TUBD1
protein-codingtubulin delta 1, the group of Tubulins
Gene summary
Predicted to enable GTP binding activity. Predicted to be a structural constituent of cytoskeleton. Involved in microtubule cytoskeleton organization. Located in centrosome. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~33.5 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 TUBD1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_016261.4. 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 | 1 | 1 | ||||
| missense | 47 | 3 | 50 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 49 | 3 | 1 | 53 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_057345.2 | 8 | MANE Select | |
| Ensembl | ENSP00000320797.3 | 8 | MANE Select | |
| RefSeq | NP_001180538.1 | 7 | Standard | |
| RefSeq | NP_001180539.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- microtubule cytoskeleton organization
- mitotic cell cycle
- microtubule-based process
- multicellular organism development
- cell projection organization
Molecular Function
- GTPase activity
- structural constituent of cytoskeleton
- GTP binding
Cellular Component
- nucleoplasm
- cytoplasm
- centriole
- cytosol
- microtubule
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000325752
- Coding exons
- 8
- Length
- 33454
- Individuals with no LoFs
- 125682
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 63
- Defined
- 125745
- p
- 0.000251
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.535 | 216 | 239 | 0.903 | 0.0000117 | 3014 |
| Missense (PolyPhen) | 52 | 64.303 | 0.80868 | 788 | ||
| Synonymous | 0.273 | 78 | 81.1 | 0.961 | 0.00000400 | 808 |
| Loss of Function | 1.85 | 13 | 22.5 | 0.579 | 0.00000113 | 273 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00062 | 0.00062 | rare |
| Latino/Admixed American | 0.00026 | 0.00026 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00033 | 0.00033 | rare |
| Finnish | 0.000092 | 0.000092 | rare |
| European (Non-Finnish) | 0.00029 | 0.00029 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Acts as a positive regulator of hedgehog signaling and regulates ciliary function. {ECO:0000250|UniProtKB:Q9R1K7}.;
Recessive Scores
- pRec
- 0.133
Intolerance Scores
- LoFtool
- 0.754
- RVIS EVS
- -0.2
- RVIS percentile EVS
- 38.82
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.537
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | High | Medium | High |
| Cancer | High | High | High |