Human Gene Module / Chromosome 5 / CDH9

CDH9cadherin 9, type 2 (T1-cadherin)

SFARI Gene Score
2
Strong Candidate Criteria 2.1
Autism Reports / Total Reports
4 / 7
Rare Variants / Common Variants
1 / 6
Aliases
CDH9, MGC125386,  cadherin-9
Associated Syndromes
-
Chromosome Band
5p14.1
Associated Disorders
-
Relevance to Autism

Genetic association has been found between the CDH9 gene and autism in two large cohorts (AGRE and ACC) of European ancestry and replicated in two other cohorts (CAP and CART) (Wang et al., 2009).

Molecular Function

cell adhesion

SFARI Genomic Platforms
Reports related to CDH9 (7 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Highly Cited Identification of three human type-II classic cadherins and frequent heterophilic interactions between different subclasses of type-II classic cadherins Shimoyama Y , et al. (2000) No -
2 Primary Common genetic variants on 5p14.1 associate with autism spectrum disorders Wang K , et al. (2009) Yes -
3 Positive Association The association of rs4307059 and rs35678 markers with autism spectrum disorders is replicated in Italian families Prandini P , et al. (2012) Yes -
4 Positive Association A genome-wide association study of autism incorporating autism diagnostic interview-revised, autism diagnostic observation schedule, and social responsiveness scale Connolly JJ , et al. (2012) Yes -
5 Support Exome sequencing of extended families with autism reveals genes shared across neurodevelopmental and neuropsychiatric disorders Cukier HN , et al. (2014) Yes -
6 Support Segregated expressions of autism risk genes Cdh11 and Cdh9 in autism-relevant regions of developing cerebellum Wang C , et al. (2019) No -
7 Recent Recommendation Sequence, map position and genome organization of the RPL17B gene, encoding ribosomal protein L17b in Saccharomyces cerevisiae Berroteran RW and Hampsey M (1995) No -
Rare Variants   (1)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
c.1808A>G p.Glu603Gly missense_variant Familial - Extended multiplex (at least one pair of ASD affec 24410847 Cukier HN , et al. (2014)
Common Variants   (6)
Status Allele Change Residue Change Variant Type Inheritance Pattern Paternal Transmission Family Type PubMed ID Author, Year
- - intergenic_variant - - - 19404256 Wang K , et al. (2009)
- - intergenic_variant - - - 22935194 Connolly JJ , et al. (2012)
- C to T intergenic_variant - - - 19404256 Wang K , et al. (2009)
- T to C intergenic_variant - - - 19404256 Wang K , et al. (2009)
- C/T intergenic_variant - - - 22739633 Prandini P , et al. (2012)
- C/T intergenic_variant - - - 22935194 Connolly JJ , et al. (2012)
SFARI Gene score
2

Strong Candidate

Flanking gene to SNP with strong association (Wang et al., 2009).

Score Delta: Score remained at 2

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
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2

Decreased from 3 to 2

Description

Flanking gene to SNP with strong association (Wang et al., 2009).

10/1/2019
4
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3

Decreased from 4 to 3

New Scoring Scheme
Description

Flanking gene to SNP with strong association (Wang et al., 2009).

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

Decreased from 4 to 4

Description

Flanking gene to SNP with strong association (Wang et al., 2009).

7/1/2014
No data
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4

Increased from No data to 4

Description

Flanking gene to SNP with strong association (Wang et al., 2009).

4/1/2014
No data
icon
4

Increased from No data to 4

Description

Flanking gene to SNP with strong association (Wang et al., 2009).

Krishnan Probability Score

Score 0.49561425204153

Ranking 2877/25841 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.
ExAC Score

Score 0.99248359037809

Ranking 1690/18225 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
Sanders TADA Score

Score 0.93945733093123

Ranking 14217/18665 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).
Larsen Cumulative Evidence Score

Score 65

Ranking 22/461 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.
Zhang D Score

Score 0.30028741476992

Ranking 2739/20870 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.
Interaction Table
Interactor Symbol Interactor Name Interactor Organism Interactor Type Entrez ID Uniprot ID
CDH10 cadherin 10, type 2 (T2-cadherin) Human Protein Binding 1008 Q9Y6N8
CDH15 Cadherin-15 Human Protein Binding 1013 P55291
CDH7 Cadherin-7 Chicken Protein Binding 374007 Q90763
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