0.289
- rvis_EVS
- -0.65
- rvis_percentile_EVS
- 16.44
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.896
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Gene ontology
- Biological process
- retinoid metabolic process;visual perception;retinol metabolic process;photoreceptor cell maintenance;response to stimulus;oxidation-reduction process
- Cellular component
- photoreceptor inner segment membrane
- Molecular function
- retinol dehydrogenase activity;protein binding;NADP-retinol dehydrogenase activity