TTLL1

gene
On this page

Also known as PGs3TPGS3

Summary

TTLL1 (TTL family tubulin polyglutamylase complex subunit L1, HGNC:1312) is a protein-coding gene on chromosome 22q13.2, encoding Polyglutamylase complex subunit TTLL1 (O95922). Catalytic subunit of a polyglutamylase complex which modifies tubulin, generating side chains of glutamate on the gamma-carboxyl group of specific glutamate residues within the C-terminal tail of tubulin.

Enables tubulin-glutamic acid ligase activity. Involved in microtubule cytoskeleton organization. Is active in microtubule.

Source: NCBI Gene 25809 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 68 total
  • MANE Select transcript: NM_012263

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1312
Approved symbolTTLL1
NameTTL family tubulin polyglutamylase complex subunit L1
Location22q13.2
Locus typegene with protein product
StatusApproved
AliasesPGs3, TPGS3
Ensembl geneENSG00000100271
Ensembl biotypeprotein_coding
OMIM608955
Entrez25809

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 13 protein_coding, 2 nonsense_mediated_decay

ENST00000266254, ENST00000331018, ENST00000439248, ENST00000440761, ENST00000903474, ENST00000903475, ENST00000903476, ENST00000903477, ENST00000903478, ENST00000903479, ENST00000903480, ENST00000903481, ENST00000947941, ENST00000947942, ENST00000947943

RefSeq mRNA: 1 — MANE Select: NM_012263 NM_012263

CCDS: CCDS14043

Canonical transcript exons

ENST00000266254 — 11 exons

ExonStartEnd
ENSE000013914164307990243079986
ENSE000015244604308927743089391
ENSE000022412784307547443075590
ENSE000034827684304641043046573
ENSE000035105884306381343063921
ENSE000035248234306419043064324
ENSE000035302244305938443059527
ENSE000036061794305180143051887
ENSE000036394154303951643039905
ENSE000036470894306963643069844
ENSE000036639964306841043068590

Expression profiles

Bgee: expression breadth ubiquitous, 222 present calls, max score 91.28.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.5858 / max 46.0107, expressed in 1555 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
1945023.18331395
1945011.4025936

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cortical plateUBERON:000534391.28gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099190.72gold quality
ganglionic eminenceUBERON:000402388.72gold quality
bronchial epithelial cellCL:000232887.77gold quality
ventricular zoneUBERON:000305387.44gold quality
epithelium of bronchusUBERON:000203187.07gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047387.04gold quality
bronchusUBERON:000218586.70gold quality
embryoUBERON:000092284.38gold quality
mucosa of paranasal sinusUBERON:000503083.63silver quality
prefrontal cortexUBERON:000045183.59gold quality
frontal poleUBERON:000279583.41silver quality
right uterine tubeUBERON:000130283.04gold quality
oocyteCL:000002382.51gold quality
stromal cell of endometriumCL:000225582.50gold quality
middle frontal gyrusUBERON:000270282.25gold quality
lateral nuclear group of thalamusUBERON:000273682.02gold quality
neocortexUBERON:000195081.48gold quality
cingulate cortexUBERON:000302781.38gold quality
frontal cortexUBERON:000187081.36gold quality
anterior cingulate cortexUBERON:000983581.28gold quality
testisUBERON:000047381.26gold quality
left testisUBERON:000453381.26gold quality
secondary oocyteCL:000065581.25gold quality
right testisUBERON:000453481.22gold quality
nucleus accumbensUBERON:000188281.21gold quality
right frontal lobeUBERON:000281081.14gold quality
C1 segment of cervical spinal cordUBERON:000646981.12gold quality
cerebral cortexUBERON:000095681.05gold quality
hypothalamusUBERON:000189880.95gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no3.03

