TMEM9

gene
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Also known as TMEM9A

Summary

TMEM9 (transmembrane protein 9, HGNC:18823) is a protein-coding gene on chromosome 1q32.1, encoding Proton-transporting V-type ATPase complex assembly regulator TMEM9 (Q9P0T7). Transmembrane protein that binds to and facilitates the assembly of lysosomal proton-transporting V-type ATPase (v-ATPase), resulting in enhanced lysosomal acidification and trafficking.

Involved in intracellular pH reduction; positive regulation of canonical Wnt signaling pathway; and proton-transporting V-type ATPase complex assembly. Located in bounding membrane of organelle; intercellular bridge; and mitotic spindle.

Source: NCBI Gene 252839 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 22 total
  • MANE Select transcript: NM_001288565

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18823
Approved symbolTMEM9
Nametransmembrane protein 9
Location1q32.1
Locus typegene with protein product
StatusApproved
AliasesTMEM9A
Ensembl geneENSG00000116857
Ensembl biotypeprotein_coding
OMIM616877
Entrez252839

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 11 protein_coding, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000367330, ENST00000367332, ENST00000367333, ENST00000367334, ENST00000414605, ENST00000435310, ENST00000455367, ENST00000472411, ENST00000485839, ENST00000495205, ENST00000497582, ENST00000904676, ENST00000904677, ENST00000904678

RefSeq mRNA: 9 — MANE Select: NM_001288565 NM_001288564, NM_001288565, NM_001288566, NM_001288567, NM_001288568, NM_001288569, NM_001288570, NM_001288571, NM_016456

CCDS: CCDS1408, CCDS73001

Canonical transcript exons

ENST00000367330 — 5 exons

ExonStartEnd
ENSE00001444236201153858201154474
ENSE00001927890201134772201135815
ENSE00003704790201151761201151852
ENSE00003709361201146740201146848
ENSE00003709991201143820201143951

Expression profiles

Bgee: expression breadth ubiquitous, 254 present calls, max score 97.46.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 19.8585 / max 169.1686, expressed in 1782 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter IDTPM avgSamples expressed
1660916.96291776
166081.2815577
166050.8275556
166110.4890254
166100.120649
166120.101553
166060.041613
166070.03386

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
anterior cingulate cortexUBERON:000983597.46gold quality
hypothalamusUBERON:000189897.38gold quality
right adrenal glandUBERON:000123397.14gold quality
right frontal lobeUBERON:000281097.14gold quality
right adrenal gland cortexUBERON:003582797.14gold quality
left adrenal glandUBERON:000123497.12gold quality
left adrenal gland cortexUBERON:003582597.04gold quality
nucleus accumbensUBERON:000188297.03gold quality
Brodmann (1909) area 9UBERON:001354097.02gold quality
amygdalaUBERON:000187697.00gold quality
secondary oocyteCL:000065596.95gold quality
prefrontal cortexUBERON:000045196.95gold quality
middle temporal gyrusUBERON:000277196.82gold quality
oocyteCL:000002396.81gold quality
adrenal cortexUBERON:000123596.70gold quality
putamenUBERON:000187496.68gold quality
caudate nucleusUBERON:000187396.64gold quality
dorsolateral prefrontal cortexUBERON:000983496.60gold quality
right ovaryUBERON:000211896.54gold quality
right uterine tubeUBERON:000130296.43gold quality
endocervixUBERON:000045896.35gold quality
neocortexUBERON:000195096.31gold quality
ventricular zoneUBERON:000305396.30gold quality
left ovaryUBERON:000211996.29gold quality
adrenal glandUBERON:000236996.22gold quality
frontal cortexUBERON:000187096.10gold quality
cerebral cortexUBERON:000095695.78gold quality
forebrainUBERON:000189095.76gold quality
islet of LangerhansUBERON:000000695.73gold quality
metanephrosUBERON:000008195.70gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes16.56

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

45 targeting TMEM9, 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-6833-3P100.0070.633197
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-4283100.0066.422097
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-185-3P99.9567.011743
HSA-MIR-539-5P99.9370.302855
HSA-MIR-311999.9271.342390
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-449299.8768.253611
HSA-MIR-394199.8670.542735
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-149-3P99.7268.223963
HSA-MIR-6883-5P99.6968.053785
HSA-MIR-5004-5P99.6866.631294
HSA-MIR-320299.6667.702737
HSA-MIR-613499.6365.681537
HSA-MIR-451699.6167.783390
HSA-MIR-24-3P99.5969.971934
HSA-MIR-76299.5866.611994
HSA-MIR-141-5P99.5767.86897
HSA-MIR-443799.5265.291266
HSA-MIR-766-5P99.4767.912225
HSA-MIR-449899.4767.422360
HSA-MIR-324-3P99.2666.311034
HSA-MIR-149-5P99.2567.161315
HSA-MIR-6815-3P99.1368.981530
HSA-MIR-443499.1067.011984
HSA-MIR-570399.1067.092053
HSA-MIR-5001-5P99.0566.761972

Literature-anchored findings (GeneRIF, showing 11)

  • phylogenetically conserved, widely expressed transmembrane protein with a potential, but unknown function in intracellular transport that localizes to lysosomes and late endosomes (PMID:12359240)
  • TMEM9B is a key component of inflammatory signaling pathways and suggest that endosomal or lysosomal compartments regulate these pathways (PMID:18541524)
  • TMEM9 knockdown by RNA interference resulted in G1 arrest. (PMID:27220462)
  • TMEM9 plays a significant role in TNF-alpha-enhanced cytokines (IL-6 and IL-1beta) secretion in LX-2 cells and that the canonical Wnt/beta-catenin signaling pathway is involved in the induction of these cytokine expressions. (PMID:30119033)
  • Data show that TMEM9 binds to and facilitates assembly of vacuolar-ATPase (v-ATPase), a vacuolar proton pump, resulting in enhanced vesicular acidification and trafficking. (PMID:30374053)
  • TMEM9-activated v-ATPase downregulates APC via lysosomal degradation, which hyperactivates WNT/beta-Catenin signaling. (PMID:32380568)
  • TMEM9-v-ATPase Activates Wnt/beta-Catenin Signaling Via APC Lysosomal Degradation for Liver Regeneration and Tumorigenesis. (PMID:32380568)
  • Lysosomal TMEM9-LAMTOR4-controlled mTOR signaling integrity is required for mammary tumorigenesis. (PMID:36336962)
  • Tumor-Promoting Properties of TMEM9A in Breast Cancer Progression via Activating the Wnt/beta-Catenin Signaling Pathway. (PMID:36596527)
  • TMEM9 promotes lung adenocarcinoma progression via activating the MEK/ERK/STAT3 pathway to induce VEGF expression. (PMID:38664392)
  • TMEM9 activates Rab9-dependent alternative autophagy through interaction with Beclin1. (PMID:39078420)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriotmem9ENSDARG00000055757
mus_musculusTmem9ENSMUSG00000026411
rattus_norvegicusTmem9ENSRNOG00000010204
drosophila_melanogasterCG1161FBGN0037313
caenorhabditis_elegansWBGENE00020026

Paralogs (1): TMEM9B (ENSG00000175348)

Protein

Protein identifiers

Proton-transporting V-type ATPase complex assembly regulator TMEM9Q9P0T7 (reviewed: Q9P0T7)

Alternative names: Dermal papilla-derived protein 4, Transmembrane protein 9

All UniProt accessions (6): Q9P0T7, B1ALM4, B1ALM5, B1ALM7, B1ALM8, F2Z389

UniProt curated annotations — full annotation on UniProt →

Function. Transmembrane protein that binds to and facilitates the assembly of lysosomal proton-transporting V-type ATPase (v-ATPase), resulting in enhanced lysosomal acidification and trafficking. By bringing the v-ATPase accessory protein ATP6AP2 and the v-ATPase subunit ATP6V0D1 together, allows v-ATPase complex formation and activation. TMEM9-controlled vesicular acidification induces hyperactivation of Wnt/beta-catenin signaling, involved in development, tissue homeostasis and tissue regeneration, through lysosomal degradation of adenomatous polyposis coli/APC. In the liver, involved in hepatic regeneration.

Subunit / interactions. Interacts with the v-ATPase accessory protein ATP6AP2 and with the v-ATPase complex subunit ATP6V0D1; these interactions lead to the assembly of the v-ATPase complex.

Subcellular location. Lysosome membrane. Late endosome membrane. Endosome. Multivesicular body membrane.

Tissue specificity. Highly expressed in adrenal gland, thyroid gland, testis, ovary and prostate. Moderate expression in trachea, spinal cord, stomach, colon, small intestine and spleen. Low expression in bone marrow, lymph node, thymus and peripheral blood lymphocytes. Expression is detected in hematopoietic cell lines including those of myeloid, erythroid, B- and T-cell origin.

Post-translational modifications. N-glycosylated.

Domain organisation. The transmembrane domain (TMD) is essential for the interaction with ATP6AP2.

Similarity. Belongs to the TMEM9 family.

RefSeq proteins (9): NP_001275493, NP_001275494, NP_001275495, NP_001275496, NP_001275497, NP_001275498, NP_001275499, NP_001275500, NP_057540 (=MANE)

Domains & families (InterPro)

IDNameType
IPR008853TMEM9/TMEM9BFamily

Pfam: PF05434

UniProt features (12 total): glycosylation site 3, sequence conflict 2, topological domain 2, modified residue 2, signal peptide 1, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

3 structures.

PDBMethodResolution (Å)
9DNXELECTRON MICROSCOPY2.86
9DNYELECTRON MICROSCOPY3.01
9DNZELECTRON MICROSCOPY3.16

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9P0T7-F173.450.18

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 (2): 137, 144

Glycosylation sites (3): 21, 38, 47

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 134 (showing top): GOBP_ENDOSOME_ORGANIZATION, GOBP_VACUOLE_ORGANIZATION, GOCC_VACUOLAR_MEMBRANE, GOBP_VESICLE_ORGANIZATION, AAGCCAT_MIR135A_MIR135B, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_REGULATION_OF_WNT_SIGNALING_PATHWAY, GOBP_REGULATION_OF_CATABOLIC_PROCESS, GOBP_CANONICAL_WNT_SIGNALING_PATHWAY, GOBP_VACUOLAR_ACIDIFICATION, GOBP_REGULATION_OF_PROTEIN_CATABOLIC_PROCESS, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, GOBP_REGULATION_OF_PH, GOBP_POSITIVE_REGULATION_OF_CANONICAL_WNT_SIGNALING_PATHWAY, GOBP_MONOATOMIC_ION_HOMEOSTASIS

GO Biological Process (6): lysosomal lumen acidification (GO:0007042), protein transport (GO:0015031), regulation of protein catabolic process (GO:0042176), endosomal lumen acidification (GO:0048388), proton-transporting V-type ATPase complex assembly (GO:0070070), positive regulation of canonical Wnt signaling pathway (GO:0090263)

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

GO Cellular Component (10): lysosome (GO:0005764), lysosomal membrane (GO:0005765), late endosome (GO:0005770), microtubule cytoskeleton (GO:0015630), multivesicular body membrane (GO:0032585), intercellular bridge (GO:0045171), mitotic spindle (GO:0072686), endosome (GO:0005768), membrane (GO:0016020), late endosome membrane (GO:0031902)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
vacuolar acidification1
transport1
intracellular protein localization1
establishment of protein localization1
regulation of catabolic process1
protein catabolic process1
regulation of protein metabolic process1
endosome organization1
intracellular pH reduction1
proton-transporting two-sector ATPase complex assembly1
positive regulation of Wnt signaling pathway1
canonical Wnt signaling pathway1
regulation of canonical Wnt signaling pathway1
binding1
lytic vacuole1
lysosome1
lytic vacuole membrane1
endosome1
cytoskeleton1
multivesicular body1
late endosome membrane1
spindle1
endomembrane system1
cytoplasmic vesicle1
late endosome1
endosome membrane1

Protein interactions and networks

STRING

682 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TMEM9MINDY3Q9H8M7775
TMEM9GHITMQ9H3K2737
TMEM9TMEM45AQ9NWC5711
TMEM9COPS7AQ9UBW8576
TMEM9C11orf86A6NJI1489
TMEM9RBM42Q9BTD8475
TMEM9MRI1Q9BV20449
TMEM9ARL6IP5O75915431
TMEM9TMEM167AQ8TBQ9397
TMEM9TM9SF2Q99805396
TMEM9DTD2Q96FN9393
TMEM9FBXL17Q9UF56377
TMEM9TMEM161AQ9NX61374
TMEM9SHISA4Q96DD7374
TMEM9WFIKKN2Q8TEU8367

IntAct

93 interactions, top by confidence:

ABTypeScore
RINT1NBASpsi-mi:“MI:0914”(association)0.830
HEATR3TMEM186psi-mi:“MI:0914”(association)0.730
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
STX6TMEM9psi-mi:“MI:0915”(physical association)0.670
TRDNTMEM223psi-mi:“MI:0914”(association)0.640
C2CD2LTMEM9psi-mi:“MI:0915”(physical association)0.560
CLDN1TMEM9psi-mi:“MI:0915”(physical association)0.560
TMEM60TMEM9psi-mi:“MI:0915”(physical association)0.560
TMEM9PGAP2psi-mi:“MI:0915”(physical association)0.560
TMEM140TMEM9psi-mi:“MI:0915”(physical association)0.560
CLDN10TMEM9psi-mi:“MI:0915”(physical association)0.560
ATP6V0CTMEM9psi-mi:“MI:0915”(physical association)0.560
TSPOTMEM9psi-mi:“MI:0915”(physical association)0.560
NINJ2TMEM9psi-mi:“MI:0915”(physical association)0.560
TUSC5TMEM9psi-mi:“MI:0915”(physical association)0.560
SLC30A8TMEM9psi-mi:“MI:0915”(physical association)0.560
EMP1TMEM9psi-mi:“MI:0915”(physical association)0.560
TMEM9ESYT2psi-mi:“MI:0914”(association)0.530
SLC27A3ATP5F1Bpsi-mi:“MI:0914”(association)0.530
TNFSF8LGALS8psi-mi:“MI:0914”(association)0.530
LGALS3PODXLpsi-mi:“MI:0914”(association)0.530
CCT8L2ACSL4psi-mi:“MI:0914”(association)0.530
SLC15A4PGRMC1psi-mi:“MI:0914”(association)0.530
NRASESYT2psi-mi:“MI:2364”(proximity)0.480
TMEM9GALNT6psi-mi:“MI:0915”(physical association)0.370
SORT1SH3PXD2Bpsi-mi:“MI:0914”(association)0.350
P/V/CPEX1psi-mi:“MI:0914”(association)0.350

BioGRID (279): TMEM9 (Proximity Label-MS), TMEM9 (Proximity Label-MS), TMEM9 (Affinity Capture-MS), TMEM9 (Affinity Capture-MS), TMEM9 (Affinity Capture-RNA), TMEM9 (Affinity Capture-MS), TMEM9 (Affinity Capture-MS), TMEM9 (Proximity Label-MS), TMEM9 (Proximity Label-MS), TMEM9 (Affinity Capture-RNA), TMEM9 (Proximity Label-MS), TMEM9 (Affinity Capture-MS), TMEM9 (Two-hybrid), EMP1 (Two-hybrid), CLDN10 (Two-hybrid)

ESM2 similar proteins: A0A1B0GVV1, A0M8S0, A0M8T1, A0M8U1, A3KN28, A4D7R9, A9JRA0, B1AZA5, E9Q2Z6, P01134, P48030, Q00PJ0, Q07DV5, Q07DW9, Q07DX8, Q07DY8, Q07E08, Q07E45, Q09YH4, Q09YI5, Q09YJ7, Q09YK8, Q09YN2, Q108U3, Q1RLU8, Q2IBA8, Q2IBD0, Q2IBE0, Q2IBE8, Q2PG42, Q2QL86, Q2QLA6, Q2QLB7, Q2QLD7, Q2QLE8, Q2QLG2, Q3KRC4, Q3SXP7, Q5T292, Q68FW3

Diamond homologs: O73698, Q9CR23, Q9JJR8, Q9NQ34, Q9P0T7, Q9VNA4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance16
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1182 predictions. Top by Δscore:

