CTNNAL1

protein-coding

catenin alpha like 1

Gene summary

Predicted to enable actin filament binding activity and cadherin binding activity. Acts upstream of or within Rho protein signal transduction. Located in cytosol. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_003798.4

Inheritance

—

ClinVar variants

U:85B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.57

Max pathogenic AF

—

Genomic locus

chr9:108,942,569-109,013,522

External References & Databases

Ensembl (ENSG00000119326)

Transcript & Mutation Effects

hg38 • Region Span ~71.0 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CTNNAL1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 79

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003798.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	2 clinvar		3
missense			81 clinvar	1 clinvar	1 clinvar	83
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	85	3	1	89

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 66 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003798.4	RefSeq	NP_003789.1	19	MANE Select
ENST00000325551.9	Ensembl	ENSP00000320434.4	19	MANE Select
NM_001286974.2	RefSeq	NP_001273903.1	19	Standard
ENST00000374593.4	Ensembl	ENSP00000363721.4	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Regulation of toll-like receptor signaling pathway
EGFR1

Biological Process

cell adhesion
Rho protein signal transduction

Molecular Function

protein binding
cadherin binding
actin filament binding

Cellular Component

cytosol
cytoskeleton
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000325551
Coding exons: 19
Length: 70959
Individuals with no LoFs: 125683
Homozygous LoFs: 0
Heterozygous LoFs: 64
Defined: 125747
p: 0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.688	317	353	0.897	0.0000172	4777
Missense (PolyPhen)		113	137.92	0.81933		1920
Synonymous	0.757	116	127	0.914	0.00000655	1371
Loss of Function	2.46	22	38.5	0.572	0.00000194	515

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00027	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00039	0.00038	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00034	0.00033	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May modulate the Rho pathway signaling by providing a scaffold for the Lbc Rho guanine nucleotide exchange factor (ARHGEF1).;

Recessive Scores

pRec: 0.139

Intolerance Scores

LoFtool: 0.951
RVIS EVS: -0.04
RVIS percentile EVS: 50.45

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.576

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium