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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
    mouse all
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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

    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
    		Compare labs

    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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