Human Gene Module / Chromosome 4 / PCDH10

PCDH10protocadherin 10

SFARI Gene Score
2
Strong Candidate Criteria 2.1
Autism Reports / Total Reports
4 / 9
Rare Variants / Common Variants
5 / 0
Aliases
PCDH10, PCDH19,  OL-PCDH,  KIAA1400,  MGC133344,  DKFZP761O2023
Associated Syndromes
-
Chromosome Band
4q28.3
Associated Disorders
-
Relevance to Autism

Rare variants in the PCDH10 gene have been identified with autism in the HMCA cohort (Morrow et al., 2008).

Molecular Function

encodes a cadherin-related neuronal receptor thought to play a role in the estab lishment and function of specific cell-cell connections in the brain.

Reports related to PCDH10 (9 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Recent Recommendation OL-Protocadherin is essential for growth of striatal axons and thalamocortical projections Uemura M , et al. (2007) No -
2 Primary Identifying autism loci and genes by tracing recent shared ancestry Morrow EM , et al. (2008) Yes -
3 Recent Recommendation Contact-dependent promotion of cell migration by the OL-protocadherin-Nap1 interaction Nakao S , et al. (2008) No -
4 Support Multiple autism-linked genes mediate synapse elimination via proteasomal degradation of a synaptic scaffold PSD-95 Tsai NP , et al. (2012) No -
5 Support Large-scale discovery of novel genetic causes of developmental disorders Deciphering Developmental Disorders Study (2014) No -
6 Support Genome-wide characteristics of de novo mutations in autism Yuen RK et al. (2016) Yes -
7 Support Integrative Analyses of De Novo Mutations Provide Deeper Biological Insights into Autism Spectrum Disorder Takata A , et al. (2018) Yes -
8 Support - Woodbury-Smith M et al. (2022) Yes -
9 Highly Cited Expression of a novel protocadherin, OL-protocadherin, in a subset of functional systems of the developing mouse brain Hirano S , et al. (1999) No -
Rare Variants   (5)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
c.*1124T>G - 3_prime_UTR_variant De novo NA Simplex 27525107 Yuen RK et al. (2016)
- - copy_number_loss Familial Both parents Simplex 18621663 Morrow EM , et al. (2008)
c.2466G>C p.Gln822His missense_variant De novo NA Simplex 29346770 Takata A , et al. (2018)
c.1044A>T p.Val348%3D synonymous_variant Unknown - - 35205252 Woodbury-Smith M et al. (2022)
c.1813G>A p.Ala605Thr missense_variant De novo NA Unknown 25533962 Deciphering Developmental Disorders Study (2014)
Common Variants  

No common variants reported.

SFARI Gene score
2

Strong Candidate

A single rare CNV in the PCDH10 gene was observed with autism (PMID: 18621663).

Score Delta: Decreased from 4 to 3

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.

10/1/2021
4
icon
3

Decreased from 4 to 3

Description

A single rare CNV in the PCDH10 gene was observed with autism (PMID: 18621663).

7/1/2021
4
icon
3

Decreased from 4 to 3

Description

A single rare CNV in the PCDH10 gene was observed with autism (PMID: 18621663).

4/1/2021
4
icon
3

Decreased from 4 to 3

Description

A single rare CNV in the PCDH10 gene was observed with autism (PMID: 18621663).

1/1/2021
4
icon
3

Decreased from 4 to 3

Description

A single rare CNV in the PCDH10 gene was observed with autism (PMID: 18621663).

10/1/2020
4
icon
3

Decreased from 4 to 3

Description

A single rare CNV in the PCDH10 gene was observed with autism (PMID: 18621663).

7/1/2020
4
icon
3

Decreased from 4 to 3

Description

A single rare CNV in the PCDH10 gene was observed with autism (PMID: 18621663).

4/1/2020
4
icon
3

Decreased from 4 to 3

Description

A single rare CNV in the PCDH10 gene was observed with autism (PMID: 18621663).

1/1/2020
4
icon
3

Decreased from 4 to 3

Description

A single rare CNV in the PCDH10 gene was observed with autism (PMID: 18621663).

10/1/2019
4
icon
3

Decreased from 4 to 3

New Scoring Scheme
Description

A single rare CNV in the PCDH10 gene was observed with autism (PMID: 18621663).

Reports Added
[New Scoring Scheme]
7/1/2019
4
icon
3

Decreased from 4 to 3

Description

A single rare CNV in the PCDH10 gene was observed with autism (PMID: 18621663).

4/1/2019
4
icon
3

Decreased from 4 to 3

Description

A single rare CNV in the PCDH10 gene was observed with autism (PMID: 18621663).

1/1/2019
4
icon
3

Decreased from 4 to 3

Description

A single rare CNV in the PCDH10 gene was observed with autism (PMID: 18621663).

10/1/2018
4
icon
3

Decreased from 4 to 3

Description

A single rare CNV in the PCDH10 gene was observed with autism (PMID: 18621663).

10/1/2017
4
icon
3

Decreased from 4 to 3

Description

A single rare CNV in the PCDH10 gene was observed with autism (PMID: 18621663).

10/1/2016
4
icon
3

Decreased from 4 to 3

Description

A single rare CNV in the PCDH10 gene was observed with autism (PMID: 18621663).

7/1/2016
4
icon
4

Decreased from 4 to 4

Description

A single rare CNV in the PCDH10 gene was observed with autism (PMID: 18621663).

10/1/2015
4
icon
3

Decreased from 4 to 3

Description

A single rare CNV in the PCDH10 gene was observed with autism (PMID: 18621663).

1/1/2015
4
icon
4

Decreased from 4 to 4

Description

A single rare CNV in the PCDH10 gene was observed with autism (PMID: 18621663).

10/1/2014
4
icon
3

Decreased from 4 to 3

Description

A single rare CNV in the PCDH10 gene was observed with autism (PMID: 18621663).

7/1/2014
No data
icon
4

Increased from No data to 4

Description

A single rare CNV in the PCDH10 gene was observed with autism (PMID: 18621663).

4/1/2014
No data
icon
4

Increased from No data to 4

Description

A single rare CNV in the PCDH10 gene was observed with autism (PMID: 18621663).

Krishnan Probability Score

Score 0.56748818343886

Ranking 1177/25841 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 0.89443021344704

Ranking 3270/18225 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 0.94673222783228

Ranking 16989/18665 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).
Zhang D Score

Score -0.019254785906904

Ranking 9325/20870 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
BEX1 brain expressed, X-linked 1 Human Protein Binding 55859 Q9HBH7
FCGRT IgG receptor FcRn large subunit p51 Human Protein Binding 2217 P55899
PCDH12 Protocadherin-12 Human Protein Binding 51294 Q9NPG4
SLC34A2 Sodium-dependent phosphate transport protein 2B Human Protein Binding 10568 O95436-2
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