Human Gene Module / Chromosome 16 / CDH11

CDH11cadherin 11

SFARI Gene Score
2
Strong Candidate Criteria 2.1
Autism Reports / Total Reports
5 / 8
Rare Variants / Common Variants
18 / 1
Aliases
CDH11, CAD11,  CDHOB,  OB,  OSF-4, CDH11
Associated Syndromes
Teebi hypertelorism syndrome 2, DD
Chromosome Band
16q21
Associated Disorders
ADHD, ID
Relevance to Autism

A de novo partial deletion of CDH11, which was associated with one of the breakpoints of a de novo complex chromosomal rearrangement, was identified in a sporadic patient with ASD, mild intellectual disability, and ADHD; in the same report, a case-control study for 14 SNP variants in the CDH11 gene in 519 ASD cases and 1,192 controls showed significant overpresentation of rs7187376C/C genotypes in the patient group (P=0.0049) (Crepel et al., 2014).

Molecular 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. Expressed mainly in brain but also found in other tissues. Expressed in neuroblasts.

External Links
Gene CardOpen Targets PlatformgnomAD browserSynGO portalPubMed
Human
Entrez GeneOMIMUniProtHumanBaseVariCarta
SFARI Genomic Platforms
GPF browser SFARI genome browser
Reports related to CDH11 (8 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Primary Association of CDH11 with non-syndromic ASD Crepel A , et al. (2014) Yes ID, ADHD
2 Support Clinical genomics expands the morbid genome of intellectual disability and offers a high diagnostic yield Anazi S , et al. (2016) No -
3 Support Mutations in Human Accelerated Regions Disrupt Cognition and Social Behavior Doan RN , et al. (2016) Yes -
4 Support Segregated expressions of autism risk genes Cdh11 and Cdh9 in autism-relevant regions of developing cerebellum Wang C , et al. (2019) No -
5 Support - Li D et al. (2021) No ASD, ADHD, ID
6 Support - Frei JA et al. (2021) Yes -
7 Support - Wu N et al. (2021) Yes -
8 Support - Zhou X et al. (2022) Yes -
Rare Variants   (18)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
G>A - intergenic_variant - - Unknown 27667684 Doan RN , et al. (2016)
TA>CT - intergenic_variant - - Unknown 27667684 Doan RN , et al. (2016)
- - copy_number_loss De novo - Simplex 24839052 Crepel A , et al. (2014)
c.418G>A p.Glu140Lys missense_variant Unknown - - 33811546 Li D et al. (2021)
c.1303C>T p.Pro435Ser missense_variant De novo - - 35982159 Zhou X et al. (2022)
c.164G>C p.Trp55Ser missense_variant De novo - Simplex 33811546 Li D et al. (2021)
c.780T>A p.Asp260Glu missense_variant De novo - Simplex 33811546 Li D et al. (2021)
c.785A>T p.Asn262Ile missense_variant De novo - Simplex 33811546 Li D et al. (2021)
c.797C>T p.Pro266Leu missense_variant De novo - Simplex 33811546 Li D et al. (2021)
c.835G>C p.Glu279Gln missense_variant De novo - Simplex 33811546 Li D et al. (2021)
c.806C>T p.Pro269Leu missense_variant Unknown - Unknown 24839052 Crepel A , et al. (2014)
c.2132C>A p.Ala711Glu missense_variant Unknown - Unknown 24839052 Crepel A , et al. (2014)
c.1369_1374del p.Thr457_Val458del inframe_deletion De novo - - 35982159 Zhou X et al. (2022)
c.979G>T p.Gly327Trp missense_variant Familial Paternal Multiplex 33811546 Li D et al. (2021)
c.999+1G>T - splice_site_variant Familial Both parents Simplex 27431290 Anazi S , et al. (2016)
c.778G>A p.Asp260Asn missense_variant Familial - Extended multiplex 33811546 Li D et al. (2021)
c.1121T>A p.Val374Glu missense_variant Familial - Multi-generational 33811546 Li D et al. (2021)
c.1562C>T p.Thr521Met missense_variant Familial Paternal Multiplex 24839052 Crepel A , et al. (2014)
Common Variants   (1)
Status Allele Change Residue Change Variant Type Inheritance Pattern Paternal Transmission Family Type PubMed ID Author, Year
c.-298+19288A>G;c.-298+21082A>G;c.-298+23178A>G;c.-298+21642A>G;c.-276+19288A>G - intron_variant - - - 24839052 Crepel A , et al. (2014)
SFARI Gene score
2

Strong Candidate

A de novo partial deletion of CDH11, which was associated with one of the breakpoints of a de novo complex chromosomal rearrangement, was identified in a sporadic patient with ASD, mild intellectual disability, and ADHD; in the same report, a case-control study for 14 SNP variants in the CDH11 gene in 519 ASD cases and 1,192 controls showed significant overpresentation of rs7187376C/C genotypes in the patient group (P=0.0049) (Crepel et al., 2014). Rare missense variants in CDH11 were also identified in ASD probands in this report.

Score Delta: Score remained at 2

criteria met
See SFARI Gene'scoring criteria
2

Strong Candidate

See all Category 2 Genes

We considered a rigorous statistical comparison between cases and controls, yielding genome-wide statistical significance, with independent replication, to be the strongest possible evidence for a gene. These criteria were relaxed slightly for category 2.

4/1/2022
3
icon
2

Decreased from 3 to 2

Description

A de novo partial deletion of CDH11, which was associated with one of the breakpoints of a de novo complex chromosomal rearrangement, was identified in a sporadic patient with ASD, mild intellectual disability, and ADHD; in the same report, a case-control study for 14 SNP variants in the CDH11 gene in 519 ASD cases and 1,192 controls showed significant overpresentation of rs7187376C/C genotypes in the patient group (P=0.0049) (Crepel et al., 2014). Rare missense variants in CDH11 were also identified in ASD probands in this report.

