Human Gene Module / Chromosome 2 / GIGYF2

GIGYF2GRB10 interacting GYF protein 2

Score
1
High Confidence Criteria 1.1
Autism Reports / Total Reports
7 / 7
Rare Variants / Common Variants
8 / 0
Aliases
GIGYF2, GYF2,  PARK11,  PERQ2,  PERQ3,  TNRC15
Associated Syndromes
-
Genetic Category
Rare Single Gene Mutation
Chromosome Band
2q37.1
Associated Disorders
-
Relevance to Autism

Three de novo variants in the GIGYF2 gene (1 nonsense, 2 missense) have been identified in simplex ASD cases, with no de novo events in this gene observed in 1,786 unaffected siblings from the Simons Simplex Collection (P=3.40 x 10-4) (De Rubeis et al., 2014; Iossifov et al., 2014; Krumm et al., 2015).

Molecular Function

This gene contains CAG trinucleotide repeats and encodes a protein containing several stretches of polyglutamine residues. The encoded protein may be involved in the regulation of tyrosine kinase receptor signaling. This gene is located in a chromosomal region that was genetically linked to Parkinson disease type 11, and mutations in this gene were thought to be causative for this disease.

Reports related to GIGYF2 (7 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Primary Synaptic, transcriptional and chromatin genes disrupted in autism. De Rubeis S , et al. (2014) Yes -
2 Support The contribution of de novo coding mutations to autism spectrum disorder. Iossifov I , et al. (2014) Yes -
3 Support Excess of rare, inherited truncating mutations in autism. Krumm N , et al. (2015) Yes -
4 Recent Recommendation Low load for disruptive mutations in autism genes and their biased transmission. Iossifov I , et al. (2015) Yes -
5 Support De novo genic mutations among a Chinese autism spectrum disorder cohort. Wang T , et al. (2016) Yes -
6 Support Association of rare missense variants in the second intracellular loop of NaV1.7 sodium channels with familial autism. Rubinstein M , et al. (2016) Yes -
7 Support Rates, distribution and implications of postzygotic mosaic mutations in autism spectrum disorder. Lim ET , et al. (2017) Yes -
Rare Variants   (8)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
C>T p.Arg637Ter stop_gained De novo - - 28714951 Lim ET , et al. (2017)
c.958G>T p.Glu320Ter stop_gained De novo - - 27824329 Wang T , et al. (2016)
c.1990C>T p.Gln664Ter stop_gained De novo - Simplex 25363768 Iossifov I , et al. (2014)
c.3527C>G p.Pro1176Arg missense_variant De novo - Simplex 25961944 Krumm N , et al. (2015)
c.2867G>A p.Arg956Gln missense_variant Unknown Not maternal - 27824329 Wang T , et al. (2016)
c.2930G>A p.Arg977Gln missense_variant De novo - Simplex 25363760 De Rubeis S , et al. (2014)
c.3102_3113del p.Ser1035_His1038del inframe_deletion Unknown Not maternal - 27824329 Wang T , et al. (2016)
c.3651G>C p.Gln1217His missense_variant Familial - Extended multiplex 27956748 Rubinstein M , et al. (2016)
Common Variants  

No common variants reported.

SFARI Gene score
1

High Confidence

Three de novo variants in the GIGYF2 gene (1 nonsense, 2 missense) have been identified in simplex ASD cases, with no de novo events in this gene observed in 1,786 unaffected siblings from the Simons Simplex Collection (P=3.40 x 10-4) (De Rubeis et al., 2014; Iossifov et al., 2014; Krumm et al., 2015). A second de novo loss-of-function (LoF) variant in GIGYF2 was identified in a Chinese ASD proband from the Autism Clinical and Genetic Resources in China (ACGC) cohort in Wang et al., 2016. A de novo postzygotic mosaic nonsense variant in GIGYF2 was identified in an ASD proband in Lim et al., 2017, bringing the total of de novo LoF variants in GIGYF2 to three.

