CDH24

protein-coding

cadherin 24, the group of Type II classical cadherins

Gene summary

Enables several functions, including alpha-catenin binding activity; beta-catenin binding activity; and delta-catenin binding activity. Acts upstream of or within cell-cell adhesion. Located in cell-cell junction. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_144985.4

Inheritance

—

ClinVar variants

U:142B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.54

Max pathogenic AF

—

Genomic locus

chr14:23,047,062-23,057,538

External References & Databases

Ensembl (ENSG00000139880)

Transcript & Mutation Effects

hg38 • Region Span ~10.5 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 CDH24 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 149

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_144985.4. 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			1
missense			140 clinvar	4 clinvar		144
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	142	4	0	146

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_144985.4	RefSeq	NP_659422.2	11	MANE Select
ENST00000487137.7	Ensembl	ENSP00000434821.2	11	MANE Select
NM_022478.4	RefSeq	NP_071923.2	12	Standard
ENST00000267383.5	Ensembl	ENSP00000267383.5	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Cell-cell junction organization
Adherens junctions interactions
Cell junction organization
Cell-Cell communication

Biological Process

cell morphogenesis
cell-cell junction assembly
homophilic cell adhesion via plasma membrane adhesion molecules
calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules
adherens junction organization

Molecular Function

calcium ion binding
cytoskeletal protein binding
protein homodimerization activity
cadherin binding

Cellular Component

plasma membrane
cell-cell junction
cell-cell adherens junction
cell surface
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000397359
Coding exons: 12
Length: 10477
Individuals with no LoFs: 125682
Homozygous LoFs: 0
Heterozygous LoFs: 64
Defined: 125746
p: 0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.39	387	472	0.820	0.0000306	5173
Missense (PolyPhen)		173	239.39	0.72266		2557
Synonymous	0.531	194	204	0.953	0.0000141	1795
Loss of Function	2.50	18	33.6	0.536	0.00000201	333

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0.00090	0.00089	rare
East Asian	0.00038	0.00038	rare
Finnish	0.00021	0.00018	rare
European (Non-Finnish)	0.00018	0.00018	rare
South Asian	0.00042	0.00033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types. Cadherin-24 mediate strong cell-cell adhesion. {ECO:0000269|PubMed:12734196}.;

Recessive Scores

pRec: 0.101

Intolerance Scores

LoFtool: 0.866
RVIS EVS: 0.02
RVIS percentile EVS: 55.76

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.634

Gene Damage Prediction

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