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

Summary

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
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 12q24.11-q24.12

Exon count:: 26

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (111034165..111350554)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (111013350..111331050)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (111471969..111788358)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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

Go to the top of the page Help

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 EBI GWAS CatalogPubMed
A genome-wide association study of a coronary artery disease risk variant. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

SGC32083 (e-PCR)
- UniSTS:68614

SHGC-145997 (e-PCR)
- UniSTS:182567

RH65418 (e-PCR)
- UniSTS:24115

A004C03 (e-PCR)
- UniSTS:3698

RH48630 (e-PCR)
- UniSTS:61079

D12S1817 (e-PCR)
- UniSTS:75210

RH15677 (e-PCR)
- UniSTS:16113

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 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
located_in chromatin	ISA Inferred from Sequence Alignment more info
located_in extracellular exosome	HDA more info	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

Go to the top of the page Help

Preferred Names: homeobox protein cut-like 2

Names: homeobox protein cux-2

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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

NG_023039.2 RefSeqGene

Range

5142..321531

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000012.12 Reference GRCh38.p14 Primary Assembly

Range

111034165..111350554

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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