CDH11
protein-codingcadherin 11, the group of Type II classical cadherins
Gene summary
This gene encodes a type II classical cadherin from the cadherin superfamily, integral membrane proteins that mediate calcium-dependent cell-cell adhesion. Mature cadherin proteins are composed of a large N-terminal extracellular domain, a single membrane-spanning domain, and a small, highly conserved C-terminal cytoplasmic domain. Type II (atypical) cadherins are defined based on their lack of a HAV cell adhesion recognition sequence specific to type I cadherins. Expression of this particular cadherin in osteoblastic cell lines, and its upregulation during differentiation, suggests a specific function in bone development and maintenance. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~182.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0008885
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0030674
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0008885
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0030674
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0030674
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0008885
Submitter: ClinGen
The *CDH11* gene located on chromosome 16 at 16q21 encodes a type II classical cadherin from the cadherin superfamily, integral membrane proteins that mediate calcium-dependent cell-cell adhesion. The protein is composed of 5 extracellular cadherin domains, one transmembrane domain, and one intracellular domain. *CDH11* was first reported in relation to Elsahy-Waters syndrome (ESWS), also known as branchioskeletogenital syndrome, in 2016 (Anazi et al., 2016 PMID: 27431290). ESWS is characterized by significant craniofacial dysmorphism (including hypertelorism, broad forehead, thick eyebrows with synophrys, flat malar regions, broad/ bulbous noses, mild prognathism), multiple congenital ocular, dental, digital, genital and vertebral anomalies, moderate intellectual disability and/or moderate hearing loss. Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we found differences in molecular mechanisms, inheritance patterns, and phenotypic variability among individuals with biallelic versus monoallelic *CDH11* variants. Therefore, the following disease entities have been split into multiple disease entities, AR Elsahy-Waters syndrome (ESWS) (OMIM:211380), and AD Teebi hypertelorism syndrome 2 (TBHS2) (OMIM:619736). The split curation for AD TBHS2 has been curated separately. All variants reported to date in the recessive condition are putative loss of function variants, including nonsense, frameshifts, essential splice donor and/or acceptor variants impacting the extracellular domains. Five homozygous probands from consanguineous families in five publications have been included in this curation (PMID:27431290; Taskiran et al., 2017 PMID: 28988429; Harms et al., 2018 PMID: 29271567; Castori et al., 2018 PMID: 30194892; Minatogawa et al., 2021 PMID: 34278706). The mechanism of pathogenicity appears to be loss of function. This gene-disease relationship is also supported by functional alteration of patient cells (PMID: 28988429) and several homozygous null animal models recapitulating cranial, femoral, and snout dysmorphology (Kawaguchi et al., 2001 PMID: 11450702), hearing loss (Kiyama et al., 2018 PMID: 29967341), and genitourinary malformations (IMPC database, Dickinson et al., 2016 PMID: 27626380). In summary, there is definitive evidence supporting the relationship between *CDH11* and AR ESWS. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This classification was approved by the ClinGen Syndromic Disorders GCEP on the meeting date May 17th, 2024 (SOP Version 10).
Inheritance Pattern: AR
Disease ID:MONDO:0008885
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0030674
Submitter: ClinGen
The *CDH11* gene located on chromsome 16 at 16q21 encodes a type II classical cadherin from the cadherin superfamily, integral membrane proteins that mediate calcium-dependent cell-cell adhesion. The protein is composed of 5 extracellular cadherin domains, one transmembrane domain, and one intracellular domain (Harms 2018). *CDH11* was first reported in relation to Teebi hypertelorism syndrome 2 (TBHS2), also known as brachycephalofrontonasal dysplasia, in 2021 (Li et al., 2021 PMID: 33811546). TBHS2 is characterized by hypertelorism, cardiac and genitourinary defects. Intellectual disability and other craniofacial dysmorphism tends to be rarer and milder than the autosomal recessive condition also caused by variants in *CDH11*, Elsahy-Waters syndrome (ESWS; OMIM:211380). Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we found differences in molecular mechanisms, inheritance patterns, and phenotypic variability among individuals with biallelic versus monoallelic *CDH11* variants. Therefore, the following disease entities have been split into multiple disease entities, AR Elsahy-Waters syndrome (ESWS) (OMIM:211380), and AD Teebi hypertelorism syndrome 2 (OMIM:619736). The split curation for AR Elsahy-Waters syndrome (ESWS) (OMIM:211380) has been curated separately. Other presenting features of TBHS2 include broad or short phalanx, large anterior fontanelle, and umbilical defects. All variants reported to date are missense variants impacting the extracellular domains. Ten probands (6 de novo, 4 consistent with AD inheritance) from two publications are included in this curation (Li 2021, PMID: 33811546; Kuroda 2024, PMID: 37646430). The mechanism of pathogenicity is unclear. This gene-disease relationship is also supported by experimental evidence including mouse models which partially recapitulate the TBHS2 phenotype, particularly with respect to cranial dysmorphology and cardiac defects (Alimperti et al., 2014 PMID: 24741067; Bowen et al., 2015 PMID: 26188246), but these present an inheritance mismatch and likely a molecular mechanism mismatch between homozygous null mice and heterozygous missense human patients. Missense functional alterations in patient fibroblasts show higher *CDH11* expression than wild type controls , and transfected L cells with missense changes found in patients display adhesion and migration defects, suggesting a possible gain of function or dominant negative molecular mechanism of pathogenicity ( PMID: 33811546). In summary, there is moderate evidence supporting the relationship between *CDH11* and AD TBHS2. This classification was approved by the ClinGen Syndromic Disorders GCEP on the meeting date May 17th, 2024 (SOP Version 10).
Inheritance Pattern: AR
Disease ID:MONDO:0008885
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0008885
Submitter: Ambry Genetics
Clinical Genomic Database (CGD)
Manifestation: Craniofacial; Dental; Genitourinary; Musculoskeletal; Neurologic; Ophthalmologic
Intervention: General
Rationale: 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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CDH11 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001797.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 20 | 20 | ||||
| missense | 4 | 4 | 122 | 9 | 139 | |
| nonsense | 1 | 1 | 2 | 4 | ||
| start loss | 0 | |||||
| frameshift | 1 | 1 | 2 | |||
| splice donor/acceptor (+/-2bp) | 1 | 4 | 5 | |||
| Total | 7 | 6 | 128 | 29 | 0 | 170 |
Highest pathogenic variant AF is 0.000006569784
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001788.2 | 11 | MANE Select | |
| Ensembl | ENSP00000268603.4 | 11 | MANE Select | |
| RefSeq | NP_001295321.1 | 12 | Standard | |
| RefSeq | NP_001317505.1 | 10 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| cdh11 | Danio rerio | Structure: retinal ganglion cell Quality: mislocalised abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Cell-cell junction organization
- Adherens junctions interactions
- Cell junction organization
- Cell-Cell communication
Biological Process
- cell morphogenesis
- skeletal system development
- ossification
- cell-cell junction assembly
- cell adhesion
Molecular Function
- calcium ion binding
- cytoskeletal protein binding
- protein homodimerization activity
- cadherin binding
Cellular Component
- cytoplasm
- plasma membrane
- cell-cell adherens junction
- cell surface
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000268603
- Coding exons
- 11
- Length
- 182360
- Individuals with no LoFs
- 125306
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 1
- Defined
- 125307
- p
- 0.00000399
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.59 | 378 | 475 | 0.795 | 0.0000281 | 5250 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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.;
Recessive Scores
- pRec
- 0.243
Intolerance Scores
- RVIS EVS
- 0.07
- RVIS percentile EVS
- 59.11
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.559
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | Medium | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |