CTNNB1

Chr 3

catenin beta 1

Also known as: CTNNB, EVR7, MRD19, NEDSDV, armadillo

NCBI Gene: 1499ENSG00000168036UniProt: P35222

The protein encoded by this gene is part of a complex of proteins that constitute adherens junctions (AJs). AJs are necessary for the creation and maintenance of epithelial cell layers by regulating cell growth and adhesion between cells. The encoded protein also anchors the actin cytoskeleton and may be responsible for transmitting the contact inhibition signal that causes cells to stop dividing once the epithelial sheet is complete. Finally, this protein binds to the product of the APC gene, which is mutated in adenomatous polyposis of the colon. Mutations in this gene are a cause of colorectal cancer (CRC), pilomatrixoma (PTR), medulloblastoma (MDB), and ovarian cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2016]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtColorectal cancer
UniProtPilomatrixoma
UniProtMedulloblastoma
UniProtOvarian cancer

Clinical highlights

Gene-disease validity (ClinGen)
CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy · ADDefinitivesufficient evidence for diagnostic panels
Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype) and the gene is intolerant of it in the population — truncating, frameshift and canonical splice variants carry more prior weight here than missense.Curated gene-level mechanism — a prior for triage, not a per-variant call.
12
Active trials
819
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.13
LOEUF· LoF intol.
LOF
Mechanism· G2P
📖
GeneReview available — CTNNB1
Authoritative clinical overview · Recommended first read
Open GeneReview ↗
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Dual constrained — LoF & missense intolerant
LoF Constraint?
0.13LOEUF
pLI 1.000
Z-score 5.46
OE 0.03 (0.01–0.13)
Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint?
3.85Z-score
OE missense 0.47 (0.42–0.53)
199 obs / 421.1 exp
Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios?
LoF OE?0.03 (0.01–0.13)
0≤0.351.4
Missense OE?0.47 (0.42–0.53)
0≤0.61.4
Synonymous OE?0.99
0≤1.21.6
LoF obs/exp: 1 / 36.7Missense obs/exp: 199 / 421.1Syn Z: 0.14

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

CTNNB1 · 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
CTNNB1L-DOPA

Study of L-dopa Treatment in Patients With a Neurodevelopmental Disorder (CTNNB1 Gene)

RECRUITING
NCT07614126Phase NAUniversity Hospital, MontpellierStarted 2026-04-08
L-Dopa
Colorectal Cancer

ASPirin Intervention for the REDuction of Colorectal Cancer Risk

ACTIVE NOT RECRUITING
NCT02394769Phase NAMassachusetts General HospitalStarted 2015-07-06
AspirinPlacebo for Aspirin
Lung Cancer

Feasibility of Targeted Bronchial Washing for Molecular Testing by Next Generation Sequencing in Early-stage Lung Cancer

ACTIVE NOT RECRUITING
NCT06301295Phase NAPusan National University HospitalStarted 2024-05-29
Ultarthin bronchoscopy with intratumoral washing
CTNNB1 Neurodevelopmental Syndrome

Gene Replacement Therapy for Treatment of Paediatric Patients With CTNNB1 Neurodevelopmental Syndrome

RECRUITING
NCT07270549Phase PHASE1, PHASE2CTNNB1 FoundationStarted 2025-11-01
Urbagen gene addition therapySirolimusMethylprednisolone (Corticosteroid)
16P11.2 Deletion Syndrome16p11.2 Duplications1Q21.1 Deletion

Online Study of People Who Have Genetic Changes and Features of Autism: Simons Searchlight

RECRUITING
NCT01238250Simons SearchlightStarted 2010-10
CTNNB1 Neurodevelopmental Syndrome

CTNNB1 Neurodevelopmental Syndrome - Natural History Study

RECRUITING
NCT07167732University Medical Centre LjubljanaStarted 2024-06-14
A General Medical and Neurological AssessmentWorld Health Organisation (WHO) Motor MilestonesBurke-Fahn-Marsden Dystonia Rating Scale
Unresectable Colorectal Neoplasm Metastasis

Study of a Tankyrase Inhibitor RK-582 for Patients With Unresectable Metastatic Colorectal Cancer

RECRUITING
NCT06853496Phase PHASE1Eiji ShinozakiStarted 2025-03-13
RK-582
Desmoid FibromatosisRecurrent Desmoid FibromatosisUnresectable Desmoid Fibromatosis

A Study of a New Drug, Nirogacestat, for Treating Desmoid Tumors That Cannot be Removed by Surgery

ACTIVE NOT RECRUITING
NCT04195399Phase PHASE2Children's Oncology GroupStarted 2020-10-07
Biospecimen CollectionComputed TomographyEchocardiography Test
Aggressive Fibromatosis

National Clinical-biological Prospective Cohort of Incident Cases of Aggressive Fibromatosis (ALTITUDES)

ACTIVE NOT RECRUITING
NCT02867033Phase NACentre Oscar LambretStarted 2016-03-22
biopsybiobank constitutionColoscopy
Post Traumatic Stress DisorderComplex Posttraumatic Stress DisorderStress

Building Resilience at Schools: Emotional and Biological Assessment and Treatment of Traumatic Stress

RECRUITING
NCT05701111Phase NAStanford UniversityStarted 2024-02-23
Start with the Heart StudentsStart with the Heart TeachersCue Centered Therapy Counselors
Metastatic Colorectal Carcinoma (mCRC)Colorectal Cancer (CRC)Adenomatous Polyposis Coli (APC) Gene Mutation

Safety and Efficacy of Tegavivint in Patients With Metastatic Colorectal Carcinoma

RECRUITING
NCT07463599Phase PHASE1, PHASE2HonorHealth Research InstituteStarted 2026-02-17
Tegavivint
Craniopharyngioma, Child

Prospective Pilot Study Identifying Clinically Relevant Biological Targets for Medical Therapy

ENROLLING BY INVITATION
NCT03610906University of Colorado, DenverStarted 2019-03-12
Tumor and Blood Specimens

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