Human Gene Module / Chromosome 2 / CLASP1

CLASP1cytoplasmic linker associated protein 1

Score
2
Strong Candidate Criteria 2.1
Autism Reports / Total Reports
3 / 3
Rare Variants / Common Variants
4 / 0
Aliases
CLASP1, MAST1
Associated Syndromes
-
Genetic Category
Rare Single Gene Mutation
Chromosome Band
2q14.2-q14.3
Associated Disorders
-
Relevance to Autism

Three de novo missense variants in the CLASP1 gene had previously been identified in ASD probands (one proband from the Autism Sequencing Consortium in De Rubeis et al., 2014, and two others from the Simons Simplex Collection in Iossifov et al., 2014). A fourth de novo missense variant in this gene was identified by whole genome sequencing in an ASD proband as part of the MSSNG initiative in Yuen et al., 2017. Based on the discovery of four de novo missense variants in ASD cases, a z-score > 2.0 for missense mutations, and a higher-than expected mutation rate (a false discovery rate < 15%), CLASP1 was determined to be an ASD candidate gene in Yuen et al., 2017.

Molecular Function

CLASPs, such as CLASP1, are nonmotor microtubule-associated proteins that interact with CLIPs. CLASP1 is involved in the regulation of microtubule dynamics at the kinetochore and throughout the spindle.

Reports related to CLASP1 (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 Support The contribution of de novo coding mutations to autism spectrum disorder. Iossifov I , et al. (2014) Yes -
3 Recent Recommendation Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder. C Yuen RK , et al. (2017) Yes -
Rare Variants   (4)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
c.3989A>C p.Lys1330Thr missense_variant De novo NA - 25363760 De Rubeis S , et al. (2014)
c.1276G>A p.Ala426Thr missense_variant De novo NA Simplex 28263302 C Yuen RK , et al. (2017)
c.3004A>G p.Ile1002Val missense_variant De novo NA Simplex 25363768 Iossifov I , et al. (2014)
c.3740T>G p.Leu1247Arg missense_variant De novo NA Simplex 25363768 Iossifov I , et al. (2014)
Common Variants  

No common variants reported.

SFARI Gene score
2

Strong Candidate

Three de novo missense variants in the CLASP1 gene had previously been identified in ASD probands (one proband from the Autism Sequencing Consortium in De Rubeis et al., 2014, and two others from the Simons Simplex Collection in Iossifov et al., 2014). A fourth de novo missense variant in this gene was identified by whole genome sequencing in an ASD proband as part of the MSSNG initiative in Yuen et al., 2017. Based on the discovery of four de novo missense variants in ASD cases, a z-score > 2.0 for missense mutations, and a higher-than expected mutation rate (a false discovery rate < 15%), CLASP1 was determined to be an ASD candidate gene in Yuen et al., 2017.

Score Delta: Decreased from 3 to 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.

10/1/2019
3
icon
2

Decreased from 3 to 2

New Scoring Scheme
Description

Three de novo missense variants in the CLASP1 gene had previously been identified in ASD probands (one proband from the Autism Sequencing Consortium in De Rubeis et al., 2014, and two others from the Simons Simplex Collection in Iossifov et al., 2014). A fourth de novo missense variant in this gene was identified by whole genome sequencing in an ASD proband as part of the MSSNG initiative in Yuen et al., 2017. Based on the discovery of four de novo missense variants in ASD cases, a z-score > 2.0 for missense mutations, and a higher-than expected mutation rate (a false discovery rate < 15%), CLASP1 was determined to be an ASD candidate gene in Yuen et al., 2017.

Reports Added
[New Scoring Scheme]
7/1/2018
4.4 + acc
icon
3

Decreased from 4.4 + acc to 3

Description

Three de novo missense variants in the CLASP1 gene had previously been identified in ASD probands (one proband from the Autism Sequencing Consortium in De Rubeis et al., 2014, and two others from the Simons Simplex Collection in Iossifov et al., 2014). A fourth de novo missense variant in this gene was identified by whole genome sequencing in an ASD proband as part of the MSSNG initiative in Yuen et al., 2017. Based on the discovery of four de novo missense variants in ASD cases, a z-score > 2.0 for missense mutations, and a higher-than expected mutation rate (a false discovery rate < 15%), CLASP1 was determined to be an ASD candidate gene in Yuen et al., 2017.

4/1/2018
3
icon
4.4 + acc

Increased from 3 to 4.4 + acc

Description

3

4/1/2017
icon
3

Increased from to 3

Description

Three de novo missense variants in the CLASP1 gene had previously been identified in ASD probands (one proband from the Autism Sequencing Consortium in De Rubeis et al., 2014, and two others from the Simons Simplex Collection in Iossifov et al., 2014). A fourth de novo missense variant in this gene was identified by whole genome sequencing in an ASD proband as part of the MSSNG initiative in Yuen et al., 2017. Based on the discovery of four de novo missense variants in ASD cases, a z-score > 2.0 for missense mutations, and a higher-than expected mutation rate (a false discovery rate < 15%), CLASP1 was determined to be an ASD candidate gene in Yuen et al., 2017.

Krishnan Probability Score

Score 0.53654001082612

Ranking 1481/25841 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 0.99999998887092

Ranking 138/18225 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 0.61248675630353

Ranking 751/18665 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 0.095000476924979

Ranking 6240/20870 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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