CDH24

cadherin 24, the group of Type II classical cadherins

Basic information

Region (hg38): 14:23047062-23057538

Links

ENSG00000139880 ∙ NCBI:64403 ∙ OMIM:618599 ∙ HGNC:14265 ∙ Uniprot:Q86UP0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CDH24 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDH24 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			75	4		79
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	75	4	0

Variants in CDH24

This is a list of pathogenic ClinVar variants found in the CDH24 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
14-23047985-G-T		not specified	Uncertain significance (Sep 29, 2023)
14-23047994-G-A		not specified	Uncertain significance (Feb 06, 2024)
14-23048035-G-A		not specified	Uncertain significance (Jul 02, 2024)
14-23048054-G-A		not specified	Uncertain significance (Nov 02, 2023)
14-23048065-C-T		not specified	Uncertain significance (Feb 22, 2025)
14-23048078-C-G		not specified	Uncertain significance (Dec 13, 2024)
14-23048093-A-C		not specified	Uncertain significance (May 08, 2024)
14-23048115-G-C		not specified	Uncertain significance (Feb 12, 2025)
14-23048132-C-G		not specified	Uncertain significance (Aug 10, 2024)
14-23048174-C-T		not specified	Likely benign (May 30, 2023)
14-23048214-C-G		not specified	Uncertain significance (Jan 17, 2025)
14-23048228-C-T		not specified	Uncertain significance (Dec 02, 2024)
14-23048249-G-C		not specified	Uncertain significance (Mar 25, 2022)
14-23048267-G-A		not specified	Uncertain significance (Nov 12, 2021)
14-23048270-G-A		not specified	Uncertain significance (Feb 21, 2024)
14-23048309-G-A		not specified	Uncertain significance (Oct 07, 2024)
14-23048311-G-A		not specified	Uncertain significance (Dec 24, 2024)
14-23048351-C-T		not specified	Uncertain significance (Jun 18, 2024)
14-23048381-C-G		not specified	Uncertain significance (Feb 11, 2025)
14-23048426-C-T		not specified	Uncertain significance (Jun 02, 2024)
14-23048429-T-A		not specified	Uncertain significance (Jul 26, 2024)
14-23048449-C-A		not specified	Uncertain significance (Jul 05, 2023)
14-23048452-C-T		not specified	Uncertain significance (Jul 13, 2022)
14-23048479-G-C		not specified	Uncertain significance (Aug 04, 2021)
14-23049066-C-T		not specified	Uncertain significance (Aug 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDH24	protein_coding	protein_coding	ENST00000397359	12	10477

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.06e-8	0.993	125682	0	64	125746	0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.39	387	472	0.820	0.0000306	5173
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000514	0.000511
Ashkenazi Jewish	0.000896	0.000893
East Asian	0.000385	0.000381
Finnish	0.000208	0.000185
European (Non-Finnish)	0.000181	0.000176
Middle Eastern	0.000385	0.000381
South Asian	0.000416	0.000327
Other	0.000164	0.000163

dbNSFP

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}.
• Pathway: Cell-cell junction organization;Adherens junctions interactions;Cell junction organization;Cell-Cell communication (Consensus)

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.866
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.76

Haploinsufficiency Scores

• pHI: 0.321
• hipred: Y
• hipred_score: 0.644
• ghis: 0.518

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.634

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdh24

Gene ontology

• 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;cell-cell adhesion mediated by cadherin;cell-cell adhesion
• Cellular component: plasma membrane;cell-cell junction;cell-cell adherens junction;cell surface;integral component of membrane;catenin complex
• Molecular function: calcium ion binding;cytoskeletal protein binding;protein homodimerization activity;cadherin binding