CAB39L

Chr 13

calcium binding protein 39 like

Also known as: MLAA-34, MO25-BETA, MO2L, bA103J18.3

NCBI Gene: 81617ENSG00000102547UniProt: Q9H9S4

This protein is a component of a complex that binds and activates the STK11/LKB1 kinase, stabilizing the interaction between CAB39/MO25 and STK11/LKB1. The gene is extremely intolerant to loss-of-function variants (pLI = 1.0), suggesting it is essential for normal cellular function, but no specific human diseases have been definitively associated with CAB39L mutations to date. Given its critical role in the LKB1 signaling pathway, mutations would likely affect cellular energy metabolism and growth control.

Summary from RefSeq, UniProt
Research Assistant →
0
Active trials
6
Pubs (1 yr)
61
P/LP submissions
0%
P/LP missense
1.00
LOEUF
DN
Mechanism· predicted
Clinical Summary— CAB39L
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
61 unique Pathogenic / Likely Pathogenic· 48 VUS of 123 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.00LOEUF
pLI 0.000
Z-score 1.56
OE 0.57 (0.34–1.00)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.64Z-score
OE missense 0.86 (0.76–0.99)
150 obs / 173.6 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.57 (0.34–1.00)
0≤0.351.4
Missense OE0.86 (0.76–0.99)
0≤0.61.4
Synonymous OE0.91
0≤1.21.6
LoF obs/exp: 9 / 15.7Missense obs/exp: 150 / 173.6Syn Z: 0.55
DN
0.74top 25%
GOF
0.5072th %ile
LOF
0.2872th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

123 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic59
Likely Pathogenic2
VUS48
Likely Benign2
59
Pathogenic
2
Likely Pathogenic
48
VUS
2
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
59
0
59
Likely Pathogenic
0
0
2
0
2
VUS
0
40
8
0
48
Likely Benign
0
1
0
1
2
Benign
0
0
0
0
0
Total041691111

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

View in ClinVar →

Protein Context — Lollipop Plot

CAB39L · protein map & ClinVar variants

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

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