Human Gene Module / Chromosome 15 / C15orf62

C15orf62chromosome 15 open reading frame 62

SFARI Gene Score
2
Strong Candidate Criteria 2.1
Autism Reports / Total Reports
3 / 3
Rare Variants / Common Variants
3 / 0
Aliases
-
Associated Syndromes
-
Chromosome Band
15q15.1
Associated Disorders
-
Relevance to Autism

A de novo stop-loss variant in the C15orf62 gene was identified in an ASD proband from the Simons Simplex Collection in O'Roak et al., 2012. Targeted sequencing of 536 Chinese ASD probands and 1457 Chinese controls in Guo et al., 2017 detected a rare inherited loss-of-function variant in this gene in a Chinese ASD proband. Transmission and De Novo Association (TADA) analysis of a combined cohort consisting of Chinese ASD cases and controls, as well as ASD probands and controls from the Simons Simplex Collection and the Autism Sequencing Consortium, in Guo et al., 2017 identified C15orf62 as an ASD candidate gene with a PTADA of 0.003927.

Molecular Function

This gene encodes for a protein of unknown function.

External Links
Gene CardOpen Targets PlatformgnomAD browserPubMed
Human
Entrez GeneUniProtHumanBaseVariCarta
SFARI Genomic Platforms
GPF browser SFARI genome browser
Reports related to C15orf62 (3 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Primary Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations O'Roak BJ , et al. (2012) Yes -
2 Recent Recommendation Targeted sequencing and functional analysis reveal brain-size-related genes and their networks in autism spectrum disorders Li J , et al. (2017) Yes -
3 Support - Cirnigliaro M et al. (2023) Yes -
Rare Variants   (3)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
c.82C>T p.Arg28Ter stop_gained Familial - - 28831199 Li J , et al. (2017)
c.527A>T p.Ter176LeuextTer3 stop_lost De novo - Simplex 22495309 O'Roak BJ , et al. (2012)
c.440dup p.Ser148LeufsTer12 frameshift_variant Familial Paternal Multiplex 37506195 Cirnigliaro M et al. (2023)
Common Variants  

No common variants reported.

SFARI Gene score
2

Strong Candidate

A de novo stop-loss variant in the C15orf62 gene was identified in an ASD proband from the Simons Simplex Collection in O'Roak et al., 2012. Targeted sequencing of 536 Chinese ASD probands and 1457 Chinese controls in Guo et al., 2017 detected a rare inherited loss-of-function variant in this gene in a Chinese ASD proband. Transmission and De Novo Association (TADA) analysis of a combined cohort consisting of Chinese ASD cases and controls, as well as ASD probands and controls from the Simons Simplex Collection and the Autism Sequencing Consortium, in Guo et al., 2017 identified C15orf62 as an ASD candidate gene with a PTADA of 0.003927.

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

A de novo stop-loss variant in the C15orf62 gene was identified in an ASD proband from the Simons Simplex Collection in O'Roak et al., 2012. Targeted sequencing of 536 Chinese ASD probands and 1457 Chinese controls in Guo et al., 2017 detected a rare inherited loss-of-function variant in this gene in a Chinese ASD proband. Transmission and De Novo Association (TADA) analysis of a combined cohort consisting of Chinese ASD cases and controls, as well as ASD probands and controls from the Simons Simplex Collection and the Autism Sequencing Consortium, in Guo et al., 2017 identified C15orf62 as an ASD candidate gene with a PTADA of 0.003927.

10/1/2019
4
icon
3

Decreased from 4 to 3

New Scoring Scheme
Description

A de novo stop-loss variant in the C15orf62 gene was identified in an ASD proband from the Simons Simplex Collection in O'Roak et al., 2012. Targeted sequencing of 536 Chinese ASD probands and 1457 Chinese controls in Guo et al., 2017 detected a rare inherited loss-of-function variant in this gene in a Chinese ASD proband. Transmission and De Novo Association (TADA) analysis of a combined cohort consisting of Chinese ASD cases and controls, as well as ASD probands and controls from the Simons Simplex Collection and the Autism Sequencing Consortium, in Guo et al., 2017 identified C15orf62 as an ASD candidate gene with a PTADA of 0.003927.

Reports Added
[New Scoring Scheme]
7/1/2017
icon
4

Increased from to 4

Description

A de novo stop-loss variant in the C15orf62 gene was identified in an ASD proband from the Simons Simplex Collection in O'Roak et al., 2012. Targeted sequencing of 536 Chinese ASD probands and 1457 Chinese controls in Guo et al., 2017 detected a rare inherited loss-of-function variant in this gene in a Chinese ASD proband. Transmission and De Novo Association (TADA) analysis of a combined cohort consisting of Chinese ASD cases and controls, as well as ASD probands and controls from the Simons Simplex Collection and the Autism Sequencing Consortium, in Guo et al., 2017 identified C15orf62 as an ASD candidate gene with a PTADA of 0.003927.

Krishnan Probability Score

Score 0.44366859898739

Ranking 16511/25841 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
Sanders TADA Score

Score 0.89871704975626

Ranking 6256/18665 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 -0.059180837125381

Ranking 10758/20870 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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