TSPAN9

gene
On this page

Also known as NET-5

Summary

TSPAN9 (tetraspanin 9, HGNC:21640) is a protein-coding gene on chromosome 12p13.33-p13.32, encoding Tetraspanin-9 (O75954).

The protein encoded by this gene is a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Most of these members are cell-surface proteins that are characterized by the presence of four hydrophobic domains. The proteins mediate signal transduction events that play a role in the regulation of cell development, activation, growth and motility. Alternatively spliced transcripts encoding the same protein have been identified.

Source: NCBI Gene 10867 — RefSeq curated summary.

At a glance

  • GWAS associations: 35
  • Clinical variants (ClinVar): 47 total
  • MANE Select transcript: NM_006675

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:21640
Approved symbolTSPAN9
Nametetraspanin 9
Location12p13.33-p13.32
Locus typegene with protein product
StatusApproved
AliasesNET-5
Ensembl geneENSG00000011105
Ensembl biotypeprotein_coding
OMIM613137
Entrez10867

Gene structure

Transcript identifiers

Ensembl transcripts: 31 — 27 protein_coding, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000011898, ENST00000407263, ENST00000431374, ENST00000444315, ENST00000492305, ENST00000537971, ENST00000539631, ENST00000640568, ENST00000649909, ENST00000865933, ENST00000865934, ENST00000865935, ENST00000865936, ENST00000865937, ENST00000865938, ENST00000865939, ENST00000865940, ENST00000865941, ENST00000865942, ENST00000865943, ENST00000865944, ENST00000865945, ENST00000865946, ENST00000865947, ENST00000865948, ENST00000865949, ENST00000865950, ENST00000865951, ENST00000865952, ENST00000971277, ENST00000971278

RefSeq mRNA: 2 — MANE Select: NM_006675 NM_001168320, NM_006675

CCDS: CCDS8520

Canonical transcript exons

ENST00000011898 — 9 exons

ExonStartEnd
ENSE0000071372132811983281329
ENSE0000071372332817343281817
ENSE0000115863332011773201256
ENSE0000126563930836533083719
ENSE0000221436532830453286559
ENSE0000346418832784213278612
ENSE0000350644832789923279066
ENSE0000360220932803823280483
ENSE0000384896030773793077453

Expression profiles

Bgee: expression breadth ubiquitous, 270 present calls, max score 97.53.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.9020 / max 382.7136, expressed in 1523 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
12347610.04691500
1234771.7911827
1234791.5378453
1234860.3960242
1234830.118579
1234820.01184

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
apex of heartUBERON:000209897.53gold quality
cerebellar hemisphereUBERON:000224597.51gold quality
cerebellar cortexUBERON:000212997.39gold quality
right hemisphere of cerebellumUBERON:001489097.25gold quality
cerebellumUBERON:000203796.63gold quality
right atrium auricular regionUBERON:000663195.90gold quality
heart left ventricleUBERON:000208495.82gold quality
cardiac ventricleUBERON:000208295.72gold quality
cardiac atriumUBERON:000208195.34gold quality
heartUBERON:000094894.67gold quality
right lungUBERON:000216793.91gold quality
right lobe of liverUBERON:000111493.85gold quality
stromal cell of endometriumCL:000225593.65gold quality
vena cavaUBERON:000408793.24gold quality
gall bladderUBERON:000211092.98gold quality
metanephros cortexUBERON:001053391.94gold quality
heart right ventricleUBERON:000208091.70gold quality
adult mammalian kidneyUBERON:000008291.57gold quality
body of uterusUBERON:000985391.25gold quality
right ovaryUBERON:000211891.17gold quality
left ovaryUBERON:000211991.06gold quality
liverUBERON:000210791.02gold quality
upper lobe of left lungUBERON:000895290.59gold quality
upper lobe of lungUBERON:000894890.31gold quality
endocervixUBERON:000045889.88gold quality
right coronary arteryUBERON:000162589.70gold quality
myocardiumUBERON:000234989.68gold quality
renal medullaUBERON:000036289.57gold quality
left uterine tubeUBERON:000130389.50gold quality
tibial arteryUBERON:000761089.47gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes5.13

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): FOXO3

miRNA regulators (miRDB)

152 targeting TSPAN9, 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-3163100.0077.238605
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-4692100.0067.322066
HSA-MIR-6127100.0066.762188
HSA-MIR-6129100.0066.462080
HSA-MIR-6856-5P100.0065.471298
HSA-MIR-6758-5P100.0066.211470
HSA-MIR-9-5P100.0072.282361
HSA-MIR-5193100.0067.261744
HSA-MIR-4510100.0066.602050
HSA-MIR-6130100.0066.692012
HSA-MIR-6133100.0066.482064
HSA-MIR-4455100.0065.481587
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-451499.9967.101870
HSA-MIR-33A-5P99.9968.621055
HSA-MIR-33B-5P99.9968.581062
HSA-MIR-1213699.9872.815713
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-548AT-5P99.9670.832666
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-426799.9666.532368
HSA-MIR-548J-3P99.9472.614881
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-548AE-3P99.9372.664867
HSA-MIR-548AH-3P99.9372.544872
HSA-MIR-548AM-3P99.9372.544872
HSA-MIR-548AQ-3P99.9372.664867
HSA-MIR-652-5P99.9167.49505

Literature-anchored findings (GeneRIF, showing 5)

  • Findings suggest a role for Tspan9 in regulating platelet function in concert with other platelet tetraspanins and their associated proteins. (PMID:18795891)
  • tetraspanin CD9 has a role in determining vascular smooth muscle cell injury phenotypes (PMID:18799160)
  • TSPAN9 is an endosomal tetraspanin whose depletion has a pronounced effect on the entry of several viruses that fuse in the early endosome. (PMID:26865714)
  • The proliferation, migration and invasion of human gastric cancer SGC7901 cells were significantly inhibited by overexpression of Tspan9. (PMID:27177197)
  • expression of the membrane protein TSPAN9 regulates gastric cancer cell migration and invasion by inhibiting the FAK-RAS-ERK1/2 signaling pathway. The extracellular secretory protein EMILIN1 can increase this tumor suppressive effect by promoting the expression of TSPAN9. (PMID:31242895)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriotspan9aENSDARG00000025299
danio_reriotspan9bENSDARG00000045706
mus_musculusTspan9ENSMUSG00000030352
rattus_norvegicusTspan9ENSRNOG00000051620

Paralogs (32): TSPAN6 (ENSG00000000003), CD9 (ENSG00000010278), TSPAN17 (ENSG00000048140), TSPAN32 (ENSG00000064201), CD82 (ENSG00000085117), TSPAN15 (ENSG00000099282), CD37 (ENSG00000104894), UPK1A (ENSG00000105668), TSPAN12 (ENSG00000106025), TSPAN13 (ENSG00000106537), TSPAN14 (ENSG00000108219), CD81 (ENSG00000110651), TSPAN11 (ENSG00000110900), PRPH2 (ENSG00000112619), UPK1B (ENSG00000114638), TSPAN1 (ENSG00000117472), TSPAN8 (ENSG00000127324), TSPAN16 (ENSG00000130167), TSPAN2 (ENSG00000134198), CD63 (ENSG00000135404), TSPAN31 (ENSG00000135452), TSPAN3 (ENSG00000140391), CD53 (ENSG00000143119), ROM1 (ENSG00000149489), TSPAN7 (ENSG00000156298), TSPAN18 (ENSG00000157570), TSPAN33 (ENSG00000158457), TSPAN5 (ENSG00000168785), CD151 (ENSG00000177697), TSPAN10 (ENSG00000182612), TSPAN4 (ENSG00000214063), TSPAN19 (ENSG00000231738)

Protein

Protein identifiers

Tetraspanin-9O75954 (reviewed: O75954)

Alternative names: Tetraspan NET-5

All UniProt accessions (5): O75954, A0A1W2PQ04, A0A3B3IST1, B5MD23, E9PHL0

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Found in a complex with GP6.

Subcellular location. Membrane.

Tissue specificity. Expressed in megakaryocytes and platelets (at protein level).

Post-translational modifications. Glycosylated.

Similarity. Belongs to the tetraspanin (TM4SF) family.

RefSeq proteins (2): NP_001161792, NP_006666* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000301Tetraspanin_animalsFamily
IPR008952Tetraspanin_EC2_sfHomologous_superfamily
IPR018499Tetraspanin/PeripherinFamily
IPR018503Tetraspanin_CSConserved_site

Pfam: PF00335

UniProt features (12 total): topological domain 5, transmembrane region 4, chain 1, glycosylation site 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O75954-F189.650.67

Functional residue map

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

Glycosylation sites (1): 180

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 212 (showing top): GOBP_MYELOID_CELL_HOMEOSTASIS, TGCACTT_MIR519C_MIR519B_MIR519A, GCANCTGNY_MYOD_Q6, GOBP_PLATELET_ACTIVATION, TERAMOTO_OPN_TARGETS_CLUSTER_6, GOBP_WOUND_HEALING, GOBP_CELL_CELL_ADHESION, BROWNE_HCMV_INFECTION_24HR_UP, ACATTCC_MIR1_MIR206, AACTTT_UNKNOWN, GOBP_REGULATION_OF_MITOCHONDRIAL_MEMBRANE_POTENTIAL, GOBP_MULTICELLULAR_ORGANISMAL_LEVEL_HOMEOSTASIS, GOBP_HOMOTYPIC_CELL_CELL_ADHESION, GOBP_HEMOSTASIS, AML1_01

GO Biological Process (6): neutrophil homeostasis (GO:0001780), collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063), regulation of mitochondrial membrane potential (GO:0051881), platelet aggregation (GO:0070527), receptor diffusion trapping (GO:0098953), mitocytosis (GO:0160040)

GO Molecular Function (1): signaling receptor binding (GO:0005102)

GO Cellular Component (6): plasma membrane (GO:0005886), focal adhesion (GO:0005925), extracellular matrix (GO:0031012), tetraspanin-enriched microdomain (GO:0097197), migrasome (GO:0140494), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
plasma membrane2
cellular anatomical structure2
leukocyte homeostasis1
myeloid cell homeostasis1
cell surface receptor protein tyrosine kinase signaling pathway1
collagen-activated signaling pathway1
regulation of membrane potential1
platelet activation1
homotypic cell-cell adhesion1
localization within membrane1
mitochondrion distribution1
establishment of mitochondrion localization1
migracytosis1
protein binding1
membrane1
cell periphery1
cell-substrate junction1
external encapsulating structure1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

944 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TSPAN9TSPAN32Q96QS1715
TSPAN9ITGB1P05556595
TSPAN9GP6Q9HCN6555
TSPAN9CD63P08962515
TSPAN9CD151P48509499
TSPAN9CD9P21926492
TSPAN9VWCEQ96DN2428
TSPAN9B4E171B4E171418
TSPAN9TSPAN14Q8NG11418
TSPAN9NRIP2Q9BQI9414
TSPAN9TSPAN2O60636410
TSPAN9PRMT8Q9NR22409
TSPAN9TSPAN10Q9H1Z9408
TSPAN9RIPOR2Q9Y4F9403
TSPAN9CRACR2AQ9BSW2401

IntAct

13 interactions, top by confidence:

ABTypeScore
TSPAN15ADAM10psi-mi:“MI:0914”(association)0.840
TSPAN5ADAM10psi-mi:“MI:0914”(association)0.800
CD9ADAM10psi-mi:“MI:0914”(association)0.750
EVA1BNRP1psi-mi:“MI:0914”(association)0.530
ADAM10TSPAN9psi-mi:“MI:0914”(association)0.350
EVA1BTMEM131Lpsi-mi:“MI:0914”(association)0.350
TSC22D3VPS37Cpsi-mi:“MI:0914”(association)0.350
SYT2SMAPpsi-mi:“MI:0914”(association)0.350
VSIG1RIMOC1psi-mi:“MI:0914”(association)0.350

BioGRID (9): TSPAN9 (Affinity Capture-RNA), TSPAN9 (Affinity Capture-MS), TSPAN9 (Affinity Capture-RNA), TSPAN9 (Affinity Capture-RNA), TSPAN9 (Affinity Capture-MS), TSPAN9 (Affinity Capture-MS), TSPAN9 (Affinity Capture-MS), TSPAN9 (Affinity Capture-RNA), TSPAN9 (Affinity Capture-RNA)

ESM2 similar proteins: B0BM39, B3VSC2, B5X3I6, F7BWT7, O14494, O14817, O35566, O42602, O42603, O43688, O60636, O62772, O75954, O88956, O95857, O95858, P35353, P47866, P48509, P60588, Q01453, Q06AA5, Q13324, Q3SYV5, Q3ZBV0, Q4L208, Q5RAP3, Q5RAZ3, Q5ZJ75, Q60748, Q6DCQ3, Q6GMK6, Q6WL85, Q86UF1, Q8BJU2, Q8K593, Q8R3S2, Q8R4D1, Q90812, Q91ZH7

