TTLL13
protein-codingtubulin tyrosine ligase like 13, 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 bundle formation. Predicted to be located in cytosol. Predicted to be active in ciliary basal body. [provided by Alliance of Genome Resources, Jul 2025]
- TTLL13P
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~16.0 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 TTLL13 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001396017.1. 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 | 1 | 1 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 1 | 1 | 0 | 2 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001382946.1 | 14 | MANE Select | |
| Ensembl | ENSP00000493387.1 | 14 | MANE Select | |
| Ensembl | ENSP00000491066.1 | 14 | Standard | |
| Ensembl | ENSP00000492322.1 | 13 | 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
Molecular Function
- ATP binding
- tubulin-glutamic acid ligase activity
Cellular Component
- cytosol
- microtubule
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000339615
- Coding exons
- 9
- Length
- 15438
- Individuals with no LoFs
- 125507
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 238
- Defined
- 125747
- p
- 0.000955
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.708 | 241 | 274 | 0.880 | 0.0000167 | 3014 |
| Missense (PolyPhen) | 56 | 68.284 | 0.8201 | 778 | ||
| Synonymous | 1.42 | 82 | 100 | 0.820 | 0.00000535 | 871 |
| Loss of Function | 0.871 | 20 | 24.7 | 0.811 | 0.00000148 | 268 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00031 | 0.00031 | rare |
| Latino/Admixed American | 0.00052 | 0.00052 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.0029 | 0.0029 | notable |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00058 | 0.00058 | rare |
| South Asian | 0.0032 | 0.0030 | notable |
| Other | 0.00066 | 0.00065 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Polyglutamylase which preferentially modifies alpha- tubulin. Involved in the side-chain elongation step of the polyglutamylation reaction rather than in the initiation step (By similarity). {ECO:0000250|UniProtKB:A4Q9F6}.;
Intolerance Scores
- RVIS EVS
- -0.47
- RVIS percentile EVS
- 23.51
Essentials
- Essential (gene trap)
- N