Human Gene Module / Chromosome 1 / SRSF11

SRSF11serine and arginine rich splicing factor 11

Score
2
Strong Candidate Criteria 2.1
Autism Reports / Total Reports
3 / 3
Rare Variants / Common Variants
3 / 0
Aliases
SRSF11, NET2,  SFRS11,  dJ677H15.2,  p54
Associated Syndromes
-
Genetic Category
Rare Single Gene Mutation
Chromosome Band
1p31.1
Associated Disorders
-
Relevance to Autism

A de novo loss-of-function (LoF) variant in the SRSF11 gene was first identified in an ASD proband from the Autism Sequencing Consortium (De Rubeis et al., 2014). A second de novo LoF variant in this gene was identified by whole genome sequencing in an ASD proband from a multiplex family as part of the MSSNG initiative in Yuen et al., 2017. Based on the discovery of two de novo LoF variants in ASD cases, a probability of LoF intolerance rate (pLI) > 0.9, and a higher-than expected mutation rate (a false discovery rate < 15%), SRSF11 was determined to be an ASD candidate gene in Yuen et al., 2017.

Molecular Function

This gene encodes 54-kD nuclear protein that contains an arginine/serine-rich region similar to segments found in pre-mRNA splicing factors. Although the function of this protein is not yet known, structure and immunolocalization data suggest that it may play a role in pre-mRNA processing.

Reports related to SRSF11 (3 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 Recent Recommendation Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder. C Yuen RK , et al. (2017) Yes -
3 Support Rates, distribution and implications of postzygotic mosaic mutations in autism spectrum disorder. Lim ET , et al. (2017) Yes -
Rare Variants   (3)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
669+A 223-! frameshift_variant De novo - - 25363760 De Rubeis S , et al. (2014)
c.371_372del p.Leu124fs frameshift_variant De novo - Multiplex 28263302 C Yuen RK , et al. (2017)
A>G p.His15Arg missense_variant De novo - - 28714951 Lim ET , et al. (2017)
Common Variants  

No common variants reported.

SFARI Gene score
2

Strong Candidate

2

Score Delta: Increased from 2 to 3.3 + acc

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.

4/1/2018
2
icon
3.3 + acc

Increased from 2 to 3.3 + acc

Description

2

7/1/2017
2
icon
2

Increased from 2 to 2

Description

A de novo loss-of-function (LoF) variant in the SRSF11 gene was first identified in an ASD proband from the Autism Sequencing Consortium (De Rubeis et al., 2014). A second de novo LoF variant in this gene was identified by whole genome sequencing in an ASD proband from a multiplex family as part of the MSSNG initiative in Yuen et al., 2017. Based on the discovery of two de novo LoF variants in ASD cases, a probability of LoF intolerance rate (pLI) > 0.9, and a higher-than expected mutation rate (a false discovery rate < 15%), SRSF11 was determined to be an ASD candidate gene in Yuen et al., 2017.

4/1/2017
icon
2

Increased from to 2

Description

A de novo loss-of-function (LoF) variant in the SRSF11 gene was first identified in an ASD proband from the Autism Sequencing Consortium (De Rubeis et al., 2014). A second de novo LoF variant in this gene was identified by whole genome sequencing in an ASD proband from a multiplex family as part of the MSSNG initiative in Yuen et al., 2017. Based on the discovery of two de novo LoF variants in ASD cases, a probability of LoF intolerance rate (pLI) > 0.9, and a higher-than expected mutation rate (a false discovery rate < 15%), SRSF11 was determined to be an ASD candidate gene in Yuen et al., 2017.

Krishnan Probability Score

Score 0.49808588056067

Ranking 2295/25841 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 0.99978776713447

Ranking 782/18225 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 0.44134497279062

Ranking 338/18665 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 0.15471275657842

Ranking 5086/20870 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.
CNVs associated with SRSF11(1 CNVs)
1p31.1 28 Deletion-Duplication 45  /  175
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