Human Gene Module / Chromosome 8 / PSD3

PSD3pleckstrin and Sec7 domain containing 3

SFARI Gene Score
2
Strong Candidate Criteria 2.1
Autism Reports / Total Reports
6 / 7
Rare Variants / Common Variants
8 / 1
Aliases
PSD3, EFA6R,  HCA67
Associated Syndromes
-
Chromosome Band
8p22
Associated Disorders
ID
Relevance to Autism

Rare mutations involving the PSD3 gene have been identified in individuals with ASD (Pinto et al., 2010).

Molecular Function

This protein is a guanine nucleotide exchange factor for ARF6.

External Links
Gene CardOpen Targets PlatformgnomAD browserPubMed
Human
Entrez GeneOMIMUniProtHumanBaseVariCarta
SFARI Genomic Platforms
GPF browser SFARI genome browser
Reports related to PSD3 (7 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Primary Functional impact of global rare copy number variation in autism spectrum disorders Pinto D , et al. (2010) Yes -
2 Support A discovery resource of rare copy number variations in individuals with autism spectrum disorder Prasad A , et al. (2013) Yes -
3 Support Prospective diagnostic analysis of copy number variants using SNP microarrays in individuals with autism spectrum disorders Nava C , et al. (2013) Yes ID
4 Support The contribution of de novo coding mutations to autism spectrum disorder Iossifov I et al. (2014) Yes -
5 Positive Association Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection Pardias AF , et al. (2018) No -
6 Support Homozygous deletions implicate non-coding epigenetic marks in Autism spectrum disorder Schmitz-Abe K et al. (2020) Yes -
7 Support - Zhou X et al. (2022) Yes -
Rare Variants   (8)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
- - copy_number_loss Unknown - Unknown 23275889 Prasad A , et al. (2013)
- - copy_number_loss Familial Maternal - 20531469 Pinto D , et al. (2010)
- - copy_number_gain Familial Maternal Simplex 23632794 Nava C , et al. (2013)
c.125A>G p.Asp42Gly missense_variant De novo - - 35982159 Zhou X et al. (2022)
- - copy_number_gain Familial Paternal Simplex 20531469 Pinto D , et al. (2010)
- - copy_number_loss Familial Both parents - 32820185 Schmitz-Abe K et al. (2020)
c.1808T>C p.Val603Ala missense_variant De novo - Multiplex 35982159 Zhou X et al. (2022)
c.209del p.Gly70GlufsTer4 frameshift_variant De novo - Simplex 25363768 Iossifov I et al. (2014)
Common Variants   (1)
Status Allele Change Residue Change Variant Type Inheritance Pattern Paternal Transmission Family Type PubMed ID Author, Year
c.2785-7612C>T;c.1183-7612C>T;c.2695-7612C>T;c.2845-7612C>T;c.2824-7612C>T;c.2782-7612C>T;c.2686-761 - intron_variant - - - 29483656 Pardias AF , et al. (2018)
SFARI Gene score
2

Strong Candidate

A single gene deletion was identified in 1 of 996 cases, with a control frequency <1% but otherwise unclear (PMID 20531469). A second single gene deletion has also been identified (PMID 19557195).

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 single gene deletion was identified in 1 of 996 cases, with a control frequency <1% but otherwise unclear (PMID 20531469). A second single gene deletion has also been identified (PMID 19557195).

7/1/2020
3
icon
3

Decreased from 3 to 3

Description

A single gene deletion was identified in 1 of 996 cases, with a control frequency <1% but otherwise unclear (PMID 20531469). A second single gene deletion has also been identified (PMID 19557195).

Reports Added
[Homozygous deletions implicate non-coding epigenetic marks in Autism spectrum disorder2020]
10/1/2019
4
icon
3

Decreased from 4 to 3

New Scoring Scheme
Description

A single gene deletion was identified in 1 of 996 cases, with a control frequency <1% but otherwise unclear (PMID 20531469). A second single gene deletion has also been identified (PMID 19557195).

Reports Added
[New Scoring Scheme]
1/1/2016
4
icon
4

Decreased from 4 to 4

Description

A single gene deletion was identified in 1 of 996 cases, with a control frequency <1% but otherwise unclear (PMID 20531469). A second single gene deletion has also been identified (PMID 19557195).

Reports Added
[Functional impact of global rare copy number variation in autism spectrum disorders.2010] [A discovery resource of rare copy number variations in individuals with autism spectrum disorder.2013] [Prospective diagnostic analysis of copy number variants using SNP microarrays in individuals with autism spectrum disorders.2013] [The contribution of de novo coding mutations to autism spectrum disorder2014]
7/1/2014
No data
icon
4

Increased from No data to 4

Description

A single gene deletion was identified in 1 of 996 cases, with a control frequency <1% but otherwise unclear (PMID 20531469). A second single gene deletion has also been identified (PMID 19557195).

4/1/2014
No data
icon
4

Increased from No data to 4

Description

A single gene deletion was identified in 1 of 996 cases, with a control frequency <1% but otherwise unclear (PMID 20531469). A second single gene deletion has also been identified (PMID 19557195).

Krishnan Probability Score

Score 0.62461811769844

Ranking 77/25841 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 0.85170564943632

Ranking 3608/18225 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 0.29269393924287

Ranking 174/18665 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
Zhang D Score

Score 0.61067692270555

Ranking 61/20870 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
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