LATS2

Chr 13

large tumor suppressor kinase 2

Also known as: KPM

NCBI Gene: 26524ENSG00000150457UniProt: Q9NRM7OMIM: 604861

This gene encodes a serine/threonine kinase that functions as a negative regulator of YAP1 in the Hippo signaling pathway, controlling organ size and tumor suppression by restricting cell proliferation and promoting apoptosis, and also plays critical roles in centrosome duplication and maintaining genomic stability. The gene is highly constrained against loss-of-function variation (pLI=0.99, LOEUF=0.30), but no established Mendelian diseases have been definitively linked to LATS2 mutations in current databases.

OMIMResearchSummary from RefSeq, UniProt
LOFmechanismLOEUF 0.30
Clinical Summary— LATS2
⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.99). One damaged copy is likely sufficient to cause disease.
📋
ClinVar Variants
45 unique Pathogenic / Likely Pathogenic· 143 VUS of 223 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint
0.30LOEUF
pLI 0.988
Z-score 4.74
OE 0.14 (0.07–0.30)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint
2.21Z-score
OE missense 0.76 (0.70–0.82)
499 obs / 658.8 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios
LoF OE0.14 (0.07–0.30)
0≤0.351.4
Missense OE0.76 (0.70–0.82)
0≤0.61.4
Synonymous OE0.94
0≤1.21.6
LoF obs/exp: 5 / 35.4Missense obs/exp: 499 / 658.8Syn Z: 0.86
DN
0.4388th %ile
GOF
0.4875th %ile
LOF
0.70top 10%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.30

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

223 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic42
Likely Pathogenic3
VUS143
Likely Benign15
Benign13
42
Pathogenic
3
Likely Pathogenic
143
VUS
15
Likely Benign
13
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
42
0
42
Likely Pathogenic
1
0
2
0
3
VUS
0
133
10
0
143
Likely Benign
0
7
3
5
15
Benign
0
4
1
8
13
Total11445813216

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

View in ClinVar →

Protein Context — Lollipop Plot

LATS2 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients