RITA1
protein-codingRBPJ interacting and tubulin associated 1
Gene summary
Enables tubulin binding activity. Involved in negative regulation of Notch signaling pathway and nuclear export. Located in centrosome; cytosol; and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]
- C12orf52
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~6.8 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 RITA1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_032848.3. 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 | 1 | 1 | ||||
| missense | 35 | 7 | 42 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 35 | 8 | 0 | 43 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_116237.1 | 2 | MANE Select | |
| Ensembl | ENSP00000449841.1 | 2 | MANE Select | |
| RefSeq | NP_001273144.1 | 3 | Standard | |
| Ensembl | ENSP00000448289.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- negative regulation of transcription by RNA polymerase II
- Notch signaling pathway
- neurogenesis
- negative regulation of Notch signaling pathway
- nuclear export
Molecular Function
- protein binding
- tubulin binding
Cellular Component
- nucleus
- cytoplasm
- centrosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000548278
- Coding exons
- 2
- Length
- 6843
- Individuals with no LoFs
- 125543
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 197
- Defined
- 125740
- p
- 0.000784
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.445 | 157 | 174 | 0.905 | 0.0000110 | 1674 |
| Missense (PolyPhen) | 42 | 43.142 | 0.97353 | 464 | ||
| Synonymous | 1.28 | 62 | 76.2 | 0.814 | 0.00000484 | 626 |
| Loss of Function | 0.564 | 4 | 5.42 | 0.738 | 3.98e-7 | 59 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00018 | rare |
| Latino/Admixed American | 0.00078 | 0.00069 | rare |
| Ashkenazi Jewish | 0.00030 | 0.00030 | rare |
| East Asian | 0.0026 | 0.0024 | notable |
| Finnish | 0.00025 | 0.00023 | rare |
| European (Non-Finnish) | 0.0010 | 0.00095 | notable |
| South Asian | 0.00020 | 0.00020 | rare |
| Other | 0.00056 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Tubulin-binding protein that acts as a negative regulator of Notch signaling pathway. Shuttles between the cytoplasm and the nucleus and mediates the nuclear export of RBPJ/RBPSUH, thereby preventing the interaction between RBPJ/RBPSUH and NICD product of Notch proteins (Notch intracellular domain), leading to down-regulate Notch-mediated transcription. May play a role in neurogenesis. {ECO:0000269|PubMed:21102556}.;
Intolerance Scores
- RVIS EVS
- 0.49
- RVIS percentile EVS
- 79.38
Essentials
- Essential (gene trap)
- N
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |