TSPAN1

Chr 1

tetraspanin 1

Also known as: NET1, TM4C, TM4SF

NCBI Gene: 10103ENSG00000117472UniProt: O60635

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. [provided by RefSeq, Jul 2008]

1324
ClinVar variants
63
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— TSPAN1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
63 Pathogenic / Likely Pathogenic· 167 VUS of 1324 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
1.37LOEUF
pLI 0.000
Z-score 0.67
OE 0.79 (0.47–1.37)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
0.54Z-score
OE missense 0.87 (0.74–1.01)
113 obs / 130.5 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.79 (0.47–1.37)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.87 (0.74–1.01)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.16
0≤1.21.6
LoF obs/exp: 9 / 11.4Missense obs/exp: 113 / 130.5Syn Z: -0.92

ClinVar Variant Classifications

1324 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic22
Likely Pathogenic41
VUS167
Likely Benign240
Benign2
Conflicting4
22
Pathogenic
41
Likely Pathogenic
167
VUS
240
Likely Benign
2
Benign
4
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
16
0
6
0
22
Likely Pathogenic
25
2
14
0
41
VUS
3
137
18
9
167
Likely Benign
0
7
154
79
240
Benign
0
0
2
0
2
Conflicting
—4
Total4414619488476

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

TSPAN1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
TETRASPANIN 1; TSPAN1
MIM #613170 · *
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
TSPAN1 promotes autophagy flux and mediates cooperation between WNT-CTNNB1 signaling and autophagy via the MIR454-FAM83A-TSPAN1 axis in pancreatic cancer.
Zhou C et al.·Autophagy
2021
Prospective cohort study integrating plasma proteomics and machine learning for early risk prediction of prostate cancer.
Chen Y et al.·Int J Surg
2025Cohort
Genomic and Immunologic Correlates in Prostate Cancer with High Expression of KLK2.
Paniagua-Herranz L et al.·Int J Mol Sci
2024
Expression of TSPAN1 and its link to thyroid nodules: one step forward on the path to thyroid tumorigenesis biomarkers.
Abooshahab R et al.·BMC Cancer
2024
TSPAN1 functions as an oncogene in gastric cancer and is downregulated by miR-573.
Lu Z et al.·FEBS Lett
2015
Decreased TSPAN1 promotes prostate cancer progression and is a marker for early biochemical recurrence after radical prostatectomy.
Xu F et al.·Oncotarget
2016
TSPAN1 upregulates MMP2 to promote pancreatic cancer cell migration and invasion via PLCγ.
Zhang X et al.·Oncol Rep
2019
Clinicopathological significance of overexpression of TSPAN1, Ki67 and CD34 in gastric carcinoma.
Chen L et al.·Tumori
2008
miR-573 suppresses pancreatic cancer cell proliferation, migration, and invasion through targeting TSPAN1.
Wang L et al.·Strahlenther Onkol
2021
Bioinformatics analysis reveals TSPAN1 as a candidate biomarker of progression and prognosis in pancreatic cancer.
Ma C et al.·Bosn J Basic Med Sci
2021
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools