TSPAN19

Summary

TSPAN19 (tetraspanin 19, HGNC:31886) is a protein-coding gene on chromosome 12q21.31, encoding Tetraspanin-19 (P0C672).

Predicted to be located in membrane. Predicted to be active in plasma membrane.

Source: NCBI Gene 144448 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 36 total
• MANE Select transcript: NM_001100917

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31886
Approved symbol	TSPAN19
Name	tetraspanin 19
Location	12q21.31
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000231738
Ensembl biotype	protein_coding
Entrez	144448

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 7 protein_coding, 2 nonsense_mediated_decay, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000433494, ENST00000525452, ENST00000529820, ENST00000532498, ENST00000532628, ENST00000547403, ENST00000547836, ENST00000552392, ENST00000900752, ENST00000965352, ENST00000965353, ENST00000965354

RefSeq mRNA: 1 — MANE Select: NM_001100917 NM_001100917

CCDS: CCDS44949

Canonical transcript exons

ENST00000532498 — 9 exons

Exon	Start	End
ENSE00001663193	85015888	85015971
ENSE00001792535	85017456	85017599
ENSE00002152814	85036204	85036277
ENSE00003594704	85029881	85029973
ENSE00003617425	85019626	85019736
ENSE00003635972	85014317	85014555
ENSE00003642234	85029719	85029791
ENSE00003675213	85023326	85023400
ENSE00003787812	85027899	85028023

Expression profiles

Bgee: expression breadth ubiquitous, 122 present calls, max score 94.45.

FANTOM5 (CAGE): breadth broad, TPM avg 0.4890 / max 28.7072, expressed in 196 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
132356	0.3650	160
132355	0.1240	49

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
olfactory segment of nasal mucosa	UBERON:0005386	94.45	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	78.63	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.96	gold quality
hypothalamus	UBERON:0001898	72.85	gold quality
pituitary gland	UBERON:0000007	71.95	gold quality
adenohypophysis	UBERON:0002196	71.04	gold quality
substantia nigra	UBERON:0002038	70.87	gold quality
ventricular zone	UBERON:0003053	70.86	gold quality
right testis	UBERON:0004534	69.42	gold quality
testis	UBERON:0000473	69.23	gold quality
left testis	UBERON:0004533	68.77	gold quality
putamen	UBERON:0001874	68.30	gold quality
caudate nucleus	UBERON:0001873	67.39	gold quality
Ammon’s horn	UBERON:0001954	67.19	gold quality
Brodmann (1909) area 9	UBERON:0013540	67.04	gold quality
prefrontal cortex	UBERON:0000451	66.29	gold quality
primary visual cortex	UBERON:0002436	65.62	gold quality
amygdala	UBERON:0001876	65.35	gold quality
brain	UBERON:0000955	65.26	gold quality
temporal lobe	UBERON:0001871	65.10	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	65.10	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	64.98	gold quality
nucleus accumbens	UBERON:0001882	64.97	gold quality
right lung	UBERON:0002167	64.97	gold quality
frontal cortex	UBERON:0001870	64.71	gold quality
cerebral cortex	UBERON:0000956	64.60	gold quality
superior frontal gyrus	UBERON:0002661	63.79	gold quality
right frontal lobe	UBERON:0002810	62.84	gold quality
anterior cingulate cortex	UBERON:0009835	61.97	gold quality
right hemisphere of cerebellum	UBERON:0014890	59.28	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-CURD-114	yes	64.25
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

21 targeting TSPAN19, 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-5692A	100.00	74.40	6850
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-374C-5P	99.80	72.06	2910
HSA-MIR-655-3P	99.80	72.19	2909
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-6505-5P	99.73	69.25	1595
HSA-MIR-33A-3P	99.70	70.27	3362
HSA-MIR-7154-5P	99.69	70.52	1900
HSA-MIR-12113	99.32	67.54	1072
HSA-MIR-16-2-3P	99.29	70.60	1954
HSA-MIR-195-3P	99.29	70.61	1954
HSA-MIR-8070	99.07	69.30	1303
HSA-MIR-8066	99.05	68.66	1532
HSA-MIR-4539	98.78	67.18	888
HSA-MIR-7850-5P	98.12	67.28	1111
HSA-MIR-582-3P	96.69	67.38	1019

Cross-species orthologs

0 orthologs

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), TSPAN4 (ENSG00000214063)

Protein

Protein identifiers

Tetraspanin-19 — P0C672 (reviewed: P0C672)

All UniProt accessions (5): P0C672, F8VV50, F8VZ36, H0YFW1, J3KQT2

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the tetraspanin (TM4SF) family.

RefSeq proteins (1): NP_001094387* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000301	Tetraspanin_animals	Family
IPR008952	Tetraspanin_EC2_sf	Homologous_superfamily
IPR018499	Tetraspanin/Peripherin	Family

Pfam: PF00335

UniProt features (6 total): transmembrane region 3, glycosylation site 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0C672-F1	90.55	0.74

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): 5, 158

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 22 (showing top): chr12q21, HES2_TARGET_GENES, HMG20B_TARGET_GENES, OVOL3_TARGET_GENES, ZNF407_TARGET_GENES, MIR3658, MIR655_3P, MIR374C_5P, MIR195_3P, MIR16_2_3P, MIR6505_5P, MIR8066, FAN_EMBRYONIC_CTX_OLIG, MANNO_MIDBRAIN_NEUROTYPES_HPROGFPL, GAO_ESOPHAGUS_25W_C1_CILIATED_EPITHELIAL_CELLS

GO Biological Process (0):

GO Molecular Function (0):

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

338 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TSPAN19	LINC03043	A4D0Y5	582
TSPAN19	TSPAN2	O60636	540
TSPAN19	LRRIQ1	Q96JM4	529
TSPAN19	FAM216B	Q8N7L0	514
TSPAN19	TSPAN32	Q96QS1	503
TSPAN19	OVCH1	Q7RTY7	467
TSPAN19	TSPAN16	Q9UKR8	447
TSPAN19	TMEM212	A6NML5	441
TSPAN19	CD81	P18582	424
TSPAN19	ST8SIA6	P61647	423
TSPAN19	CLEC19A	Q6UXS0	413
TSPAN19	TSPAN14	Q8NG11	399
TSPAN19	TSPAN13	O95857	397
TSPAN19	TSPAN10	Q9H1Z9	372
TSPAN19	SLC4A10	Q6U841	371

IntAct

1 interactions, top by confidence:

A	B	Type	Score
KRAS	IGKV2D-29	psi-mi:“MI:0914”(association)	0.350

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: O60635, P0C672

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	33
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1750 predictions. Top by Δscore:

Variant	Effect	Δscore
12:85019624:A:AC	donor_gain	1.0000
12:85019625:C:CC	donor_gain	1.0000
12:85014555:CCTG:C	acceptor_loss	0.9900
12:85014556:C:CC	acceptor_gain	0.9900
12:85014556:C:CG	acceptor_loss	0.9900
12:85014557:T:C	acceptor_loss	0.9900
12:85023319:T:A	donor_gain	0.9900
12:85023401:C:CC	acceptor_gain	0.9900
12:85015970:CC:C	acceptor_gain	0.9800
12:85015971:CC:C	acceptor_gain	0.9800
12:85019625:CTG:C	donor_gain	0.9800
12:85023327:T:TA	donor_gain	0.9800
12:85023399:TA:T	acceptor_gain	0.9800
12:85017075:C:CA	donor_gain	0.9700
12:85023398:ATACT:A	acceptor_gain	0.9700
12:85014552:AAAC:A	acceptor_gain	0.9600
12:85014553:AAC:A	acceptor_gain	0.9600
12:85023397:CATA:C	acceptor_gain	0.9600
12:85029917:A:AC	donor_gain	0.9600
12:85015967:CAACC:C	acceptor_gain	0.9500
12:85019625:CT:C	donor_gain	0.9500
12:85029918:A:C	donor_gain	0.9500
12:85014554:AC:A	acceptor_gain	0.9400
12:85014555:CC:C	acceptor_gain	0.9400
12:85036218:AAGCT:A	donor_gain	0.9400
12:85017039:A:AC	donor_gain	0.9300
12:85017040:C:CC	donor_gain	0.9300
12:85036199:TCTA:T	donor_loss	0.9300
12:85036200:CTAC:C	donor_loss	0.9300
12:85036201:TAC:T	donor_loss	0.9300

AlphaMissense

1636 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:85017564:C:A	W162C	0.994
12:85017564:C:G	W162C	0.994
12:85017566:A:G	W162R	0.976
12:85017566:A:T	W162R	0.976
12:85017592:C:G	C153S	0.976
12:85017593:A:T	C153S	0.976
12:85017587:C:A	G155C	0.974
12:85017589:C:G	C154S	0.971
12:85017590:A:T	C154S	0.971
12:85015967:C:G	C200S	0.968
12:85015968:A:T	C200S	0.968
12:85017489:A:C	F187L	0.968
12:85017489:A:T	F187L	0.968
12:85017491:A:G	F187L	0.968
12:85017517:C:G	C178S	0.968
12:85017518:A:T	C178S	0.968
12:85019653:C:A	W141C	0.966
12:85019653:C:G	W141C	0.966
12:85017593:A:G	C153R	0.965
12:85017586:C:A	G155V	0.961
12:85027952:A:G	C71R	0.956
12:85017555:A:C	N165K	0.953
12:85017555:A:T	N165K	0.953
12:85017589:C:T	C154Y	0.946
12:85017516:G:C	C178W	0.945
12:85017518:A:G	C178R	0.941
12:85019690:T:C	Y129C	0.941
12:85017490:A:C	F187C	0.939
12:85017591:A:C	C153W	0.939
12:85015971:C:A	G199C	0.938

dbSNP variants (sampled 300 via entrez): RS1000093558 (12:85036595 T>C), RS1000132839 (12:85021736 T>A), RS1000206728 (12:85021502 T>C), RS1000411524 (12:85015531 T>C), RS1000688336 (12:85018615 T>C), RS1000691746 (12:85028488 G>C), RS1000784009 (12:85015714 C>A,T), RS1001151936 (12:85013899 A>G), RS1001252578 (12:85015089 A>T), RS1001313165 (12:85037001 CCTAA>C), RS1001432090 (12:85026313 G>A,T), RS1001585389 (12:85034452 T>C), RS1001686202 (12:85021372 T>A), RS1001759533 (12:85020981 G>A,C), RS1001920646 (12:85033144 G>A,C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST003262_580	Post bronchodilator FEV1	3.000000e-06
GCST008155_21	Waist-hip ratio	8.000000e-06
GCST009311_8	Letter-number span reordering	6.000000e-06
GCST009391_2047	Metabolite levels	6.000000e-06

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004314	forced expiratory volume
EFO:0004343	waist-hip ratio
EFO:0004874	memory performance
EFO:0010508	malate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
propionaldehyde	increases expression	1
abrine	increases expression	1
licochalcone B	decreases expression	1
bisphenol S	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	increases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Valproic Acid	decreases methylation	1
Aflatoxin B1	decreases methylation	1
Cadmium Chloride	decreases expression	1

Clinical trials (associated diseases)

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