TTLL11
protein-codingtubulin tyrosine ligase like 11, the group of Tubulin tyrosine ligase family
Gene summary
Predicted to enable tubulin binding activity and tubulin-glutamic acid ligase activity. Predicted to be involved in microtubule cytoskeleton organization. Predicted to act upstream of or within microtubule severing and protein polyglutamylation. Predicted to be located in cytosol. Predicted to be active in ciliary basal body. [provided by Alliance of Genome Resources, Apr 2025]
- C9orf20
- TTLL11-IT1
- C9orf148
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~277.9 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 TTLL11 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001139442.2. 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 | 95 | 4 | 99 | |||
| nonsense | 0 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 99 | 4 | 0 | 103 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001132914.2 | 9 | MANE Select | |
| Ensembl | ENSP00000321346.6 | 9 | MANE Select | |
| RefSeq | NP_001373760.1 | 9 | Standard | |
| RefSeq | NP_001373761.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Post-translational protein modification
- Metabolism of proteins
- Carboxyterminal post-translational modifications of tubulin
Biological Process
- protein polyglutamylation
- microtubule severing
Molecular Function
- ATP binding
- tubulin-glutamic acid ligase activity
Cellular Component
- cytosol
- microtubule
- cilium
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000321582
- Coding exons
- 9
- Length
- 271679
- Individuals with no LoFs
- 125728
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 20
- Defined
- 125748
- p
- 0.0000795
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.03 | 308 | 426 | 0.723 | 0.0000243 | 5137 |
| Missense (PolyPhen) | 80 | 118.08 | 0.67749 | 1416 | ||
| Synonymous | 0.0191 | 180 | 180 | 0.998 | 0.0000108 | 1643 |
| Loss of Function | 1.30 | 16 | 22.7 | 0.705 | 9.66e-7 | 305 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00013 | 0.00012 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00011 | 0.00011 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Polyglutamase which preferentially modifies alpha- tubulin. Involved in the side-chain elongation step of the polyglutamylation reaction rather than in the initiation step (By similarity). Required for CCSAP localization to both spindle and cilia microtubules (PubMed:22493317). Generates long side-chains (By similarity). {ECO:0000250|UniProtKB:A4Q9F4, ECO:0000269|PubMed:22493317}.;
Intolerance Scores
- LoFtool
- 0.497
- RVIS EVS
- -0.27
- RVIS percentile EVS
- 34.6
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.338
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |