TUBA3E
protein-codingtubulin alpha 3e, 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. This gene encodes an alpha tubulin that highly conserved among species. A missense mutation in this gene has been potentially linked to microlissencephaly and global developmental delay. [provided by RefSeq, Jul 2016]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~6.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0100038
Submitter: Ambry Genetics
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TUBA3E variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_207312.3. 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 | 5 | 5 | ||||
| missense | 1 | 41 | 3 | 45 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 1 | 42 | 8 | 0 | 51 |
Highest pathogenic variant AF is 0.000053316602
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_997195.2 | 5 | MANE Select | |
| Ensembl | ENSP00000318197.7 | 5 | MANE Select | |
| Ensembl | ENSP00000771680.1 | 4 | Standard | |
| Ensembl | ENSP00000771681.1 | 5 | 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
- microtubule cytoskeleton organization
- mitotic cell cycle
- microtubule-based process
- biological_process
Molecular Function
- molecular_function
- GTPase activity
- structural constituent of cytoskeleton
- protein binding
- GTP binding
Cellular Component
- nucleus
- cytoplasm
- microtubule
- microtubule cytoskeleton
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000312988
- Coding exons
- 5
- Length
- 6717
- Individuals with no LoFs
- 125019
- Homozygous LoFs
- 7
- Heterozygous LoFs
- 722
- Defined
- 125748
- p
- 0.00290
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.296 | 299 | 285 | 1.05 | 0.0000181 | 2921 |
| Missense (PolyPhen) | 160 | 145.1 | 1.1027 | 1495 | ||
| Synonymous | 0.144 | 117 | 119 | 0.983 | 0.00000812 | 892 |
| Loss of Function | 0.509 | 13 | 15.1 | 0.859 | 7.34e-7 | 170 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.036 | 0.037 | notable |
| Latino/Admixed American | 0.0016 | 0.0016 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00048 | 0.00047 | rare |
| South Asian | 0.00085 | 0.00085 | rare |
| Other | 0.00098 | 0.00098 | 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 (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.172
Intolerance Scores
- LoFtool
- 0.527
- RVIS EVS
- 0.38
- RVIS percentile EVS
- 75.58
Essentials
- Essential (CRISPR)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |