Human Gene Module / Chromosome 1 / AGBL4

AGBL4ATP/GTP binding protein-like 4

SFARI Gene Score
2
Strong Candidate Criteria 2.1
Autism Reports / Total Reports
3 / 3
Rare Variants / Common Variants
6 / 0
Aliases
AGBL4, RP11-342A17.1,  CCP6
Associated Syndromes
-
Chromosome Band
1p33
Associated Disorders
ID
Relevance to Autism

Rare deletions involving the AGBL4 gene have been identified in individuals with ASD (Pinto et al., 2010).

Molecular Function

Metallocarboxypeptidase that mediates deglutamylation of target proteins such as tubulins and MYLK.

External Links
Gene CardOpen Targets PlatformgnomAD browserPubMed
Human
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SFARI Genomic Platforms
GPF browser SFARI genome browser
Reports related to AGBL4 (3 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
Rare Variants   (6)
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 Simplex 20531469 Pinto D , et al. (2010)
- - copy_number_loss Familial Paternal Simplex 20531469 Pinto D , et al. (2010)
- - copy_number_loss Familial Maternal Unknown 20531469 Pinto D , et al. (2010)
- - copy_number_loss Familial Paternal Unknown 20531469 Pinto D , et al. (2010)
- - copy_number_loss Familial Paternal Multiplex 23632794 Nava C , et al. (2013)
Common Variants  

No common variants reported.

SFARI Gene score
2

Strong Candidate

Intronic deletions were identified in 13 / 996 vs. 6 / 1287, with a nominal combined P value = 0.02 (PMID 20531469). This gene does not qualify for Cat. 2.1 because these CNVs are not 'convincing'.

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
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2

Decreased from 3 to 2

Description

Intronic deletions were identified in 13 / 996 vs. 6 / 1287, with a nominal combined P value = 0.02 (PMID 20531469). This gene does not qualify for Cat. 2.1 because these CNVs are not 'convincing'.

10/1/2019
4
icon
3

Decreased from 4 to 3

New Scoring Scheme
Description

Intronic deletions were identified in 13 / 996 vs. 6 / 1287, with a nominal combined P value = 0.02 (PMID 20531469). This gene does not qualify for Cat. 2.1 because these CNVs are not 'convincing'.

Reports Added
[New Scoring Scheme]
7/1/2014
No data
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4

Increased from No data to 4

Description

Intronic deletions were identified in 13 / 996 vs. 6 / 1287, with a nominal combined P value = 0.02 (PMID 20531469). This gene does not qualify for Cat. 2.1 because these CNVs are not 'convincing'.

4/1/2014
No data
icon
4

Increased from No data to 4

Description

Intronic deletions were identified in 13 / 996 vs. 6 / 1287, with a nominal combined P value = 0.02 (PMID 20531469). This gene does not qualify for Cat. 2.1 because these CNVs are not 'convincing'.

Krishnan Probability Score

Score 0.48405310074729

Ranking 7610/25841 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 3.5783005724045E-6

Ranking 14607/18225 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 0.94864733584057

Ranking 17769/18665 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 13

Ranking 147/461 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 0.30612551280987

Ranking 2645/20870 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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