10/1/2019
4
icon
3

Decreased from 4 to 3

New Scoring Scheme
Description

A de novo partial deletion of CDH11, which was associated with one of the breakpoints of a de novo complex chromosomal rearrangement, was identified in a sporadic patient with ASD, mild intellectual disability, and ADHD; in the same report, a case-control study for 14 SNP variants in the CDH11 gene in 519 ASD cases and 1,192 controls showed significant overpresentation of rs7187376C/C genotypes in the patient group (P=0.0049) (Crepel et al., 2014). Rare missense variants in CDH11 were also identified in ASD probands in this report.

Reports Added
[New Scoring Scheme]
4/1/2019
4
icon
4

Decreased from 4 to 4

Description

A de novo partial deletion of CDH11, which was associated with one of the breakpoints of a de novo complex chromosomal rearrangement, was identified in a sporadic patient with ASD, mild intellectual disability, and ADHD; in the same report, a case-control study for 14 SNP variants in the CDH11 gene in 519 ASD cases and 1,192 controls showed significant overpresentation of rs7187376C/C genotypes in the patient group (P=0.0049) (Crepel et al., 2014). Rare missense variants in CDH11 were also identified in ASD probands in this report.

Reports Added
[Segregated expressions of autism risk genes Cdh11 and Cdh9 in autism-relevant regions of developing cerebellum.2019]
7/1/2018
icon
4

Increased from to 4

Description

A de novo partial deletion of CDH11, which was associated with one of the breakpoints of a de novo complex chromosomal rearrangement, was identified in a sporadic patient with ASD, mild intellectual disability, and ADHD; in the same report, a case-control study for 14 SNP variants in the CDH11 gene in 519 ASD cases and 1,192 controls showed significant overpresentation of rs7187376C/C genotypes in the patient group (P=0.0049) (Crepel et al., 2014). Rare missense variants in CDH11 were also identified in ASD probands in this report.

Krishnan Probability Score

Score 0.58790046685746

Ranking 496/25841 scored genes


[Show Scoring Methodology]
Krishnan and colleagues generated probability scores genome-wide by using a machine learning approach on a human brain-specific gene network. The method was first presented in Nat Neurosci 19, 1454-1462 (2016), and scores for more than 25,000 RefSeq genes can be accessed in column G of supplementary table 3 (see: http://www.nature.com/neuro/journal/v19/n11/extref/nn.4353-S5.xlsx). A searchable browser, with the ability to view networks of associated ASD risk genes, can be found at asd.princeton.edu.
Original Source
ExAC Score

Score 0.99926714496455

Ranking 1012/18225 scored genes


[Show Scoring Methodology]
The Exome Aggregation Consortium (ExAC) is a summary database of 60,706 exomes that has been widely used to estimate 'constraint' on mutation for individual genes. It was introduced by Lek et al. Nature 536, 285-291 (2016), and the ExAC browser can be found at exac.broadinstitute.org. The pLI score was developed as measure of intolerance to loss-of- function mutation. A pLI > 0.9 is generally viewed as highly constrained, and thus any loss-of- function mutations in autism in such a gene would be more likely to confer risk. For a full list of pLI scores see: ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3.1/functional_gene_constraint/fordist_cle aned_exac_nonTCGA_z_pli_rec_null_data.txt
Original Source
Sanders TADA Score

Score 0.94161992157272

Ranking 15000/18665 scored genes


[Show Scoring Methodology]
The TADA score ('Transmission and De novo Association') was introduced by He et al. PLoS Genet 9(8):e1003671 (2013), and is a statistic that integrates evidence from both de novo and transmitted mutations. It forms the basis for the claim of 65 individual genes being strongly associated with autism risk at a false discovery rate of 0.1 (Sanders et al. Neuron 87, 1215-1233 (2015)). The calculated TADA score for 18,665 RefSeq genes can be found in column P of Supplementary Table 6 in the Sanders et al. paper (the column headed 'tadaFdrAscSscExomeSscAgpSmallDel'), which represents a combined analysis of exome data and small de novo deletions (see www.cell.com/cms/attachment/2038545319/2052606711/mmc7.xlsx).
Original Source
Larsen Cumulative Evidence Score

Score 11

Ranking 169/461 scored genes


[Show Scoring Methodology]
Larsen and colleagues generated gene scores based on the sum of evidence for all available ASD-associated variants in a gene, with assessments based on mode of inheritance, effect size, and variant frequency in the general population. The approach was first presented in Mol Autism 7:44 (2016), and scores for 461 genes can be found in column I in supplementary table 4 from that paper.
Original Source
Zhang D Score

Score 0.02873551982557

Ranking 7825/20870 scored genes


[Show Scoring Methodology]
The DAMAGES score (disease-associated mutation analysis using gene expression signatures), or D score, was developed to combine evidence from de novo loss-of- function mutation with evidence from cell-type- specific gene expression in the mouse brain (specifically translational profiles of 24 specific mouse CNS cell types isolated from 6 different brain regions). Genes with positive D scores are more likely to be associated with autism risk, with higher-confidence genes having higher D scores. This statistic was first presented by Zhang & Shen (Hum Mutat 38, 204- 215 (2017), and D scores for more than 20,000 RefSeq genes can be found in column M in supplementary table 2 from that paper.
Original Source
Interactome
Interaction Table
Interactor Symbol Interactor Name Interactor Organism Interactor Type Entrez ID Uniprot ID
sdc4-a syndecan 4 African clawed frog Protein Binding 734218 Q1AGV7
Submit New Gene

Report an Error