TUBA3E
Basic information
Region (hg38): 2:130191745-130198439
Links
Phenotypes
GenCC
Source:
- complex neurodevelopmental disorder (Limited), mode of inheritance: AR
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (34 variants)
- not_provided (7 variants)
- Neurodevelopmental_disorder (1 variants)
- Lissencephaly (1 variants)
- Primary_microcephaly (1 variants)
- Global_developmental_delay (1 variants)
- Seizure (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TUBA3E gene is commonly pathogenic or not. These statistics are base on transcript: NM_000207312.3. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 5 | |||||
missense | 33 | 37 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
Total | 0 | 1 | 34 | 8 | 0 |
Highest pathogenic variant AF is 0.000053316602
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
TUBA3E | protein_coding | protein_coding | ENST00000312988 | 5 | 6717 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
2.03e-8 | 0.258 | 125019 | 7 | 722 | 125748 | 0.00290 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.296 | 299 | 285 | 1.05 | 0.0000181 | 2921 |
Missense in 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 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0380 | 0.0382 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000218 | 0.000217 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000483 | 0.000475 |
Middle Eastern | 0.000218 | 0.000217 |
South Asian | 0.000850 | 0.000850 |
Other | 0.000979 | 0.000978 |
dbNSFP
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}.;
- Pathway
- 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);Pathogenic Escherichia coli infection;Parkin-Ubiquitin Proteasomal System pathway;Post-translational protein modification;Metabolism of proteins;Chaperonin-mediated protein folding;Formation of tubulin folding intermediates by CCT/TriC;Carboxyterminal post-translational modifications of tubulin;Protein folding;Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding;Post-chaperonin tubulin folding pathway
(Consensus)
Recessive Scores
- pRec
- 0.172
Intolerance Scores
- loftool
- 0.527
- rvis_EVS
- 0.38
- rvis_percentile_EVS
- 75.58
Haploinsufficiency Scores
- pHI
- 0.514
- hipred
- N
- hipred_score
- 0.396
- ghis
- 0.392
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.539
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tuba3b
- Phenotype
Gene ontology
- Biological process
- microtubule cytoskeleton organization;mitotic cell cycle;microtubule-based process;biological_process
- Cellular component
- nucleus;cytoplasm;microtubule;microtubule cytoskeleton
- Molecular function
- molecular_function;GTPase activity;structural constituent of cytoskeleton;protein binding;GTP binding