CDH6

cadherin 6, the group of Type II classical cadherins

Basic information

Region (hg38): 5:31193686-31329146

Links

ENSG00000113361 ∙ NCBI:1004 ∙ OMIM:603007 ∙ HGNC:1765 ∙ Uniprot:P55285 ∙ 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 CDH6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDH6 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			20			20
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	0	0

Variants in CDH6

This is a list of pathogenic ClinVar variants found in the CDH6 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-31267528-A-G		not specified	Uncertain significance (Sep 26, 2024)
5-31267592-T-C		not specified	Uncertain significance (Mar 25, 2024)
5-31267640-T-A		not specified	Uncertain significance (Jun 06, 2023)
5-31267660-C-G		not specified	Uncertain significance (Nov 21, 2024)
5-31267672-A-G		not specified	Uncertain significance (Jul 09, 2024)
5-31293981-G-A		not specified	Uncertain significance (Sep 09, 2021)
5-31294077-G-A		not specified	Uncertain significance (Nov 10, 2024)
5-31294100-G-A		not specified	Uncertain significance (Jun 11, 2021)
5-31294122-C-T		not specified	Uncertain significance (Dec 13, 2023)
5-31294148-G-A		not specified	Uncertain significance (Oct 05, 2021)
5-31299580-G-A		not specified	Uncertain significance (May 30, 2024)
5-31302284-A-G		not specified	Uncertain significance (May 27, 2022)
5-31305235-T-C		not specified	Uncertain significance (Dec 03, 2024)
5-31305244-G-A		not specified	Uncertain significance (Feb 03, 2022)
5-31305398-A-C		not specified	Uncertain significance (May 25, 2022)
5-31313394-A-C		not specified	Uncertain significance (Mar 07, 2023)
5-31316223-G-A		not specified	Uncertain significance (Aug 11, 2022)
5-31316243-A-G		not specified	Uncertain significance (Oct 24, 2024)
5-31317411-C-T		not specified	Uncertain significance (Mar 22, 2023)
5-31317802-G-A		not specified	Uncertain significance (Jan 03, 2024)
5-31317822-C-T		not specified	Uncertain significance (Aug 05, 2024)
5-31317880-C-G		not specified	Uncertain significance (Jan 24, 2024)
5-31322836-C-G		not specified	Uncertain significance (Feb 27, 2023)
5-31322977-A-G		not specified	Uncertain significance (May 03, 2023)
5-31322991-A-G		not specified	Uncertain significance (Apr 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDH6	protein_coding	protein_coding	ENST00000265071	11	135397

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.920	0.0803	125736	0	11	125747	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.39	308	451	0.684	0.0000249	5185
Missense in Polyphen		128	192.39	0.66532		2169
Synonymous	0.583	171	181	0.945	0.0000116	1552
Loss of Function	4.74	7	38.9	0.180	0.00000252	404

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.0000998	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000531	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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: Neural Crest Differentiation;Ectoderm Differentiation;TGF-B Signaling in Thyroid Cells for Epithelial-Mesenchymal Transition;Cell-cell junction organization;Adherens junctions interactions;Cell junction organization;Cell-Cell communication (Consensus)

Recessive Scores

• pRec: 0.0817

Intolerance Scores

• loftool: 0.386
• rvis_EVS: -1.31
• rvis_percentile_EVS: 4.85

Haploinsufficiency Scores

• pHI: 0.857
• hipred: Y
• hipred_score: 0.739
• ghis: 0.591

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.668

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdh6
• Phenotype: renal/urinary system phenotype

Zebrafish Information Network

• Gene name: cdh6
• Affected structure: eye photoreceptor cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: cell morphogenesis;cell-cell junction assembly;cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules;Notch signaling pathway;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