Human Gene Module / Chromosome 15 / NEO1

NEO1Neogenin 1

Score
3
Suggestive Evidence Criteria 3.1
Autism Reports / Total Reports
1 / 1
Rare Variants / Common Variants
6 / 0
Aliases
NEO1, IGDCC2,  NGN,  NTN1R2
Associated Syndromes
-
Genetic Category
-
Chromosome Band
15q24.1
Associated Disorders
-
Relevance to Autism

Biallelic variants in the NEO1 gene were identified in two ASD patients of Han Chinese descent (Siu et al., 2015).

Molecular Function

Multi-functional cell surface receptor for members of the BMP, netrin, and repulsive guidance molecule (RGM) families that regulates cell adhesion in many diverse developmental processes, including neural tube and mammary gland formation, myogenesis and angiogenesis. Netrin-Neogenin interactions result in a chemoattractive axon guidance response and cell-cell adhesion.

Reports related to NEO1 (1 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Primary Unmasking a novel disease gene NEO1 associated with autism spectrum disorders by a hemizygous deletion on chromosome 15 and a functional polymorphism. Siu WK , et al. (2015) Yes -
Rare Variants   (6)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
- - copy_number_loss Unknown Not maternal Simplex 26518331 Siu WK , et al. (2015)
c.2204-14_2204-2dup - intron_variant Familial Maternal Simplex 26518331 Siu WK , et al. (2015)
c.302G>A p.Arg101His missense_variant Familial Maternal Simplex 26518331 Siu WK , et al. (2015)
c.2204-14_2204-2dup - intron_variant Unknown Not maternal Simplex 26518331 Siu WK , et al. (2015)
c.3388C>T p.Arg1130Cys missense_variant Familial Maternal Simplex 26518331 Siu WK , et al. (2015)
c.3388C>T p.Arg1130Cys missense_variant Unknown Not maternal Simplex 26518331 Siu WK , et al. (2015)
Common Variants  

No common variants reported.

SFARI Gene score
3

Suggestive Evidence

Biallelic variants in the NEO1 gene were identified in two ASD patients of Han Chinese descent (Siu et al., 2015).

Score Delta: Decreased from 4 to 3

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

Biallelic variants in the NEO1 gene were identified in two ASD patients of Han Chinese descent (Siu et al., 2015).

Reports Added
[New Scoring Scheme]
10/1/2015
icon
4

Increased from to 4

Description

Biallelic variants in the NEO1 gene were identified in two ASD patients of Han Chinese descent (Siu et al., 2015).

Krishnan Probability Score

Score 0.49571815192683

Ranking 2831/25841 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 0.99985462014738

Ranking 735/18225 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 0.94601465496199

Ranking 16700/18665 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 0.22876620063948

Ranking 3797/20870 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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