Human Gene Module / Chromosome 5 / PCDHA9

PCDHA9Protocadherin alpha 9

Score
3
Suggestive Evidence Criteria 3.1
Autism Reports / Total Reports
3 / 4
Rare Variants / Common Variants
2 / 5
Aliases
PCDHA9, PCDH-ALPHA9
Associated Syndromes
-
Genetic Category
Rare Single Gene Mutation, Genetic Association
Chromosome Band
5q31.3
Associated Disorders
-
Relevance to Autism

Five SNPs within PCDHA9 (rs251379, rs1119032, rs17119271, rs155806, and rs17119346) showed significant association with autism in a family-based association study using 14 SNPs within the PCDHA gene cluster in 841 ASD families (574 of which were multiplex) obtained from the Autism Genetic Resource Exchange (AGRE) (Anitha et al., 2012). A novel de novo missense variant in this gene was identified in an ASD proband from the Simons Simplex Collection in Iossifov et al., 2014; however, this variant was predicted to be benign in Sanders et al., 2015.

Molecular Function

This gene is a member of the protocadherin alpha gene cluster, one of three related gene clusters tandemly linked on chromosome five that demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The alpha gene cluster is composed of 15 cadherin superfamily genes related to the mouse CNR genes and consists of 13 highly similar and 2 more distantly related coding sequences. The tandem array of 15 N-terminal exons, or variable exons, are followed by downstream C-terminal exons, or constant exons, which are shared by all genes in the cluster. The large, uninterrupted N-terminal exons each encode six cadherin ectodomains while the C-terminal exons encode the cytoplasmic domain. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins that most likely play a critical role in the establishment and function of specific cell-cell connections in the brain.

Reports related to PCDHA9 (4 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Recent Recommendation Identification of CTCF as a master regulator of the clustered protocadherin genes. Golan-Mashiach M , et al. (2012) No -
2 Support De novo gene disruptions in children on the autistic spectrum. Iossifov I , et al. (2012) Yes -
3 Primary Protocadherin (PCDHA) as a novel susceptibility gene for autism. Anitha A , et al. (2012) Yes -
4 Support The contribution of de novo coding mutations to autism spectrum disorder. Iossifov I , et al. (2014) Yes -
Rare Variants   (2)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
del(4) - intron_variant De novo - Simplex 22542183 Iossifov I , et al. (2012)
c.212G>T p.Arg71Leu missense_variant De novo - Simplex 25363768 Iossifov I , et al. (2014)
Common Variants   (5)
Status Allele Change Residue Change Variant Type Inheritance Pattern Paternal Transmission Family Type PubMed ID Author, Year
c.2394+51957A>G - intron_variant - - - 23031252 Anitha A , et al. (2012)
c.2395-48828T>C - intron_variant - - - 23031252 Anitha A , et al. (2012)
c.2542+11686G>A - intron_variant - - - 23031252 Anitha A , et al. (2012)
c.2395-8694A>G T/C intron_variant - - - 23031252 Anitha A , et al. (2012)
c.2394+28448G>A T/C intron_variant - - - 23031252 Anitha A , et al. (2012)
SFARI Gene score
3

Suggestive Evidence

Five SNPs within PCDHA9 (rs251379, rs1119032, rs17119271, rs155806, and rs17119346) showed significant association with autism in a family-based association study using 14 SNPs within the PCDHA gene cluster in 841 ASD families (574 of which were multiplex) obtained from the Autism Genetic Resource Exchange (AGRE) (Anitha et al., 2012). A novel de novo missense variant in this gene was identified in an ASD proband from the Simons Simplex Collection in Iossifov et al., 2014; however, this variant was predicted to be benign in Sanders et al., 2015.

Score Delta: Score remained at 4

3

Suggestive Evidence

See all Category 3 Genes

The literature is replete with relatively small studies of candidate genes, using either common or rare variant approaches, which do not reach the criteria set out for categories 1 and 2. Genes that had two such lines of supporting evidence were placed in category 3, and those with one line of evidence were placed in category 4. Some additional lines of "accessory evidence" (indicated as "acc" in the score cards) could also boost a gene from category 4 to 3.

4/1/2018
icon
4.3

Increased from to 4.3

Description

4

Krishnan Probability Score

Score 0.50086408950229

Ranking 2055/25841 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 7.8893945081967E-14

Ranking 17519/18225 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 0.93739335039549

Ranking 13510/18665 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 9

Ranking 210/461 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.
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