TUBA4A
protein-codingtubulin alpha 4a, the group of Tubulins
Gene summary
Microtubules of the eukaryotic cytoskeleton perform essential and diverse functions and are composed of a heterodimer of alpha and beta tubulin. The genes encoding these microtubule constituents are part of the tubulin superfamily, which is composed of six distinct families. Genes from the alpha, beta and gamma tubulin families are found in all eukaryotes. The alpha and beta tubulins represent the major components of microtubules, while gamma tubulin plays a critical role in the nucleation of microtubule assembly. There are multiple alpha and beta tubulin genes and they are highly conserved among and between species. This gene encodes an alpha tubulin that is a highly conserved homolog of a rat testis-specific alpha tubulin. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2013]
- TUBA1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~28.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0979231
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0979231
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0014531
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0979230
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0019952
Submitter: PanelApp Australia
Inheritance Pattern: Unknown
Disease ID:MONDO:0014531
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0014531
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0014531
Submitter: ClinGen
TUBA4A was first reported in relation to autosomal dominant amyotrophic lateral sclerosis 22 (ALS) in 2014 (Smith BN, et al., 2014, PMID: 25374358). TUBA4A encodes an α-tubulin subunit, which together with β-tubulin constitutes the tubulin heterodimer, the building block of microtubules. ALS-associated TUBA4A variants are suggested to dysregulate neuronal function by disruption of microtubule dynamics and stability. ALS is a neurodegenerative disorder affecting upper motor neurons in the brain and lower motor neurons in the brain stem and spinal cord, resulting in fatal paralysis. Evidence supporting this gene-disease relationship includes case-level data and experimental data. At least 14 variants have been reported in relation to ALS (mostly missense, as well as one nonsense, one splice site, and one frameshift). Variants in this gene have been reported in at least 14 probands in 4 publications (PMIDs: 25374358, 25893256, 28069311, and 295405137). Experimentally, this gene-disease relationship is supported by its role as a constituent of cytoskeleton (PMID: 25374358), expression in the nervous system (PMID: 25374358, PMID: 30030593), and a zebrafish model with overlapping phenotypes though mechanism may differ from that proposed in patients (PMID: 38463699). TUBA4A mutants appear to disrupt microtubule dynamics and stability through a dominant-negative mechanism, however there is an absence of functional data from primary tissue of TUBA4A mutation carriers. In summary, there is moderate evidence to support this gene-disease relationship. While more evidence is needed to establish this relationship definitively, no convincing contradictory evidence has emerged. This classification was previously approved by the ClinGen ALS GCEP on 09/14/2021, it was recurated on 03/27/2025 and a new zebrafish model (PMID: 38463699) was identified but there was no change of classification.
Inheritance Pattern: AD
Disease ID:MONDO:0015372
Submitter: ClinGen
*TUBA4A* was first reported in relation to autosomal dominant macrothrombocytopenia in 2019 (Strassel et al., 2019, PMID: 30760556). *TUBA4A* encodes an α-tubulin subunit, which together with β-tubulin constitutes the tubulin heterodimer, the building block of microtubules and it is well established that microtubules are key actors in the formation of proplatelets from mature megakaryocytes (Reviewed in PMID: 31315202). Evidence supporting this gene-disease relationship includes case-level data and experimental data. One macrothrombocytopenia patient has been reported with two rare *TUBA4A* missense variants in cis (PMID: 30760556). No functional evidence is yet available to support one, or both, variants as deleterious. This gene-disease relationship is supported by its shared function with *TUBB1* as a building block of microtubules. *TUBA4A* has a high level of microtubule incorporation (PMID: 25374358) and expression of *TUBA4A* is particularly enriched in platelet microtubules (PMID: 30760556). Additionally, mice carrying a missense mutation in the Tuba4a gene, displayed macrothrombocytopenia and structural abnormalities in the marginal band of platelets, similar to the patient. In summary, there is very limited genetic evidence and more evidence is needed to support a causal role, however no convincing evidence has emerged that contradicts the gene-disease relationship. Two additional macrothrombocytopenia families have been identified with *TUBA4A* variants but are not reported in a peer reviewed article or ClinVar submission. These families were presented at the ISTH 2024 Congress (https://isth2024.eventscribe.net/fsPopup.asp?efp=R0tKSkNBT0ExNjMzNg&PresentationID=1433440&mode=presInfo). Five macrothrombocytopenic patients from two unrelated families carrying two heterozygous variants, respectively (p.(Lys430del) in family A and p.(Asp431Tyr) in family B (CATCH study, ClinicalTrials.gov identifier: NCT04272970) were identified by WES. Of note, *TUBA4A* has also been implicated in autosomal dominant amyotrophic lateral sclerosis (ALS). ALS is a neurodegenerative disorder affecting upper motor neurons in the brain and lower motor neurons in the brain stem and spinal cord, resulting in fatal paralysis. and apparently dominant negative *TUBA4A* variants are suggested to dysregulate neuronal function by disruption of microtubule dynamics and stability. Based on differences in phenotype and proposed molecular mechanisms these disease entiteis have been considered seperately and the relationship to ALS was curated by the ALS GCEP. This gene-disease pair was originally evaluated by the HT GCEP on 2021 Jun 23. It was reevaluated on 2023 Nov 06. As a result of this reevaluation no additional patients were scored and the classification remained Limited. Three additional disease assertions have been made in OMIM in relation to *TUBA4A*, Congenital myopathy 26, Oocyte/zygote/embryo maturation arrest 23, and Spastic ataxia 11, autosomal dominant. There is no variant or phenotype overlap with these additional diseases and autosomal dominant macrothrombocytopenia is still considered seperately.
