TCP11L1

Summary

TCP11L1 (t-complex 11 like 1, HGNC:25655) is a protein-coding gene on chromosome 11p13, encoding T-complex protein 11-like protein 1 (Q9NUJ3).

Predicted to be involved in signal transduction. Located in microtubule.

Source: NCBI Gene 55346 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 67 total
• MANE Select transcript: NM_018393

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25655
Approved symbol	TCP11L1
Name	t-complex 11 like 1
Location	11p13
Locus type	gene with protein product
Status	Approved
Aliases	FLJ11336
Ensembl gene	ENSG00000176148
Ensembl biotype	protein_coding
Entrez	55346

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 11 protein_coding, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000334274, ENST00000432887, ENST00000527661, ENST00000528107, ENST00000528898, ENST00000528962, ENST00000530171, ENST00000530419, ENST00000531632, ENST00000532687, ENST00000602733, ENST00000862423, ENST00000862424, ENST00000949219, ENST00000949220

RefSeq mRNA: 2 — MANE Select: NM_018393 NM_001145541, NM_018393

CCDS: CCDS7882

Canonical transcript exons

ENST00000334274 — 10 exons

Exon	Start	End
ENSE00001612247	33054593	33054725
ENSE00002142261	33039572	33039792
ENSE00003478120	33068687	33068859
ENSE00003485810	33058959	33059095
ENSE00003501420	33057919	33058139
ENSE00003583607	33061530	33061726
ENSE00003662531	33057115	33057235
ENSE00003684938	33065830	33066011
ENSE00003799950	33043750	33043936
ENSE00003845903	33072474	33073550

Expression profiles

Bgee: expression breadth ubiquitous, 214 present calls, max score 88.24.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.3157 / max 287.0723, expressed in 1806 samples.

FANTOM5 promoters (11 alternative TSS)

Promoter ID	TPM avg	Samples expressed
113651	12.3729	1789
113658	2.6470	1145
113653	1.1515	724
113656	0.9137	610
113650	0.7724	429
113659	0.7339	468
113652	0.5743	322
113657	0.3865	188
113649	0.3067	140
113654	0.2955	104

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.24	gold quality
vena cava	UBERON:0004087	87.85	silver quality
type B pancreatic cell	CL:0000169	87.35	gold quality
olfactory bulb	UBERON:0002264	86.96	gold quality
diaphragm	UBERON:0001103	85.54	gold quality
calcaneal tendon	UBERON:0003701	84.89	gold quality
triceps brachii	UBERON:0001509	84.57	gold quality
corpus callosum	UBERON:0002336	84.16	gold quality
parotid gland	UBERON:0001831	84.03	silver quality
colonic epithelium	UBERON:0000397	83.97	gold quality
prefrontal cortex	UBERON:0000451	83.96	gold quality
gluteal muscle	UBERON:0002000	83.58	gold quality
tendon of biceps brachii	UBERON:0008188	83.53	gold quality
tendon	UBERON:0000043	83.35	gold quality
stromal cell of endometrium	CL:0002255	83.12	gold quality
male germ cell	CL:0000015	82.66	gold quality
sperm	CL:0000019	82.02	gold quality
smooth muscle tissue	UBERON:0001135	82.02	gold quality
cortical plate	UBERON:0005343	81.45	gold quality
tongue squamous epithelium	UBERON:0006919	81.45	gold quality
bone marrow cell	CL:0002092	81.26	gold quality
monocyte	CL:0000576	80.87	gold quality
hair follicle	UBERON:0002073	80.82	gold quality
mononuclear cell	CL:0000842	80.74	gold quality
leukocyte	CL:0000738	80.53	gold quality
gall bladder	UBERON:0002110	80.45	gold quality
ganglionic eminence	UBERON:0004023	80.45	gold quality
descending thoracic aorta	UBERON:0002345	79.96	gold quality
popliteal artery	UBERON:0002250	79.87	gold quality
tibial artery	UBERON:0007610	79.86	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

80 targeting TCP11L1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	tcp11l1	ENSDARG00000031890
mus_musculus	Tcp11l1	ENSMUSG00000027175
rattus_norvegicus	Tcp11l1	ENSRNOG00000042576
drosophila_melanogaster	CG16721	FBGN0029820
caenorhabditis_elegans		WBGENE00010875

Paralogs (4): TCP11 (ENSG00000124678), TCP11L2 (ENSG00000166046), TCP11X2 (ENSG00000215029), TCP11X1 (ENSG00000268235)

Protein

Protein identifiers

T-complex protein 11-like protein 1 — Q9NUJ3 (reviewed: Q9NUJ3)

All UniProt accessions (7): Q9NUJ3, E9PJ55, E9PMB0, E9PP52, E9PS88, H0YES4, R4GNF5

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the TCP11 family.

RefSeq proteins (2): NP_001139013, NP_060863* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR008862	Tcp11	Family

Pfam: PF05794

UniProt features (6 total): sequence variant 2, chain 1, region of interest 1, compositionally biased region 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NUJ3-F1	82.20	0.59

Functional residue map

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

Post-translational modifications (1): 56

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 72 (showing top): GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_DN, SENESE_HDAC1_AND_HDAC2_TARGETS_DN, RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN, BASAKI_YBX1_TARGETS_UP, SENESE_HDAC3_TARGETS_DN, KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP, SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A12, FORTSCHEGGER_PHF8_TARGETS_DN, GOCC_SUPRAMOLECULAR_COMPLEX, GOCC_POLYMERIC_CYTOSKELETAL_FIBER, GOCC_SUPRAMOLECULAR_POLYMER, CIITA_TARGET_GENES, DACH1_TARGET_GENES, E2F5_TARGET_GENES, HOXB4_TARGET_GENES

GO Biological Process (1): signal transduction (GO:0007165)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (1): microtubule (GO:0005874)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cell communication	1
cellular process	1
signaling	1
regulation of cellular process	1
cellular response to stimulus	1
binding	1
microtubule cytoskeleton	1
polymeric cytoskeletal fiber	1

Protein interactions and networks

STRING

447 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TCP11L1	CCDC73	Q6ZRK6	645
TCP11L1	QSER1	Q2KHR3	618
TCP11L1	DEPDC7	Q96QD5	609
TCP11L1	PRRG4	Q9BZD6	584
TCP11L1	CSTF3	Q12996	558
TCP11L1	EIF3M	Q7L2H7	527
TCP11L1	COMMD9	Q9P000	517
TCP11L1	C11orf91	Q3C1V1	507
TCP11L1	DNAJC24	Q6P3W2	488
TCP11L1	ARL14EP	Q8N8R7	475
TCP11L1	CCDC47	Q96A33	472
TCP11L1	ELP4	Q96EB1	450
TCP11L1	MYZAP	P0CAP1	430
TCP11L1	SMIM14	Q96QK8	419
TCP11L1	CCDC34	Q96HJ3	405

IntAct

138 interactions, top by confidence:

A	B	Type	Score
ARPC5	ARPC3	psi-mi:“MI:0914”(association)	0.730
TUBB	PLD2	psi-mi:“MI:0914”(association)	0.640
VPS52	TCP11L1	psi-mi:“MI:0915”(physical association)	0.560
HMG20A	TCP11L1	psi-mi:“MI:0915”(physical association)	0.560
MEOX1	TCP11L1	psi-mi:“MI:0915”(physical association)	0.560
REL	TCP11L1	psi-mi:“MI:0915”(physical association)	0.560
PAX6	TCP11L1	psi-mi:“MI:0915”(physical association)	0.560
ERCC6L2	TCP11L1	psi-mi:“MI:0915”(physical association)	0.560
MAGEA12	TCP11L1	psi-mi:“MI:0915”(physical association)	0.560
LHX2	TCP11L1	psi-mi:“MI:0915”(physical association)	0.560
TBX6	TCP11L1	psi-mi:“MI:0915”(physical association)	0.560
TCP11L1	CNOT7	psi-mi:“MI:0915”(physical association)	0.560
DDIT4L	TCP11L1	psi-mi:“MI:0915”(physical association)	0.560
PRXL2B	TCP11L1	psi-mi:“MI:0915”(physical association)	0.560
TSNAX	TCP11L1	psi-mi:“MI:0915”(physical association)	0.560
PSMD4	TCP11L1	psi-mi:“MI:0915”(physical association)	0.560
SNW1	TCP11L1	psi-mi:“MI:0915”(physical association)	0.560
IPO4	TCP11L1	psi-mi:“MI:0915”(physical association)	0.560
TCP11L1	PLEKHS1	psi-mi:“MI:0915”(physical association)	0.560
SDCBP2	TCP11L1	psi-mi:“MI:0915”(physical association)	0.560
TRIM21	TCP11L1	psi-mi:“MI:0915”(physical association)	0.560
WWTR1	TCP11L1	psi-mi:“MI:0915”(physical association)	0.560
PRSS22	PPM1A	psi-mi:“MI:0914”(association)	0.560
TUBB3	POTEF	psi-mi:“MI:0914”(association)	0.530
TUBB2B	EML2	psi-mi:“MI:0914”(association)	0.530
TTC5	TUBA4A	psi-mi:“MI:0914”(association)	0.530
FAM174A	BLTP3B	psi-mi:“MI:0914”(association)	0.530

BioGRID (89): TCP11L1 (Affinity Capture-MS), TCP11L1 (Affinity Capture-MS), TCP11L1 (Affinity Capture-MS), TCP11L1 (Affinity Capture-MS), TCP11L1 (Affinity Capture-MS), TCP11L1 (Affinity Capture-MS), TCP11L1 (Affinity Capture-MS), TCP11L1 (Affinity Capture-MS), TCP11L1 (Affinity Capture-MS), TCP11L1 (Affinity Capture-MS), TCP11L1 (Affinity Capture-MS), TCP11L1 (Affinity Capture-MS), TCP11L1 (Affinity Capture-RNA), TCP11L1 (Affinity Capture-MS), TCP11L1 (Affinity Capture-MS)

ESM2 similar proteins: A0JMW6, A1L1K3, A1L2I9, A2BID5, A2RV06, A7Z033, B4DZS4, O70481, O75153, P52590, P57740, Q01755, Q08CY4, Q0IHW8, Q14746, Q2PW47, Q568Z0, Q5BLE2, Q5FWU8, Q5H9J9, Q5PQS3, Q5SW19, Q5U249, Q5XI00, Q62825, Q68F70, Q68Y81, Q6GPP1, Q6GR21, Q6IV68, Q6KAR6, Q6NRB7, Q7SYB2, Q7T0S7, Q80V62, Q8BH74, Q8BTG3, Q8CDT7, Q8CIM8, Q8IWV7

Diamond homologs: A7Z033, B4DZS4, Q01755, Q568Z0, Q5H9J9, Q5XI00, Q8BTG3, Q8K1H7, Q8N4U5, Q8WWU5, Q9NUJ3

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 117 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane	13	104.0×	1e-22
Transport of connexons to the plasma membrane	13	104.0×	1e-22
Gap junction trafficking and regulation	13	91.0×	6e-22
Gap junction trafficking	13	91.0×	6e-22
Post-chaperonin tubulin folding pathway	13	91.0×	6e-22
Formation of tubulin folding intermediates by CCT/TriC	13	80.9×	4e-21
Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding	13	78.0×	7e-21
Activation of AMPK downstream of NMDARs	13	72.8×	2e-20

GO biological processes:

GO term	Partners	Fold	FDR
microtubule cytoskeleton organization	17	21.0×	2e-15
mitotic cell cycle	14	19.1×	5e-12
cerebral cortex development	6	12.6×	1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	60
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3026 predictions. Top by Δscore:

Variant	Effect	Δscore
11:33043937:G:GG	donor_gain	1.0000
11:33054586:GTTAC:G	acceptor_loss	1.0000
11:33054587:TTACA:T	acceptor_loss	1.0000
11:33054589:ACAG:A	acceptor_loss	1.0000
11:33054590:CA:C	acceptor_loss	1.0000
11:33054591:A:AG	acceptor_gain	1.0000
11:33054592:G:GA	acceptor_gain	1.0000
11:33054592:GCT:G	acceptor_gain	1.0000
11:33054592:GCTA:G	acceptor_gain	1.0000
11:33054724:AGGT:A	donor_loss	1.0000
11:33054726:G:GG	donor_gain	1.0000
11:33054726:GTA:G	donor_loss	1.0000
11:33054727:T:A	donor_loss	1.0000
11:33057105:A:AG	acceptor_gain	1.0000
11:33057105:ACT:A	acceptor_gain	1.0000
11:33057106:C:G	acceptor_gain	1.0000
11:33057107:T:A	acceptor_gain	1.0000
11:33057913:TTGTA:T	acceptor_loss	1.0000
11:33057917:A:AG	acceptor_gain	1.0000
11:33057918:G:GG	acceptor_gain	1.0000
11:33057918:G:GT	acceptor_loss	1.0000
11:33057918:GA:G	acceptor_gain	1.0000
11:33057918:GACT:G	acceptor_gain	1.0000
11:33057938:T:A	acceptor_gain	1.0000
11:33057942:T:TA	acceptor_gain	1.0000
11:33058093:G:GT	donor_gain	1.0000
11:33058097:T:G	donor_gain	1.0000
11:33058111:GACAT:G	donor_gain	1.0000
11:33058120:G:GT	donor_gain	1.0000
11:33058121:A:T	donor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000066821 (11:33051333 A>G), RS1000141753 (11:33040111 T>C), RS1000212540 (11:33039277 A>G), RS1000486041 (11:33061079 C>T), RS1000486281 (11:33068096 T>C), RS1000513619 (11:33039954 G>A,C,T), RS1000669400 (11:33049891 C>G,T), RS1000684146 (11:33063126 G>A), RS1000820247 (11:33069657 C>G,T), RS1000843521 (11:33057337 A>G,T), RS1000959989 (11:33063812 G>A,T), RS1000976831 (11:33067478 T>C), RS1001082173 (11:33051279 T>G), RS1001248437 (11:33073754 T>A), RS1001281424 (11:33060829 C>A,T)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:258040

GenCC curated gene-disease

Mondo (1): exstrophy-epispadias complex (MONDO:0017919)

Orphanet (2): Exstrophy-epispadias complex (Orphanet:322), Cloacal exstrophy (Orphanet:93929)

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST002324_8	Anger	2.000000e-06
GCST90002401_179	Platelet distribution width	1.000000e-14

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0003015	aggressive behavior
EFO:0007984	platelet component distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases methylation, increases expression, increases mutagenesis	4
Valproic Acid	affects cotreatment, increases expression	3
Aflatoxin B1	affects expression, increases expression, increases methylation	2
beauvericin	affects cotreatment, decreases expression	1
methylmercuric chloride	increases expression	1
bisphenol A	decreases expression	1
sulforaphane	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	increases expression	1
cobaltous chloride	decreases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
coumarin	decreases phosphorylation	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
perfluorooctane sulfonic acid	increases expression	1
CGP 52608	affects binding, increases reaction	1
enniatins	affects cotreatment, decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment	1
dorsomorphin	affects cotreatment, increases expression	1
bisphenol S	decreases methylation	1
Acetaminophen	increases expression	1
Doxorubicin	decreases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Ethyl Methanesulfonate	increases expression	1
Methyl Methanesulfonate	increases expression	1
Perfume	increases expression	1
Quercetin	increases expression	1
Silicon Dioxide	decreases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	increases expression	1
Cyclosporine	increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT04760028	PHASE4	COMPLETED	Study on the Influencing Factors of Electroencephalogram Parameters Under Anesthesia
NCT06106425	Not specified	UNKNOWN	Diagnostic and Prognostic Criteria of EEG in Neonatal Convulsions at Assiut University Children Hospital