Human Gene Module / Chromosome 3 / GPX1

GPX1glutathione peroxidase 1

SFARI Gene Score
2
Strong Candidate Criteria 2.1
Autism Reports / Total Reports
2 / 6
Rare Variants / Common Variants
1 / 1
Aliases
GPX1, GSHPX1,  MGC14399,  MGC88245,  GPX1
Associated Syndromes
-
Chromosome Band
3p21.31
Associated Disorders
-
Relevance to Autism

Genetic association has been found between the GPX1 gene and autism in a US population cohort (Ming et al., 2010).

Molecular Function

It functions in the detoxification of hydrogen peroxide

SFARI Genomic Platforms
Reports related to GPX1 (6 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Highly Cited Targeted mutation of the gene for cellular glutathione peroxidase (Gpx1) increases noise-induced hearing loss in mice Ohlemiller KK , et al. (2001) No -
2 Recent Recommendation Glutathione peroxidase 1-deficient mice are more susceptible to doxorubicin-induced cardiotoxicity Gao J , et al. (2008) No -
3 Recent Recommendation Cellular glutathione peroxidase in human brain: cellular distribution, and its potential role in the degradation of Lewy bodies in Parkinson's disease and dementia with Lewy bodies Power JH and Blumbergs PC (2008) No -
4 Primary Genetic variant of glutathione peroxidase 1 in autism Ming X , et al. (2009) Yes -
5 Support - Cirnigliaro M et al. (2023) Yes -
6 Highly Cited Mice with a homozygous null mutation for the most abundant glutathione peroxidase, Gpx1, show increased susceptibility to the oxidative stress-inducing agents paraquat and hydrogen peroxide de Haan JB , et al. (1998) No -
Rare Variants   (1)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
c.199_200insCG p.Gly67AlafsTer? frameshift_variant Familial Maternal Multiplex 37506195 Cirnigliaro M et al. (2023)
Common Variants   (1)
Status Allele Change Residue Change Variant Type Inheritance Pattern Paternal Transmission Family Type PubMed ID Author, Year
N/A N/A microsatellite - - - 19195803 Ming X , et al. (2009)
SFARI Gene score
2

Strong Candidate

Unreplicated association of trinucleotide repeat polymorphism in Ming et al., 2010 (PMID: 19195803)

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
icon
2

Decreased from 3 to 2

Description

Unreplicated association of trinucleotide repeat polymorphism in Ming et al., 2010 (PMID: 19195803)

10/1/2019
4
icon
3

Decreased from 4 to 3

New Scoring Scheme
Description

Unreplicated association of trinucleotide repeat polymorphism in Ming et al., 2010 (PMID: 19195803)

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

Increased from No data to 4

Description

Unreplicated association of trinucleotide repeat polymorphism in Ming et al., 2010 (PMID: 19195803)

4/1/2014
No data
icon
4

Increased from No data to 4

Description

Unreplicated association of trinucleotide repeat polymorphism in Ming et al., 2010 (PMID: 19195803)

Krishnan Probability Score

Score 0.48841055660428

Ranking 6748/25841 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 0.0069316511169313

Ranking 10314/18225 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 0.93043819134822

Ranking 11429/18665 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 1

Ranking 421/461 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 -0.54805630426069

Ranking 19602/20870 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
FAM9B family with sequence similarity 9, member B Human Protein Binding 171483 A0A024RBV3
Submit New Gene

Report an Error