Human Gene Module / Chromosome 12 / CCDC91

CCDC91coiled-coil domain containing 91

SFARI Gene Score
2
Strong Candidate Criteria 2.1
Autism Reports / Total Reports
5 / 6
Rare Variants / Common Variants
5 / 0
Aliases
CCDC91, HSD8,  p56
Associated Syndromes
-
Chromosome Band
12p11.22
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 de novo single gene deletion in Shen et al., 2010, and a maternally-inherited single gene deletion in Nava et al., 2014).

Molecular Function

Involved in the regulation of membrane traffic through the trans-Golgi network (TGN).

External Links
Gene CardOpen Targets PlatformgnomAD browserPubMed
Human
Entrez GeneUniProtHumanBaseVariCarta
SFARI Genomic Platforms
GPF browser SFARI genome browser
Reports related to CCDC91 (6 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Primary Clinical genetic testing for patients with autism spectrum disorders Shen Y , et al. (2010) Yes -
2 Support Prospective diagnostic analysis of copy number variants using SNP microarrays in individuals with autism spectrum disorders Nava C , 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 -
4 Support Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks Ruzzo EK , et al. (2019) Yes -
5 Support - Zhou X et al. (2022) Yes -
6 Support - Cirnigliaro M et al. (2023) Yes -
Rare Variants   (5)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
- - copy_number_loss De novo - Unknown 20231187 Shen Y , et al. (2010)
- - copy_number_loss Familial Maternal Simplex 23632794 Nava C , et al. (2013)
c.946T>C p.Ser316Pro missense_variant De novo - - 35982159 Zhou X et al. (2022)
c.-14-31064A>G - splice_site_variant Familial Paternal Multiplex 31398340 Ruzzo EK , et al. (2019)
c.-14-31002G>T - splice_site_variant Familial Maternal Multiplex 37506195 Cirnigliaro M et al. (2023)
Common Variants  

No common variants reported.

SFARI Gene score
2

Strong Candidate

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 de novo single gene deletion in Shen et al., 2010, and a maternally-inherited single gene deletion in Nava et al., 2014).

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

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 de novo single gene deletion in Shen et al., 2010, and a maternally-inherited single gene deletion in Nava et al., 2014).

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 de novo single gene deletion in Shen et al., 2010, and a maternally-inherited single gene deletion in Nava et al., 2014).

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

Decreased from 4 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 de novo single gene deletion in Shen et al., 2010, and a maternally-inherited single gene deletion in Nava et al., 2014).

Reports Added
[Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks.2019]
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 de novo single gene deletion in Shen et al., 2010, and a maternally-inherited single gene deletion in Nava et al., 2014).

Krishnan Probability Score

Score 0.41905427384826

Ranking 21191/25841 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 3.15157303302E-5

Ranking 13678/18225 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 0.92200559929284

Ranking 9487/18665 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 -0.43076333766957

Ranking 18642/20870 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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