SDR16C5
protein-codingshort chain dehydrogenase/reductase family 16C member 5, the group of Short chain dehydrogenase/reductase superfamily
Gene summary
This gene encodes a member of the short-chain alcohol dehydrogenase/reductase superfamily of proteins and is involved in the oxidation of retinol to retinaldehyde. The encoded protein is associated with the endoplasmic reticulum and is predicted to contain three transmembrane helices, suggesting that it is an integral membrane protein. It recognizes all-trans-retinol and all-trans-retinaldehyde as substrates and exhibits a strong preference for NAD(+)/NADH as cofactors. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~20.8 kbGenCC 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 SDR16C5 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_138969.4. 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 | 2 | 2 | ||||
| missense | 46 | 4 | 50 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 49 | 4 | 0 | 53 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_620419.2 | 6 | MANE Select | |
| Ensembl | ENSP00000307607.3 | 6 | MANE Select | |
| RefSeq | NP_001304978.1 | 6 | Standard | |
| RefSeq | NP_001304979.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Retinol metabolism - Homo sapiens (human)
- Vitamin A and Carotenoid Metabolism
- Signal Transduction
- RA biosynthesis pathway
- retinoate biosynthesis I
Biological Process
- negative regulation of transcription by RNA polymerase II
- positive regulation of histone deacetylation
- negative regulation of histone acetylation
- retinol metabolic process
- retinal metabolic process
Molecular Function
- DNA-binding transcription factor activity
- retinol dehydrogenase activity
- transcription factor binding
- activating transcription factor binding
Cellular Component
- chromatin
- nucleus
- endoplasmic reticulum
- endoplasmic reticulum membrane
- lipid droplet
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000303749
- Coding exons
- 6
- Length
- 20767
- Individuals with no LoFs
- 125672
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 76
- Defined
- 125748
- p
- 0.000302
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.261 | 174 | 165 | 1.06 | 0.00000826 | 2017 |
| Missense (PolyPhen) | 70 | 65.587 | 1.0673 | 795 | ||
| Synonymous | 0.178 | 61 | 62.8 | 0.971 | 0.00000351 | 592 |
| Loss of Function | 1.86 | 5 | 11.9 | 0.419 | 5.01e-7 | 169 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00017 | 0.00017 | rare |
| Ashkenazi Jewish | 0.00020 | 0.00020 | rare |
| East Asian | 0.0021 | 0.0018 | notable |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000079 | 0.000079 | rare |
| South Asian | 0.00082 | 0.00082 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Oxidoreductase with strong preference for NAD. Active in both the oxidative and reductive directions. Oxidizes all-trans- retinol in all-trans-retinaldehyde. No activity was detected with 11-cis-retinol or 11-cis-retinaldehyde as substrates with either NAD(+)/NADH or NADP(+)/NADPH. {ECO:0000269|PubMed:18926804}.;
Recessive Scores
- pRec
- 0.0803
Intolerance Scores
- RVIS EVS
- 0.1
- RVIS percentile EVS
- 61.49
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.300
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |