Human Gene Module / Chromosome 7 / CUX1

CUX1cut like homeobox 1

Score
2
Strong Candidate Criteria 2.1
Autism Reports / Total Reports
3 / 6
Rare Variants / Common Variants
10 / 0
Aliases
CUX1, CASP,  CDP,  CDP/Cut,  CDP1,  COY1,  CUTL1,  CUX,  Clox,  Cux/CDP,  GOLIM6,  Nbla10317,  p100,  p110,  p200,  p75
Associated Syndromes
-
Genetic Category
Rare Single Gene Mutation, Functional
Chromosome Band
7q22.1
Associated Disorders
ID, ASD
Relevance to Autism

A rare G>A mutation within the human accelerated region HAR426, for which existing ChIA-Pet data showed an interaction with the dosage-sensitive CUX1 promoter 200 kb distal, was homozygous in three individuals presenting with ASD and ID from two unrelated consanguineous families; functional analysis of this variant in luciferase reporter assays demonstrated that while HAR426 joined to the human CUX1 promoter showed strong enhancer activity (1.5-fold increase), the G>A variant boosted activity over 3-fold (Doan et al., 2016). In the same report, overexpression of CUX1 in cortical cultured neurons was shown to increase synaptic spine density and spine head area in an activity-dependent manner. CUX1 was found to bind to a transcriptional activator containing an ASD-associated intronic haplotype in the EN2 gene (Choi et al., 2012).

Molecular Function

The protein encoded by this gene is a member of the homeodomain family of DNA binding proteins. It may regulate gene expression, morphogenesis, and differentiation and it may also play a role in the cell cycle progession.

Reports related to CUX1 (6 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Support Cux1 and Cux2 regulate dendritic branching, spine morphology, and synapses of the upper layer neurons of the cortex. Cubelos B , et al. (2010) No -
2 Support Cut-like homeobox 1 and nuclear factor I/B mediate ENGRAILED2 autism spectrum disorder-associated haplotype function. Choi J , et al. (2011) No -
3 Support Synaptic, transcriptional and chromatin genes disrupted in autism. De Rubeis S , et al. (2014) Yes -
4 Primary Mutations in Human Accelerated Regions Disrupt Cognition and Social Behavior. Doan RN , et al. (2016) Yes -
5 Support Haploinsufficiency of CUX1 Causes Nonsyndromic Global Developmental Delay With Possible Catch-up Development. Mitter D , et al. (2018) No ID, ASD
6 Support Whole genome sequencing and variant discovery in the ASPIRE autism spectrum disorder cohort. Callaghan DB , et al. (2019) Yes -
Rare Variants   (10)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
- - copy_number_loss De novo NA - 30014507 Mitter D , et al. (2018)
c.61C>T p.Gln21Ter stop_gained De novo NA Simplex 30014507 Mitter D , et al. (2018)
G>A - intergenic_variant Familial Both parents Simplex 27667684 Doan RN , et al. (2016)
c.2617C>T p.Gln873Ter stop_gained De novo NA Simplex 30014507 Mitter D , et al. (2018)
c.902T>C p.Val301Ala missense_variant De novo NA - 25363760 De Rubeis S , et al. (2014)
G>A - intergenic_variant Familial Both parents Multiplex 27667684 Doan RN , et al. (2016)
c.115G>A p.Glu39Lys missense_variant Unknown - Simplex 31038196 Callaghan DB , et al. (2019)
c.3783_3784dup p.Leu1262ArgfsTer10 frameshift_variant De novo NA - 30014507 Mitter D , et al. (2018)
c.2398del p.Gln800ArgfsTer19 frameshift_variant De novo NA Simplex 30014507 Mitter D , et al. (2018)
c.3197dup p.Ala1067CysfsTer3 frameshift_variant Familial Maternal Multiplex 30014507 Mitter D , et al. (2018)
Common Variants  

No common variants reported.

SFARI Gene score
2

Strong Candidate

A rare G>A mutation within the human accelerated region HAR426, for which existing ChIA-Pet data showed an interaction with the dosage-sensitive CUX1 promoter 200 kb distal, was homozygous in three individuals presenting with ASD and ID from two unrelated consanguineous families; functional analysis of this variant in luciferase reporter assays demonstrated that while HAR426 joined to the human CUX1 promoter showed strong enhancer activity (1.5-fold increase), the G>A variant boosted activity over 3-fold (Doan et al., 2016). In the same report, overexpression of CUX1 in cortical cultured neurons was shown to increase synaptic spine density and spine head area in an activity-dependent manner. Platzer et al., 2018 reported nine individuals harboring null-allele variants in the CUX1 gene that presented with developmental delay (primarily speech delay), motor delay, and intellectual disability.

