TIMM9

gene
On this page

Also known as TIM9A

Summary

TIMM9 (translocase of inner mitochondrial membrane 9, HGNC:11819) is a protein-coding gene on chromosome 14q23.1, encoding Mitochondrial import inner membrane translocase subunit Tim9 (Q9Y5J7). Mitochondrial intermembrane chaperone that participates in the import and insertion of multi-pass transmembrane proteins into the mitochondrial inner membrane. It is a selective cancer dependency (DepMap: 68.4% of cell lines).

TIMM9 belongs to a family of evolutionarily conserved proteins that are organized in heterooligomeric complexes in the mitochondrial intermembrane space. These proteins mediate the import and insertion of hydrophobic membrane proteins into the mitochondrial inner membrane.

Source: NCBI Gene 26520 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 16 total
  • Druggable target: yes
  • Cancer dependency (DepMap): dependent in 68.4% of screened cell lines
  • MANE Select transcript: NM_012460

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:11819
Approved symbolTIMM9
Nametranslocase of inner mitochondrial membrane 9
Location14q23.1
Locus typegene with protein product
StatusApproved
AliasesTIM9A
Ensembl geneENSG00000100575
Ensembl biotypeprotein_coding
OMIM607384
Entrez26520

Gene structure

Transcript identifiers

Ensembl transcripts: 36 — 34 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000216463, ENST00000395159, ENST00000555061, ENST00000555097, ENST00000555404, ENST00000555593, ENST00000555930, ENST00000556007, ENST00000556367, ENST00000557397, ENST00000871598, ENST00000871599, ENST00000871600, ENST00000871601, ENST00000871602, ENST00000871603, ENST00000922994, ENST00000922995, ENST00000922996, ENST00000922997, ENST00000922998, ENST00000922999, ENST00000923000, ENST00000923001, ENST00000923002, ENST00000923003, ENST00000923004, ENST00000923005, ENST00000923006, ENST00000923007, ENST00000923008, ENST00000923009, ENST00000923010, ENST00000923011, ENST00000923012, ENST00000941474

RefSeq mRNA: 8 — MANE Select: NM_012460 NM_001304485, NM_001304486, NM_001304487, NM_001304488, NM_001304489, NM_001304490, NM_001304491, NM_012460

CCDS: CCDS76685, CCDS86393, CCDS86394, CCDS9735

Canonical transcript exons

ENST00000395159 — 6 exons

ExonStartEnd
ENSE000015207545840849558409168
ENSE000015207735842400858424095
ENSE000015207745842705458427242
ENSE000024525925842739258427531
ENSE000036559995841084358410938
ENSE000038041855841190758411971

Expression profiles

Bgee: expression breadth ubiquitous, 283 present calls, max score 97.32.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 23.9392 / max 288.0773, expressed in 1807 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
14343420.39511797
1434331.4184892
1434361.3266686
1434370.3239139
2072360.2777122
1434350.197553

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
body of pancreasUBERON:000115097.32gold quality
ganglionic eminenceUBERON:000402395.63gold quality
hindlimb stylopod muscleUBERON:000425295.52gold quality
pancreasUBERON:000126494.83gold quality
colonic epitheliumUBERON:000039794.77gold quality
ventricular zoneUBERON:000305394.77gold quality
gastrocnemiusUBERON:000138894.57gold quality
left ovaryUBERON:000211994.36gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099194.31gold quality
muscle of legUBERON:000138394.30gold quality
muscle layer of sigmoid colonUBERON:003580593.82gold quality
right ovaryUBERON:000211893.69gold quality
cortical plateUBERON:000534393.69gold quality
omental fat padUBERON:001041493.47gold quality
peritoneumUBERON:000235893.41gold quality
islet of LangerhansUBERON:000000693.36gold quality
popliteal arteryUBERON:000225093.34gold quality
tibial arteryUBERON:000761093.34gold quality
endocervixUBERON:000045893.03gold quality
olfactory segment of nasal mucosaUBERON:000538693.01gold quality
ovaryUBERON:000099292.98gold quality
lower esophagus muscularis layerUBERON:003583392.96gold quality
body of uterusUBERON:000985392.94gold quality
lower esophagusUBERON:001347392.94gold quality
body of stomachUBERON:000116192.92gold quality
mucosa of stomachUBERON:000119992.91gold quality
right adrenal gland cortexUBERON:003582792.87gold quality
left adrenal glandUBERON:000123492.77gold quality
esophagogastric junction muscularis propriaUBERON:003584192.77gold quality
left adrenal gland cortexUBERON:003582592.76gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes11.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