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

20 targeting TTLL1, 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-3613-3P100.0076.367965
HSA-MIR-548AZ-5P99.8369.943230
HSA-MIR-548T-5P99.8369.913220
HSA-MIR-451799.7669.191867
HSA-MIR-128399.6972.423009
HSA-MIR-360999.5269.892587
HSA-MIR-548AH-5P99.5269.732626
HSA-MIR-5584-5P99.4968.222814
HSA-MIR-127699.3668.181642
HSA-MIR-124499.3368.38832
HSA-MIR-154-5P98.9266.65733
HSA-MIR-519A-2-5P98.7871.741401
HSA-MIR-520B-5P98.7871.741401
HSA-MIR-6796-3P98.6865.49689
HSA-MIR-374B-3P98.6368.241360
HSA-MIR-219A-2-3P98.6268.78797
HSA-MIR-3158-3P98.4564.25560
HSA-MIR-6773-3P98.1765.511213
HSA-MIR-215-3P97.0268.011209
HSA-MIR-317494.6363.64577

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriottll1ENSDARG00000090778
mus_musculusTtll1ENSMUSG00000022442
rattus_norvegicusTtll1ENSRNOG00000010141
drosophila_melanogasterTTLL1AFBGN0030823
drosophila_melanogasterTTLL1BFBGN0052238

Paralogs (12): TTLL12 (ENSG00000100304), TTLL2 (ENSG00000120440), TTLL9 (ENSG00000131044), TTLL4 (ENSG00000135912), TTLL7 (ENSG00000137941), TTLL8 (ENSG00000138892), TTLL10 (ENSG00000162571), TTLL6 (ENSG00000170703), TTLL11 (ENSG00000175764), KPRP (ENSG00000203786), TTLL13 (ENSG00000213471), TTLL3 (ENSG00000214021)

Protein

Protein identifiers

Polyglutamylase complex subunit TTLL1O95922 (reviewed: O95922)

Alternative names: Tubulin polyglutamylase TTLL1, Tubulin polyglutamylase complex subunit 3, Tubulin–tyrosine ligase-like protein 1

All UniProt accessions (1): O95922

UniProt curated annotations — full annotation on UniProt →

Function. Catalytic subunit of a polyglutamylase complex which modifies tubulin, generating side chains of glutamate on the gamma-carboxyl group of specific glutamate residues within the C-terminal tail of tubulin. Probably involved in the side-chain elongation step of the polyglutamylation reaction rather than the initiation step. Modifies both alpha- and beta-tubulins with a preference for the alpha-tail. Unlike most polyglutamylases of the tubulin–tyrosine ligase family, only displays a catalytic activity when in complex with other proteins as it is most likely lacking domains important for autonomous activity. Part of the neuronal tubulin polyglutamylase complex. Mediates cilia and flagella polyglutamylation which is essential for their biogenesis and motility. Involved in respiratory motile cilia function through the regulation of beating asymmetry. Essential for sperm flagella biogenesis, motility and male fertility. Involved in KLF4 glutamylation which impedes its ubiquitination, thereby leading to somatic cell reprogramming, pluripotency maintenance and embryogenesis.

Subunit / interactions. Part of the neuronal tubulin polyglutamylase complex which contains TPGS1, TPGS2, TTLL1, LRRC49 and NICN1. Interacts with PCM1, CSTPP1 and LRRC49.

Subcellular location. Cytoplasm. Cytoskeleton. Cilium basal body. Cilium axoneme. Cell projection. Cilium. Flagellum.

Tissue specificity. Expressed in a wide range of tissues. Has a stronger expression in heart, brain and testis.

Domain organisation. Gln-144 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 polyglutamylase family.

Isoforms (3)

UniProt IDNamesCanonical?
O95922-1A, TTLL1ayes
O95922-2B, TTLL1b, Truncated
O95922-44

RefSeq proteins (1): NP_036395* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR004344TTL/TTLL_famFamily

Pfam: PF03133

Catalyzed reactions (Rhea), 1 shown:

  • (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 (22 total): binding site 13, splice variant 3, chain 1, domain 1, site 1, region of interest 1, sequence variant 1, mutagenesis site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O95922-F186.070.63

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): 144 (essential for specifying alpha-elongation versus initiation step of the polyglutamylase activity)

