Human Gene Module / Chromosome 9 / CYLC2

CYLC2cylicin, basic protein of sperm head cytoskeleton 2

Score
3
Suggestive Evidence Criteria 3.1
Autism Reports / Total Reports
2 / 3
Rare Variants / Common Variants
2 / 0
Aliases
-
Associated Syndromes
-
Genetic Category
Rare Single Gene Mutation
Chromosome Band
9q31.1
Associated Disorders
-
Relevance to Autism

This gene was identified as a novel ASD candidate gene in Gonzalez-Mantilla et al., 2016 based on the presence of two potentially pathogenic loss-of-function variants in ASD cases (a maternally-inherited single gene deletion in an SSC proband in Levy et al., 2011, and a single gene deletion of unknown origin in Stobbe et al., 2013).

Molecular Function

Possible architectural role during spermatogenesis. May be involved in spermatid differentiation.

Reports related to CYLC2 (3 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Primary Rare de novo and transmitted copy-number variation in autistic spectrum disorders. Levy D , et al. (2011) Yes -
2 Support Diagnostic yield of array comparative genomic hybridization in adults with autism spectrum disorders. Stobbe G , et al. (2013) Yes -
3 Recent Recommendation A Cross-Disorder Method to Identify Novel Candidate Genes for Developmental Brain Disorders. Gonzalez-Mantilla AJ , et al. (2016) No -
Rare Variants   (2)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
- - copy_number_loss Unknown - Unknown 23765050 Stobbe G , et al. (2013)
- - copy_number_loss Familial Maternal Simplex 21658582 Levy D , et al. (2011)
Common Variants  

No common variants reported.

SFARI Gene score
3

Suggestive Evidence

This gene was identified as a novel ASD candidate gene in Gonzalez-Mantilla et al., 2016 based on the presence of two potentially pathogenic loss-of-function variants in ASD cases (a maternally-inherited single gene deletion in an SSC proband in Levy et al., 2011, and a single gene deletion of unknown origin in Stobbe et al., 2013).

Score Delta: Score remained at 4

3

Suggestive Evidence

See all Category 3 Genes

The literature is replete with relatively small studies of candidate genes, using either common or rare variant approaches, which do not reach the criteria set out for categories 1 and 2. Genes that had two such lines of supporting evidence were placed in category 3, and those with one line of evidence were placed in category 4. Some additional lines of "accessory evidence" (indicated as "acc" in the score cards) could also boost a gene from category 4 to 3.

10/1/2019
4
icon
3

Decreased from 4 to 3

New Scoring Scheme
Description

This gene was identified as a novel ASD candidate gene in Gonzalez-Mantilla et al., 2016 based on the presence of two potentially pathogenic loss-of-function variants in ASD cases (a maternally-inherited single gene deletion in an SSC proband in Levy et al., 2011, and a single gene deletion of unknown origin in Stobbe et al., 2013).

Reports Added
[New Scoring Scheme]
1/1/2016
icon
4

Increased from to 4

Description

This gene was identified as a novel ASD candidate gene in Gonzalez-Mantilla et al., 2016 based on the presence of two potentially pathogenic loss-of-function variants in ASD cases (a maternally-inherited single gene deletion in an SSC proband in Levy et al., 2011, and a single gene deletion of unknown origin in Stobbe et al., 2013).

Krishnan Probability Score

Score 0.49976568445977

Ranking 2135/25841 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 5.14081582239E-7

Ranking 15245/18225 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 0.85441340279221

Ranking 3625/18665 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 0.05541406691423

Ranking 7089/20870 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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SFARI Gene Update

We are pleased to announce some changes to the ongoing curation of the data in SFARI Gene. In the context of a continued effort to develop the human gene module and its manually curated list of autism risk genes, we are modifying other aspects of the site to focus on the information that is of greatest interest to the research community. The version of SFARI Gene that has been developed until now will be frozen and will remain available as “SFARI Gene Archive”. Please see the announcement for more details.
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