CDH26

cadherin 26, the group of Major cadherins

Basic information

Region (hg38): 20:59958423-60034011

Links

ENSG00000124215 ∙ NCBI:60437 ∙ OMIM:617685 ∙ HGNC:15902 ∙ Uniprot:Q8IXH8 ∙ 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 CDH26 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDH26 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			58	5		63
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	58	5	0

Variants in CDH26

This is a list of pathogenic ClinVar variants found in the CDH26 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-59958742-G-A		not specified	Likely benign (Aug 02, 2023)
20-59958769-C-G		not specified	Uncertain significance (Jul 12, 2022)
20-59958784-T-C		not specified	Uncertain significance (Nov 15, 2024)
20-59969006-C-A		not specified	Uncertain significance (Mar 14, 2023)
20-59970088-A-G		not specified	Uncertain significance (Feb 17, 2024)
20-59970090-C-G		not specified	Uncertain significance (Mar 18, 2024)
20-59970094-C-G		not specified	Uncertain significance (Aug 20, 2024)
20-59970103-C-G		not specified	Uncertain significance (Dec 21, 2022)
20-59971962-C-G		not specified	Uncertain significance (Nov 18, 2023)
20-59971986-A-G		not specified	Uncertain significance (May 03, 2023)
20-59972037-A-T		not specified	Uncertain significance (Jun 23, 2021)
20-59972056-A-G		not specified	Uncertain significance (Mar 18, 2024)
20-59972062-A-G		not specified	Uncertain significance (Jun 01, 2023)
20-59972089-G-A		not specified	Uncertain significance (May 30, 2023)
20-59972103-G-C		not specified	Uncertain significance (May 28, 2024)
20-59972119-T-C		not specified	Uncertain significance (Mar 29, 2024)
20-59982945-G-T		not specified	Uncertain significance (Nov 04, 2023)
20-59984647-A-G		not specified	Uncertain significance (Mar 01, 2024)
20-59984752-C-T		not specified	Uncertain significance (Jul 26, 2021)
20-59985050-C-T		not specified	Uncertain significance (Aug 19, 2024)
20-59985056-T-C		not specified	Uncertain significance (Oct 03, 2023)
20-59985123-G-C		not specified	Uncertain significance (Apr 01, 2024)
20-59987492-G-A		not specified	Uncertain significance (May 17, 2023)
20-59987492-G-C		not specified	Uncertain significance (May 30, 2022)
20-59987537-G-T		not specified	Uncertain significance (Aug 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDH26	protein_coding	protein_coding	ENST00000348616	18	75596

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.38e-26	0.000623	125293	3	452	125748	0.00181

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.282	460	477	0.964	0.0000263	5425
Missense in Polyphen		124	129.09	0.96057		1650
Synonymous	0.204	188	192	0.981	0.0000116	1666
Loss of Function	0.297	40	42.1	0.951	0.00000245	451

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00367	0.00367
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.00223	0.00223
Finnish	0.000232	0.000231
European (Non-Finnish)	0.00133	0.00132
Middle Eastern	0.00223	0.00223
South Asian	0.00482	0.00475
Other	0.00278	0.00261

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. Ligand for integrins alpha- E/beta-7, ITGAE:ITGAB7, alpha-4/beta-7, ITGA4:ITGAB7 and alpha- 4/beta-1, ITGA4:ITGAB1 through which modulates CD4(+) T cells activation (PubMed:28051089). {ECO:0000269|PubMed:28051089}.

Recessive Scores

• pRec: 0.0683

Intolerance Scores

• loftool: 0.981
• rvis_EVS: 0.92
• rvis_percentile_EVS: 89.58

Haploinsufficiency Scores

• pHI: 0.0294
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.173

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdh26

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;CD4-positive, alpha-beta T cell activation;cell-cell adhesion mediated by cadherin;cell-cell adhesion
• Cellular component: plasma membrane;cell-cell adherens junction;cell surface;integral component of membrane;catenin complex
• Molecular function: integrin binding;calcium ion binding;protein binding;beta-catenin binding;cytoskeletal protein binding;protein homodimerization activity;alpha-catenin binding;cadherin binding;delta-catenin binding