RIDA
protein-codingreactive intermediate imine deaminase A homolog
Gene summary
Enables mRNA binding activity. Involved in mRNA catabolic process and mRNA destabilization. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Jul 2025]
- HRSP12
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~14.8 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 RIDA variants in ClinVar
No annotated ClinVar phenotypes.
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_005836.3. 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 | 0 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 3 | 0 | 0 | 3 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005827.1 | 6 | MANE Select | |
| Ensembl | ENSP00000254878.3 | 6 | MANE Select | |
| Ensembl | ENSP00000428596.1 | 6 | Standard | |
| Ensembl | ENSP00000430482.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Metabolism of amino acids and derivatives
- Metabolism
- Threonine catabolism
Biological Process
- kidney development
- brain development
- negative regulation of translation
- L-threonine catabolic process to glycine
- lung development
Molecular Function
- RNA binding
- endoribonuclease activity, producing 3'-phosphomonoesters
- deaminase activity
- long-chain fatty acid binding
- protein homodimerization activity
Cellular Component
- nucleus
- cytoplasm
- mitochondrial matrix
- peroxisome
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000254878
- Coding exons
- 6
- Length
- 14898
- Individuals with no LoFs
- 125724
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 13
- Defined
- 125737
- p
- 0.0000517
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.0945 | 71 | 73.3 | 0.969 | 0.00000342 | 875 |
| Missense (PolyPhen) | 16 | 18.609 | 0.85981 | 273 | ||
| Synonymous | 1.32 | 17 | 25.5 | 0.667 | 0.00000117 | 276 |
| Loss of Function | 1.62 | 3 | 7.94 | 0.378 | 3.34e-7 | 100 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00049 | 0.00049 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000044 | 0.000044 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes the hydrolytic deamination of enamine/imine intermediates that form during the course of normal metabolism. May facilitate the release of ammonia from these potentially toxic reactive metabolites, reducing their impact on cellular components. It may act on enamine/imine intermediates formed by several types of pyridoxal-5'-phosphate-dependent dehydratases including L-threonine dehydratase. {ECO:0000269|PubMed:20817725, ECO:0000269|PubMed:22094463}.;
Recessive Scores
- pRec
- 0.167
Intolerance Scores
- RVIS EVS
- -0.05
- RVIS percentile EVS
- 49.39
Essentials
- Essential (gene trap)
- N