33 targeting TIMM9, 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-4795-3P100.0074.624024
HSA-MIR-428299.9975.366408
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-3605-5P99.9667.12932
HSA-MIR-144-3P99.9473.982698
HSA-MIR-182-5P99.8774.032589
HSA-MIR-576-5P99.8470.462582
HSA-MIR-442099.8270.081624
HSA-MIR-181B-2-3P99.8170.061646
HSA-MIR-181B-3P99.8170.061646
HSA-MIR-432099.7565.80793
HSA-MIR-132-3P99.7370.561424
HSA-MIR-212-3P99.7370.651424
HSA-MIR-472999.6972.184233
HSA-MIR-58799.6470.862611
HSA-MIR-182799.6368.573265
HSA-MIR-4753-5P99.5468.511356
HSA-MIR-7159-3P99.5170.171920
HSA-MIR-766-3P99.4765.241811
HSA-MIR-807099.0769.301303
HSA-MIR-1304-5P98.9068.581054
HSA-MIR-3145-3P98.8569.072031
HSA-MIR-6894-5P98.7063.78809
HSA-MIR-299-5P98.5671.141140
HSA-MIR-4766-3P98.4867.941347
HSA-MIR-1910-3P98.4467.511695
HSA-MIR-4704-3P98.2869.331300
HSA-MIR-445098.2668.35725
HSA-MIR-126398.1369.18459
HSA-MIR-6511A-5P98.1367.471770

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 68.4% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 3)

  • in contrast to yeast, only a small fraction of Tim9-Tim10a-Tim10b complex is in a stable association with Tim22 (PMID:14726512)
  • The crystal structure of TIM9.10 described here reveals a previously undescribed alpha-propeller topology in which helical “blades” radiate from a narrow central pore lined with polar residues. (PMID:16387659)
  • in gastric cancer patients, a borderline association was found between overexpression of TIMM9 and vascular invasion; patients with high expression levels of TIMM9 achieved a significantly lower disease-free survival rate compared with those with low expression levels (PMID:27720672)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriotimm9ENSDARG00000043865
mus_musculusTimm9ENSMUSG00000021079
rattus_norvegicusTimm9ENSRNOG00000008222
drosophila_melanogasterTim9aFBGN0030480
caenorhabditis_elegansWBGENE00006572

Protein

Protein identifiers

Mitochondrial import inner membrane translocase subunit Tim9Q9Y5J7 (reviewed: Q9Y5J7)

All UniProt accessions (5): Q9Y5J7, A0A1W2PQS5, A0A1W2PRH9, G3V2F3, G3V502

UniProt curated annotations — full annotation on UniProt →

Function. Mitochondrial intermembrane chaperone that participates in the import and insertion of multi-pass transmembrane proteins into the mitochondrial inner membrane. May also be required for the transfer of beta-barrel precursors from the TOM complex to the sorting and assembly machinery (SAM complex) of the outer membrane. Acts as a chaperone-like protein that protects the hydrophobic precursors from aggregation and guide them through the mitochondrial intermembrane space.

Subunit / interactions. Heterohexamer; composed of 3 copies of TIMM9 and 3 copies of TIMM10/TIM10A, named soluble 70 kDa complex. The complex forms a 6-bladed alpha-propeller structure and associates with the TIMM22 component of the TIM22 complex. Interacts with multi-pass transmembrane proteins in transit. Also forms a complex composed of TIMM9, TIMM10/TIM10A and FXC1/TIM10B.

Subcellular location. Mitochondrion inner membrane.

Tissue specificity. Ubiquitous, with highest expression in heart, kidney, liver and skeletal muscle.

