CDH5

cadherin 5, the group of CD molecules|Type II classical cadherins

Basic information

Region (hg38): 16:66366690-66404784

Links

ENSG00000179776 ∙ NCBI:1003 ∙ OMIM:601120 ∙ HGNC:1764 ∙ Uniprot:P33151 ∙ 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 CDH5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDH5 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
missense			60	6		66
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	60	6	1

Variants in CDH5

This is a list of pathogenic ClinVar variants found in the CDH5 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-66379362-G-A		not specified	Uncertain significance (Jan 23, 2023)
16-66379374-G-A		not specified	Likely benign (Jul 19, 2023)
16-66379374-G-T		not specified	Uncertain significance (Jul 21, 2021)
16-66379389-C-G		not specified	Uncertain significance (Jan 23, 2024)
16-66379398-G-A		not specified	Uncertain significance (May 30, 2023)
16-66379435-G-A		not specified	Uncertain significance (Dec 13, 2021)
16-66379464-C-G		not specified	Uncertain significance (Nov 30, 2021)
16-66379468-G-A		not specified	Uncertain significance (Oct 05, 2023)
16-66379539-G-A		not specified	Uncertain significance (Nov 07, 2022)
16-66386827-C-T		not specified	Uncertain significance (Feb 12, 2024)
16-66386863-G-A		Marfanoid habitus and intellectual disability	Uncertain significance (-)
16-66386872-G-A		not specified	Uncertain significance (Dec 19, 2023)
16-66386949-C-A		not specified	Uncertain significance (May 06, 2024)
16-66386983-G-C		not specified	Uncertain significance (Oct 22, 2021)
16-66387038-A-T		not specified	Uncertain significance (Dec 13, 2023)
16-66387056-A-G		not specified	Uncertain significance (Jun 17, 2024)
16-66388425-G-T		not specified	Uncertain significance (Jun 06, 2023)
16-66389361-G-A		not specified	Uncertain significance (Jun 23, 2021)
16-66389366-A-G		not specified	Likely benign (Jun 06, 2023)
16-66389376-C-T		not specified	Uncertain significance (Feb 06, 2023)
16-66389417-G-C		not specified	Uncertain significance (Jul 30, 2023)
16-66389447-C-T		not specified	Uncertain significance (Nov 30, 2022)
16-66389471-G-A		not specified	Uncertain significance (Aug 23, 2021)
16-66390419-C-T			Benign (Aug 20, 2018)
16-66390420-G-A		not specified	Uncertain significance (Dec 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDH5	protein_coding	protein_coding	ENST00000341529	11	38154

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.513	0.487	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.518	479	512	0.936	0.0000344	5138
Missense in Polyphen		155	184.65	0.8394		1984
Synonymous	-0.515	240	230	1.04	0.0000184	1567
Loss of Function	4.15	7	32.6	0.215	0.00000184	345

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000129	0.000123
Middle Eastern	0.00	0.00
South Asian	0.0000328	0.0000327
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. This cadherin may play a important role in endothelial cell biology through control of the cohesion and organization of the intercellular junctions. It associates with alpha-catenin forming a link to the cytoskeleton. Acts in concert with KRIT1 to establish and maintain correct endothelial cell polarity and vascular lumen. These effects are mediated by recruitment and activation of the Par polarity complex and RAP1B. Required for activation of PRKCZ and for the localization of phosphorylated PRKCZ, PARD3, TIAM1 and RAP1B to the cell junction. {ECO:0000269|PubMed:20332120, ECO:0000269|PubMed:21269602}.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Fluid shear stress and atherosclerosis - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);VEGFA-VEGFR2 Signaling Pathway;Signal Transduction;VEGFA-VEGFR2 Pathway;Signaling by VEGF;Cell-cell junction organization;Adherens junctions interactions;Cell junction organization;Signaling by Receptor Tyrosine Kinases;Cell-Cell communication;Signaling events mediated by VEGFR1 and VEGFR2;S1P2 pathway;VEGFR2 mediated vascular permeability (Consensus)

Recessive Scores

• pRec: 0.222

Intolerance Scores

• loftool: 0.498
• rvis_EVS: -1.06
• rvis_percentile_EVS: 7.58

Haploinsufficiency Scores

• pHI: 0.503
• hipred: Y
• hipred_score: 0.670
• ghis: 0.595

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.713

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdh5
• Phenotype: reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); embryo phenotype; liver/biliary system phenotype; immune system phenotype; vision/eye phenotype; craniofacial phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: cdh5
• Affected structure: nucleate erythrocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: cell morphogenesis;blood vessel maturation;cell-cell junction assembly;homophilic cell adhesion via plasma membrane adhesion molecules;transforming growth factor beta receptor signaling pathway;calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules;adherens junction organization;cell-cell adhesion mediated by cadherin;positive regulation of angiogenesis;negative regulation of inflammatory response;cell-cell adhesion;positive regulation of establishment of endothelial barrier;regulation of establishment of cell polarity
• Cellular component: plasma membrane;cell-cell junction;cell-cell adherens junction;bicellular tight junction;cell surface;membrane;integral component of membrane;catenin complex;cell junction
• Molecular function: signaling receptor binding;calcium ion binding;protein binding;beta-catenin binding;cytoskeletal protein binding;protein homodimerization activity;ion channel binding;cadherin binding