TSPAN13

Summary

TSPAN13 (tetraspanin 13, HGNC:21643) is a protein-coding gene on chromosome 7p21.1, encoding Tetraspanin-13 (O95857).

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.

Source: NCBI Gene 27075 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 21 total
• MANE Select transcript: NM_014399

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21643
Approved symbol	TSPAN13
Name	tetraspanin 13
Location	7p21.1
Locus type	gene with protein product
Status	Approved
Aliases	NET-6
Ensembl gene	ENSG00000106537
Ensembl biotype	protein_coding
OMIM	613139
Entrez	27075

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 10 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000262067, ENST00000466195, ENST00000889428, ENST00000889429, ENST00000889430, ENST00000889431, ENST00000889432, ENST00000889433, ENST00000889434, ENST00000889435, ENST00000912970

RefSeq mRNA: 1 — MANE Select: NM_014399 NM_014399

CCDS: CCDS5363

Canonical transcript exons

ENST00000262067 — 6 exons

Exon	Start	End
ENSE00000831822	16783417	16784536
ENSE00000976318	16753755	16754030
ENSE00001739245	16779003	16779116
ENSE00003475469	16776211	16776378
ENSE00003603565	16777042	16777122
ENSE00003643381	16777798	16777911

Expression profiles

Bgee: expression breadth ubiquitous, 285 present calls, max score 99.82.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 23.1489 / max 319.9064, expressed in 1520 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
77326	22.5227	1518
77328	0.3028	177
77327	0.2339	129
77325	0.0896	33

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
parotid gland	UBERON:0001831	99.82	gold quality
visceral pleura	UBERON:0002401	99.78	gold quality
jejunal mucosa	UBERON:0000399	99.74	gold quality
endothelial cell	CL:0000115	99.70	gold quality
mucosa of sigmoid colon	UBERON:0004993	99.65	gold quality
Brodmann (1909) area 23	UBERON:0013554	99.64	gold quality
lower lobe of lung	UBERON:0008949	99.63	gold quality
germinal epithelium of ovary	UBERON:0001304	99.56	gold quality
bronchial epithelial cell	CL:0002328	99.51	gold quality
middle temporal gyrus	UBERON:0002771	99.44	gold quality
nasal cavity epithelium	UBERON:0005384	99.43	gold quality
colonic mucosa	UBERON:0000317	99.37	gold quality
epithelium of bronchus	UBERON:0002031	99.23	gold quality
bronchus	UBERON:0002185	99.23	gold quality
epithelial cell of pancreas	CL:0000083	99.20	gold quality
trachea	UBERON:0003126	99.17	gold quality
pigmented layer of retina	UBERON:0001782	99.07	gold quality
retina	UBERON:0000966	99.04	gold quality
nasal cavity mucosa	UBERON:0001826	99.02	gold quality
palpebral conjunctiva	UBERON:0001812	98.94	gold quality
esophagus squamous epithelium	UBERON:0006920	98.94	gold quality
epithelium of nasopharynx	UBERON:0001951	98.93	gold quality
adult organism	UBERON:0007023	98.86	gold quality
tibia	UBERON:0000979	98.83	gold quality
orbitofrontal cortex	UBERON:0004167	98.82	gold quality
seminal vesicle	UBERON:0000998	98.73	gold quality
amniotic fluid	UBERON:0000173	98.68	gold quality
pancreatic ductal cell	CL:0002079	98.66	gold quality
pylorus	UBERON:0001166	98.66	gold quality
mucosa of paranasal sinus	UBERON:0005030	98.55	gold quality

Single-cell (SCXA)

Detected in 22 experiment(s), a significant marker in 21.

Experiment	Marker?	Max mean expression
E-MTAB-8498	yes	1555.54
E-MTAB-10662	yes	502.91
E-MTAB-7381	yes	449.43
E-HCAD-32	yes	335.31
E-MTAB-10137	yes	308.36
E-MTAB-6701	yes	123.32
E-HCAD-4	yes	47.50
E-GEOD-125970	yes	25.82
E-HCAD-1	yes	24.46
E-MTAB-8142	yes	21.20
E-MTAB-9467	yes	17.40
E-MTAB-5061	yes	16.99
E-GEOD-81547	yes	15.51
E-GEOD-93593	yes	15.07
E-CURD-122	yes	15.06

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

98 targeting TSPAN13, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-4775	99.98	75.00	6394
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-338-5P	99.92	72.34	2951
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-3681-3P	99.88	70.46	2254
HSA-MIR-30A-3P	99.87	69.74	2928
HSA-MIR-30D-3P	99.87	69.92	2917
HSA-MIR-30E-3P	99.87	69.68	2942
HSA-MIR-221-3P	99.86	71.56	1329
HSA-MIR-222-3P	99.86	71.35	1337
HSA-MIR-944	99.82	70.85	3042
HSA-MIR-3180-5P	99.82	69.12	2422
HSA-MIR-4639-5P	99.81	67.37	1028
HSA-MIR-548AG	99.77	69.25	1492
HSA-MIR-3617-5P	99.75	69.41	1968

Literature-anchored findings (GeneRIF, showing 10)

• NET-6 may represent a novel breast cancer suppressor gene. (PMID:15958618)
• NET-6 is a potent new breast cancer suppressor gene. (PMID:17486367)
• TSPAN13 is overexpressed in prostate cancer and its expression correlates with factors of favourable outcome. (PMID:19148481)
• tspan13 is overexpressed in prostate cancer and its expression correlates with factors of favourable outcome (PMID:19148481)
• The TSPAN13-to-S100A9 ratio was selected to determine the diagnostic value of urinary nucleic acids in prostate cancer (PCa) (P = 0.037) and shown to be significantly higher in PCa than in benign prostatic hyperplasia. (PMID:26713053)
• The expression of PFKFB3, PFKFB4, NAMPT, and TSPAN13 is strongly up-regulated in pediatric glioma. (PMID:27491149)
• Knocking down of TSAPN13 in human TERT overexpressing osteosarcoma cells enhanced the apoptosis of the cells. TSPAN13 knockdown in these cells suppressed mesenchymal properties and enhanced epithelial character. (PMID:29722072)
• downregulation of miR-369-3p and consequent upregulation of its target TSPAN13 appear to be involved in pathophysiology of papillary thyroid cancer (PMID:30114378)
• The results suggested that miR-4732-5p may serve as a tumor suppressor in the initiation of breast cancer, but as a tumor promoter in breast cancer progression by targeting TSPAN13. (PMID:30701690)
• The expression of tetraspanins NET-6 and CD151 may indicate an alteration of their biological function during neoplastic transformation. (PMID:31004251)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	tspan13a	ENSDARG00000068883
danio_rerio	tspan13b	ENSDARG00000070479
mus_musculus	Tspan13	ENSMUSG00000020577
rattus_norvegicus	Tspan13	ENSRNOG00000005046

Paralogs (32): TSPAN6 (ENSG00000000003), CD9 (ENSG00000010278), TSPAN9 (ENSG00000011105), TSPAN17 (ENSG00000048140), TSPAN32 (ENSG00000064201), CD82 (ENSG00000085117), TSPAN15 (ENSG00000099282), CD37 (ENSG00000104894), UPK1A (ENSG00000105668), TSPAN12 (ENSG00000106025), 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-13 — O95857 (reviewed: O95857)

Alternative names: Tetraspan NET-6, Transmembrane 4 superfamily member 13

All UniProt accessions (2): O95857, Q6FGK0

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the tetraspanin (TM4SF) family.

RefSeq proteins (1): NP_055214* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000301	Tetraspanin_animals	Family
IPR018499	Tetraspanin/Peripherin	Family

Pfam: PF00335

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O95857-F1	90.20	0.71

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): 143

Glycosylation sites (2): 113, 137

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 360 (showing top): VERHAAK_AML_WITH_NPM1_MUTATED_DN, GAANYNYGACNY_UNKNOWN, YANG_BREAST_CANCER_ESR1_BULK_UP, GCANCTGNY_MYOD_Q6, GOZGIT_ESR1_TARGETS_DN, ROVERSI_GLIOMA_COPY_NUMBER_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_DN, RACCACAR_AML_Q6, TAL1ALPHAE47_01, FOXO4_01, GGGTGGRR_PAX4_03, GOBP_MONOATOMIC_CATION_TRANSPORT, GOBP_REGULATION_OF_CALCIUM_ION_TRANSMEMBRANE_TRANSPORT

GO Biological Process (1): regulation of calcium ion transmembrane transport (GO:1903169)

GO Molecular Function (1): calcium channel regulator activity (GO:0005246)

GO Cellular Component (2): plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of calcium ion transport	1
calcium ion transmembrane transport	1
regulation of monoatomic cation transmembrane transport	1
calcium channel activity	1
ion channel regulator activity	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

636 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TSPAN13	B4E171	B4E171	761
TSPAN13	ANKMY2	Q8IV38	640
TSPAN13	BZW2	Q9Y6E2	602
TSPAN13	TSPAN17	Q96FV3	578
TSPAN13	ITGB1	P05556	566
TSPAN13	TSPAN11	A1L157	540
TSPAN13	TSPAN5	P62079	535
TSPAN13	TSPAN1	O60635	523
TSPAN13	TSPAN15	O95858	500
TSPAN13	TSPAN18	Q96SJ8	481
TSPAN13	TSPAN32	Q96QS1	478
TSPAN13	SNX13	Q9Y5W8	472
TSPAN13	TSPAN6	O43657	454
TSPAN13	NUDT13	Q86X67	425
TSPAN13	ZNF414	Q96IQ9	424

IntAct

4 interactions, top by confidence:

A	B	Type	Score
TSPAN13	GLP1R	psi-mi:“MI:0915”(physical association)	0.540
GLP1R	TSPAN13	psi-mi:“MI:0915”(physical association)	0.540
TSPAN13	GLP1R	psi-mi:“MI:0403”(colocalization)	0.540

BioGRID (5): TSPAN13 (Proximity Label-MS), TSPAN13 (Affinity Capture-RNA), APP (Reconstituted Complex), TSPAN13 (PCA), TSPAN13 (Affinity Capture-Western)

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: O95857, Q12999, Q29257, Q32KP1, Q3ZBV0, Q5FVL6, Q5RAP8, Q5U1V9, Q5XHG6, Q7ZUB3, Q7ZWW7, Q9CQ88, Q9D8C2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	15
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1403 predictions. Top by Δscore:

Variant	Effect	Δscore
7:16777908:GGCT:G	donor_gain	1.0000
7:16777909:GCTG:G	donor_gain	1.0000
7:16777912:G:GG	donor_gain	1.0000
7:16778992:A:AG	acceptor_gain	1.0000
7:16778995:T:A	acceptor_gain	1.0000
7:16779002:GAGCT:G	acceptor_gain	1.0000
7:16782284:T:G	donor_gain	1.0000
7:16782298:G:GG	donor_gain	1.0000
7:16753961:TTCC:T	donor_gain	0.9900
7:16754026:ACACC:A	donor_gain	0.9900
7:16754027:CACC:C	donor_gain	0.9900
7:16754027:CACCG:C	donor_loss	0.9900
7:16754028:ACC:A	donor_gain	0.9900
7:16754029:CC:C	donor_gain	0.9900
7:16754030:CGTG:C	donor_loss	0.9900
7:16754031:G:GG	donor_gain	0.9900
7:16754031:GT:G	donor_loss	0.9900
7:16754032:T:TC	donor_loss	0.9900
7:16754033:G:GG	donor_loss	0.9900
7:16754034:AGTA:A	donor_loss	0.9900
7:16776197:G:A	acceptor_gain	0.9900
7:16776209:AGTT:A	acceptor_gain	0.9900
7:16776210:GTTG:G	acceptor_gain	0.9900
7:16776301:G:GG	donor_gain	0.9900
7:16776331:G:GG	donor_gain	0.9900
7:16777793:ACTAG:A	acceptor_gain	0.9900
7:16777909:GCT:G	donor_gain	0.9900
7:16778277:A:AG	donor_gain	0.9900
7:16778278:G:GG	donor_gain	0.9900
7:16778992:AATT:A	acceptor_gain	0.9900

AlphaMissense

1320 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:16776217:A:C	S24R	0.999
7:16776219:T:A	S24R	0.999
7:16776219:T:G	S24R	0.999
7:16777821:G:C	W112C	0.999
7:16777821:G:T	W112C	0.999
7:16779105:A:C	S177R	0.999
7:16779107:T:A	S177R	0.999
7:16779107:T:G	S177R	0.999
7:16783448:G:C	R191T	0.999
7:16783448:G:T	R191M	0.999
7:16783449:G:C	R191S	0.999
7:16783449:G:T	R191S	0.999
7:16754018:C:A	N17K	0.998
7:16754018:C:G	N17K	0.998
7:16776304:G:C	G53R	0.998
7:16776334:G:C	G63R	0.998
7:16777819:T:A	W112R	0.998
7:16777819:T:C	W112R	0.998
7:16777869:C:G	C128W	0.998
7:16779038:T:G	C154W	0.998
7:16783423:G:C	G183R	0.998
7:16783483:T:C	F203L	0.998
7:16783485:C:A	F203L	0.998
7:16783485:C:G	F203L	0.998
7:16776335:G:A	G63D	0.997
7:16776344:G:A	G66E	0.997
7:16777867:T:A	C128S	0.997
7:16777868:G:C	C128S	0.997
7:16779037:G:A	C154Y	0.997
7:16779085:G:A	G170D	0.997

dbSNP variants (sampled 300 via entrez): RS1000120794 (7:16754991 T>C), RS1000136546 (7:16773486 A>G), RS1000208927 (7:16763105 T>A), RS1000289772 (7:16751856 T>C), RS1000297476 (7:16773216 A>G), RS1000313912 (7:16761746 G>T), RS1000333707 (7:16757705 A>G,T), RS1000337793 (7:16777285 T>C), RS1000427123 (7:16757376 T>G), RS1000472458 (7:16764201 G>T), RS1000541925 (7:16771949 A>C), RS1000982415 (7:16752139 TC>T), RS1001068250 (7:16766814 A>AG), RS1001089846 (7:16766298 C>T), RS1001127963 (7:16755440 G>C)

Disease associations

OMIM: gene MIM:613139 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST001915_18	Alzheimer’s disease (cognitive decline)	6.000000e-11
GCST004573_9	Iron status biomarkers (ferritin levels)	9.000000e-08
GCST008821_11	Neurofibrillary tangles	2.000000e-08

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004459	ferritin measurement
EFO:0006797	neurofibrillary tangles measurement

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.

Chemical	Actions (top 5)	PubMed papers
trichostatin A	affects cotreatment, decreases expression, affects expression	3
sodium arsenite	affects methylation, increases expression	3
Valproic Acid	affects expression, increases expression	3
bisphenol A	decreases expression	2
Acetaminophen	increases expression, affects response to substance	2
Doxorubicin	affects expression, affects response to substance	2
aristolochic acid I	decreases expression	1
fluorene-9-bisphenol	decreases expression	1
dicrotophos	decreases expression	1
2-methyl-4-isothiazolin-3-one	increases expression	1
potassium chromate(VI)	increases expression	1
cupric chloride	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
ICG 001	decreases expression	1
abrine	decreases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	decreases expression, affects cotreatment	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Temozolomide	decreases expression	1
Arsenic	affects methylation	1
Carbamazepine	affects expression	1
Catechin	affects cotreatment, increases expression	1
Cisplatin	affects cotreatment, decreases expression	1
Phenobarbital	affects expression	1
Rotenone	increases expression	1
Silicon Dioxide	decreases expression	1
Smoke	decreases expression	1
Tretinoin	increases expression	1
Triclosan	decreases expression	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_TU93	HAP1 TSPAN13 (-) 1	Cancer cell line	Male
CVCL_TU94	HAP1 TSPAN13 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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