Domain organisation. The twin CX3C motif contains 4 conserved Cys residues that form 2 disulfide bonds in the mitochondrial intermembrane space. However, during the transit of TIMM9 from cytoplasm into mitochondrion, the Cys residues probably coordinate zinc, thereby preventing folding and allowing its transfer across mitochondrial outer membrane.

Similarity. Belongs to the small Tim family.

RefSeq proteins (8): NP_001291414, NP_001291415, NP_001291416, NP_001291417, NP_001291418, NP_001291419, NP_001291420, NP_036592* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR004217Tim10-likeDomain
IPR035427Tim10-like_dom_sfHomologous_superfamily
IPR050673Mito_inner_translocase_subFamily

Pfam: PF02953

UniProt features (11 total): helix 3, disulfide bond 2, strand 2, initiator methionine 1, chain 1, short sequence motif 1, modified residue 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
2BSKX-RAY DIFFRACTION3.3
7CGPELECTRON MICROSCOPY3.7

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9Y5J7-F191.300.82

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): 2

Disulfide bonds (2): 28–52, 32–48

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-1268020Mitochondrial protein import
R-HSA-9837999Mitochondrial protein degradation

MSigDB gene sets: 199 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_UP, RORA1_01, GOBP_SENSORY_PERCEPTION_OF_MECHANICAL_STIMULUS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_PROTEIN_TARGETING, TGACCTY_ERR1_Q2, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_ORGANELLE, GGGTGGRR_PAX4_03, USF_C, FREAC3_01, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM4, GOBP_INNER_MITOCHONDRIAL_MEMBRANE_ORGANIZATION, MYCMAX_01, GROSS_HYPOXIA_VIA_HIF1A_UP

GO Biological Process (4): obsolete protein targeting to mitochondrion (GO:0006626), sensory perception of sound (GO:0007605), protein transport (GO:0015031), protein insertion into mitochondrial inner membrane (GO:0045039)

GO Molecular Function (7): zinc ion binding (GO:0008270), membrane insertase activity (GO:0032977), protein homodimerization activity (GO:0042803), protein-folding chaperone binding (GO:0051087), protein transporter activity (GO:0140318), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (6): mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), mitochondrial intermembrane space (GO:0005758), mitochondrial intermembrane space chaperone complex (GO:0042719), TIM22 mitochondrial import inner membrane insertion complex (GO:0042721), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Protein localization1
Metabolism of proteins1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
sensory perception of mechanical stimulus1
transport1
intracellular protein localization1
establishment of protein localization1
inner mitochondrial membrane organization1
mitochondrial protein import pathway1
transition metal ion binding1
establishment of protein localization to membrane1
protein carrier activity1
identical protein binding1
protein dimerization activity1
protein binding1
transporter activity1
binding1
cation binding1
cytoplasm1
intracellular membrane-bounded organelle1
organelle inner membrane1
mitochondrial membrane1
mitochondrial envelope1
organelle envelope lumen1
mitochondrial intermembrane space1
mitochondrial protein-containing complex1
inner mitochondrial membrane protein complex1
cellular anatomical structure1

Protein interactions and networks

STRING

1520 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TIMM9TIMM10P62072999
TIMM9TIMM8AO60220982
TIMM9TIMM13P62206981
TIMM9TIMM23O14925904
TIMM9TIMM22Q9Y584897
TIMM9CHCHD4Q8N4Q1883
TIMM9TIMM10BQ9Y5J6820
TIMM9TIMM17AQ99595807
TIMM9TIMM29Q9BSF4783
TIMM9TIMM21Q9BVV7773
TIMM9TOMM70O94826744
TIMM9TIMM50Q3ZCQ8736
TIMM9TIMM44O43615733
TIMM9SLC25A12O75746733
TIMM9TOMM40O96008733

IntAct

33 interactions, top by confidence:

ABTypeScore
TIMM9TIMM10psi-mi:“MI:0914”(association)0.830
TIMM10TIMM9psi-mi:“MI:0915”(physical association)0.830
TIMM9TIMM10psi-mi:“MI:0915”(physical association)0.830
TIMM10BTIMM10psi-mi:“MI:0914”(association)0.710
TIMM10TIMM10Bpsi-mi:“MI:0914”(association)0.710
TIMM10BTIMM10psi-mi:“MI:0915”(physical association)0.710
TIMM10AGKpsi-mi:“MI:0914”(association)0.640
repIDEpsi-mi:“MI:0914”(association)0.530
ANKS6DCAF7psi-mi:“MI:0914”(association)0.510
TIMM22TIMM10psi-mi:“MI:0914”(association)0.350
BADPPP6Cpsi-mi:“MI:0914”(association)0.350
BADERLIN1psi-mi:“MI:0914”(association)0.350
repCEBPZOSpsi-mi:“MI:0914”(association)0.350
FEVPSMB4psi-mi:“MI:0914”(association)0.350
FOXQ1TIMM8Apsi-mi:“MI:0914”(association)0.350
PRDM1HSPD1psi-mi:“MI:0914”(association)0.350
FGFR3TIMM8Apsi-mi:“MI:0914”(association)0.350
TIMM10DCTN6psi-mi:“MI:0914”(association)0.350
TIMM10IGLL5psi-mi:“MI:0914”(association)0.350
AGKRAB29psi-mi:“MI:0914”(association)0.350
ATF2CLIC1psi-mi:“MI:0914”(association)0.350
SLC14A2SMCHD1psi-mi:“MI:0914”(association)0.350
SCO1HAX1psi-mi:“MI:2364”(proximity)0.270
SFXN1HAX1psi-mi:“MI:2364”(proximity)0.270
PARLHAX1psi-mi:“MI:2364”(proximity)0.270
KLF15TAF4psi-mi:“MI:2364”(proximity)0.270
PRDM1ZNF609psi-mi:“MI:2364”(proximity)0.270

BioGRID (66): COX5A (Co-fractionation), NUDC (Co-fractionation), PTGES3 (Co-fractionation), TIMM10 (Co-fractionation), TIMM13 (Co-fractionation), TIMM8A (Co-fractionation), TIMM8B (Co-fractionation), TIMM9 (Co-fractionation), TIMM9 (Affinity Capture-MS), TIMM9 (Affinity Capture-MS), TIMM9 (Affinity Capture-MS), TIMM9 (Negative Genetic), TIMM9 (Positive Genetic), TIMM9 (Positive Genetic), TIMM9 (Negative Genetic)

ESM2 similar proteins: A4QNC6, B0BN94, O74700, P0CR96, P0CR97, P0CS00, P0CS01, P30629, P62075, P62076, P62077, P62078, Q10481, Q2HJI3, Q2KIV2, Q3SZ93, Q4I6B0, Q4V7R1, Q59MI8, Q59R24, Q5ZIR8, Q616Q2, Q61TH2, Q63ZH8, Q66L32, Q6BN23, Q6BU42, Q6CM57, Q6DEM5, Q6DGJ3, Q6FK81, Q6GPY0, Q6PBU0, Q75DU7, Q7SBR3, Q8AVK1, Q90YI5, Q96C01, Q9CR98, Q9N408

Diamond homologs: O74700, P0CR96, P0CR97, P57745, Q17754, Q2KIV2, Q4IB65, Q4V7R1, Q4WIQ2, Q559H1, Q568N4, Q59R24, Q5ZIR8, Q61TH2, Q6BU42, Q6C6Z2, Q6CM57, Q6FRT3, Q757S0, Q8J1Z1, Q9P7K0, Q9VYD7, Q9W762, Q9WV97, Q9WV98, Q9XGX7, Q9XGX8, Q9XGX9, Q9Y0V2, Q9Y5J7, Q9Y8A7, Q3SZW4, Q5RDJ0, Q6CWH5, Q6GR66, Q9R1B1, Q9WV96, Q9Y0V3, Q9Y5J6, P57744

SIGNOR signaling

2 interactions.

AEffectBMechanism
TIMM9“form complex”“TIM22 complex”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 34 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
Mitochondrial protein import536.5×4e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance9
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1141 predictions. Top by Δscore:

VariantEffectΔscore
14:58410605:G:Cdonor_gain1.0000
14:58410838:CATA:Cdonor_loss1.0000
14:58410839:ATAC:Adonor_loss1.0000
14:58410840:TA:Tdonor_loss1.0000
14:58410841:A:Cdonor_loss1.0000
14:58410842:CCT:Cdonor_gain1.0000
14:58410934:TTAAA:Tacceptor_gain1.0000
14:58410935:TAAA:Tacceptor_gain1.0000
14:58410936:AAA:Aacceptor_gain1.0000
14:58410937:AA:Aacceptor_gain1.0000
14:58410937:AAC:Aacceptor_gain1.0000
14:58410937:AACTA:Aacceptor_loss1.0000
14:58410938:ACT:Aacceptor_gain1.0000
14:58410938:ACTA:Aacceptor_loss1.0000
14:58410939:C:CCacceptor_gain1.0000
14:58410939:CT:Cacceptor_gain1.0000
14:58410939:CTACA:Cacceptor_loss1.0000
14:58410940:T:Gacceptor_gain1.0000
14:58410859:T:TAdonor_gain0.9900
14:58410935:TAAAC:Tacceptor_gain0.9900
14:58410936:AAACT:Aacceptor_gain0.9900
14:58411901:CCTTA:Cdonor_loss0.9900
14:58411902:CTTA:Cdonor_loss0.9900
14:58411903:TTAC:Tdonor_loss0.9900
14:58411904:TA:Tdonor_loss0.9900
14:58411905:ACCTG:Adonor_loss0.9900
14:58411970:ACCTA:Aacceptor_loss0.9900
14:58411972:CTA:Cacceptor_loss0.9900
14:58411973:T:Gacceptor_loss0.9900
14:58424091:CTTAC:Cacceptor_gain0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000199336 (14:58416477 C>T), RS1000242201 (14:58409647 C>T), RS1000296070 (14:58409959 G>A), RS1000418708 (14:58428917 A>G), RS1000477156 (14:58416109 T>G), RS1000605697 (14:58411763 C>A,T), RS1000671722 (14:58422158 C>G,T), RS1000775294 (14:58428896 C>T), RS1000807956 (14:58418352 A>G), RS1000819036 (14:58425068 T>C), RS1000912350 (14:58424696 C>T), RS1001074810 (14:58418628 A>T), RS1001177257 (14:58417199 C>G), RS1001251105 (14:58411205 T>C), RS1001364294 (14:58423916 A>G)

Disease associations

OMIM: gene MIM:607384 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST010703_93Brain morphology (MOSTest)6.000000e-54

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004346neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066451 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

42 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Air Pollutantsdecreases expression, increases abundance, increases expression3
Cyclosporineincreases expression, increases methylation3
Particulate Matterdecreases expression, increases abundance, increases expression3
bisphenol Aaffects expression, increases expression2
Acetaminophenaffects response to substance, decreases expression2
Tunicamycinincreases expression2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression2
Cadmium Chloridedecreases expression2
aristolochic acid Idecreases expression1
bisphenol Fincreases expression, affects cotreatment1
beauvericinaffects cotreatment, decreases expression1
deoxynivalenolincreases expression1
beta-lapachoneincreases expression1
sodium arsenitedecreases expression1
perfluorooctanoic acidincreases expression1
beta-methylcholineaffects expression1
enniatinsaffects cotreatment, decreases expression1
perfluoro-n-nonanoic acidincreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic aciddecreases expression1
Resveratrolaffects cotreatment, decreases expression1
Sunitinibincreases expression1
Vehicle Emissionsincreases abundance, increases expression1
Benzo(a)pyreneincreases methylation1
Cannabidiolincreases expression1
Dichlorodiphenyl Dichloroethyleneincreases expression1
Dexamethasoneaffects cotreatment, increases expression1
Doxorubicindecreases expression1
Indomethacinaffects cotreatment, increases expression1
Ivermectindecreases expression1
Plant Extractsaffects cotreatment, decreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5652633BindingBinding affinity to human TIMM9 incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

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.