Ligand- & substrate-binding residues (13): 259; 313; 326; 326; 328; 344; 138; 144–145; 144; 181–184; 194–196; 220

Mutagenesis-validated functional residues (1):

PositionPhenotype
326abolishes microtubule polyglutamylation. decreases map4 recruitment to microtubules.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

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

MSigDB gene sets: 172 (showing top): GOBP_HINDBRAIN_DEVELOPMENT, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, GOBP_METENCEPHALON_DEVELOPMENT, GOBP_RESPIRATORY_GASEOUS_EXCHANGE_BY_RESPIRATORY_SYSTEM, TGCGCANK_UNKNOWN, GOBP_CEREBELLAR_PURKINJE_CELL_LAYER_FORMATION, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GOBP_CEREBELLAR_CORTEX_MORPHOGENESIS, GOBP_RESPIRATORY_SYSTEM_PROCESS, GOBP_NEUROGENESIS, GOBP_MALE_GAMETE_GENERATION, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_IN_UTERO_EMBRYONIC_DEVELOPMENT, GOBP_CEREBELLAR_CORTEX_DEVELOPMENT

GO Biological Process (13): microtubule cytoskeleton organization (GO:0000226), immune response in nasopharyngeal-associated lymphoid tissue (GO:0002395), sperm axoneme assembly (GO:0007288), protein polyglutamylation (GO:0018095), cerebellar Purkinje cell differentiation (GO:0021702), mucociliary clearance (GO:0120197), regulation of blastocyst development (GO:0120222), epithelial cilium movement involved in extracellular fluid movement (GO:0003351), flagellated sperm motility (GO:0030317), axoneme assembly (GO:0035082), protein modification process (GO:0036211), microtubule polymerization (GO:0046785), cilium disassembly (GO:0061523)

GO Molecular Function (7): 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, elongating (GO:0106438), nucleotide binding (GO:0000166), ligase activity (GO:0016874)

GO Cellular Component (9): extracellular region (GO:0005576), microtubule (GO:0005874), axoneme (GO:0005930), motile cilium (GO:0031514), 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
cellular anatomical structure4
protein-glutamic acid ligase activity2
cilium2
cytoskeleton organization1
microtubule-based process1
immune response in gut-associated lymphoid tissue1
developmental process involved in reproduction1
axoneme assembly1
sperm flagellum assembly1
peptidyl-glutamic acid modification1
cell differentiation in hindbrain1
cerebellar Purkinje cell layer formation1
central nervous system neuron differentiation1
respiratory system process1
epithelial cilium movement involved in extracellular fluid movement1
blastocyst development1
regulation of developmental process1
cilium movement1
extracellular transport1
microtubule-based transport1
cilium-dependent cell motility1
cilium movement involved in cell motility1
sperm motility1
microtubule bundle formation1
cellular component assembly1
cilium assembly1
protein metabolic process1
macromolecule modification1
microtubule nucleation1
microtubule polymerization or depolymerization1
protein polymerization1
supramolecular fiber organization1
cilium organization1
organelle disassembly1
adenyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
cytoskeletal protein binding1
cation binding1
nucleoside phosphate binding1
heterocyclic compound binding1

Protein interactions and networks

STRING

656 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TTLL1CEP41Q9BYV8643
TTLL1AGTPBP1Q9UPW5612
TTLL1TTLL12Q14166609
TTLL1LRRC49Q8IUZ0595
TTLL1SPASTQ9UBP0545
TTLL1AGBL4Q5VU57543
TTLL1IQUBQ8NA54512
TTLL1AGBL5Q8NDL9506
TTLL1TTLL5Q6EMB2483
TTLL1TTLL11Q8NHH1483
TTLL1NICN1Q9BSH3483
TTLL1CPXM2Q8N436474
TTLL1CHCHD1Q96BP2473
TTLL1CFAP97Q9P2B7457
TTLL1TTLL4Q14679451

IntAct

13 interactions, top by confidence:

