TSPAN4

gene
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Also known as NAG-2TSPAN-4TETRASPAN

Summary

TSPAN4 (tetraspanin 4, HGNC:11859) is a protein-coding gene on chromosome 11p15.5, encoding Tetraspanin-4 (O14817). Structural component of specialized membrane microdomains known as tetraspanin-enriched microdomains (TERMs), which act as platforms for receptor clustering and signaling.

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. This encoded protein is a cell surface glycoprotein and is similar in sequence to its family member CD53 antigen. It is known to complex with integrins and other transmembrane 4 superfamily proteins. Alternatively spliced transcript variants encoding different isoforms have been identified.

Source: NCBI Gene 7106 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 60 total
  • MANE Select transcript: NM_003271

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:11859
Approved symbolTSPAN4
Nametetraspanin 4
Location11p15.5
Locus typegene with protein product
StatusApproved
AliasesNAG-2, TSPAN-4, TETRASPAN
Ensembl geneENSG00000214063
Ensembl biotypeprotein_coding
OMIM602644
Entrez7106

Gene structure

Transcript identifiers

Ensembl transcripts: 76 — 70 protein_coding, 6 retained_intron

ENST00000346501, ENST00000397396, ENST00000397397, ENST00000397404, ENST00000397406, ENST00000397408, ENST00000397411, ENST00000409531, ENST00000409543, ENST00000464987, ENST00000468468, ENST00000494815, ENST00000524895, ENST00000525201, ENST00000525334, ENST00000526055, ENST00000527644, ENST00000529566, ENST00000530404, ENST00000532375, ENST00000894461, ENST00000894462, ENST00000894463, ENST00000894464, ENST00000894465, ENST00000894466, ENST00000894467, ENST00000894468, ENST00000894469, ENST00000894470, ENST00000894471, ENST00000894472, ENST00000894473, ENST00000894474, ENST00000894475, ENST00000894476, ENST00000894477, ENST00000894478, ENST00000894479, ENST00000894480, ENST00000894481, ENST00000894482, ENST00000894483, ENST00000894484, ENST00000894485, ENST00000894486, ENST00000894487, ENST00000894488, ENST00000894489, ENST00000912168, ENST00000912169, ENST00000912170, ENST00000912171, ENST00000912172, ENST00000912173, ENST00000912174, ENST00000912175, ENST00000912176, ENST00000912177, ENST00000912178, ENST00000912179, ENST00000971873, ENST00000971874, ENST00000971875, ENST00000971876, ENST00000971877, ENST00000971878, ENST00000971879, ENST00000971880, ENST00000971881, ENST00000971882, ENST00000971883, ENST00000971884, ENST00000971885, ENST00000971886, ENST00000971887

RefSeq mRNA: 7 — MANE Select: NM_003271 NM_001025234, NM_001025235, NM_001025236, NM_001025237, NM_001025238, NM_001025239, NM_003271

CCDS: CCDS41589, CCDS7721

Canonical transcript exons

ENST00000397397 — 9 exons

ExonStartEnd
ENSE00001301323847201847300
ENSE00002189838842852842915
ENSE00003537950864437864511
ENSE00003545594865694865825
ENSE00003548838866562867111
ENSE00003566913865918866001
ENSE00003585196865513865614
ENSE00003640300850288850367
ENSE00003787171862550862741

Expression profiles

Bgee: expression breadth ubiquitous, 278 present calls, max score 98.88.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 61.0147 / max 579.0660, expressed in 1804 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter IDTPM avgSamples expressed
11232227.25011782
11232518.85871418
1123247.12231431
1123262.60971013
1123232.51451124
1123291.7509559
1123210.5401312
1123280.3683188

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
stromal cell of endometriumCL:000225598.88gold quality
right lungUBERON:000216797.92gold quality
omental fat padUBERON:001041497.77gold quality
peritoneumUBERON:000235897.71gold quality
adipose tissue of abdominal regionUBERON:000780897.51gold quality
left uterine tubeUBERON:000130397.40gold quality
right ovaryUBERON:000211897.38gold quality
endocervixUBERON:000045897.36gold quality
left ovaryUBERON:000211997.35gold quality
body of uterusUBERON:000985397.32gold quality
subcutaneous adipose tissueUBERON:000219097.28gold quality
upper lobe of left lungUBERON:000895297.20gold quality
tibial nerveUBERON:000132397.06gold quality
right lobe of thyroid glandUBERON:000111997.03gold quality
left lobe of thyroid glandUBERON:000112096.95gold quality
mucosa of stomachUBERON:000119996.92gold quality
right coronary arteryUBERON:000162596.86gold quality
upper lobe of lungUBERON:000894896.72gold quality
lower esophagus muscularis layerUBERON:003583396.29gold quality
esophagogastric junction muscularis propriaUBERON:003584196.28gold quality
adipose tissueUBERON:000101396.27gold quality
thyroid glandUBERON:000204696.25gold quality
metanephros cortexUBERON:001053396.23gold quality
lower esophagusUBERON:001347396.22gold quality
spleenUBERON:000210696.05gold quality
connective tissueUBERON:000238495.73gold quality
ectocervixUBERON:001224995.69gold quality
apex of heartUBERON:000209895.53gold quality
coronary arteryUBERON:000162195.29gold quality
left coronary arteryUBERON:000162695.25gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 7.

ExperimentMarker?Max mean expression
E-MTAB-6701yes59.01
E-MTAB-8410yes56.94
E-ANND-3yes19.01
E-HCAD-1yes17.11
E-CURD-112yes13.99
E-HCAD-13yes11.65
E-MTAB-6678yes11.39

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

17 targeting TSPAN4, 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-453199.9969.703181
HSA-MIR-1213699.9872.815713
HSA-MIR-96-5P99.9572.802140
HSA-MIR-1-3P99.9372.351914
HSA-MIR-20699.9372.501893
HSA-MIR-61399.9171.501710
HSA-MIR-990299.8969.152250
HSA-MIR-182-5P99.8774.032589
HSA-MIR-3663-3P99.8470.39798
HSA-MIR-1213199.4868.721673
HSA-MIR-4667-3P99.2665.451608
HSA-MIR-442699.1766.741949
HSA-MIR-4477A98.8369.752952
HSA-MIR-1178-3P98.5767.09890
HSA-MIR-216B-3P98.5567.191223
HSA-MIR-66597.6065.641781
HSA-MIR-342-3P96.4467.481344

Literature-anchored findings (GeneRIF, showing 4)

  • TM4SF4/il-TMP has the potential to be biomarker in a hepatocellular carcinoma and plays a crucial role in promotion of cancer cell proliferation (PMID:22236579)
  • Exome sequencing of child-parent trios with bladder exstrophy: Findings in 26 children. (PMID:34355505)
  • Identification of TSPAN4 as Novel Histamine H4 Receptor Interactor. (PMID:34439793)
  • TSPAN4 and migrasomes in atherosclerosis regression correlated to myocardial infarction and pan-cancer progression. (PMID:36513632)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriotspan4aENSDARG00000089354
mus_musculusTspan4ENSMUSG00000025511
rattus_norvegicusTspan4ENSRNOG00000029810

Paralogs (32): TSPAN6 (ENSG00000000003), CD9 (ENSG00000010278), TSPAN9 (ENSG00000011105), 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), TSPAN19 (ENSG00000231738)

Protein

Protein identifiers

Tetraspanin-4O14817 (reviewed: O14817)

Alternative names: Novel antigen 2, Transmembrane 4 superfamily member 7

All UniProt accessions (8): A8MVV6, E9PMX4, E9PN41, E9PPX8, E9PSH3, O14817, J3KNL1, J3KQ42

UniProt curated annotations — full annotation on UniProt →

Function. Structural component of specialized membrane microdomains known as tetraspanin-enriched microdomains (TERMs), which act as platforms for receptor clustering and signaling. Plays an essential role in migrasome formation and migration on retracting fibers at the rear end of migrating cells. Migrasomes are cellular organelles that form as large vesicle-like structures on retraction fibers of migrating cells. Mechanistically, acts as a membrane curvature sensor and participates in stabilizing the migrasome structure in a late stage of biogenesis. May also play a regulatory role for the histamine H4 receptor/HRH4 without affecting histamine binding to HRH4 or signaling.

Subunit / interactions. Forms a complex with integrins. Interacts with HRH4.

Subcellular location. Cell membrane.

Tissue specificity. Expressed in multiple tissues but is absent in brain, lymphoid cells, and platelets.

Similarity. Belongs to the tetraspanin (TM4SF) family.

RefSeq proteins (7): NP_001020405, NP_001020406, NP_001020407, NP_001020408, NP_001020409, NP_001020410, NP_003262* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000301Tetraspanin_animalsFamily
IPR008952Tetraspanin_EC2_sfHomologous_superfamily
IPR018499Tetraspanin/PeripherinFamily
IPR018503Tetraspanin_CSConserved_site

Pfam: PF00335

UniProt features (13 total): topological domain 5, transmembrane region 4, glycosylation site 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O14817-F189.950.69

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 (2): 152, 161

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 217 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_DN, MODULE_64, FOXO4_01, GGGTGGRR_PAX4_03, USF_C, YU_MYC_TARGETS_UP, UEDA_PERIFERAL_CLOCK, ACATTCC_MIR1_MIR206, TGACATY_UNKNOWN, ABBUD_LIF_SIGNALING_1_UP, GOMF_SIGNALING_RECEPTOR_BINDING, ZAMORA_NOS2_TARGETS_DN, FOXO4_02

GO Biological Process (1): protein-containing complex assembly (GO:0065003)

GO Molecular Function (3): antigen binding (GO:0003823), integrin binding (GO:0005178), protein binding (GO:0005515)

GO Cellular Component (4): plasma membrane (GO:0005886), focal adhesion (GO:0005925), vesicle (GO:0031982), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding2
cellular component assembly1
protein-containing complex organization1
signaling receptor binding1
protein-containing complex binding1
cell adhesion molecule binding1
membrane1
cell periphery1
cell-substrate junction1
membrane-bounded organelle1
cellular anatomical structure1

Protein interactions and networks

STRING

756 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TSPAN4GDF15P78360880
TSPAN4CHD7Q9P2D1649
TSPAN4SERPINA7P05543643
TSPAN4ADCY10Q96PN6637
TSPAN4NISCHQ9Y2I1573
TSPAN4CD81P18582571
TSPAN4TMEM8BA6NDV4571
TSPAN4ITGB1P05556508
TSPAN4CCDC136Q96JN2507
TSPAN4ASPDHA6ND91488
TSPAN4CD9P21926487
TSPAN4ITGA6P23229441
TSPAN4TSPAN31Q12999439
TSPAN4CTIFO43310425
TSPAN4B4E171B4E171416

IntAct

128 interactions, top by confidence:

ABTypeScore
NOTCH2NLATSPAN4psi-mi:“MI:0915”(physical association)0.670
TSPAN4NOTCH2NLApsi-mi:“MI:0915”(physical association)0.670
CYSRT1TSPAN4psi-mi:“MI:0915”(physical association)0.560
TSPAN4MDFIpsi-mi:“MI:0915”(physical association)0.560
TSPAN4NOTCH2NLCpsi-mi:“MI:0915”(physical association)0.560
TSPAN4NR4A3psi-mi:“MI:0915”(physical association)0.560
TSPAN4LCE2Dpsi-mi:“MI:0915”(physical association)0.560
TSPAN4CREB5psi-mi:“MI:0915”(physical association)0.560
TSPAN4CLEC2Dpsi-mi:“MI:0915”(physical association)0.560
FCHO1TSPAN4psi-mi:“MI:0915”(physical association)0.560
TSPAN4LCE3Apsi-mi:“MI:0915”(physical association)0.560
TSPAN4CATSPER1psi-mi:“MI:0915”(physical association)0.560
TSPAN4LCE3Dpsi-mi:“MI:0915”(physical association)0.560
TSPAN4LCE4Apsi-mi:“MI:0915”(physical association)0.560
TSPAN4psi-mi:“MI:0915”(physical association)0.560
PHLDA1TSPAN4psi-mi:“MI:0915”(physical association)0.560
TSPAN4GNEpsi-mi:“MI:0915”(physical association)0.560
TSPAN4LCE3Cpsi-mi:“MI:0915”(physical association)0.560
TSPAN4KRTAP9-2psi-mi:“MI:0915”(physical association)0.560
TSPAN4HOXA1psi-mi:“MI:0915”(physical association)0.560
TSPAN4KRTAP9-3psi-mi:“MI:0915”(physical association)0.560
TSPAN4GRNpsi-mi:“MI:0915”(physical association)0.560
TSPAN4GUCD1psi-mi:“MI:0915”(physical association)0.560
TSPAN4CHRDpsi-mi:“MI:0915”(physical association)0.560
TSPAN4FRS3psi-mi:“MI:0915”(physical association)0.560
VGLL3TSPAN4psi-mi:“MI:0915”(physical association)0.560

BioGRID (58): NOTCH2NL (Two-hybrid), TSPAN4 (Two-hybrid), TSPAN4 (Affinity Capture-RNA), TSPAN4 (Affinity Capture-RNA), TSPAN4 (Two-hybrid), TSPAN4 (Two-hybrid), TSPAN4 (Two-hybrid), TSPAN4 (Two-hybrid), TSPAN4 (Two-hybrid), TSPAN4 (Two-hybrid), TSPAN4 (Two-hybrid), TSPAN4 (Two-hybrid), TSPAN4 (Two-hybrid), TSPAN4 (Two-hybrid), TSPAN4 (Two-hybrid)

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.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 40 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
Keratinization1325.9×2e-14
Formation of the cornified envelope722.0×3e-07

GO biological processes:

GO termPartnersFoldFDR
keratinization852.0×4e-10

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance44
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1977 predictions. Top by Δscore:

VariantEffectΔscore
11:842412:AC:Adonor_gain1.0000
11:842412:ACC:Adonor_gain1.0000
11:842413:CC:Cdonor_gain1.0000
11:842413:CCC:Cdonor_gain1.0000
11:842413:CCCCT:Cdonor_gain1.0000
11:850366:GG:Gdonor_gain1.0000
11:850367:GG:Gdonor_gain1.0000
11:862537:T:TAacceptor_gain1.0000
11:862540:T:Aacceptor_gain1.0000
11:862548:AGCTG:Aacceptor_gain1.0000
11:862549:GCTGG:Gacceptor_gain1.0000
11:862641:C:Aacceptor_gain1.0000
11:862741:TG:Tdonor_loss1.0000
11:862742:G:GGdonor_gain1.0000
11:862742:GTGA:Gdonor_loss1.0000
11:864434:CA:Cacceptor_loss1.0000
11:864435:A:AGacceptor_gain1.0000
11:864435:AGTTC:Aacceptor_loss1.0000
11:864436:G:GAacceptor_gain1.0000
11:864436:GTT:Gacceptor_gain1.0000
11:864509:AAGG:Adonor_loss1.0000
11:864510:AGGT:Adonor_loss1.0000
11:864511:GGTA:Gdonor_loss1.0000
11:865511:A:AGacceptor_gain1.0000
11:865511:AGATT:Aacceptor_gain1.0000
11:865512:G:GAacceptor_gain1.0000
11:865512:GA:Gacceptor_gain1.0000
11:865512:GAT:Gacceptor_gain1.0000
11:865512:GATT:Gacceptor_gain1.0000
11:865512:GATTG:Gacceptor_gain1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000141388 (11:852064 G>A,T), RS1000218968 (11:845084 C>G,T), RS1000285576 (11:861438 C>T), RS1000390673 (11:847480 G>A,T), RS1000441734 (11:843285 G>T), RS1000639494 (11:863458 C>A,T), RS1000695966 (11:844245 G>A), RS1000920457 (11:852944 G>A,C), RS1000934032 (11:855855 C>T), RS1000977106 (11:861181 A>C), RS1000987371 (11:844421 C>G), RS1000994924 (11:857638 C>G,T), RS1001029418 (11:860949 C>T), RS1001167936 (11:862519 T>C), RS1001175730 (11:846884 C>T)

Disease associations

OMIM: gene MIM:602644 | 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
GCST90012857_13Falling risk2.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, increases expression, increases methylation6
sodium arsenitedecreases expression, affects cotreatment, increases abundance, increases expression4
Air Pollutantsaffects cotreatment, increases abundance, increases oxidation, decreases expression4
Tobacco Smoke Pollutiondecreases expression, increases methylation3
Tretinoindecreases expression, increases expression3
Particulate Matterdecreases reaction, increases abundance, decreases expression3
Arsenicincreases abundance, increases expression, affects cotreatment, decreases expression2
Phenylmercuric Acetateincreases expression, affects cotreatment2
Smokeincreases expression, decreases expression, increases abundance2
aristolochic acid Iincreases expression1
triphenyl phosphateaffects expression1
alpha-pineneaffects cotreatment, increases oxidation, increases abundance1
pirinixic acidaffects binding, decreases expression, increases activity1
bisphenol Aaffects cotreatment, decreases methylation1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
cobaltous chloridedecreases expression1
2-bromopalmitatedecreases reaction, increases abundance, increases palmitoylation1
manganese chlorideaffects cotreatment, decreases expression, increases abundance1
benzo(e)pyreneincreases methylation1
aflatoxin B2decreases methylation1
methacrylaldehydeaffects cotreatment, increases oxidation, increases abundance1
entinostatincreases expression1
monomethylarsonous aciddecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amidedecreases expression, decreases reaction1
dorsomorphinaffects cotreatment, increases expression1
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
Arsenic Trioxidedecreases expression1
Fulvestrantaffects cotreatment, decreases methylation1
Acetaminophendecreases expression1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

CellosaurusNameCategorySex
CVCL_XU79HAP1 TSPAN4 (-)Cancer cell lineMale

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.