VariantEffectΔscore
1:201135812:CATC:Cacceptor_gain1.0000
1:201143814:TCTTA:Tdonor_loss1.0000
1:201143815:CTTAC:Cdonor_loss1.0000
1:201143816:TTAC:Tdonor_loss1.0000
1:201143817:TA:Tdonor_loss1.0000
1:201143818:A:ACdonor_gain1.0000
1:201143819:C:CCdonor_gain1.0000
1:201143819:C:CTdonor_loss1.0000
1:201143819:CCT:Cdonor_gain1.0000
1:201143948:TGAC:Tacceptor_gain1.0000
1:201146844:AGTTG:Aacceptor_gain1.0000
1:201146845:GTTGC:Gacceptor_loss1.0000
1:201146846:TTG:Tacceptor_gain1.0000
1:201146846:TTGC:Tacceptor_loss1.0000
1:201146847:TG:Tacceptor_gain1.0000
1:201146848:GC:Gacceptor_loss1.0000
1:201146849:C:CCacceptor_gain1.0000
1:201146849:C:Tacceptor_loss1.0000
1:201146850:T:Aacceptor_loss1.0000
1:201135811:GCATC:Gacceptor_gain0.9900
1:201135812:CATCC:Cacceptor_gain0.9900
1:201135813:ATC:Aacceptor_gain0.9900
1:201135814:TC:Tacceptor_gain0.9900
1:201135815:CC:Cacceptor_gain0.9900
1:201135816:C:CAacceptor_loss0.9900
1:201135816:C:CCacceptor_gain0.9900
1:201135817:T:Cacceptor_loss0.9900
1:201135818:G:Cacceptor_gain0.9900
1:201135821:G:GCacceptor_gain0.9900
1:201143807:AAAGC:Adonor_gain0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000204387 (1:201138097 A>C,G), RS1000274154 (1:201159228 T>C), RS1000317074 (1:201147093 C>A), RS1000344153 (1:201147941 A>C), RS1000418202 (1:201153165 G>A), RS1000424324 (1:201153023 A>G), RS1000591259 (1:201159781 ACT>A), RS1000763948 (1:201151380 A>G), RS1000861338 (1:201172490 T>C), RS1000868453 (1:201171322 C>T), RS1000952616 (1:201164953 T>C), RS1000998227 (1:201138563 A>T), RS1001008849 (1:201157594 A>G), RS1001207594 (1:201165806 G>A), RS1001217589 (1:201152401 T>C,G)

Disease associations

OMIM: gene MIM:616877 | 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
GCST005212_6Asthma2.000000e-06
GCST009391_1089Metabolite levels5.000000e-06

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0010543uridine diphosphate galactose measurement
EFO:0010544uridine diphosphate glucose 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 expression2
GSK-J4decreases expression1
FR900359decreases phosphorylation1
sodium arseniteaffects cotreatment, increases abundance, increases expression1
manganese chlorideincreases expression, affects cotreatment, increases abundance1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic acidincreases expression1
CGP 52608increases reaction, affects binding1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acidincreases expression1
Resveratrolaffects cotreatment, decreases expression1
Sunitinibincreases expression1
Acetaminophenaffects response to substance1
Arsenicaffects cotreatment, increases abundance, increases expression1
Atrazineincreases expression1
Benzo(a)pyreneaffects methylation1
Cadmiumincreases abundance, increases expression1
Cisplatinincreases expression1
Doxorubicinincreases expression1
Hydralazineaffects cotreatment, increases expression1
Ivermectindecreases expression1
Leadaffects expression1
Manganeseaffects cotreatment, increases abundance, increases expression1
Plant Extractsdecreases expression, affects cotreatment1
Thiramdecreases expression1
Tretinoindecreases expression1
Cyclosporinedecreases methylation1
Cadmium Chlorideincreases abundance, increases expression1
Okadaic Aciddecreases expression1

Cellosaurus cell lines

2 cell lines: 2 embryonic stem cell

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_E2VXH9 AAVS1-TRE3G-NGN2 Flag-EEA1 TMEM9-/-Embryonic stem cellFemale
CVCL_E2VYH9 AAVS1-TRE3G-NGN2 Flag-EEA1 TMEM9-/-; TMEM9B-/-Embryonic stem cellFemale

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.