Human Gene Module / Chromosome 15 / MEGF11

MEGF11multiple EGF like domains 11

SFARI Gene Score
2
Strong Candidate Criteria 2.1
Autism Reports / Total Reports
7 / 9
Rare Variants / Common Variants
8 / 0
Aliases
-
Associated Syndromes
-
Chromosome Band
15q22.31
Associated Disorders
-
Relevance to Autism

Three de novo missense variants in the MEGF11 gene were identified in ASD probands from the Simons Simplex Collection (Sanders et al., 2012; O'Roak et al., 2012) and the Autism Sequencing Consortium (De Rubeis et al., 2014). Two of these variants were later determined to be postzygotic mosaic mutations (PZMs) in Lim et al., 2017; comparison with a background set of 84,448 privately inherited variants demonstrated that this gene harbored more PZMs than expected based on background rates (2/571 observed vs. 10/84,448 expected; hypergeometric P-value of 2.0E-03).

Molecular Function

May regulate the mosaic spacing of specific neuron subtypes in the retina through homotypic retinal neuron repulsion.

External Links
Gene CardOpen Targets PlatformgnomAD browserPubMed
Human
Entrez GeneOMIMUniProtHumanBaseVariCarta
SFARI Genomic Platforms
GPF browser SFARI genome browser
Reports related to MEGF11 (9 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Primary De novo mutations revealed by whole-exome sequencing are strongly associated with autism Sanders SJ , et al. (2012) Yes -
2 Support Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations O'Roak BJ , et al. (2012) Yes -
3 Support Synaptic, transcriptional and chromatin genes disrupted in autism De Rubeis S , et al. (2014) Yes -
4 Recent Recommendation Rates, distribution and implications of postzygotic mosaic mutations in autism spectrum disorder Lim ET , et al. (2017) No -
5 Support Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks Ruzzo EK , et al. (2019) Yes -
6 Support - Zhou X et al. (2022) Yes -
7 Support - Chen WX et al. (2022) Yes -
8 Support - Cirnigliaro M et al. (2023) Yes -
9 Support - et al. () No -
Rare Variants   (8)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
c.2385A>G p.Leu795%3D synonymous_variant De novo - - 35982159 Zhou X et al. (2022)
c.272G>A p.Gly91Asp missense_variant De novo - Simplex 36320054 Chen WX et al. (2022)
c.2066T>C p.Ile689Thr missense_variant De novo - - 25363760 De Rubeis S , et al. (2014)
c.2306C>T p.Thr769Ile missense_variant De novo - Simplex 22495309 O'Roak BJ , et al. (2012)
c.2731C>T p.Arg911Cys missense_variant De novo - Simplex 22495306 Sanders SJ , et al. (2012)
c.1155G>A p.Trp385Ter stop_gained Familial Paternal Multiplex 31398340 Ruzzo EK , et al. (2019)
c.180G>A p.Trp60Ter stop_gained Familial Paternal Multiplex 37506195 Cirnigliaro M et al. (2023)
c.3233C>A p.Ser1078Ter stop_gained Familial Paternal Multiplex 37506195 Cirnigliaro M et al. (2023)
Common Variants  

No common variants reported.

SFARI Gene score
2

Strong Candidate

Three de novo missense variants in the MEGF11 gene were identified in ASD probands from the Simons Simplex Collection (Sanders et al., 2012; O'Roak et al., 2012) and the Autism Sequencing Consortium (De Rubeis et al., 2014). Two of these variants were later determined to be postzygotic mosaic mutations (PZMs) in Lim et al., 2017; comparison with a background set of 84,448 privately inherited variants demonstrated that this gene harbored more PZMs than expected based on background rates (2/571 observed vs. 10/84,448 expected; hypergeometric P-value of 2.0E-03).

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

Three de novo missense variants in the MEGF11 gene were identified in ASD probands from the Simons Simplex Collection (Sanders et al., 2012; O'Roak et al., 2012) and the Autism Sequencing Consortium (De Rubeis et al., 2014). Two of these variants were later determined to be postzygotic mosaic mutations (PZMs) in Lim et al., 2017; comparison with a background set of 84,448 privately inherited variants demonstrated that this gene harbored more PZMs than expected based on background rates (2/571 observed vs. 10/84,448 expected; hypergeometric P-value of 2.0E-03).

10/1/2019
4
icon
3

Decreased from 4 to 3

New Scoring Scheme
Description

Three de novo missense variants in the MEGF11 gene were identified in ASD probands from the Simons Simplex Collection (Sanders et al., 2012; O'Roak et al., 2012) and the Autism Sequencing Consortium (De Rubeis et al., 2014). Two of these variants were later determined to be postzygotic mosaic mutations (PZMs) in Lim et al., 2017; comparison with a background set of 84,448 privately inherited variants demonstrated that this gene harbored more PZMs than expected based on background rates (2/571 observed vs. 10/84,448 expected; hypergeometric P-value of 2.0E-03).

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

Decreased from 4 to 4

Description

Three de novo missense variants in the MEGF11 gene were identified in ASD probands from the Simons Simplex Collection (Sanders et al., 2012; O'Roak et al., 2012) and the Autism Sequencing Consortium (De Rubeis et al., 2014). Two of these variants were later determined to be postzygotic mosaic mutations (PZMs) in Lim et al., 2017; comparison with a background set of 84,448 privately inherited variants demonstrated that this gene harbored more PZMs than expected based on background rates (2/571 observed vs. 10/84,448 expected; hypergeometric P-value of 2.0E-03).

Reports Added
[Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks.2019]
7/1/2017
icon
4

Increased from to 4

Description

Three de novo missense variants in the MEGF11 gene were identified in ASD probands from the Simons Simplex Collection (Sanders et al., 2012; O'Roak et al., 2012) and the Autism Sequencing Consortium (De Rubeis et al., 2014). Two of these variants were later determined to be postzygotic mosaic mutations (PZMs) in Lim et al., 2017; comparison with a background set of 84,448 privately inherited variants demonstrated that this gene harbored more PZMs than expected based on background rates (2/571 observed vs. 10/84,448 expected; hypergeometric P-value of 2.0E-03).

Krishnan Probability Score

Score 0.49604978571576

Ranking 2704/25841 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 2.5182184269378E-24

Ranking 18081/18225 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 0.84623012084277

Ranking 3332/18665 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 0.12936574563563

Ranking 5554/20870 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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