CUX1cut like homeobox 1
Autism Reports / Total Reports
7 / 11Rare Variants / Common Variants
19 / 0Aliases
CUX1, CASP, CDP, CDP/Cut, CDP1, COY1, CUTL1, CUX, Clox, Cux/CDP, GOLIM6, Nbla10317, p100, p110, p200, p75Associated Syndromes
-Chromosome Band
7q22.1Associated Disorders
ID, ASDRelevance 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.
External Links
SFARI Genomic Platforms
Reports related to CUX1 (11 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 | - |
7 | Support | - | Li D et al. (2022) | Yes | - |
8 | Support | - | Woodbury-Smith M et al. (2022) | Yes | - |
9 | Support | - | Suzuki T et al. (2022) | No | ASD, DD, ID |
10 | Support | - | Zhou X et al. (2022) | Yes | - |
11 | Support | - | Chan AJS et al. (2022) | Yes | - |
Rare Variants (19)
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.1943G>T | p.Ser648Ile | missense_variant | Unknown | - | - | 34968013 | Li D et al. (2022) | |
c.3161C>T | p.Ser1054Leu | missense_variant | Unknown | - | - | 35581205 | Suzuki T et al. (2022) | |
c.3815G>A | p.Arg1272Gln | missense_variant | Unknown | - | - | 35581205 | Suzuki T et al. (2022) | |
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) | |
c.2839G>A | p.Glu947Lys | missense_variant | De novo | NA | Simplex | 35982159 | Zhou X et al. (2022) | |
G>A | - | intergenic_variant | Familial | Both parents | Multiplex | 27667684 | Doan RN , et al. (2016) | |
c.3986C>G | p.Ala1329Gly | missense_variant | De novo | NA | Simplex | 35982159 | Zhou X et al. (2022) | |
c.3281C>T | p.Ala1094Val | missense_variant | Unknown | - | Simplex | 35581205 | Suzuki T et al. (2022) | |
c.4172C>T | p.Thr1391Ile | missense_variant | Unknown | - | Simplex | 35581205 | Suzuki T et al. (2022) | |
c.115G>A | p.Glu39Lys | missense_variant | Unknown | - | Simplex | 31038196 | Callaghan DB , et al. (2019) | |
c.3081C>T | p.Pro1027%3D | synonymous_variant | Unknown | - | - | 35205252 | Woodbury-Smith M et al. (2022) | |
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.1702del | p.Ala568ProfsTer8 | frameshift_variant | Familial | Paternal | Simplex | 36309498 | Chan AJS et al. (2022) | |
c.3197dup | p.Ala1067CysfsTer3 | frameshift_variant | Familial | Maternal | Multiplex | 30014507 | Mitter D , et al. (2018) |
Common Variants
No common variants reported.
SFARI Gene score
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
criteria met
See SFARI Gene'scoring criteriaWe 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

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

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

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

Decreased from 3 to 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.
10/1/2016

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
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ExAC Score
Score 0.99998887753519
Ranking 465/18225 scored genes
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Sanders TADA Score
Score 0.94890537013454
Ranking 17874/18665 scored genes
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Zhang D Score
Score -0.42867633751742
Ranking 18624/20870 scored genes
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