Score Delta: Score remained at 2

1

High Confidence

See all Category 1 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.

7/1/2017
2
icon
2

Score remained at 2

Description

Three de novo variants in the GIGYF2 gene (1 nonsense, 2 missense) have been identified in simplex ASD cases, with no de novo events in this gene observed in 1,786 unaffected siblings from the Simons Simplex Collection (P=3.40 x 10-4) (De Rubeis et al., 2014; Iossifov et al., 2014; Krumm et al., 2015). A second de novo loss-of-function (LoF) variant in GIGYF2 was identified in a Chinese ASD proband from the Autism Clinical and Genetic Resources in China (ACGC) cohort in Wang et al., 2016. A de novo postzygotic mosaic nonsense variant in GIGYF2 was identified in an ASD proband in Lim et al., 2017, bringing the total of de novo LoF variants in GIGYF2 to three.

1/1/2017
2
icon
2

Score remained at 2

Description

Three de novo variants in the GIGYF2 gene (1 nonsense, 2 missense) have been identified in simplex ASD cases, with no de novo events in this gene observed in 1,786 unaffected siblings from the Simons Simplex Collection (P=3.40 x 10-4) (De Rubeis et al., 2014; Iossifov et al., 2014; Krumm et al., 2015). A fourth de novo LoF variant in GIGYF2 was identified in a Chinese ASD proband from the Autism Clinical and Genetic Resources in China (ACGC) cohort in Wang et al., 2016.

10/1/2016
3
icon
2

Decreased from 3 to 2

Description

Three de novo variants in the GIGYF2 gene (1 nonsense, 2 missense) have been identified in simplex ASD cases, with no de novo events in this gene observed in 1,786 unaffected siblings from the Simons Simplex Collection (P=3.40 x 10-4) (De Rubeis et al., 2014; Iossifov et al., 2014; Krumm et al., 2015). A fourth de novo LoF variant in GIGYF2 was identified in a Chinese ASD proband from the Autism Clinical and Genetic Resources in China (ACGC) cohort in Wang et al., 2016.

1/1/2016
3
icon
3

Decreased from 3 to 3

Description

Three de novo variants in the GIGYF2 gene (1 nonsense, 2 missense) have been identified in simplex ASD cases, with no de novo events in this gene observed in 1,786 unaffected siblings from the Simons Simplex Collection (P=3.40 x 10-4) (De Rubeis et al., 2014; Iossifov et al., 2014; Krumm et al., 2015).

7/1/2015
icon
3

Increased from to 3

Description

Three de novo variants in the GIGYF2 gene (1 nonsense, 2 missense) have been identified in simplex ASD cases, with no de novo events in this gene observed in 1,786 unaffected siblings from the Simons Simplex Collection (P=3.40 x 10-4) (De Rubeis et al., 2014; Iossifov et al., 2014; Krumm et al., 2015).

Krishnan Probability Score

Score 0.49228277258555

Ranking 4627/25841 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 0.99999999997935

Ranking 53/18225 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
Iossifov Probability Score

Score 0.948

Ranking 84/239 scored genes


[Show Scoring Methodology]
Supplementary dataset S2 in the paper by Iossifov et al. (PNAS 112, E5600-E5607 (2015)) lists 239 genes with a probability of at least 0.8 of being associated with autism risk (column I). This probability metric combines the evidence from de novo likely-gene- disrupting and missense mutations and assesses it against the background mutation rate in unaffected individuals from the University of Washington’s Exome Variant Sequence database (evs.gs.washington.edu/EVS/). The list of probability scores can be found here: www.pnas.org/lookup/suppl/doi:10.1073/pnas.1516376112/- /DCSupplemental/pnas.1516376112.sd02.xlsx
Sanders TADA Score

Score 0.25896648523786

Ranking 149/18665 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 0.34279934511242

Ranking 2107/20870 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.
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