TTC4

gene
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Also known as MGC5097FLJ41930CNS1

Summary

TTC4 (tetratricopeptide repeat domain 4, HGNC:12394) is a protein-coding gene on chromosome 1p32.3, encoding Hsp70/Hsp90 co-chaperone CNS1 homolog (O95801). Co-chaperone that recruits molecular chaperones Hsp90 (HSC82 and HSP82) and Hsp70 (SSA1) to nascent polypeptides, facilitating their proper folding into functional proteins. It is a selective cancer dependency (DepMap: 81.2% of cell lines).

This gene encodes a protein that contains tetratricopeptide (TPR) repeats, which often mediate protein-protein interactions and chaperone activity. The encoded protein interacts with heat shock proteins 70 and 90. Alternative splicing results in multiple transcript variants. Naturally-occuring readthrough transcription occurs from upstream gene MROH (maestro heat-like repeat family member 7) to this gene.

Source: NCBI Gene 7268 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 1 total
  • Cancer dependency (DepMap): dependent in 81.2% of screened cell lines
  • MANE Select transcript: NM_004623

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:12394
Approved symbolTTC4
Nametetratricopeptide repeat domain 4
Location1p32.3
Locus typegene with protein product
StatusApproved
AliasesMGC5097, FLJ41930, CNS1
Ensembl geneENSG00000243725
Ensembl biotypeprotein_coding
OMIM606753
Entrez7268

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 7 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000371281, ENST00000371284, ENST00000486091, ENST00000486621, ENST00000876949, ENST00000876950, ENST00000934475, ENST00000934476, ENST00000970583, ENST00000970584

RefSeq mRNA: 2 — MANE Select: NM_004623 NM_001291333, NM_004623

CCDS: CCDS596

Canonical transcript exons

ENST00000371281 — 10 exons

ExonStartEnd
ENSE000019162595471586154716019
ENSE000019506355474141154742657
ENSE000034757595473362954733710
ENSE000034765385473758254737664
ENSE000034863125472267554722799
ENSE000034929445472116354721240
ENSE000035335615471749254717653
ENSE000035895115472834654728432
ENSE000035982025473148654731700
ENSE000036805105471660054716717

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 91.43.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 28.7301 / max 265.9175, expressed in 1819 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
296227.65031818
29611.0797682

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
gastrocnemiusUBERON:000138891.43gold quality
muscle of legUBERON:000138391.02gold quality
islet of LangerhansUBERON:000000690.51gold quality
hindlimb stylopod muscleUBERON:000425289.72gold quality
skeletal muscle tissueUBERON:000113489.34gold quality
muscle tissueUBERON:000238588.77gold quality
C1 segment of cervical spinal cordUBERON:000646988.70gold quality
pituitary glandUBERON:000000788.45gold quality
adenohypophysisUBERON:000219688.45gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047387.42gold quality
ventricular zoneUBERON:000305387.41gold quality
apex of heartUBERON:000209887.34gold quality
heart left ventricleUBERON:000208486.88gold quality
hypothalamusUBERON:000189886.78gold quality
right frontal lobeUBERON:000281086.65gold quality
caudate nucleusUBERON:000187386.59gold quality
Brodmann (1909) area 9UBERON:001354086.08gold quality
smooth muscle tissueUBERON:000113586.04gold quality
lower esophagus muscularis layerUBERON:003583385.99gold quality
lower esophagusUBERON:001347385.98gold quality
heartUBERON:000094885.95gold quality
nucleus accumbensUBERON:000188285.94gold quality
endometriumUBERON:000129585.89gold quality
dorsolateral prefrontal cortexUBERON:000983485.87gold quality
brainUBERON:000095585.80gold quality
amygdalaUBERON:000187685.79gold quality
pancreasUBERON:000126485.78gold quality
skin of legUBERON:000151185.77gold quality
esophagogastric junction muscularis propriaUBERON:003584185.74gold quality
putamenUBERON:000187485.66gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes2.86

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

34 targeting TTC4, 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-118499.9968.191458
HSA-MIR-33A-5P99.9968.621055
HSA-MIR-33B-5P99.9968.581062
HSA-MIR-806899.9873.852376
HSA-MIR-145-5P99.9271.131836
HSA-MIR-5195-3P99.9270.921877
HSA-MIR-132399.8369.892471
HSA-MIR-808099.8267.521342
HSA-MIR-453099.6966.471509
HSA-MIR-58699.6570.402051
HSA-MIR-3120-3P99.5470.282669
HSA-MIR-5009-3P99.4569.431341
HSA-MIR-942-5P99.4168.401977
HSA-MIR-183-5P99.3172.271164
HSA-MIR-3678-3P99.3167.101432
HSA-MIR-6815-3P99.1368.981530
HSA-MIR-1207-3P98.9966.221532
HSA-MIR-143-5P98.9868.87946
HSA-MIR-3194-3P98.8366.221167
HSA-MIR-5006-5P98.7966.921246
HSA-MIR-797798.6566.182590
HSA-MIR-2467-3P98.6567.181969
HSA-MIR-6728-3P98.6367.631534
HSA-MIR-950098.6266.541845
HSA-MIR-147A98.3366.40795
HSA-MIR-316698.2466.631223
HSA-MIR-6787-3P97.7566.171233
HSA-MIR-3928-3P97.6166.531096
HSA-MIR-6818-5P97.5067.101167
HSA-MIR-128997.4665.37655

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 81.2% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 4)

  • TTC4 is highly expressed in malignant melanoma (PMID:18320024)
  • Studies identi fi ed a novel signal of nuclear localization (NLS) in all MSL1 protein isoforms and found that the combination of both NLS allows for its intra-nuclear focal accumulation and nuclear transport of TTC4 while all MSL1 isoforms affect H4K16Ac. (PMID:24913909)
  • Study identified TTC4 as a TBK1 interactor and positive regulator of Sendai virus-induced innate immunity. (PMID:29251827)
  • Promoting TTC4 and HSP70 interaction and translocation of annexin A7 to lysosome inhibits apoptosis in vascular endothelial cells. (PMID:33000523)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriottc4ENSDARG00000044405
mus_musculusTtc4ENSMUSG00000025413
rattus_norvegicusTtc4ENSRNOG00000042467
drosophila_melanogasterDpit47FBGN0266518
caenorhabditis_elegansWBGENE00015916

Paralogs (18): RPAP3 (ENSG00000005175), TOMM34 (ENSG00000025772), ST13 (ENSG00000100380), STUB1 (ENSG00000103266), SPAG1 (ENSG00000104450), SGTA (ENSG00000104969), TTC1 (ENSG00000113312), TTC31 (ENSG00000115282), UNC45A (ENSG00000140553), UNC45B (ENSG00000141161), SPATA16 (ENSG00000144962), TTC12 (ENSG00000149292), TOMM70 (ENSG00000154174), SUGT1 (ENSG00000165416), STIP1 (ENSG00000168439), TTC32 (ENSG00000183891), SGTB (ENSG00000197860), DNAAF4 (ENSG00000256061)

Protein

Protein identifiers

Hsp70/Hsp90 co-chaperone CNS1 homologO95801 (reviewed: O95801)

Alternative names: Tetratricopeptide repeat protein 4

All UniProt accessions (1): O95801

UniProt curated annotations — full annotation on UniProt →

Function. Co-chaperone that recruits molecular chaperones Hsp90 (HSC82 and HSP82) and Hsp70 (SSA1) to nascent polypeptides, facilitating their proper folding into functional proteins. Client proteins include eukaryotic elongation factor eEF2, a key player in cellular translation. Stimulates SSA1 ATPase activity, but not Hsp90 ATPase activity. Promotes Sendai virus (SeV)-induced host cell innate immune responses.

Subunit / interactions. Interacts (via TPR repeats) with HSP90AB1. Interacts with HSPA8 and CDC6. Interacts with TBK1. Interacts with MSL1.

Subcellular location. Nucleus. Nucleoplasm. Cytoplasm.

Tissue specificity. Highly expressed in proliferating tissue and tumor cell lines but not in normal cell lines.

Similarity. Belongs to the TTC4 family.

RefSeq proteins (2): NP_001278262, NP_004614* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR011990TPR-like_helical_dom_sfHomologous_superfamily
IPR019734TPR_rptRepeat
IPR044059Csn1/TTC4_wheelDomain

Pfam: PF18972

UniProt features (37 total): strand 7, mutagenesis site 6, helix 6, modified residue 4, turn 4, site 4, repeat 3, chain 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
6HFOX-RAY DIFFRACTION1.65

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O95801-F187.310.65

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 (4): 77 (essential for interaction with cdc6); 152 (essential for interaction with hspa8); 156 (essential for interaction with hspa8); 217 (essential for interaction with cdc6)

Post-translational modifications (4): 51, 243, 1, 47

Mutagenesis-validated functional residues (6):

PositionPhenotype
42no effect on interaction with hspa8, hsp90ab1 and cdc6.
67no effect on interaction with hspa8, hsp90ab1 and cdc6.
77no effect on interaction with hspa8 and hsp90ab1. loss of interaction with cdc6.
152loss of interaction with hspa8.
156loss of interaction with hspa8.
217no effect on interaction with hspa8 and hsp90ab1. loss of interaction with cdc6.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 120 (showing top): GSE45365_NK_CELL_VS_BCELL_DN, GOBP_PROTEIN_MATURATION, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, GOBP_PROTEIN_FOLDING, GOBP_DEFENSE_RESPONSE_TO_VIRUS, DANG_BOUND_BY_MYC, GOBP_RESPONSE_TO_VIRUS, GOCC_INTERMEDIATE_FILAMENT_CYTOSKELETON, BENPORATH_MYC_MAX_TARGETS, GOMF_HEAT_SHOCK_PROTEIN_BINDING, GOMF_HSP90_PROTEIN_BINDING, GOMF_PROTEIN_FOLDING_CHAPERONE_BINDING, GOMF_HSP70_PROTEIN_BINDING, ALKBH3_TARGET_GENES, DIDO1_TARGET_GENES

GO Biological Process (4): protein folding (GO:0006457), innate immune response (GO:0045087), defense response to virus (GO:0051607), immune system process (GO:0002376)

GO Molecular Function (3): Hsp70 protein binding (GO:0030544), Hsp90 protein binding (GO:0051879), protein binding (GO:0005515)

GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
heat shock protein binding2
cellular anatomical structure2
cellular process1
protein maturation1
immune response1
defense response to symbiont1
defense response1
response to virus1
biological_process1
protein-folding chaperone binding1
binding1
intracellular membrane-bounded organelle1
nuclear lumen1
intracellular anatomical structure1

Protein interactions and networks

STRING

2882 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TTC4SMAD3P84022771
TTC4CDC37Q16543677
TTC4RAXQ9Y2V3665
TTC4PPIDQ08752658
TTC4FOXP3Q9BZS1608
TTC4GATA3P23771602
TTC4SATB1Q01826599
TTC4CBFBQ13951596
TTC4IL4P05112589
TTC4TNFRSF18Q9Y5U5586
TTC4TTC9CQ8N5M4573
TTC4HSP90AA1P07900573
TTC4TBX21Q9UL17567
TTC4HSP90AB1P08238566
TTC4GPS1Q13098565

IntAct

82 interactions, top by confidence:

ABTypeScore
TTC4HGH1psi-mi:“MI:0915”(physical association)0.770
TTC4HSP90AB1psi-mi:“MI:0915”(physical association)0.750
TTC4HSP90AB1psi-mi:“MI:0407”(direct interaction)0.750
TTC4HSP90AB1psi-mi:“MI:0914”(association)0.750
TTC4EDRF1psi-mi:“MI:0914”(association)0.730
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
HSP90AA1CHUKpsi-mi:“MI:0914”(association)0.670
SLC27A6TTC4psi-mi:“MI:0914”(association)0.640
TTC4SNAPC3psi-mi:“MI:0915”(physical association)0.560
TBK1TTC4psi-mi:“MI:0914”(association)0.540
TBK1TTC4psi-mi:“MI:0915”(physical association)0.540
TBK1TTC4psi-mi:“MI:0403”(colocalization)0.540
HSP90AA1USP19psi-mi:“MI:0914”(association)0.530
SERPINB13TTC4psi-mi:“MI:0914”(association)0.530
EDAAP3B1psi-mi:“MI:0914”(association)0.530
TTC4HSPA8psi-mi:“MI:0915”(physical association)0.480
TTC4CDC6psi-mi:“MI:0915”(physical association)0.480
TUBA1ATUBAL3psi-mi:“MI:2364”(proximity)0.420
MTRF1LTTC4psi-mi:“MI:0915”(physical association)0.400
TTC4psi-mi:“MI:0915”(physical association)0.400
TTC4psi-mi:“MI:0915”(physical association)0.400
TTC4RXFP4psi-mi:“MI:0915”(physical association)0.370
TTC4psi-mi:“MI:0915”(physical association)0.370
HSCBRBP5psi-mi:“MI:0914”(association)0.350
TBK1FMNL1psi-mi:“MI:0914”(association)0.350

BioGRID (190): HSP90AB3P (Affinity Capture-MS), GCC2 (Affinity Capture-MS), EDRF1 (Affinity Capture-MS), HGH1 (Affinity Capture-MS), TTC4 (Affinity Capture-MS), CTPS1 (Co-fractionation), HAT1 (Co-fractionation), PCID2 (Co-fractionation), SAC3D1 (Co-fractionation), TLN2 (Co-fractionation), TTC4 (Co-fractionation), TTC4 (Co-fractionation), TTC4 (Co-fractionation), TTC4 (Co-fractionation), TTC4 (Co-fractionation)

ESM2 similar proteins: A0A1L8G016, A1A5Q0, B3DH20, D3Z8X7, D4A1F2, E1BTG2, F1MF74, F1RA39, O14730, O60308, O88978, O94851, O95801, P51432, P70566, Q1RMR5, Q1RMT7, Q28FY0, Q2YDM7, Q3UHZ5, Q3UM18, Q4KLT3, Q4R3F0, Q4R8L2, Q5BJT6, Q5EA11, Q5ZJD3, Q6AZN0, Q6P5Q4, Q7Z569, Q80V31, Q863A4, Q863A5, Q863A6, Q863A7, Q86X45, Q8BML1, Q8CCP0, Q8R368, Q8R3H9

Diamond homologs: A1Z6M6, O95801, Q28IV3, Q5EA11, Q6NU95, Q8R3H9, A4K2V0, A6HD62, A6ZRW3, D7REX8, F1RBN2, F4IRM4, F4JTI1, F4K487, F4KCL7, O13754, O14217, O16259, O35814, O48802, O54981, O94826, P07213, P23231, P25638, P31948, P33313, P38825, P53041, P53042, Q07617, Q12118, Q13451, Q15785, Q32PZ3, Q3KRD5, Q3ZBR5, Q43207, Q4R8N7, Q5PPS5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 73 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:

PathwayPartnersFoldFDR
HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand827.2×2e-07
Autophagy513.0×2e-03
Macroautophagy510.1×3e-03
SARS-CoV-2 activates/modulates innate and adaptive immune responses57.8×8e-03

GO biological processes:

GO termPartnersFoldFDR
protein folding913.5×1e-05
protein stabilization87.8×2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance0
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1476 predictions. Top by Δscore:

VariantEffectΔscore
1:54716005:G:GTdonor_gain1.0000
1:54716015:AGAAG:Adonor_loss1.0000
1:54716017:AAG:Adonor_loss1.0000
1:54716018:AGG:Adonor_loss1.0000
1:54716019:GG:Gdonor_loss1.0000
1:54716020:G:GAdonor_loss1.0000
1:54717488:GCA:Gacceptor_loss1.0000
1:54717490:A:AGacceptor_gain1.0000
1:54717491:G:GAacceptor_gain1.0000
1:54717491:GA:Gacceptor_gain1.0000
1:54717491:GAA:Gacceptor_gain1.0000
1:54717491:GAAC:Gacceptor_gain1.0000
1:54717491:GAACA:Gacceptor_gain1.0000
1:54717638:GCACA:Gdonor_gain1.0000
1:54717643:G:GGdonor_gain1.0000
1:54717650:CTGG:Cdonor_loss1.0000
1:54717651:TGGGT:Tdonor_loss1.0000
1:54717652:GG:Gdonor_gain1.0000
1:54717653:GG:Gdonor_gain1.0000
1:54717655:T:Adonor_loss1.0000
1:54721146:AAAC:Aacceptor_gain1.0000
1:54721149:C:CAacceptor_gain1.0000
1:54728345:GC:Gacceptor_gain1.0000
1:54731485:GGCTA:Gacceptor_gain1.0000
1:54733706:TGGAG:Tdonor_loss1.0000
1:54733709:AGG:Adonor_loss1.0000
1:54733709:AGGTA:Adonor_loss1.0000
1:54733710:GG:Gdonor_loss1.0000
1:54733711:G:Adonor_loss1.0000
1:54733711:GTAAG:Gdonor_loss1.0000

AlphaMissense

2558 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:54717630:G:CR123P0.997
1:54717511:A:CK83N0.993
1:54717511:A:TK83N0.993
1:54717554:G:CA98P0.992
1:54717632:G:CA124P0.992
1:54731630:T:AW276R0.992
1:54731630:T:CW276R0.992
1:54717518:G:CG86R0.991
1:54717519:G:AG86D0.991
1:54722675:G:AG157D0.991
1:54717555:C:AA98D0.990
1:54717633:C:AA124E0.990
1:54717575:G:CG105R0.989
1:54722683:T:CC160R0.989
1:54722685:C:GC160W0.989
1:54722725:T:CC174R0.988
1:54722734:G:AG177R0.988
1:54722734:G:CG177R0.988
1:54722785:G:CA194P0.988
1:54717519:G:TG86V0.987
1:54716621:T:CF45L0.986
1:54716623:T:AF45L0.986
1:54716623:T:GF45L0.986
1:54721199:C:AA143D0.986
1:54733672:T:AW314R0.986
1:54733672:T:CW314R0.986
1:54722713:G:CA170P0.985
1:54717576:G:AG105D0.984
1:54717638:G:CA126P0.984
1:54721198:G:CA143P0.982

dbSNP variants (sampled 300 via entrez): RS1000162021 (1:54730026 A>G), RS1000189006 (1:54719220 G>A), RS1000235241 (1:54732455 T>C,G), RS1000291350 (1:54726390 A>C), RS1000363913 (1:54726040 A>C), RS1000889200 (1:54737433 C>T), RS1000976834 (1:54718566 A>G), RS1001163720 (1:54731784 T>G), RS1001278133 (1:54732022 G>A), RS1001391709 (1:54724742 T>G), RS1001597126 (1:54718086 A>C,G), RS1001941720 (1:54736049 C>T), RS1002109186 (1:54737800 C>T), RS1002169926 (1:54738245 C>A,T), RS1002213250 (1:54733160 A>AAT)

Disease associations

OMIM: gene MIM:606753 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

ChemicalActions (top 5)PubMed papers
Air Pollutantsaffects expression, increases abundance, increases expression2
beta-lapachoneincreases expression1
benzo(e)pyrenedecreases methylation1
S-(1,2-dichlorovinyl)cysteineaffects cotreatment, increases expression1
beta-methylcholineaffects expression1
CGP 52608affects binding, increases reaction1
abrineincreases expression1
Acetaminophenaffects expression1
Benzo(a)pyreneaffects methylation1
Caffeinedecreases phosphorylation1
Enzyme Inhibitorsdecreases activity, increases O-linked glycosylation1
Lipopolysaccharidesaffects cotreatment, increases expression1
Methapyrilenedecreases methylation1
Ozoneaffects expression, increases abundance1
Tobacco Smoke Pollutionincreases expression1
Valproic Acidincreases methylation1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression1
Cyclosporineincreases expression1
Cadmium Chloridedecreases expression1
Particulate Matterincreases abundance, increases 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.