GeneBe

CUX2

cut like homeobox 2, the group of MicroRNA protein coding host genes|CUT class homeoboxes and pseudogenes

Basic information

Region (hg38): 12:111034165-111350554

Previous symbols: [ "CUTL2" ]

Links

ENSG00000111249 ∙ NCBI:23316 ∙ OMIM:610648 ∙ HGNC:19347 ∙ Uniprot:O14529 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • developmental and epileptic encephalopathy, 67 (Strong), mode of inheritance: AD
  • Lennox-Gastaut syndrome (Supportive), mode of inheritance: AD
  • developmental and epileptic encephalopathy, 67 (Strong), mode of inheritance: AD
  • developmental and epileptic encephalopathy, 67 (Strong), mode of inheritance: AD
  • genetic developmental and epileptic encephalopathy (Moderate), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Developmental and epileptic encephalopathy 67ADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingNeurologic29630738; 29795476

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CUX2 gene.

  • not_provided (172 variants)
  • Inborn_genetic_diseases (171 variants)
  • Developmental_and_epileptic_encephalopathy,_67 (65 variants)
  • CUX2-related_disorder (57 variants)
  • not_specified (16 variants)
  • Intellectual_disability (6 variants)
  • See_cases (2 variants)
  • Russell-Silver_syndrome (1 variants)
  • Cone-rod_dystrophy (1 variants)
  • Bilateral_tonic-clonic_seizure (1 variants)
  • Hypertrophic_cardiomyopathy (1 variants)
  • Autism_spectrum_disorder (1 variants)
  • Developmental_and_epileptic_encephalopathy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CUX2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015267.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
56
clinvar
5
clinvar
 62
missense
1
clinvar
2
clinvar
243
clinvar
68
clinvar
5
clinvar
 319
nonsense
3
clinvar
 3
start loss
0
frameshift
1
clinvar
6
clinvar
 7
splice donor/acceptor (+/-2bp)
4
clinvar
 4
Total 1 3 257 124 10

Highest pathogenic variant AF is 6.2468e-7

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CUX2protein_codingprotein_codingENST00000261726 22316531
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.000.00000193124785091247940.0000361
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.186158810.6980.00005759418
Missense in Polyphen161324.110.496753372
Synonymous1.623654070.8980.00002923110
Loss of Function6.67663.20.09490.00000305753

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002010.000129
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00004790.0000464
European (Non-Finnish)0.00004610.0000441
Middle Eastern0.000.00
South Asian0.000.00
Other0.0001650.000165

dbNSFP

Source: dbNSFP

Function
FUNCTION: May be a transcription factor involved in neural specification. Binds to DNA in a sequence-specific manner (By similarity). {ECO:0000250}.;

Recessive Scores

pRec
0.118

Intolerance Scores

loftool
0.280
rvis_EVS
-2.08
rvis_percentile_EVS
1.6

Haploinsufficiency Scores

pHI
0.247
hipred
Y
hipred_score
0.711
ghis
0.532

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.227

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Cux2
Phenotype
embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); cellular phenotype;

Gene ontology

Biological process
negative regulation of transcription by RNA polymerase II;short-term memory;positive regulation of gene expression;Golgi vesicle transport;positive regulation of dendrite morphogenesis;cognition;positive regulation of synapse assembly;positive regulation of dendritic spine morphogenesis;cellular response to organic substance;positive regulation of excitatory postsynaptic potential
Cellular component
Golgi membrane;nucleus;extracellular exosome
Molecular function
RNA polymerase II regulatory region sequence-specific DNA binding;RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;sequence-specific DNA binding