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CUX2 cut like homeobox 2 [ Homo sapiens (human) ]

Gene ID: 23316, updated on 5-Mar-2024

Summary

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Official Symbol
CUX2provided by HGNC
Official Full Name
cut like homeobox 2provided by HGNC
Primary source
HGNC:HGNC:19347
See related
Ensembl:ENSG00000111249 MIM:610648; AllianceGenome:HGNC:19347
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CDP2; CUTL2; DEE67; EIEE67
Summary
This gene encodes a protein which contains three CUT domains and a homeodomain; both domains are DNA-binding motifs. A similar gene, whose gene product possesses different DNA-binding activities, is located on chromosome on chromosome 7. Two pseudogenes of this gene have been identified on chromosomes 10 and 4. [provided by RefSeq, Jan 2013]
Expression
Biased expression in prostate (RPKM 4.9), liver (RPKM 4.6) and 3 other tissues See more
Orthologs
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Genomic context

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Location:
12q24.11-q24.12
Exon count:
26
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (111034165..111350554)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (111013350..111331050)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (111471969..111788358)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:111394805-111396004 Neighboring gene long intergenic non-protein coding RNA 1404 Neighboring gene uncharacterized LOC105369981 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:111478778-111479544 Neighboring gene VISTA enhancer hs611 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:111498362-111498864 Neighboring gene NANOG hESC enhancer GRCh37_chr12:111510029-111510544 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7029 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7030 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:111537905-111538524 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:111542473-111542974 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:111598487-111599098 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:111620445-111620945 Neighboring gene uncharacterized LOC124903018 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:111631064-111631574 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:111655517-111656018 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:111656019-111656518 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:111686753-111687420 Neighboring gene uncharacterized LOC105369983 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:111730689-111731190 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:111733063-111733233 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:111736695-111737688 Neighboring gene microRNA 6760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:111791286-111791786 Neighboring gene RNA, 5S ribosomal pseudogene 373 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:111799560-111800216 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4865 Neighboring gene long intergenic non-protein coding RNA 2356 Neighboring gene PH domain containing endocytic trafficking adaptor 1 Neighboring gene heat shock protein family A (Hsp70) member 8 pseudogene 14

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. A recurrent de novo CUX2 missense variant associated with intellectual disability, seizures, and autism spectrum disorder. Barington M, et al. Eur J Hum Genet, 2018 Sep. PMID 29795476, Free PMC Article
  2. The epilepsy phenotypic spectrum associated with a recurrent CUX2 variant. Chatron N, et al. Ann Neurol, 2018 May. PMID 29630738, Free PMC Article
  3. CUX2, a potential regulator of NCAM expression: genomic characterization and analysis as a positional candidate susceptibility gene for bipolar disorder. Jacobsen NJ, et al. Am J Med Genet, 2001 Apr 8. PMID 11353453
  4. Linkage disequilibrium mapping of bipolar affective disorder at 12q23-q24 provides evidence for association at CUX2 and FLJ32356. Glaser B, et al. Am J Med Genet B Neuropsychiatr Genet, 2005 Jan 5. PMID 15389760
  5. CUX2/KDM5B/SOX17 Axis Affects the Occurrence and Development of Breast Cancer. Li L, et al. Endocrinology, 2022 Sep 1. PMID 35881915

See all (27) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CUX2/KDM5B/SOX17 Axis Affects the Occurrence and Development of Breast Cancer.
    Title: CUX2/KDM5B/SOX17 Axis Affects the Occurrence and Development of Breast Cancer.
  2. CUX2, BRAP and ALDH2 are associated with metabolic traits in people with excessive alcohol consumption.
    Title: CUX2, BRAP and ALDH2 are associated with metabolic traits in people with excessive alcohol consumption.
  3. this is the first study to explore and validate the relationships between seven SNPs in the FAM65B, AGBL4, and CUX2 genes and ATDH in a Chinese population. On the basis of this case-control study, SNP rs10946737 in FAM65B may be associated with susceptibility to ATDH in Chinese Han anti-TB treatment patients.
    Title: Association of FAM65B, AGBL4, and CUX2 genetic polymorphisms with susceptibility to antituberculosis drug-induced hepatotoxicity: validation study in a Chinese Han population.
  4. Significant allelic and genotypic associations were identified between NEURL variant rs6584555 and GJA1 variant rs13216675 and Atrial fibrillation (AF). Significant genotypic association was found between CUX2 SNP rs6490029 and AF
    Title: Genomic Variants in NEURL, GJA1 and CUX2 Significantly Increase Genetic Susceptibility to Atrial Fibrillation.
  5. Patients with CUX2 p.Glu590Lys display a distinctive phenotypic spectrum, which is predominantly generalized epilepsy
    Title: The epilepsy phenotypic spectrum associated with a recurrent CUX2 variant.
  6. De novo variant c.1768G>A; p.(Glu590Lys) in CUX2 was identifies in a patient with intellectual disability, seizures, and autism spectrum disorder.
    Title: A recurrent de novo CUX2 missense variant associated with intellectual disability, seizures, and autism spectrum disorder.
  7. results suggest that the persistent expression of CUX2 in postmitotic neurons contributes to the maintenance of genome integrity through its stimulation of oxidative DNA damage repair.
    Title: CUX2 protein functions as an accessory factor in the repair of oxidative DNA damage.
  8. Observational study of gene-disease association. (HuGE Navigator)
    Title: Maternal genes and facial clefts in offspring: a comprehensive search for genetic associations in two population-based cleft studies from Scandinavia.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Developmental and epileptic encephalopathy, 67
MedGen: C4748341 OMIM: 618141 GeneReviews: Not available
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EBI GWAS Catalog

Description
1000 Genomes-based imputation identifies novel and refined associations for the Wellcome Trust Case Control Consortium phase 1 Data.
EBI GWAS Catalog
A genome-wide association study of a coronary artery disease risk variant.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
enables DNA-binding transcription repressor activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in cellular response to organic substance IEA
Inferred from Electronic Annotation
more info
  
involved_in cognition IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of dendrite morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of dendritic spine morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of excitatory postsynaptic potential ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of gene expression ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of synapse assembly ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in short-term memory ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
part_of chromatin ISA
Inferred from Sequence Alignment
more info
  
located_in extracellular exosome HDA PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
homeobox protein cut-like 2
Names
homeobox protein cux-2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_023039.2 RefSeqGene

    Range
    5142..321531
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001370598.1 → NP_001357527.1  homeobox protein cut-like 2 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC002352, AC002978, AC002979, AC005805
    Conserved Domains (3) summary
    TIGR02168
    Location:111 → 308
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type
    pfam02376
    Location:981 → 1057
    CUT; CUT domain
    pfam00046
    Location:1109 → 1163
    Homeobox; Homeobox domain

  2. NM_015267.4 → NP_056082.2  homeobox protein cut-like 2 isoform 1

    See identical proteins and their annotated locations for NP_056082.2

    Status: REVIEWED

    Source sequence(s)
    AC005805, BC151245
    Consensus CDS
    CCDS41837.1
    UniProtKB/Swiss-Prot
    A7E2Y4, O14529
    Related
    ENSP00000261726.6, ENST00000261726.11
    Conserved Domains (3) summary
    PHA03418
    Location:1218 → 1378
    PHA03418; hypothetical E4 protein; Provisional
    pfam00046
    Location:1171 → 1224
    Homeobox; Homeobox domain
    pfam02376
    Location:1043 → 1119
    CUT; CUT domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    111034165..111350554
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017019081.2 → XP_016874570.1  homeobox protein cut-like 2 isoform X2

    Conserved Domains (3) summary
    TIGR02168
    Location:111 → 308
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type
    pfam02376
    Location:981 → 1057
    CUT; CUT domain
    pfam00046
    Location:1109 → 1163
    Homeobox; Homeobox domain

  2. XM_011538069.3 → XP_011536371.1  homeobox protein cut-like 2 isoform X2

    See identical proteins and their annotated locations for XP_011536371.1

    Conserved Domains (3) summary
    TIGR02168
    Location:111 → 308
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type
    pfam02376
    Location:981 → 1057
    CUT; CUT domain
    pfam00046
    Location:1109 → 1163
    Homeobox; Homeobox domain

  3. XM_017019080.2 → XP_016874569.1  homeobox protein cut-like 2 isoform X2

    Conserved Domains (3) summary
    TIGR02168
    Location:111 → 308
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type
    pfam02376
    Location:981 → 1057
    CUT; CUT domain
    pfam00046
    Location:1109 → 1163
    Homeobox; Homeobox domain

  4. XM_011538070.3 → XP_011536372.1  homeobox protein cut-like 2 isoform X2

    See identical proteins and their annotated locations for XP_011536372.1

    Conserved Domains (3) summary
    TIGR02168
    Location:111 → 308
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type
    pfam02376
    Location:981 → 1057
    CUT; CUT domain
    pfam00046
    Location:1109 → 1163
    Homeobox; Homeobox domain

  5. XM_011538063.4 → XP_011536365.2  homeobox protein cut-like 2 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    111013350..111331050
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054371554.1 → XP_054227529.1  homeobox protein cut-like 2 isoform X2

  2. XM_054371552.1 → XP_054227527.1  homeobox protein cut-like 2 isoform X2

  3. XM_054371553.1 → XP_054227528.1  homeobox protein cut-like 2 isoform X2

  4. XM_054371551.1 → XP_054227526.1  homeobox protein cut-like 2 isoform X2

  5. XM_054371550.1 → XP_054227525.1  homeobox protein cut-like 2 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O14529.4 GenPept UniProtKB/Swiss-Prot:O14529

Gene LinkOut

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