Human Gene Module / Chromosome 1 / OR2T10

OR2T10olfactory receptor family 2 subfamily T member 10

SFARI Gene Score
2
Strong Candidate Criteria 2.1
Autism Reports / Total Reports
3 / 4
Rare Variants / Common Variants
3 / 0
Aliases
OR2T10, OR1-64
Associated Syndromes
-
Chromosome Band
1q44
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 nonsense variant in an SSC proband in Iossifov et al., 2014, and a paternally-inherited frameshift variant in a Spanish male ASD proband in Codina-Sola et al., 2015).

Molecular Function

odorant receptor

External Links
Gene CardOpen Targets PlatformgnomAD browserPubMed
Human
Entrez GeneUniProtHumanBaseVariCarta
SFARI Genomic Platforms
GPF browser SFARI genome browser
Reports related to OR2T10 (4 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Primary The contribution of de novo coding mutations to autism spectrum disorder Iossifov I et al. (2014) Yes -
2 Support Integrated analysis of whole-exome sequencing and transcriptome profiling in males with autism spectrum disorders Codina-Sol M , et al. (2015) 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 - 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.795C>A p.Tyr265Ter stop_gained De novo - Simplex 25363768 Iossifov I et al. (2014)
c.771C>A p.Tyr257Ter stop_gained Familial Paternal Multiplex 37506195 Cirnigliaro M et al. (2023)
c.910del p.Met304CysfsTer2 frameshift_variant Familial Paternal - 25969726 Codina-Sol M , et al. (2015)
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 nonsense variant in an SSC proband in Iossifov et al., 2014, and a paternally-inherited frameshift variant in a Spanish male ASD proband in Codina-Sola et al., 2015).

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 nonsense variant in an SSC proband in Iossifov et al., 2014, and a paternally-inherited frameshift variant in a Spanish male ASD proband in Codina-Sola et al., 2015).

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 nonsense variant in an SSC proband in Iossifov et al., 2014, and a paternally-inherited frameshift variant in a Spanish male ASD proband in Codina-Sola et al., 2015).

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 de novo nonsense variant in an SSC proband in Iossifov et al., 2014, and a paternally-inherited frameshift variant in a Spanish male ASD proband in Codina-Sola et al., 2015).

Krishnan Probability Score

Score 0.44735346949272

Ranking 12608/25841 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 0.0001557488406987

Ranking 12847/18225 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 0.26879408440591

Ranking 156/18665 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
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