ABTypeScore
NICN1TTLL1psi-mi:“MI:0914”(association)0.640
TTLL1CDC27psi-mi:“MI:0914”(association)0.640
TTLL1LRRK2psi-mi:“MI:0407”(direct interaction)0.440
TTLL1TCP1psi-mi:“MI:0915”(physical association)0.400
TTLL1H1-5psi-mi:“MI:0915”(physical association)0.400
TTLL1H1-2psi-mi:“MI:0915”(physical association)0.400
TTLL1CAMK2Bpsi-mi:“MI:0914”(association)0.350
CSTPP1KRBA1psi-mi:“MI:0914”(association)0.350
S1PR1ISLRpsi-mi:“MI:0914”(association)0.350
TTLL1RGS12psi-mi:“MI:0914”(association)0.350

BioGRID (80): CDC27 (Affinity Capture-MS), CCT6B (Affinity Capture-MS), ANAPC5 (Affinity Capture-MS), CDC16 (Affinity Capture-MS), HECTD1 (Affinity Capture-MS), ANAPC1 (Affinity Capture-MS), ANAPC4 (Affinity Capture-MS), DNAJB4 (Affinity Capture-MS), ANAPC16 (Affinity Capture-MS), TBC1D19 (Affinity Capture-MS), LRRC49 (Affinity Capture-MS), CDC23 (Affinity Capture-MS), TPGS2 (Affinity Capture-MS), ANAPC2 (Affinity Capture-MS), HERC1 (Affinity Capture-MS)

ESM2 similar proteins: A2APC3, A4Q9E4, A8X9V4, A9X4T1, B2GUB3, B2RR83, H2KZM9, O16102, O43314, O95922, P08487, P10686, P16259, P16885, P19174, P20807, P23678, P24135, P43368, P49619, P49620, P49621, P51186, Q09639, Q09647, Q0VC71, Q14562, Q14BI7, Q22070, Q23SI8, Q3SXZ7, Q3SZH6, Q564U4, Q5PPI9, Q5R746, Q5REW0, Q62077, Q641W7, Q64691, Q6NS52

Diamond homologs: A2APC3, A4Q9E4, A4Q9E5, A4Q9E8, A4Q9F6, A6NNM8, A6PVC2, A8CVX7, B2GUB3, O95922, P0CAZ0, Q0VC71, Q1ECV4, Q23K29, Q23SI8, Q3SXZ7, Q3SZH6, Q4R7H0, Q564U4, Q5PPI9, Q5R978, Q641W7, Q6EEF3, Q6EMB2, Q8CHB8, Q8N841, Q91V51, Q9BWV7, Q9Y4R7, A4Q9F0, A4Q9F1, A4Q9F4, A8X9V4, E9P886, F7E540, H2KZM9, P38160, P38584, Q09647, Q14679

SIGNOR signaling

1 interactions.

AEffectBMechanism
TTLL1“form complex”“Tubulin polyglutamylase complex”binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance45
Likely benign2
Benign6

Top pathogenic / likely-pathogenic (0)

SpliceAI

2369 predictions. Top by Δscore:

VariantEffectΔscore
22:43046401:CACA:Cdonor_gain1.0000
22:43046403:CA:Cdonor_gain1.0000
22:43046404:A:ACdonor_gain1.0000
22:43046405:C:CCdonor_gain1.0000
22:43046406:TTACA:Tdonor_loss1.0000
22:43046408:A:ACdonor_gain1.0000
22:43046408:A:Cdonor_loss1.0000
22:43046409:C:CAdonor_gain1.0000
22:43046409:CA:Cdonor_gain1.0000
22:43046409:CAG:Cdonor_gain1.0000
22:43046409:CAGA:Cdonor_gain1.0000
22:43046409:CAGAA:Cdonor_gain1.0000
22:43046434:T:TAdonor_gain1.0000
22:43046435:C:Adonor_gain1.0000
22:43051796:GTTA:Gdonor_loss1.0000
22:43051797:TTA:Tdonor_loss1.0000
22:43051798:TA:Tdonor_loss1.0000
22:43051799:A:AGdonor_loss1.0000
22:43051800:CCTC:Cdonor_loss1.0000
22:43051883:ACCGG:Aacceptor_gain1.0000
22:43051884:CCGG:Cacceptor_gain1.0000
22:43051884:CCGGC:Cacceptor_gain1.0000
22:43051885:CGG:Cacceptor_gain1.0000
22:43051885:CGGC:Cacceptor_gain1.0000
22:43059379:CTCA:Cdonor_loss1.0000
22:43059381:CAC:Cdonor_loss1.0000
22:43059382:A:ACdonor_gain1.0000
22:43059383:C:CAdonor_loss1.0000
22:43059383:C:CCdonor_gain1.0000
22:43063811:AC:Adonor_gain1.0000

