CDH7

cadherin 7, the group of Type II classical cadherins

Basic information

Region (hg38): 18:65750251-65890337

Links

ENSG00000081138 ∙ NCBI:1005 ∙ OMIM:605806 ∙ HGNC:1766 ∙ Uniprot:Q9ULB5 ∙ 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 CDH7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDH7 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	11	12
missense			38		2	40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					23	23
Total	0	0	38	1	36

Variants in CDH7

This is a list of pathogenic ClinVar variants found in the CDH7 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-65762670-C-A			Benign (Nov 10, 2018)
18-65762848-G-A			Benign (Mar 29, 2018)
18-65762893-T-A			Benign (Jul 04, 2018)
18-65762926-A-G			Benign (Jul 04, 2018)
18-65763104-G-A			Benign (Nov 10, 2018)
18-65763108-T-G			Benign (Nov 10, 2018)
18-65763257-A-G			Benign (Nov 10, 2018)
18-65809574-C-T			Benign (Jun 18, 2021)
18-65809757-C-T			Benign (Jun 27, 2018)
18-65809771-C-G		not specified	Uncertain significance (Mar 06, 2023)
18-65809871-T-C			Benign (Jun 27, 2018)
18-65809890-G-A		not specified	Uncertain significance (Mar 01, 2023)
18-65809968-A-G		not specified	Uncertain significance (Jun 23, 2023)
18-65809970-G-A			Benign (Jun 09, 2021)
18-65809982-C-G			Benign (Jun 09, 2021)
18-65814178-A-T			Benign (Nov 10, 2018)
18-65814579-G-A			Benign (Jun 27, 2018)
18-65821778-A-G			Benign (Nov 10, 2018)
18-65821923-C-A			Benign (Jun 18, 2021)
18-65822007-C-T			Benign (Jun 18, 2021)
18-65822106-C-G		not specified	Uncertain significance (Mar 31, 2024)
18-65822140-G-A		not specified	Uncertain significance (Jan 23, 2023)
18-65822142-C-T			Benign (Nov 10, 2018)
18-65822425-G-A			Benign (Nov 10, 2018)
18-65824561-A-G			Benign (Nov 10, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDH7	protein_coding	protein_coding	ENST00000397968	11	131151

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.598	0.403	125727	0	20	125747	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.87	338	449	0.752	0.0000247	5136
Missense in Polyphen		96	185.3	0.51809		2103
Synonymous	-0.827	190	176	1.08	0.0000106	1537
Loss of Function	4.24	7	33.5	0.209	0.00000190	404

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000974	0.0000974
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.0000544	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000882	0.0000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000983	0.0000980
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;Cell-cell junction organization;Adherens junctions interactions;Cell junction organization;Cell-Cell communication (Consensus)

Recessive Scores

• pRec: 0.132

Intolerance Scores

• loftool: 0.577
• rvis_EVS: -0.89
• rvis_percentile_EVS: 10.46

Haploinsufficiency Scores

• pHI: 0.380
• hipred: Y
• hipred_score: 0.771
• ghis: 0.573

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.831

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdh7

Zebrafish Information Network

• Gene name: cdh7a
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: undulate

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