CDH11

protein-coding

cadherin 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

NM_001797.4

Inheritance

AR, AD

ClinVar variants

P:13U:128B:29

Top phenotype

Teebi hypertelorism syndrome 2; Elsahy-Waters syndrome

gnomAD constraint

pLI —, LoF o/e 0.03

Max pathogenic AF

—

Genomic locus

chr16:64,943,753-65,126,112

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~182.4 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Elsahy-Waters syndromeMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0008885

Submitter: Ambry Genetics

Teebi hypertelorism syndrome 2MODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0030674

Submitter: Ambry Genetics

Elsahy-Waters syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0008885

Submitter: Labcorp Genetics (formerly Invitae)

Teebi hypertelorism syndrome 2STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0030674

Submitter: Labcorp Genetics (formerly Invitae)

Teebi hypertelorism syndrome 2MODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0030674

Submitter: G2P

Elsahy-Waters syndromeDEFINITIVE

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).

Elsahy-Waters syndromeSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0008885

Submitter: Orphanet

Teebi hypertelorism syndrome 2MODERATE

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).

Elsahy-Waters syndromeDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0008885

Submitter: G2P

Elsahy-Waters syndromeMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0008885

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Teebi hypertelorism syndrome 2; Elsahy-Waters syndromeAD/AR

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

Refs: 27431290; 28988429; 29271567; 33811546Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CDH11 variants in ClinVar

7 Conditions Cataloged
Inborn genetic diseasesTotal: 82
not providedTotal: 56
CDH11-related disorderTotal: 13
Elsahy-Waters syndromeTotal: 13
not specifiedTotal: 11
Teebi hypertelorism syndrome 2Total: 11
Oromandibular-limb hypogenesis spectrumTotal: 2

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.

EffectPLPVUSLBBSum
synonymous
20
clinvar
20
missense
4
clinvar
4
clinvar
122
clinvar
9
clinvar
139
nonsense
1
clinvar
1
clinvar
2
clinvar
4
start loss
0
frameshift
1
clinvar
1
clinvar
2
splice donor/acceptor (+/-2bp)
1
clinvar
4
clinvar
5
Total76128290170

Highest pathogenic variant AF is 0.000006569784

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001797.4RefSeqNP_001788.211MANE Select
ENST00000268603.9EnsemblENSP00000268603.411MANE Select
NM_001308392.2RefSeqNP_001295321.112Standard
NM_001330576.2RefSeqNP_001317505.110Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
cdh11Danio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.593784750.7950.00002815250
Missense (PolyPhen)140197.040.71052272
Synonymous0.5381891990.9510.00001381564
Loss of Function4.95130.50.03280.00000155375

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.0000290.000029rare
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)00.0absent
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

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.;

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

AllRecessiveDominant
MendelianHighMediumHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh
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