Intellectual disability
Gene: CUX1

CUX1 (cut like homeobox 1)
EnsemblGeneIds (GRCh38): ENSG00000257923
EnsemblGeneIds (GRCh37): ENSG00000257923
OMIM: 116896, Gene2Phenotype
CUX1 is in 4 panels

2 reviews

Catherine Snow (Genomics England)

Comment on list classification: Expert review by Konstantinos Varvagiannis on CUX1. Platzer et al. (PMID: 30014507) reports on 9 individuals from 7 families with heterozygous null-allele variants in CUX1, 5 LoF variants (Gln21*, Gln800Argfs*19, Gln873*, Ala1067Cysfs*3, Leu1262Argfs*10) and 2 intragenic deletions (deletion of exons 9-24 in one subject and 3-24 in another).

All individuals displayed DD, mild/moderate ID was a feature in 5/8. Catch up was observed in 3/8 individuals who - despite a history of previous significant DD - displayed a normal age-related intelligence. For one individual information about ID was not available.

CUX1 is in OMIM with relevant phenotypes, but not in G2P.

Overall sufficient (>3) unrelated cases of DD (and ID) in patients with CUX1 variants, for inclusion on ID panel.
Created: 16 May 2019, 1:33 p.m.

Created: 16 May 2019, 1:33 p.m.

Panel version: Imported from Intellectual disability update May 2019 panel version 0.22

Konstantinos Varvagiannis (Other)

Green List (high evidence)

Heterozygous pathogenic variants in CUX1 cause Global developmental delay with or without impaired intellectual development (MIM 618330).

Platzer et al. (2018 - PMID: 30014507) report on 9 individuals from 7 families with heterozygous null-allele variants in CUX1.

All individuals displayed DD (speech delay 9/9 - motor delay 7/9 - hypotonia 3/7 for whom this information was available). Mild/moderate ID was a feature in 5/8. Catch up was observed in 3/8 individuals who - despite a history of previous significant DD - displayed a normal age-related intelligence. For 1/9 individual (Decipher 338131) information on eventual ID was unavailable. Overall the phenotype was compatible with non-syndromic DD with possible ID.

CUX1 encodes Cut homebox-1 transcription factor.

5 LoF variants (Gln21*, Gln800Argfs*19, Gln873*, Ala1067Cysfs*3, Leu1262Argfs*10) and 2 intragenic deletions (deletion of exons 9-24 in one subject and 3-24 in another) are reported.

In 6/9 individuals the variant (SNV/CNV) had occurred as a de novo event. Mosaic de novo intragenic deletion was reported for the subject from Decipher. In one family 2 sibs with mild ID had inherited a LoF variant from their affected mother with moderate ID (origin of the variant unknown in her case).

Leu1262Argfs*10 lies in the penultimate exon (NM_001202543.1 used as ref.) and is presumed to escape NMD.

Expression studies (or functional studies) are not performed for any of the variants.

As Gln800Argfs*19, found in one subject with mild ID in the present study, has been reported once in gnomAD, and given the presence of 12 individuals overall with LoF variants in the specific database, plausible explanations are discussed (among others : mild phenotype, incomplete penetrance, somatic mosaicism, exclusion of individuals with severe early-onset disorders in gnomAD, etc).

Given the reported variants, the probability of LoF intolerance (pLI:1.00), and the haploinsufficiency score (% HI) of 7.19, haploinsufficiency is thought to be the underlying mechanism. CUX1 however appears to be intolerant also to missense SNVs (z-score : 5.05).

Mouse models suggest a role for Cux1 in brain development and signaling. As the authors note, Cux1 (similar to its paralog, Cux2) is selectively expressed in layer II to IV cortical neurons. In Cux1-deficient mice, dendrites display a simpler morphology with decrease in dendritic length and number of branches (PMIDs cited: 20510857, 25059644). (MGI db for Cux1 - http://www.informatics.jax.org/marker/MGI:88568 : "Homozygotes for a targeted null mutation exhibit delayed lung development and neonatal mortality. Survivors show growth retardation and hair defects. Homozygotes for a partially deleted protein have curly hair, and females tend to lose their litters").

Finally, heterozygous mutations in CUX2, encoding cut-like homeobox-2 transcription factor, cause Epileptic encephalopathy, early infantile, 67 (MIM 618141 - in all cases reported to date due to a recurrent missense variant. Gene rated green in the current panel).
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CUX1 is not associated with any phenotype in G2P.
This gene is included in panels for ID offered by diagnostic laboratories (incl. Radboudumc).
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As a result, CUX1 can be considered for inclusion in the ID panel as green (or amber).
Sources: Literature, Radboud University Medical Center, Nijmegen
Created: 17 Feb 2019, 8:06 p.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Phenotypes
Global developmental delay with or without impaired intellectual development, 618330

Publications

Variants in this GENE are reported as part of current diagnostic practice

Created: 17 Feb 2019, 8:06 p.m.

Panel version: 2.654

Details

Mode of Inheritance

MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Sources

Expert Review
Expert Review Green
Expert Review

Phenotypes

Global developmental delay with or without impaired intellectual development, 618330

OMIM

116896

Clinvar variants

Variants in CUX1

Penetrance

unknown

Publications

Panels with this gene

History Filter Activity

25 Jul 2019, Gel status: 3

Added New Source, Added New Source, Set Phenotypes, Set publications, Status Update

Catherine Snow (Genomics England)

Source Expert Review Green was added to CUX1. Source Expert Review was added to CUX1. Added phenotypes Global developmental delay with or without impaired intellectual development, 618330 for gene: CUX1 Publications for gene CUX1 were changed from 30014507; 20510857; 25059644 to 25059644; 20510857; 30014507 Rating Changed from No List (delete) to Green List (high evidence)

17 Feb 2019, Gel status: 0

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes, Set penetrance

Konstantinos Varvagiannis (Other)

gene: CUX1 was added gene: CUX1 was added to Intellectual disability. Sources: Literature,Radboud University Medical Center, Nijmegen Mode of inheritance for gene: CUX1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: CUX1 were set to 30014507; 20510857; 25059644 Phenotypes for gene: CUX1 were set to Global developmental delay with or without impaired intellectual development, 618330 Penetrance for gene: CUX1 were set to unknown Review for gene: CUX1 was set to GREEN gene: CUX1 was marked as current diagnostic

Intellectual disability Gene: CUX1