CDH11

cadherin 11, the group of Type II classical cadherins

Basic information

Region (hg38): 16:64943752-65126112

Links

ENSG00000140937 ∙ NCBI:1009 ∙ OMIM:600023 ∙ HGNC:1750 ∙ Uniprot:P55287 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Elsahy-Waters syndrome (Moderate), mode of inheritance: AR
• Elsahy-Waters syndrome (Supportive), mode of inheritance: AR
• Elsahy-Waters syndrome (Strong), mode of inheritance: AR
• Elsahy-Waters syndrome (Definitive), mode of inheritance: AR
• Teebi hypertelorism syndrome 2 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Teebi hypertelorism syndrome 2; Elsahy-Waters syndrome	AD/AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Dental; Genitourinary; Musculoskeletal; Neurologic; Ophthalmologic	27431290; 28988429; 29271567; 33811546

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CDH11 gene.

• not provided (29 variants)
• Inborn genetic diseases (27 variants)
• Elsahy-Waters syndrome (10 variants)
• Orofacial cleft 1 (1 variants)
• CDH11-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDH11 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				6	3	9
missense		1	30	6	3	40
nonsense		2				2
start loss						0
frameshift		1	2			3
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	1		2
non coding			1	1	4	6
Total	0	4	33	13	10

Highest pathogenic variant AF is 0.00000657

Variants in CDH11

This is a list of pathogenic ClinVar variants found in the CDH11 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-64947363-G-GT		Orofacial cleft 1	Uncertain significance (Nov 22, 2022)
16-64947595-C-G		CDH11-related disorder	Likely benign (Jun 24, 2019)
16-64947596-G-A		CDH11-related disorder	Likely benign (Dec 31, 2023)
16-64947611-C-T		Inborn genetic diseases	Uncertain significance (Oct 20, 2023)
16-64947612-G-A			Likely benign (Mar 01, 2023)
16-64947620-A-G		Inborn genetic diseases	Uncertain significance (Sep 26, 2023)
16-64947698-C-T		Inborn genetic diseases	Uncertain significance (Feb 27, 2023)
16-64947765-G-A			Likely benign (Jan 01, 2024)
16-64947807-G-T		Inborn genetic diseases	Uncertain significance (May 04, 2022)
16-64947861-C-T			Likely benign (Aug 01, 2022)
16-64947921-G-C		CDH11-related disorder	Benign/Likely benign (Dec 01, 2023)
16-64947970-G-A		Inborn genetic diseases	Uncertain significance (Jun 12, 2023)
16-64947970-G-C			Uncertain significance (May 21, 2020)
16-64947992-C-T		Elsahy-Waters syndrome	Uncertain significance (Dec 30, 2022)
16-64948049-T-C		Inborn genetic diseases	Uncertain significance (Aug 23, 2021)
16-64948602-G-C		CDH11-related disorder	Likely benign (Jun 12, 2019)
16-64948606-T-C			Likely benign (Oct 01, 2022)
16-64948645-GA-G			Uncertain significance (Sep 01, 2023)
16-64948660-T-C			Uncertain significance (Nov 01, 2023)
16-64948667-A-AC		CDH11-related disorder	Uncertain significance (Mar 21, 2023)
16-64948698-T-A			Likely pathogenic (May 03, 2020)
16-64950780-G-C		Inborn genetic diseases	Uncertain significance (Feb 12, 2024)
16-64950809-C-T			Uncertain significance (Jul 13, 2022)
16-64950875-C-A		Inborn genetic diseases	Uncertain significance (Jul 25, 2023)
16-64950887-C-T		Inborn genetic diseases	Uncertain significance (Jul 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDH11	protein_coding	protein_coding	ENST00000268603	11	182360

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000105	125306	0	1	125307	0.00000399

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.59	378	475	0.795	0.0000281	5250
Missense in Polyphen		140	197.04	0.7105		2272
Synonymous	0.538	189	199	0.951	0.0000138	1564
Loss of Function	4.95	1	30.5	0.0328	0.00000155	375

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
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.
• Disease: DISEASE: Note=A chromosomal aberration involving CDH11 is a common genetic feature of aneurysmal bone cyst, a benign osseous neoplasm. Translocation t(16;17)(q22;p13) with USP6. The translocation generates a fusion gene in which the strong CDH11 promoter is fused to the entire USP6 coding sequence, resulting in USP6 transcriptional up-regulation.; DISEASE: Elsahy-Waters syndrome (ESWS) [MIM:211380]: An autosomal recessive syndrome characterized by moderate mental retardation, hypospadias and characteristic craniofacial morphology, which includes brachycephaly, facial asymmetry, exotropia, hypertelorism, telechantus, broad nose, concave nasal ridge, underdeveloped mid-face, prognathism, and radicular dentin dysplasia. {ECO:0000269|PubMed:28988429, ECO:0000269|PubMed:29271567}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Cell-cell junction organization;Adherens junctions interactions;Cell junction organization;Cell-Cell communication (Consensus)

Recessive Scores

• pRec: 0.243

Intolerance Scores

• rvis_EVS: 0.07
• rvis_percentile_EVS: 59.11

Haploinsufficiency Scores

• pHI: 0.165
• hipred: Y
• hipred_score: 0.786
• ghis: 0.539

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.559

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdh11
• 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); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); embryo phenotype

Zebrafish Information Network

• Gene name: cdh11
• Affected structure: retinal ganglion cell
• Phenotype tag: abnormal
• Phenotype quality: mislocalised

Gene ontology

• Biological process: cell morphogenesis;skeletal system development;ossification;cell-cell junction assembly;cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules;calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules;corticospinal tract morphogenesis;adherens junction organization;cell-cell adhesion mediated by cadherin;modulation of chemical synaptic transmission;cell-cell adhesion
• Cellular component: cytoplasm;plasma membrane;cell-cell adherens junction;cell surface;integral component of membrane;catenin complex;extracellular exosome;Schaffer collateral - CA1 synapse;glutamatergic synapse
• Molecular function: calcium ion binding;cytoskeletal protein binding;protein homodimerization activity;cadherin binding