TTLL11

gene
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Also known as bA244O19.1

Summary

TTLL11 (tubulin tyrosine ligase like 11, HGNC:18113) is a protein-coding gene on chromosome 9q33.2, encoding Tubulin polyglutamylase TTLL11 (Q8NHH1). Polyglutamylase which modifies tubulin, generating polyglutamate side chains of variable lengths on the gamma-carboxyl group of specific glutamate residues within the C-terminal tail of tubulin.

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.

Source: NCBI Gene 158135 — RefSeq curated summary.

At a glance

  • GWAS associations: 14
  • Clinical variants (ClinVar): 117 total
  • MANE Select transcript: NM_001139442

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18113
Approved symbolTTLL11
Nametubulin tyrosine ligase like 11
Location9q33.2
Locus typegene with protein product
StatusApproved
AliasesbA244O19.1
Ensembl geneENSG00000175764
Ensembl biotypeprotein_coding
OMIM620694
Entrez158135

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 5 protein_coding, 3 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

ENST00000321582, ENST00000373776, ENST00000373778, ENST00000411790, ENST00000474723, ENST00000486362, ENST00000487468, ENST00000685478, ENST00000687938, ENST00000882246

RefSeq mRNA: 4 — MANE Select: NM_001139442 NM_001139442, NM_001386831, NM_001386833, NM_194252

CCDS: CCDS48012, CCDS6834

Canonical transcript exons

ENST00000321582 — 9 exons

ExonStartEnd
ENSE00001725722122031723122031856
ENSE00001729651121815674121822879
ENSE00003558395121989195121989770
ENSE00003559221121974884121974979
ENSE00003562868121860337121860443
ENSE00003621013121870497121870748
ENSE00003656625121974009121974124
ENSE00003729403122039272122039368
ENSE00003918396122092687122093308

Expression profiles

Bgee: expression breadth ubiquitous, 176 present calls, max score 89.98.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.0370 / max 200.4495, expressed in 1697 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
1023766.52561615
1023771.0503628
1023730.232782
1023720.181888
1023710.033315
1023700.01335

Top tissues by expression

249 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
C1 segment of cervical spinal cordUBERON:000646989.98gold quality
tibialis anteriorUBERON:000138587.26silver quality
spinal cordUBERON:000224087.06gold quality
muscle of legUBERON:000138385.25gold quality
gastrocnemiusUBERON:000138885.11gold quality
hindlimb stylopod muscleUBERON:000425284.32gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047383.65gold quality
popliteal arteryUBERON:000225082.89gold quality
tibial arteryUBERON:000761082.86gold quality
smooth muscle tissueUBERON:000113582.64gold quality
aortaUBERON:000094782.45gold quality
thoracic aortaUBERON:000151582.28gold quality
muscle layer of sigmoid colonUBERON:003580582.26gold quality
ascending aortaUBERON:000149682.18gold quality
prefrontal cortexUBERON:000045182.05gold quality
descending thoracic aortaUBERON:000234581.94gold quality
lower esophagus muscularis layerUBERON:003583381.78gold quality
lower esophagusUBERON:001347381.75gold quality
right coronary arteryUBERON:000162581.36gold quality
esophagogastric junction muscularis propriaUBERON:003584181.06gold quality
cortical plateUBERON:000534380.77gold quality
left testisUBERON:000453379.87gold quality
left coronary arteryUBERON:000162679.39gold quality
right testisUBERON:000453478.85gold quality
cerebellar hemisphereUBERON:000224578.31gold quality
right frontal lobeUBERON:000281078.28gold quality
cerebellar cortexUBERON:000212978.18gold quality
mucosa of stomachUBERON:000119978.16gold quality
anterior cingulate cortexUBERON:000983578.07gold quality
right hemisphere of cerebellumUBERON:001489078.00gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no3.30

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

27 targeting TTLL11, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-477599.9875.006394
HSA-MIR-103A-3P99.9869.141595
HSA-MIR-10799.9869.141595
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-3682-5P99.9367.971163
HSA-MIR-6715A-3P99.8368.051473
HSA-MIR-4649-3P99.5666.901783
HSA-MIR-7162-5P99.4668.081368
HSA-MIR-516A-3P99.4667.961378
HSA-MIR-516B-3P99.4667.961378
HSA-MIR-5589-3P99.2968.301443
HSA-MIR-4758-3P99.1263.96869
HSA-MIR-655-5P98.7465.93888
HSA-MIR-7158-3P98.4666.45728
HSA-MIR-4733-3P98.3565.20994
HSA-MIR-6773-3P98.1765.511213
HSA-MIR-429497.8665.721110
HSA-MIR-66597.6065.641781
HSA-MIR-3189-5P97.5566.71655
HSA-MIR-1226-3P97.5166.321063
HSA-MIR-5699-5P97.3667.031014
HSA-MIR-2467-5P97.3667.71991
HSA-MIR-797695.7565.671186
HSA-MIR-24-1-5P95.5765.85492
HSA-MIR-24-2-5P95.5766.16484
HSA-MIR-63883.9364.4666

Literature-anchored findings (GeneRIF, showing 2)

  • Genetic variant of TTLL11 gene and subsequent ciliary defects are associated with idiopathic scoliosis in a 5-generation UK family. (PMID:34040021)
  • TTLL11 gene is associated with sustained attention performance and brain networks: A genome-wide association study of a healthy Chinese sample. (PMID:36511133)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriottll11ENSDARG00000060374
mus_musculusTtll11ENSMUSG00000026885
rattus_norvegicusTtll11ENSRNOG00000019339
caenorhabditis_elegansWBGENE00019230

Paralogs (12): TTLL1 (ENSG00000100271), TTLL12 (ENSG00000100304), TTLL2 (ENSG00000120440), TTLL9 (ENSG00000131044), TTLL4 (ENSG00000135912), TTLL7 (ENSG00000137941), TTLL8 (ENSG00000138892), TTLL10 (ENSG00000162571), TTLL6 (ENSG00000170703), KPRP (ENSG00000203786), TTLL13 (ENSG00000213471), TTLL3 (ENSG00000214021)

Protein

Protein identifiers

Tubulin polyglutamylase TTLL11Q8NHH1 (reviewed: Q8NHH1)

Alternative names: Tubulin–tyrosine ligase-like protein 11

All UniProt accessions (5): Q8NHH1, A0A087WU58, A0A087WUG8, A0A087WVF6, A0AA75MRL2

UniProt curated annotations — full annotation on UniProt →

Function. Polyglutamylase which modifies tubulin, generating polyglutamate side chains of variable lengths on the gamma-carboxyl group of specific glutamate residues within the C-terminal tail of tubulin. Preferentially mediates ATP-dependent polyglutamate long side-chain elongation over the initiation step of the polyglutamylation reaction. Preferentially modifies the alpha-tubulin tail over a beta-tail. Required for CCSAP localization to both spindle and cilia microtubules. Promotes tubulin polyglutamylation which stimulates spastin/SPAST-mediated microtubule severing, thereby regulating microtubule functions.

Subcellular location. Cytoplasm. Cytoskeleton. Cilium basal body.

Domain organisation. The flexible c-MTBD (cationic microtubule binding domain) region mediates binding to microtubules. It is positively charged and becomes ordered when bound to microtubules: it interacts with a negatively charged patch on tubulin. The presence of positive charges in the c-MTBD region is essential for proper binding. Gln-345 is the main determinant for regioselectivity, which segregates between initiases and elongases in all tubulin–tyrosine ligase family. A glutamine residue at this position is found in elongases TTLL6, TTLL9, TTLL11, TTLL13, TTLL10 and favors glutamate-chain elongation, whereas an arginine residue is found in initiases TTLL2, TTLL4, TTLL5, TTLL3, TTLL8 and favors initiation.

Similarity. Belongs to the tubulin–tyrosine ligase family.

Isoforms (2)

UniProt IDNamesCanonical?
Q8NHH1-11yes
Q8NHH1-22

RefSeq proteins (3): NP_001132914, NP_001373760, NP_919228 (=MANE)

Domains & families (InterPro)

IDNameType
IPR004344TTL/TTLL_famFamily

Pfam: PF03133

Catalyzed reactions (Rhea), 2 shown:

  • L-glutamyl-[protein] + L-glutamate + ATP = gamma-L-glutamyl-L-glutamyl-[protein] + ADP + phosphate + H(+) (RHEA:60144)
  • (L-glutamyl)(n)-gamma-L-glutamyl-L-glutamyl-[protein] + L-glutamate + ATP = (L-glutamyl)(n+1)-gamma-L-glutamyl-L-glutamyl-[protein] + ADP + phosphate + H(+) (RHEA:60148)

UniProt features (28 total): binding site 15, compositionally biased region 4, region of interest 3, splice variant 2, chain 1, domain 1, site 1, mutagenesis site 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
9HQ4ELECTRON MICROSCOPY3.28

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8NHH1-F178.040.55

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 255 (essential for specifying alpha-elongation versus initiation step of the polyglutamylase activity)

Ligand- & substrate-binding residues (15): 255–256; 255; 282–285; 295–297; 321; 343–344; 345; 346; 365; 428; 441; 441

Mutagenesis-validated functional residues (1):

PositionPhenotype
488–491decreased binding to microtubules and polyglutamylase activity; when associated with e-326 and e-329.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-8955332Carboxyterminal post-translational modifications of tubulin

MSigDB gene sets: 88 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_UP, GSE45365_NK_CELL_VS_CD8A_DC_UP, DARWICHE_SKIN_TUMOR_PROMOTER_UP, DARWICHE_PAPILLOMA_RISK_LOW_DN, DARWICHE_PAPILLOMA_RISK_HIGH_DN, DARWICHE_SQUAMOUS_CELL_CARCINOMA_UP, GOCC_MICROTUBULE_ORGANIZING_CENTER, RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN, GGARNTKYCCA_UNKNOWN, GOBP_PEPTIDYL_GLUTAMIC_ACID_MODIFICATION, GOMF_LIGASE_ACTIVITY_FORMING_CARBON_NITROGEN_BONDS, GOMF_ACID_AMINO_ACID_LIGASE_ACTIVITY, YY1_01, GCCATNTTG_YY1_Q6, GOCC_CILIUM

GO Biological Process (3): microtubule cytoskeleton organization (GO:0000226), microtubule severing (GO:0051013), protein modification process (GO:0036211)

GO Molecular Function (8): ATP binding (GO:0005524), tubulin binding (GO:0015631), metal ion binding (GO:0046872), tubulin-glutamic acid ligase activity (GO:0070740), protein-glutamic acid ligase activity, initiating (GO:0106437), protein-glutamic acid ligase activity, elongating (GO:0106438), nucleotide binding (GO:0000166), ligase activity (GO:0016874)

GO Cellular Component (7): cytosol (GO:0005829), microtubule (GO:0005874), ciliary basal body (GO:0036064), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), cilium (GO:0005929), cell projection (GO:0042995)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Post-translational protein modification1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
protein-glutamic acid ligase activity3
cellular anatomical structure3
cytoskeleton organization1
microtubule-based process1
microtubule cytoskeleton organization1
protein metabolic process1
macromolecule modification1
adenyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
cytoskeletal protein binding1
cation binding1
nucleoside phosphate binding1
heterocyclic compound binding1
catalytic activity1
cytoplasm1
microtubule cytoskeleton1
polymeric cytoskeletal fiber1
microtubule organizing center1
cilium1
intracellular anatomical structure1
intracellular membraneless organelle1
intraciliary transport particle1
membrane-bounded organelle1
plasma membrane bounded cell projection1

Protein interactions and networks

STRING

552 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TTLL11TTLL12Q14166664
TTLL11LCN9Q8WX39534
TTLL11TTLL5Q6EMB2532
TTLL11ZSCAN20P17040509
TTLL11Q5T8A5Q5T8A5508
TTLL11TTLL1O95922483
TTLL11TRMT10BQ6PF06483
TTLL11SPASTQ9UBP0476
TTLL11ZNF362Q5T0B9476
TTLL11AGBL5Q8NDL9474
TTLL11SACK1EQ2M2I3465
TTLL11DAB2IPQ5VWQ8462
TTLL11TTLL9Q3SXZ7462
TTLL11POC5Q8NA72456
TTLL11PSMD5Q16401455
TTLL11TMEM214Q6NUQ4455

IntAct

6 interactions, top by confidence:

ABTypeScore
TTLL11Dlg4psi-mi:“MI:0407”(direct interaction)0.440
HSCBRBP5psi-mi:“MI:0914”(association)0.350
MAPTSHTN1psi-mi:“MI:0914”(association)0.350

