CDH22

cadherin 22, the group of Type II classical cadherins

Basic information

Region (hg38): 20:46173738-46308498

Previous symbols: [ "C20orf25" ]

Links

ENSG00000149654 ∙ NCBI:64405 ∙ OMIM:609920 ∙ HGNC:13251 ∙ Uniprot:Q9UJ99 ∙ 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 CDH22 gene.

• Inborn genetic diseases (31 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDH22 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				1	1	2
missense			31		1	32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	1	2

Variants in CDH22

This is a list of pathogenic ClinVar variants found in the CDH22 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-46174514-C-T		not specified	Uncertain significance (Jun 21, 2023)
20-46174529-C-T		not specified	Uncertain significance (Jul 13, 2022)
20-46174535-G-A		not specified	Uncertain significance (Nov 09, 2021)
20-46174540-C-A		not specified	Uncertain significance (Dec 05, 2022)
20-46174630-A-G		not specified	Uncertain significance (Feb 28, 2024)
20-46174631-G-T		not specified	Uncertain significance (Jun 28, 2022)
20-46174648-G-A			Benign (Jan 15, 2021)
20-46174705-G-A		not specified	Uncertain significance (Nov 08, 2022)
20-46174772-C-G		not specified	Uncertain significance (Dec 19, 2023)
20-46174840-G-C		not specified	Uncertain significance (Sep 15, 2021)
20-46174841-C-G		not specified	Uncertain significance (Mar 01, 2024)
20-46174843-C-G		not specified	Uncertain significance (Jul 28, 2021)
20-46174852-G-C		not specified	Uncertain significance (Sep 15, 2021)
20-46174860-G-C			Likely benign (Nov 01, 2022)
20-46174862-C-T		not specified	Uncertain significance (Jan 03, 2024)
20-46174864-G-C		not specified	Uncertain significance (Feb 09, 2022)
20-46174889-C-T		not specified	Uncertain significance (May 05, 2023)
20-46174890-G-T		not specified	Uncertain significance (Feb 02, 2022)
20-46174940-T-A		not specified	Uncertain significance (May 17, 2023)
20-46174955-T-C		not specified	Uncertain significance (Feb 05, 2024)
20-46174990-A-T		not specified	Uncertain significance (Mar 01, 2023)
20-46175018-C-G		not specified	Uncertain significance (Feb 28, 2023)
20-46177989-G-A			Benign (Jun 20, 2018)
20-46177992-G-C		not specified	Uncertain significance (Feb 01, 2023)
20-46178098-G-A		not specified	Uncertain significance (May 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDH22	protein_coding	protein_coding	ENST00000372262	11	134766

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.500	0.500	125737	0	9	125746	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.78	333	510	0.653	0.0000330	5274
Missense in Polyphen		136	231.62	0.58718		2246
Synonymous	1.39	209	236	0.885	0.0000172	1744
Loss of Function	3.85	6	28.0	0.214	0.00000129	307

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000917	0.0000916
Ashkenazi Jewish	0.00	0.00
East Asian	0.000121	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000179	0.0000176
Middle Eastern	0.000121	0.000109
South Asian	0.0000654	0.0000653
Other	0.00	0.00

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. PB-cadherins may have a role in the morphological organization of pituitary gland and brain tissues (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.226
• rvis_EVS: -1.15
• rvis_percentile_EVS: 6.27

Haploinsufficiency Scores

• pHI: 0.175
• ghis: 0.646

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.309

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdh22

Gene ontology

• Biological process: cell morphogenesis;cell-cell junction assembly;homophilic cell adhesion via plasma membrane adhesion molecules;brain development;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 adherens junction;cell surface;integral component of membrane;catenin complex
• Molecular function: calcium ion binding;cytoskeletal protein binding;protein homodimerization activity;cadherin binding