Diamond homologs: A0A8M2B5N2, A0A8V0ZLT4, B0BM39, B3VSC2, B5X3I6, O14817, O60635, O75954, O97703, P11049, P60033, P60034, Q06AA5, Q11098, Q26499, Q3T0S3, Q4R7W6, Q4V8E0, Q58CY8, Q5RAP3, Q5RC27, Q61470, Q6AYR9, Q6DCQ3, Q6GMK6, Q80WR1, Q8BJU2, Q922J6, Q96SJ8, Q99J59, Q9DCK3, O60636, P19397, P24485, P30932, P35762, P40240, P62079, P62080, Q17QJ5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance35
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3797 predictions. Top by Δscore:

VariantEffectΔscore
12:3077449:GCGCG:Gdonor_gain1.0000
12:3077452:CGG:Cdonor_loss1.0000
12:3077454:G:GGdonor_gain1.0000
12:3077455:T:Adonor_loss1.0000
12:3278609:CAGC:Cdonor_gain1.0000
12:3278611:GC:Gdonor_gain1.0000
12:3278613:G:GGdonor_gain1.0000
12:3278990:A:AGacceptor_gain1.0000
12:3278991:G:GAacceptor_gain1.0000
12:3279063:CAAGG:Cdonor_loss1.0000
12:3279064:AAGGT:Adonor_loss1.0000
12:3279066:GGT:Gdonor_loss1.0000
12:3279067:GTAAG:Gdonor_loss1.0000
12:3279068:T:Gdonor_loss1.0000
12:3280372:C:CAacceptor_gain1.0000
12:3280376:T:TAacceptor_gain1.0000
12:3280378:GCAGG:Gacceptor_loss1.0000
12:3280379:CA:Cacceptor_loss1.0000
12:3280380:A:AGacceptor_gain1.0000
12:3280380:AG:Aacceptor_gain1.0000
12:3280380:AGGT:Aacceptor_gain1.0000
12:3280380:AGGTG:Aacceptor_loss1.0000
12:3280381:G:GCacceptor_gain1.0000
12:3280381:GG:Gacceptor_gain1.0000
12:3280381:GGT:Gacceptor_gain1.0000
12:3280381:GGTG:Gacceptor_gain1.0000
12:3280381:GGTGA:Gacceptor_gain1.0000
12:3280478:GC:Gdonor_gain1.0000
12:3280479:C:Gdonor_gain1.0000
12:3280482:AGG:Adonor_loss1.0000

AlphaMissense

1588 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:3281233:G:CW156C0.999
12:3281233:G:TW156C0.999
12:3280407:T:CL119P0.998
12:3281210:G:TG149C0.998
12:3281231:T:AW156R0.998
12:3281231:T:CW156R0.998
12:3280463:T:AW138R0.997
12:3280463:T:CW138R0.997
12:3281204:T:CC147R0.997
12:3278428:G:AG24D0.996
12:3278442:G:AG29R0.996
12:3278442:G:CG29R0.996
12:3278448:G:CG31R0.996
12:3278538:G:CG61R0.996
12:3278539:G:AG61D0.996
12:3278559:G:CG68R0.996
12:3278578:G:AG74E0.996
12:3280465:G:CW138C0.996
12:3280465:G:TW138C0.996
12:3281204:T:AC147S0.996
12:3281205:G:CC147S0.996
12:3281207:T:AC148S0.996
12:3281208:G:AC148Y0.996
12:3281208:G:CC148S0.996
12:3281211:G:AG149D0.996
12:3281211:G:TG149V0.996
12:3278449:G:AG31D0.995
12:3278458:T:CL34P0.995
12:3278560:G:AG68D0.995
12:3278568:G:CG71R0.995

dbSNP variants (sampled 300 via entrez): RS1000025806 (12:3083828 G>A), RS1000032889 (12:3147285 C>T), RS1000034161 (12:3212229 C>T), RS1000044296 (12:3180968 G>A,T), RS1000100527 (12:3190262 A>G), RS1000101937 (12:3217809 C>T), RS1000116956 (12:3080632 G>A), RS1000119236 (12:3157240 C>G,T), RS1000132034 (12:3105943 C>T), RS1000154416 (12:3190016 A>G), RS1000175498 (12:3265925 G>A), RS1000184924 (12:3141906 A>G), RS1000185946 (12:3175644 C>A,T), RS1000203157 (12:3116327 C>T), RS1000204843 (12:3085680 A>C)