BioGRID (7): TTLL11 (Affinity Capture-RNA), TTLL11 (Affinity Capture-RNA), TTLL11 (Affinity Capture-RNA), TTLL11 (Affinity Capture-MS), TTLL11 (Affinity Capture-MS), TTLL11 (Affinity Capture-MS), TTLL11 (Affinity Capture-MS)

ESM2 similar proteins: A4FUF0, A4Q9F4, D2XV59, E1C1R4, O94888, O95267, P42694, P54198, P79987, Q15139, Q49A26, Q4R8V9, Q4SS66, Q562D5, Q5R372, Q5R5M3, Q5R7T2, Q5RDU9, Q5REY7, Q5RKH0, Q5RKN4, Q5T6S3, Q5ZIA0, Q5ZJ17, Q5ZLS2, Q5ZLS7, Q61666, Q62101, Q6DC64, Q6DFV5, Q6P5G6, Q6ZPY2, Q6ZWH5, Q70Z35, Q75Q39, Q80VL1, Q86W50, Q8BY87, Q8BYN5, Q8CIW5

Diamond homologs: A2APC3, A4Q9E4, A4Q9E5, A4Q9E8, A4Q9F0, A4Q9F1, A4Q9F4, A4Q9F6, A6NNM8, A6PVC2, A8CVX7, A8X9V4, B2GUB3, E9P886, F7E540, H2KZM9, O95922, P38160, P38584, Q09647, Q0VC71, Q14679, Q1ECV4, Q23AS2, Q23K29, Q23MT7, Q23SI8, Q3SXZ7, Q3SZH6, Q564U4, Q5PPI9, Q5R978, Q641W7, Q6EEF3, Q6EMB2, Q6ZT98, Q80UG8, Q8CHB8, Q8N841, Q8NG68

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

117 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance105
Likely benign5
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2721 predictions. Top by Δscore:

VariantEffectΔscore
9:121822875:CATCC:Cacceptor_gain1.0000
9:121870493:TGA:Tdonor_loss1.0000
9:121870494:GAC:Gdonor_loss1.0000
9:121870495:A:ATdonor_loss1.0000
9:121870576:T:TAdonor_gain1.0000
9:121870746:GAC:Gacceptor_gain1.0000
9:121870746:GACCT:Gacceptor_gain1.0000
9:121870747:ACCTG:Aacceptor_gain1.0000
9:121870749:C:CCacceptor_gain1.0000
9:121870750:T:Cacceptor_loss1.0000
9:121974007:A:ACdonor_gain1.0000
9:121974008:C:CTdonor_gain1.0000
9:121974008:CT:Cdonor_gain1.0000
9:121974008:CTG:Cdonor_gain1.0000
9:121974008:CTGA:Cdonor_gain1.0000
9:121989769:ACCT:Aacceptor_loss1.0000
9:121989772:T:Gacceptor_loss1.0000
9:122031718:TCTAC:Tdonor_loss1.0000
9:122031719:CTA:Cdonor_loss1.0000
9:122031720:TAC:Tdonor_loss1.0000
9:122031721:AC:Adonor_loss1.0000
9:122031722:C:CAdonor_loss1.0000
9:122031857:C:CCacceptor_gain1.0000
9:122039273:TGGAA:Tdonor_gain1.0000
9:122092681:CCTCA:Cdonor_loss1.0000
9:122092682:CTCA:Cdonor_loss1.0000
9:122092683:TCA:Tdonor_loss1.0000
9:122092684:CAC:Cdonor_loss1.0000
9:122092685:A:AGdonor_loss1.0000
9:122092685:ACCT:Adonor_gain1.0000

AlphaMissense

5237 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
9:121974048:A:GL571P1.000
9:121974054:T:AD569V1.000
9:121974966:T:AD518V1.000
9:121974966:T:GD518A1.000
9:121989369:T:AK455N1.000
9:121989369:T:GK455N1.000
9:121989432:G:CN434K1.000
9:121989432:G:TN434K1.000
9:121989495:A:CC413W1.000
9:121989622:A:TV371D1.000
9:122039282:G:CN273K1.000
9:122039282:G:TN273K1.000
9:122039332:A:GW257R1.000
9:122039332:A:TW257R1.000
9:122092695:A:GW242R1.000
9:122092695:A:TW242R1.000
9:122092721:A:GL233P1.000
9:121870509:C:GR664P0.999
9:121870510:G:TR664S0.999
9:121870635:A:GL622P0.999
9:121870635:A:TL622H0.999
9:121974055:C:GD569H0.999
9:121974071:T:AK563N0.999
9:121974071:T:GK563N0.999
9:121974912:G:TP536H0.999
9:121974927:T:AE531V0.999
9:121974960:A:GL520P0.999
9:121974965:G:CD518E0.999
9:121974965:G:TD518E0.999
9:121974966:T:CD518G0.999

dbSNP variants (sampled 300 via entrez): RS1000006713 (9:121856506 T>A), RS1000009527 (9:122057781 G>A,C), RS1000011735 (9:121843935 A>G), RS1000015114 (9:122082456 A>G), RS1000037547 (9:121889579 T>C), RS1000054477 (9:121850622 T>C), RS1000054713 (9:121884343 C>T), RS1000076913 (9:121927297 T>C), RS1000092212 (9:121968679 C>G,T), RS1000101404 (9:121897672 G>C), RS1000107773 (9:122009686 AT>A), RS1000108070 (9:121884541 G>A,C), RS1000119492 (9:121838941 C>T), RS1000127784 (9:121850849 C>T), RS1000137972 (9:121984741 A>G)

Disease associations

OMIM: gene MIM:620694 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

14 associations (top):

StudyTraitp-value
GCST001588_11Periodontal microbiota5.000000e-07
GCST005141_67Cognitive ability (MTAG)7.000000e-09
GCST005246_6Inhibitory control3.000000e-06
GCST005316_63Intelligence (MTAG)3.000000e-09
GCST008338_2Blood cell traits (multivariate analysis)3.000000e-08
GCST008595_136Cognitive ability, years of educational attainment or schizophrenia (pleiotropy)2.000000e-09
GCST009524_297Household income (MTAG)1.000000e-09
GCST009524_34Household income (MTAG)5.000000e-10
GCST009524_68Household income (MTAG)1.000000e-10
GCST010725_17Malaria5.000000e-06
GCST010725_29Malaria1.000000e-06
GCST010725_96Malaria9.000000e-07
GCST010988_406Adult body size2.000000e-09
GCST90000047_200Age at first sexual intercourse4.000000e-08

EFO canonical traits (12, from GWAS)

EFO IDTrait name
EFO:0004337intelligence
EFO:0004784self reported educational attainment
EFO:0008467behavioural inhibitory control measurement
EFO:0004305erythrocyte count
EFO:0004309platelet count
EFO:0004528mean corpuscular hemoglobin concentration
EFO:0004833neutrophil count
EFO:0004842eosinophil count
EFO:0005090basophil count
EFO:0005091monocyte count
EFO:0009695household income
EFO:0009749age at first sexual intercourse measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression5
bisphenol Aaffects cotreatment, decreases methylation, decreases expression2
sodium arseniteaffects cotreatment, increases abundance, increases expression2
Cyclosporinedecreases expression, increases expression2
bisphenol Faffects cotreatment, decreases expression1
triphenyl phosphateaffects expression1
ethyl-p-hydroxybenzoateincreases expression1
manganese chlorideincreases expression, affects cotreatment, increases abundance1
CGP 52608affects binding, increases reaction1
perfluoro-n-nonanoic acidincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
dorsomorphinincreases expression, affects cotreatment1
jinfukangaffects cotreatment, decreases expression1
(+)-JQ1 compounddecreases expression1
Resveratrolaffects cotreatment, decreases expression1
Fulvestrantdecreases methylation, affects cotreatment1
Acetaminophenincreases expression1
Arsenicincreases abundance, increases expression, affects cotreatment1
Cisplatinaffects cotreatment, decreases expression1
Copperaffects cotreatment, decreases expression1
Dexamethasonedecreases expression, affects cotreatment1
Doxorubicindecreases expression1
Estradiolincreases expression1
Indomethacinaffects cotreatment, decreases expression1
Manganeseaffects cotreatment, increases abundance, increases expression1
1-Methyl-3-isobutylxanthineaffects cotreatment, decreases expression1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression1
S-Nitrosoglutathionedecreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): periodontitis