TSPAN6

gene
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Also known as T245TSPAN-6

Summary

TSPAN6 (tetraspanin 6, HGNC:11858) is a protein-coding gene on chromosome Xq22.1, encoding Tetraspanin-6 (O43657).

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. The protein encoded by this gene is a cell surface glycoprotein and is highly similar in sequence to the transmembrane 4 superfamily member 2 protein. It functions as a negative regulator of retinoic acid-inducible gene I-like receptor-mediated immune signaling via its interaction with the mitochondrial antiviral signaling-centered signalosome. This gene uses alternative polyadenylation sites, and multiple transcript variants result from alternative splicing.

Source: NCBI Gene 7105 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 72 total
  • MANE Select transcript: NM_003270

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:11858
Approved symbolTSPAN6
Nametetraspanin 6
LocationXq22.1
Locus typegene with protein product
StatusApproved
AliasesT245, TSPAN-6
Ensembl geneENSG00000000003
Ensembl biotypeprotein_coding
OMIM300191
Entrez7105

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 11 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000373020, ENST00000494424, ENST00000496771, ENST00000612152, ENST00000867886, ENST00000867887, ENST00000867888, ENST00000867889, ENST00000867890, ENST00000867891, ENST00000867892, ENST00000966005, ENST00000966006

RefSeq mRNA: 5 — MANE Select: NM_003270 NM_001278740, NM_001278741, NM_001278742, NM_001278743, NM_003270

CCDS: CCDS14470, CCDS76001

Canonical transcript exons

ENST00000373020 — 8 exons

ExonStartEnd
ENSE00000401072100632485100632568
ENSE00000868868100630759100630866
ENSE00001459322100627108100629986
ENSE00001855382100636608100636806
ENSE00003554016100633405100633539
ENSE00003654571100635178100635252
ENSE00003658810100633931100634029
ENSE00003662440100635558100635746

Expression profiles

Bgee: expression breadth ubiquitous, 279 present calls, max score 99.96.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 35.8982 / max 1008.5052, expressed in 1444 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter IDTPM avgSamples expressed
19992029.36061425
1999223.23471084
1999241.2345571
1999211.1978735
1999250.3975201
1999260.3411175
1999270.078011
1999190.054119

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
spermCL:000001999.96gold quality
parotid glandUBERON:000183199.35gold quality
bronchial epithelial cellCL:000232899.24gold quality
epithelium of bronchusUBERON:000203199.08gold quality
male germ cellCL:000001599.04gold quality
bronchusUBERON:000218598.95gold quality
nasal cavity epitheliumUBERON:000538498.83gold quality
epithelium of nasopharynxUBERON:000195197.98gold quality
nasal cavity mucosaUBERON:000182697.62gold quality
tibiaUBERON:000097997.52gold quality
mucosa of paranasal sinusUBERON:000503097.28gold quality
olfactory segment of nasal mucosaUBERON:000538697.26gold quality
colonic mucosaUBERON:000031796.96gold quality
mucosa of sigmoid colonUBERON:000499396.94gold quality
esophagus squamous epitheliumUBERON:000692096.86gold quality
renal medullaUBERON:000036296.84gold quality
oral cavityUBERON:000016796.75gold quality
right testisUBERON:000453496.61gold quality
epithelium of esophagusUBERON:000197696.55gold quality
left testisUBERON:000453396.47gold quality
choroid plexus epitheliumUBERON:000391195.95gold quality
palpebral conjunctivaUBERON:000181295.72gold quality
ventricular zoneUBERON:000305395.58gold quality
pharyngeal mucosaUBERON:000035595.56gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099195.47gold quality
left ovaryUBERON:000211995.36gold quality
adult organismUBERON:000702395.34gold quality
testisUBERON:000047395.33gold quality
ovaryUBERON:000099295.03gold quality
right ovaryUBERON:000211894.91gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 6.

ExperimentMarker?Max mean expression
E-GEOD-75140yes542.78
E-HCAD-10yes26.68
E-GEOD-93593yes15.28
E-ANND-3yes13.63
E-CURD-114yes7.89
E-CURD-112yes6.12
E-GEOD-99795no122.96

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

111 targeting TSPAN6, 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-6758-5P100.0066.211470
HSA-MIR-6856-5P100.0065.471298
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-3925-3P100.0069.951237
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-366299.9973.825684
HSA-MIR-569699.9872.364487
HSA-MIR-477599.9875.006394
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-548P99.9872.253784
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-590-3P99.9674.346478
HSA-MIR-651-3P99.9473.485177
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-381-3P99.9371.872854
HSA-MIR-5195-3P99.9270.921877
HSA-MIR-515-5P99.9269.822343
HSA-MIR-145-5P99.9271.131836
HSA-MIR-519E-5P99.9269.622358
HSA-MIR-30099.9271.762856
HSA-MIR-568099.9169.833421
HSA-MIR-130599.9171.433443
HSA-MIR-808799.9069.551351

Literature-anchored findings (GeneRIF, showing 7)

  • TSPAN6 functions as a negative regulator of the RLR pathway by interacting with MAVS in a ubiquitination-dependent manner. (PMID:22908223)
  • Results shows that TSPAN6 is a crucial player in Amyloid Precursor Protein-C-terminal fragment turnover (PMID:28279219)
  • Tetraspanin 7 and its closest paralog tetraspanin 6: membrane organizers with key functions in brain development, viral infection, innate immunity, diabetes and cancer. (PMID:32468130)
  • Tetraspanin 6 is a regulator of carcinogenesis in colorectal cancer. (PMID:34521767)
  • TSPAN6 is a suppressor of Ras-driven cancer. (PMID:35184157)
  • TSPAN6 reinforces the malignant progression of glioblastoma via interacting with CDK5RAP3 and regulating STAT3 signaling pathway. (PMID:38725860)
  • New insights into the role of tetraspanin 6, 7, and 8 in physiology and pathology. (PMID:39031113)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriotspan6ENSDARG00000015759
mus_musculusTspan6ENSMUSG00000067377
rattus_norvegicusTspan6ENSRNOG00000003786

Paralogs (32): 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), TSPAN4 (ENSG00000214063), TSPAN19 (ENSG00000231738)

Protein

Protein identifiers

Tetraspanin-6O43657 (reviewed: O43657)

Alternative names: A15 homolog, Putative NF-kappa-B-activating protein 321, T245 protein, Tetraspanin TM4-D, Transmembrane 4 superfamily member 6

All UniProt accessions (2): A0A087WYV6, O43657

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the tetraspanin (TM4SF) family.

RefSeq proteins (5): NP_001265669, NP_001265670, NP_001265671, NP_001265672, NP_003261* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000301Tetraspanin_animalsFamily
IPR008952Tetraspanin_EC2_sfHomologous_superfamily
IPR018499Tetraspanin/PeripherinFamily
IPR018503Tetraspanin_CSConserved_site
IPR048232TSN6/7_LELDomain

Pfam: PF00335

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O43657-F188.170.66

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): 134

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 210 (showing top): GOBP_CANONICAL_NF_KAPPAB_SIGNAL_TRANSDUCTION, CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_DN, AREB6_01, GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_DN, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, GOBP_POSITIVE_REGULATION_OF_RESPONSE_TO_EXTERNAL_STIMULUS, BROWNE_HCMV_INFECTION_48HR_DN, WANG_ESOPHAGUS_CANCER_VS_NORMAL_DN, GOBP_REGULATION_OF_IMMUNE_RESPONSE, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, BLALOCK_ALZHEIMERS_DISEASE_UP, GOBP_REGULATION_OF_RESPONSE_TO_STRESS, TSENG_IRS1_TARGETS_DN, GOBP_NEGATIVE_REGULATION_OF_CANONICAL_NF_KAPPAB_SIGNAL_TRANSDUCTION

GO Biological Process (3): negative regulation of cytoplasmic pattern recognition receptor signaling pathway (GO:0039532), positive regulation of canonical NF-kappaB signal transduction (GO:0043123), negative regulation of canonical NF-kappaB signal transduction (GO:0043124)

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

GO Cellular Component (3): plasma membrane (GO:0005886), extracellular exosome (GO:0070062), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
negative regulation of intracellular signal transduction2
canonical NF-kappaB signal transduction2
regulation of canonical NF-kappaB signal transduction2
negative regulation of immune system process1
cytoplasmic pattern recognition receptor signaling pathway1
regulation of cytoplasmic pattern recognition receptor signaling pathway1
positive regulation of intracellular signal transduction1
binding1
membrane1
cell periphery1
extracellular vesicle1
cellular anatomical structure1

Protein interactions and networks

STRING

922 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TSPAN6SDCBPO00560742
TSPAN6TM4SF1P30408584
TSPAN6MAVSQ7Z434524
TSPAN6SH2D7A6NKC9514
TSPAN6TSG101Q99816477
TSPAN6ZNF253O75346472
TSPAN6ITGB1P05556470
TSPAN6CLEC5AQ9NY25465
TSPAN6TSPAN13O95857454
TSPAN6CD63P08962432
TSPAN6TM4SF5O14894427
TSPAN6PNMA1Q8ND90425
TSPAN6SLC39A6Q13433412
TSPAN6ECM1Q16610412
TSPAN6TSPAN31Q12999395

IntAct

44 interactions, top by confidence:

ABTypeScore
TMEM30BKLRG2psi-mi:“MI:0914”(association)0.530
EVA1CUPK3BL1psi-mi:“MI:0914”(association)0.530
GPR141STXBP3psi-mi:“MI:0914”(association)0.530
SERPINA12TSPAN6psi-mi:“MI:0914”(association)0.530
TNFRSF17TSPAN6psi-mi:“MI:0914”(association)0.530
TMEM185ATSPAN6psi-mi:“MI:0914”(association)0.530
CDS1TSPAN6psi-mi:“MI:0914”(association)0.530
CLEC5ATSPAN6psi-mi:“MI:0914”(association)0.530
LRRTM1UPK3BL1psi-mi:“MI:0914”(association)0.530
TSPAN6psi-mi:“MI:0915”(physical association)0.370
TSPAN6NSG2psi-mi:“MI:0915”(physical association)0.370
LRRTM1TMEM223psi-mi:“MI:0914”(association)0.350
ASIC4UPK3BL1psi-mi:“MI:0914”(association)0.350
LYPD4DPYSL4psi-mi:“MI:0914”(association)0.350
VNN2ATP2A1psi-mi:“MI:0914”(association)0.350
CANXHLA-Apsi-mi:“MI:0914”(association)0.350
RAB14TSPAN6psi-mi:“MI:0914”(association)0.350
TSPAN15TMEM223psi-mi:“MI:0914”(association)0.350
SCN4AC2CD4Bpsi-mi:“MI:0914”(association)0.350
KIR2DL4GPR89Apsi-mi:“MI:0914”(association)0.350
LYPD4PIK3C2Apsi-mi:“MI:0914”(association)0.350

BioGRID (80): TSPAN6 (Affinity Capture-MS), TSPAN6 (Affinity Capture-MS), TSPAN6 (Affinity Capture-MS), TSPAN6 (Affinity Capture-MS), TSPAN6 (Affinity Capture-MS), TSPAN6 (Affinity Capture-MS), TSPAN6 (Affinity Capture-MS), TSPAN6 (Affinity Capture-MS), TSPAN6 (Affinity Capture-MS), TSPAN6 (Affinity Capture-MS), TSPAN6 (Affinity Capture-MS), TSPAN6 (Affinity Capture-MS), TSPAN6 (Affinity Capture-MS), TSPAN6 (Affinity Capture-MS), TSPAN6 (Affinity Capture-MS)

ESM2 similar proteins: O43657, O46101, O60635, O70352, O70401, O75508, P08962, P0C672, P19331, P19397, P27591, P27701, P28648, P34285, P40237, P41731, P41732, P91799, Q11098, Q22495, Q24188, Q26499, Q28709, Q2KIS9, Q32KU6, Q3MHK4, Q3T0S3, Q4R3L1, Q4R7W6, Q55CV4, Q55CV5, Q55CV7, Q55CW7, Q58DM3, Q5RAS5, Q5RC27, Q5REK8, Q5WRN1, Q60771, Q61451

Diamond homologs: A1L157, B0BM39, B5X3I6, O14817, O35566, O43657, O60636, O70401, O75954, P08962, P19397, P21926, P24485, P27701, P30409, P30932, P40239, P40240, P40241, P41731, P41732, P48509, P61170, P61171, Q06AA5, Q0VC33, Q28709, Q2KIS9, Q32KU6, Q3ZBH3, Q568Y5, Q58CY8, Q58DM3, Q5RAP3, Q5RAS5, Q61451, Q62283, Q6DCQ3, Q7YQK9, Q7YQL0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance23
Likely benign4
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

965 predictions. Top by Δscore:

VariantEffectΔscore
X:100630864:CAG:Cacceptor_gain1.0000
X:100630867:C:CCacceptor_gain1.0000
X:100632483:A:ACdonor_gain1.0000
X:100632484:C:CCdonor_gain1.0000
X:100633403:A:ACdonor_gain1.0000
X:100633404:C:CCdonor_gain1.0000
X:100633406:T:TAdonor_gain1.0000
X:100633535:TGCAA:Tacceptor_gain1.0000
X:100633540:C:CCacceptor_gain1.0000
X:100633926:CTTA:Cdonor_loss1.0000
X:100633927:TTA:Tdonor_loss1.0000
X:100633928:TACCG:Tdonor_loss1.0000
X:100633929:A:ACdonor_gain1.0000
X:100633929:AC:Adonor_gain1.0000
X:100633929:ACCG:Adonor_loss1.0000
X:100633930:C:CTdonor_gain1.0000
X:100633930:CC:Cdonor_gain1.0000
X:100633930:CCGT:Cdonor_gain1.0000
X:100633930:CCGTA:Cdonor_gain1.0000
X:100634025:TTAAT:Tacceptor_gain1.0000
X:100634026:TAAT:Tacceptor_gain1.0000
X:100634027:AAT:Aacceptor_gain1.0000
X:100634028:AT:Aacceptor_gain1.0000
X:100634028:ATC:Aacceptor_loss1.0000
X:100634030:C:CCacceptor_gain1.0000
X:100634032:A:Cacceptor_gain1.0000
X:100635172:GCTTA:Gdonor_loss1.0000
X:100635173:CTTA:Cdonor_loss1.0000
X:100635174:TTA:Tdonor_loss1.0000
X:100635175:TA:Tdonor_loss1.0000

AlphaMissense

1611 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
X:100633504:C:AW162C1.000
X:100633504:C:GW162C1.000
X:100633527:C:AG155C0.999
X:100633506:A:GW162R0.998
X:100633506:A:TW162R0.998
X:100632563:A:CC197W0.997
X:100632564:C:GC197S0.997
X:100632565:A:TC197S0.997
X:100633529:C:GC154S0.997
X:100633530:A:TC154S0.997
X:100633531:A:CC153W0.997
X:100633532:C:GC153S0.997
X:100633533:A:GC153R0.997
X:100633533:A:TC153S0.997
X:100635632:C:GG68R0.997
X:100635719:C:GG39R0.997
X:100635740:C:GG32R0.997
X:100632564:C:TC197Y0.996
X:100632565:A:GC197R0.996
X:100633460:C:GC177S0.996
X:100633460:C:TC177Y0.996
X:100633461:A:TC177S0.996
X:100633526:C:AG155V0.996
X:100633529:C:TC154Y0.996
X:100633532:C:TC153Y0.996
X:100633938:T:GQ148P0.996
X:100635631:C:TG68D0.996
X:100635718:C:TG39D0.996
X:100635739:C:TG32D0.996
X:100630860:C:GG226R0.995

dbSNP variants (sampled 300 via entrez): RS1000035902 (X:100629330 C>T), RS1000083682 (X:100633561 T>C), RS1000201757 (X:100627962 C>A,T), RS1000602171 (X:100627169 C>A,T), RS1000909706 (X:100627638 G>T), RS1001169815 (X:100636279 G>A), RS1001403098 (X:100632675 T>A,C), RS1001755243 (X:100628734 T>A), RS1001974420 (X:100635037 T>C), RS1002043793 (X:100633103 G>A), RS1002065612 (X:100637415 A>G), RS1002555233 (X:100631932 A>G), RS1002642058 (X:100631305 G>C), RS1003162958 (X:100631491 TA>T,TAA), RS1003841651 (X:100634617 G>A,C)

Disease associations

OMIM: gene MIM:300191 | disease phenotypes: MIM:300088, MIM:300643

GenCC curated gene-disease

Mondo (2): developmental and epileptic encephalopathy, 9 (MONDO:0010246), rolandic epilepsy, intellectual disability, and speech dyspraxia, X-linked (MONDO:0010388)

Orphanet (2): Female restricted epilepsy with intellectual disability (Orphanet:101039), X-linked intellectual disability-epilepsy syndrome (Orphanet:2076)

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (2)

DescriptorNameTree numbers
C564715Epilepsy, Female-Restricted, with Mental Retardation (supp.)
C564467Rolandic Epilepsy, Mental Retardation, and Speech Dyspraxia, X-Linked (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects expression, affects cotreatment, increases methylation, decreases methylation, increases expression3
Cyclosporinedecreases expression3
sodium arsenitedecreases expression2
Nickeldecreases expression2
Tobacco Smoke Pollutionaffects expression, decreases expression2
Valproic Acidaffects expression, decreases expression2
aristolochic acid Idecreases expression1
dicrotophosdecreases expression1
mono-(2-ethylhexyl)phthalateaffects response to substance1
perfluorooctanoic aciddecreases expression1
epigallocatechin gallatedecreases expression1
CGP 52608affects binding, increases reaction1
K 7174decreases expression1
bisphenol Bincreases expression1
abrinedecreases expression1
bisphenol Sdecreases methylation1
bisphenol AFincreases expression1
Temozolomideincreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Acetaminophendecreases expression1
Acetylcysteinedecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Atrazinedecreases expression1
Benzo(a)pyreneaffects methylation, increases methylation1
Dexamethasoneaffects cotreatment, increases expression1
Indomethacinaffects cotreatment, increases expression1
Piroxicamdecreases expression1
Smokedecreases expression1
Thiramdecreases expression1
1-Methyl-3-isobutylxanthineincreases expression, affects cotreatment1

Clinical trials (associated diseases)

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