Score Delta: Score remained at 2

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.

10/1/2019
2
icon
2

Score remained at 2

New Scoring Scheme
Description

A rare G>A mutation within the human accelerated region HAR426, for which existing ChIA-Pet data showed an interaction with the dosage-sensitive CUX1 promoter 200 kb distal, was homozygous in three individuals presenting with ASD and ID from two unrelated consanguineous families; functional analysis of this variant in luciferase reporter assays demonstrated that while HAR426 joined to the human CUX1 promoter showed strong enhancer activity (1.5-fold increase), the G>A variant boosted activity over 3-fold (Doan et al., 2016). In the same report, overexpression of CUX1 in cortical cultured neurons was shown to increase synaptic spine density and spine head area in an activity-dependent manner. Platzer et al., 2018 reported nine individuals harboring null-allele variants in the CUX1 gene that presented with developmental delay (primarily speech delay), motor delay, and intellectual disability.

Reports Added
[New Scoring Scheme]
4/1/2019
2
icon
2

Score remained at 2

Description

A rare G>A mutation within the human accelerated region HAR426, for which existing ChIA-Pet data showed an interaction with the dosage-sensitive CUX1 promoter 200 kb distal, was homozygous in three individuals presenting with ASD and ID from two unrelated consanguineous families; functional analysis of this variant in luciferase reporter assays demonstrated that while HAR426 joined to the human CUX1 promoter showed strong enhancer activity (1.5-fold increase), the G>A variant boosted activity over 3-fold (Doan et al., 2016). In the same report, overexpression of CUX1 in cortical cultured neurons was shown to increase synaptic spine density and spine head area in an activity-dependent manner. Platzer et al., 2018 reported nine individuals harboring null-allele variants in the CUX1 gene that presented with developmental delay (primarily speech delay), motor delay, and intellectual disability.

10/1/2018
2
icon
2

Score remained at 2

Description

A rare G>A mutation within the human accelerated region HAR426, for which existing ChIA-Pet data showed an interaction with the dosage-sensitive CUX1 promoter 200 kb distal, was homozygous in three individuals presenting with ASD and ID from two unrelated consanguineous families; functional analysis of this variant in luciferase reporter assays demonstrated that while HAR426 joined to the human CUX1 promoter showed strong enhancer activity (1.5-fold increase), the G>A variant boosted activity over 3-fold (Doan et al., 2016). In the same report, overexpression of CUX1 in cortical cultured neurons was shown to increase synaptic spine density and spine head area in an activity-dependent manner. Platzer et al., 2018 reported nine individuals harboring null-allele variants in the CUX1 gene that presented with developmental delay (primarily speech delay), motor delay, and intellectual disability.

7/1/2018
2.4
icon
2

Score remained at 2

Description

A rare G>A mutation within the human accelerated region HAR426, for which existing ChIA-Pet data showed an interaction with the dosage-sensitive CUX1 promoter 200 kb distal, was homozygous in three individuals presenting with ASD and ID from two unrelated consanguineous families; functional analysis of this variant in luciferase reporter assays demonstrated that while HAR426 joined to the human CUX1 promoter showed strong enhancer activity (1.5-fold increase), the G>A variant boosted activity over 3-fold (Doan et al., 2016). In the same report, overexpression of CUX1 in cortical cultured neurons was shown to increase synaptic spine density and spine head area in an activity-dependent manner. Platzer et al., 2018 reported nine individuals harboring null-allele variants in the CUX1 gene that presented with developmental delay (primarily speech delay), motor delay, and intellectual disability.

4/1/2018
3
icon
2.4

Decreased from 3 to 2.4

Description

2

10/1/2016
icon
3

Increased from to 3

Description

A rare G>A mutation within the human accelerated region HAR426, for which existing ChIA-Pet data showed an interaction with the dosage-sensitive CUX1 promoter 200 kb distal, was homozygous in three individuals presenting with ASD and ID from two unrelated consanguineous families; functional analysis of this variant in luciferase reporter assays demonstrated that while HAR426 joined to the human CUX1 promoter showed strong enhancer activity (1.5-fold increase), the G>A variant boosted activity over 3-fold (Doan et al., 2016). In the same report, overexpression of CUX1 in cortical cultured neurons was shown to increase synaptic spine density and spine head area in an activity-dependent manner.

Krishnan Probability Score

Score 0.49198153073878

Ranking 4853/25841 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 0.99998887753519

Ranking 465/18225 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 0.94890537013454

Ranking 17874/18665 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 -0.42867633751742

Ranking 18624/20870 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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