Inheritance Pattern: AD
Disease ID:MONDO:0014531
Submitter: Genomics England PanelApp
Clinical Genomic Database (CGD)
Manifestation: Neurologic
Intervention: General
Rationale: 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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TUBA4A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006000.3. 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 | 2 | 74 | 3 | 79 | ||
| missense | 17 | 9 | 35 | 1 | 62 | |
| nonsense | 1 | 3 | 4 | |||
| start loss | 2 | 2 | ||||
| frameshift | 1 | 4 | 5 | |||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 19 | 13 | 43 | 75 | 3 | 153 |
Highest pathogenic variant AF is 0.0000049562673
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005991.1 | 4 | MANE Select | |
| Ensembl | ENSP00000248437.4 | 4 | MANE Select | |
| RefSeq | NP_001265481.1 | 3 | Standard | |
| Ensembl | ENSP00000375938.2 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Tight junction - Homo sapiens (human)
- Phagosome - Homo sapiens (human)
- Gap junction - Homo sapiens (human)
- Pathogenic Escherichia coli infection - Homo sapiens (human)
- Apoptosis - Homo sapiens (human)
Biological Process
- G2/M transition of mitotic cell cycle
- microtubule cytoskeleton organization
- mitotic cell cycle
- platelet degranulation
- microtubule-based process
Molecular Function
- GTPase activity
- structural constituent of cytoskeleton
- protein binding
- GTP binding
- protein kinase binding
Cellular Component
- extracellular region
- cytoplasm
- cytosol
- cytoskeleton
- microtubule
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000248437
- Coding exons
- 4
- Length
- 28460
- Individuals with no LoFs
- 125738
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 10
- Defined
- 125748
- p
- 0.0000398
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.30 | 120 | 274 | 0.438 | 0.0000170 | 2942 |
| Missense (PolyPhen) | 29 | 102.58 | 0.28271 | 1204 | ||
| Synonymous | 0.0670 | 108 | 109 | 0.992 | 0.00000690 | 910 |
| Loss of Function | 2.60 | 4 | 14.8 | 0.271 | 8.11e-7 | 169 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.0000088 | 0.0000088 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Tubulin is the major constituent of microtubules. It binds two moles of GTP, one at an exchangeable site on the beta chain and one at a non-exchangeable site on the alpha chain.;
- Disease
- DISEASE: Amyotrophic lateral sclerosis 22, with or without frontotemporal dementia (ALS22) [MIM:616208]: A neurodegenerative disorder affecting upper motor neurons in the brain and lower motor neurons in the brain stem and spinal cord, resulting in fatal paralysis. Sensory abnormalities are absent. The pathologic hallmarks of the disease include pallor of the corticospinal tract due to loss of motor neurons, presence of ubiquitin-positive inclusions within surviving motor neurons, and deposition of pathologic aggregates. The etiology of amyotrophic lateral sclerosis is likely to be multifactorial, involving both genetic and environmental factors. The disease is inherited in 5-10% of the cases. Patients with ALS22 may develop frontotemporal dementia. {ECO:0000269|PubMed:25374358}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.649
Intolerance Scores
- LoFtool
- 0.294
- RVIS EVS
- -0.36
- RVIS percentile EVS
- 28.63
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.731
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Low | Medium |