Disease associations

OMIM: gene MIM:613137 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

35 associations (top):

StudyTraitp-value
GCST002029_1Temporomandibular joint disorder8.000000e-06
GCST002337_62Amyotrophic lateral sclerosis (sporadic)3.000000e-06
GCST003210_6Low vWF levels1.000000e-07
GCST003372_36Glomerular filtration rate (creatinine)5.000000e-14
GCST004292_4Glomerular filtration rate (creatinine)2.000000e-09
GCST004616_90Platelet distribution width1.000000e-18
GCST005196_60Coronary artery disease1.000000e-06
GCST005984_36Glomerular filtration rate7.000000e-10
GCST005985_36Creatinine levels7.000000e-11
GCST006479_80Diverticular disease1.000000e-06
GCST006979_881Heel bone mineral density6.000000e-16
GCST007344_94Estimated glomerular filtration rate4.000000e-09
GCST007876_94Estimated glomerular filtration rate5.000000e-20
GCST008058_55Estimated glomerular filtration rate8.000000e-29
GCST008059_59Estimated glomerular filtration rate1.000000e-24
GCST008060_27Estimated glomerular filtration rate9.000000e-06
GCST008506_9Stress sensitivity (neuroticism score x major depressive disorder status interaction)8.000000e-06
GCST008747_73Estimated glomerular filtration rate2.000000e-19
GCST008790_44Urinary albumin-to-creatinine ratio2.000000e-08
GCST009462_113Optic disc size5.000000e-15
GCST011739_6Cutaneous leishmaniasis2.000000e-06
GCST012228_545Waist-hip index2.000000e-11
GCST012230_38Waist-to-hip ratio adjusted for BMI2.000000e-11
GCST012231_106A body shape index1.000000e-08
GCST90000025_1013Appendicular lean mass7.000000e-22
GCST90000025_1014Appendicular lean mass8.000000e-60
GCST90000025_1015Appendicular lean mass2.000000e-55
GCST90002398_136Neutrophil count8.000000e-12
GCST90002401_227Platelet distribution width4.000000e-46
GCST90002401_228Platelet distribution width5.000000e-10

EFO canonical traits (11, from GWAS)

EFO IDTrait name
EFO:0007984platelet component distribution width
EFO:0009959diverticular disease
EFO:0009270heel bone mineral density
EFO:0007660neuroticism measurement
EFO:0007778urinary albumin to creatinine ratio
EFO:0007788BMI-adjusted waist-hip ratio
EFO:0007789BMI-adjusted waist circumference
EFO:0004980appendicular lean mass
EFO:0004833neutrophil count
EFO:0004305erythrocyte count
EFO:0004736aspartate aminotransferase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, decreases expression, increases methylation4
Estradioldecreases expression3
bisphenol Adecreases expression, decreases methylation, increases expression2
Silicon Dioxidedecreases expression, decreases methylation2
Valproic Acidincreases methylation, increases expression2
Cadmium Chloridedecreases reaction, increases abundance, increases palmitoylation, increases expression2
Particulate Matterdecreases expression, increases abundance, affects cotreatment2
aristolochic acid Idecreases expression1
2,4,6-tribromophenolincreases expression1
triphenyl phosphateaffects expression1
pirinixic acidaffects binding, decreases expression, increases activity1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
sodium arseniteincreases expression1
2-bromopalmitatedecreases reaction, increases abundance, increases palmitoylation1
perfluorooctanoic aciddecreases expression1
benzo(e)pyreneaffects methylation, increases methylation1
potassium chromate(VI)increases expression1
aflatoxin B2increases methylation1
S-(1,2-dichlorovinyl)cysteineaffects cotreatment, decreases expression1
isobutyl alcoholaffects cotreatment, decreases expression, increases abundance1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
ICG 001increases expression1
abrineincreases expression1
bisphenol Sdecreases methylation1
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
Sunitinibincreases expression1
Air Pollutantsdecreases expression, increases abundance1
Cadmiumdecreases reaction, increases abundance, increases palmitoylation1
Cisplatindecreases expression1

Clinical trials (associated diseases)

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