CDH12

cadherin 12, the group of Type II classical cadherins

Basic information

Region (hg38): 5:21750673-22853344

Links

ENSG00000154162 ∙ NCBI:1010 ∙ OMIM:600562 ∙ HGNC:1751 ∙ Uniprot:P55289 ∙ 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 CDH12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDH12 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				10	6	16
missense			40	3	3	46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	40	13	9

Variants in CDH12

This is a list of pathogenic ClinVar variants found in the CDH12 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-21751755-G-T		not specified	Uncertain significance (Apr 15, 2024)
5-21751766-C-T		not specified	Uncertain significance (Dec 17, 2023)
5-21751782-G-A			Likely benign (Dec 05, 2018)
5-21751838-C-A		not specified	Uncertain significance (Apr 25, 2022)
5-21751852-A-G			Likely benign (Jul 22, 2018)
5-21751862-T-C		not specified	Uncertain significance (Jan 22, 2024)
5-21751899-G-A			Benign (Jan 01, 2019)
5-21751918-G-A		not specified	Uncertain significance (Jan 16, 2024)
5-21751934-C-T		not specified	Uncertain significance (Jan 04, 2022)
5-21751943-C-T		not specified	Uncertain significance (Feb 10, 2022)
5-21751951-T-G		not specified	Uncertain significance (Dec 26, 2023)
5-21751969-T-C		not specified	Uncertain significance (Mar 29, 2024)
5-21752003-T-C		not specified	Likely benign (May 27, 2022)
5-21752020-G-C		not specified	Uncertain significance (Jan 04, 2024)
5-21752141-C-T		not specified	Uncertain significance (Feb 28, 2023)
5-21752146-T-A		not specified	Uncertain significance (Sep 07, 2022)
5-21755628-C-T			Likely benign (Apr 20, 2018)
5-21755629-G-A		not specified	Uncertain significance (May 10, 2022)
5-21755632-C-T		not specified	Uncertain significance (Jan 30, 2024)
5-21755678-A-T		not specified	Uncertain significance (Mar 30, 2024)
5-21755682-G-A			Likely benign (Dec 21, 2018)
5-21755713-C-T		not specified	Uncertain significance (Apr 12, 2023)
5-21755721-C-T		not specified	Uncertain significance (Jan 03, 2024)
5-21755832-C-T			Likely benign (May 15, 2018)
5-21755833-G-A		not specified	Uncertain significance (Mar 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDH12	protein_coding	protein_coding	ENST00000382254	11	1102950

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000364	1.00	125720	0	26	125746	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.931	393	449	0.876	0.0000240	5203
Missense in Polyphen		132	189.49	0.6966		2288
Synonymous	-0.944	186	170	1.09	0.0000101	1562
Loss of Function	3.42	12	33.3	0.360	0.00000176	400

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000245	0.000242
Ashkenazi Jewish	0.00	0.00
East Asian	0.000234	0.000217
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000890	0.0000879
Middle Eastern	0.000234	0.000217
South Asian	0.000131	0.000131
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.
• Pathway: Cell-cell junction organization;Adherens junctions interactions;Cell junction organization;Cell-Cell communication (Consensus)

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.638
• rvis_EVS: -0.35
• rvis_percentile_EVS: 29.49

Haploinsufficiency Scores

• pHI: 0.260
• hipred: Y
• hipred_score: 0.544
• ghis: 0.403

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.293

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdh12

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 adherens junction;cell surface;integral component of membrane;catenin complex
• Molecular function: calcium ion binding;cytoskeletal protein binding;protein homodimerization activity;cadherin binding