LST1

Chr 6

leukocyte specific transcript 1

Also known as: B144, D6S49E, LST-1

NCBI Gene: 7940ENSG00000204482UniProt: O00453

The protein encoded by this gene is a membrane protein that can inhibit the proliferation of lymphocytes. Expression of this gene is enhanced by lipopolysaccharide, interferon-gamma, and bacteria. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

24
ClinVar variants
7
Pathogenic / LP
0.00
pLI score
3
Active trials
Clinical Summary— LST1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
7 Pathogenic / Likely Pathogenic· 12 VUS of 24 total submissions
💊
Clinical Trials
3 active or recruiting trials — potential therapeutic options may be available

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.
1.88LOEUF
pLI 0.001
Z-score -0.26
OE 1.15 (0.54–1.88)
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.
0.01Z-score
OE missense 0.99 (0.80–1.25)
53 obs / 53.3 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.1.15 (0.54–1.88)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.99 (0.80–1.25)
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.1.24
0≤1.21.6
LoF obs/exp: 4 / 3.5Missense obs/exp: 53 / 53.3Syn Z: -0.93

ClinVar Variant Classifications

24 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic4
Likely Pathogenic3
VUS12
Likely Benign5
4
Pathogenic
3
Likely Pathogenic
12
VUS
5
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
4
0
4
Likely Pathogenic
0
0
3
0
3
VUS
0
9
3
0
12
Likely Benign
0
4
0
1
5
Benign
0
0
0
0
0
Total01310124

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

View in ClinVar →

Protein Context — Lollipop Plot

LST1 · 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
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Association of albumin trajectories and cumulative exposure with in-hospital mortality in acute pancreatitis: a retrospective cohort study.
Zou Y et al.·Int J Surg
2026Cohort
LST1: a gene with extensive alternative splicing and immunomodulatory function.
Rollinger-Holzinger I et al.·J Immunol
2000
Expression of ERAP2 and LST1 is increased before start of therapy in rheumatoid arthritis patients with good clinical response to glucocorticoids.
Fritsch-Stork RD et al.·Clin Exp Rheumatol
2016Cohort
Significance of leukocyte-specific transcript 1 levels in nasal mucosal tissue to predict recurrence of nasal polyps.
Zhang J et al.·Braz J Otorhinolaryngol
2023
Identification of functional haplotypes in the promoter region of the LST1 gene.
Woo J et al.·Biochem Genet
2014Functional
Conserved 33-kb haplotype in the MHC class III region regulates chronic arthritis.
Yau AC et al.·Proc Natl Acad Sci U S A
2016
Postmortem Study of Validation of Low Signal on Fat-Suppressed T1-Weighted Magnetic Resonance Imaging as Marker of Lipid Core in Middle Cerebral Artery Atherosclerosis.
Yang WJ et al.·Stroke
2016
The clinical and bioinformatics analysis for the role of antihypertension drugs on mortality among patients with hypertension hospitalized with COVID-19.
Zhao L et al.·J Med Virol
2022Cohort
Identification and validation of immune-associated gene signatures for prognostic prediction in acute myeloid leukemia.
Xu C et al.·Medicine (Baltimore)
2025
Identification and experimental validation of cuproptosis regulatory program in a sepsis immune microenvironment through a combination of single-cell and bulk RNA sequencing.
Zhao T et al.·Front Immunol
2024
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
Cardiovascular Diseases

Personalised Hyperlipidaemia Therapies Guided by Pharmacogenomics

NOT YET RECRUITING
NCT06217523Phase NANational University of SingaporeStarted 2024-04
Pharmacogenomics-directed Hyperlipidaemia Management
Gene PolymorphismEdoxabanRenal Insufficiency

Prospective Observational Association Between SLCO1B1 Gene Polymorphism and the Anti-factor Xa Activity of Edoxaban in Patients With Moderate to Severe Renal Insufficiency

RECRUITING
NCT06431789Yi HanStarted 2024-05-01
PRS-based Primary Prevention of CVD

Polygenic Risk Driven Pragmatic Statin Trial for Heart Disease Prevention

ENROLLING BY INVITATION
NCT06820086Phase PHASE4Mikk JÜRISSONStarted 2025-04
Rosuvastatin 20mg

External Resources

Links to major genomics databases and tools