AlphaMissense

2798 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
22:43046512:A:GL347P1.000
22:43046520:C:AK344N1.000
22:43046520:C:GK344N1.000
22:43046522:T:CK344E1.000
22:43046524:A:GL343P1.000
22:43046530:C:GR341P1.000
22:43046533:T:AD340V1.000
22:43046533:T:GD340A1.000
22:43046534:C:GD340H1.000
22:43046554:A:GL333P1.000
22:43046560:G:CP331R1.000
22:43046560:G:TP331Q1.000
22:43046561:G:AP331S1.000
22:43046561:G:TP331T1.000
22:43046566:G:TA329E1.000
22:43046568:A:CN328K1.000
22:43046568:A:TN328K1.000
22:43046570:T:CN328D1.000
22:43051801:C:AE326D1.000
22:43051801:C:GE326D1.000
22:43051802:T:AE326V1.000
22:43051802:T:GE326A1.000
22:43051803:C:TE326K1.000
22:43051808:A:GL324P1.000
22:43051840:G:CD313E1.000
22:43051840:G:TD313E1.000
22:43051841:T:AD313V1.000
22:43051841:T:CD313G1.000
22:43051841:T:GD313A1.000
22:43051842:C:AD313Y1.000

dbSNP variants (sampled 300 via entrez): RS1000020795 (22:43077778 G>A), RS1000030097 (22:43058720 G>A), RS1000061890 (22:43044575 A>G), RS1000184333 (22:43052722 G>A), RS1000188188 (22:43087922 C>T), RS1000349576 (22:43082754 C>A,T), RS1000362001 (22:43046855 G>C), RS1000433953 (22:43074033 A>G), RS1000460867 (22:43039410 C>T), RS1000470527 (22:43041285 A>G), RS1000479128 (22:43084547 G>C), RS1000562930 (22:43077496 T>C), RS1000564319 (22:43069411 C>A,T), RS1000583417 (22:43045069 G>C), RS1000613732 (22:43072928 G>A)

Disease associations

OMIM: gene MIM:608955 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST009319_2Uric acid elevation in response to thiazide-like diuretic in hypertension1.000000e-07
GCST012490_28Femur bone mineral density x serum urate levels interaction2.000000e-12

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004761uric acid measurement
EFO:0004531urate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidincreases expression, decreases expression3
Acetaminophenincreases expression2
GSK-J4decreases expression1
afuresertibincreases expression1
urushioldecreases expression1
bisphenol Aincreases expression1
sodium arseniteaffects splicing, decreases expression1
potassium chromate(VI)affects cotreatment, decreases expression1
epigallocatechin gallatedecreases expression, affects cotreatment1
di-n-butylphosphoric acidaffects expression1
abrinedecreases expression1
jinfukangaffects cotreatment, increases expression1
(+)-JQ1 compoundincreases expression1
Sunitinibincreases expression1
Cisplatinaffects cotreatment, increases expression1
Dichlorodiphenyl Dichloroethylenedecreases expression1
Doxorubicindecreases expression1
Endosulfanincreases expression1
Nickeldecreases expression1
Niclosamideincreases expression1
Silicon Dioxidedecreases expression1
Tobacco Smoke Pollutiondecreases expression1
Okadaic Aciddecreases expression1
Copper Sulfatedecreases expression1
Acrylamidedecreases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.