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    NKX2-5 NK2 homeobox 5 [ Homo sapiens (human) ]

    Gene ID: 1482, updated on 8-Jul-2021

    Summary

    Official Symbol
    NKX2-5provided by HGNC
    Official Full Name
    NK2 homeobox 5provided by HGNC
    Primary source
    HGNC:HGNC:2488
    See related
    Ensembl:ENSG00000183072 MIM:600584
    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
    CSX; CSX1; VSD3; CHNG5; HLHS2; NKX2E; NKX2.5; NKX4-1
    Summary
    This gene encodes a homeobox-containing transcription factor. This transcription factor functions in heart formation and development. Mutations in this gene cause atrial septal defect with atrioventricular conduction defect, and also tetralogy of Fallot, which are both heart malformation diseases. Mutations in this gene can also cause congenital hypothyroidism non-goitrous type 5, a non-autoimmune condition. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
    Expression
    Restricted expression toward heart (RPKM 9.4) See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See NKX2-5 in Genome Data Viewer
    Location:
    5q35.1
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (173232109..173235321, complement)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (172659112..172662209, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene BCL2 interacting protein 1 Neighboring gene ribosomal protein L7a pseudogene 33 Neighboring gene VISTA enhancer hs2185 Neighboring gene uncharacterized LOC105377731 Neighboring gene RNA, 5S ribosomal pseudogene 200

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Atrial septal defect 7 with or without atrioventricular conduction defects
    MedGen: C3276096 OMIM: 108900 GeneReviews: Not available
    Compare labs
    Common variants near MBNL1 and NKX2-5 are associated with infantile hypertrophic pyloric stenosis.
    GeneReviews: Not available
    Conotruncal heart malformations
    MedGen: C1857586 OMIM: 217095 GeneReviews: Not available
    Compare labs
    Genome-wide association study of PR interval.
    GeneReviews: Not available
    Hypoplastic left heart syndrome 2
    MedGen: C3280795 OMIM: 614435 GeneReviews: Not available
    Compare labs
    Hypothyroidism, congenital, nongoitrous, 5
    MedGen: C2673630 OMIM: 225250 GeneReviews: Not available
    Compare labs
    Identification of heart rate-associated loci and their effects on cardiac conduction and rhythm disorders.
    GeneReviews: Not available
    Tetralogy of Fallot
    MedGen: C0039685 OMIM: 187500 GeneReviews: Not available
    Compare labs
    Ventricular septal defect 3
    MedGen: C3280785 OMIM: 614432 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2020-07-22)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2020-07-22)

    ClinGen Genome Curation PagePubMed

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ52202, FLJ97166, FLJ97195, FLJ97197, FLJ99536

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription activator activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    contributes_to DNA-binding transcription factor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription factor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription factor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
     
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    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 
    enables transcription cis-regulatory region binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in adult heart development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in aortic valve morphogenesis TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in atrial cardiac muscle cell development ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in atrial cardiac muscle tissue development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in atrial septum morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in atrioventricular node development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within bundle of His development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within cardiac conduction system development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cardiac conduction system development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cardiac muscle cell development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cardiac muscle cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in cardiac muscle contraction IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cardiac muscle tissue morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cardiac muscle tissue morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in embryonic heart tube development ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in heart looping ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in heart morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in hemopoiesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in negative regulation of apoptotic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in negative regulation of canonical Wnt signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of cardiac muscle cell apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of myotube differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in negative regulation of transcription, DNA-templated ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in outflow tract septum morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in pharyngeal system development ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in positive regulation of cardioblast differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in positive regulation of cell population proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in positive regulation of heart contraction ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of neuron differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of sodium ion transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in positive regulation of transcription initiation from RNA polymerase II promoter ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in positive regulation of transcription via serum response element binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in positive regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription, DNA-templated ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in regulation of cardiac conduction ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in regulation of cardiac muscle contraction ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in right ventricular cardiac muscle tissue morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in septum secundum development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in spleen development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in spleen development ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in thyroid gland development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in vasculogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in ventricular cardiac muscle cell development ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in ventricular septum morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of RNA polymerase II transcription regulator complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of protein-DNA complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of transcription regulator complex IC
    Inferred by Curator
    more info
    PubMed 

    General protein information

    Preferred Names
    homeobox protein Nkx-2.5
    Names
    NK2 transcription factor related, locus 5
    NKX 2-5
    cardiac-specific homeobox 1
    homeobox protein CSX
    homeobox protein NK-2 homolog E
    homeobox protein NKX 2-5
    tinman homolog
    tinman paralog

    NCBI Reference Sequences (RefSeq)

    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

    1. NG_013340.1 RefSeqGene

      Range
      5107..8204
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_671

    mRNA and Protein(s)

    1. NM_001166175.2NP_001159647.1  homeobox protein Nkx-2.5 isoform 2

      See identical proteins and their annotated locations for NP_001159647.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AI609745, AK290615, AK307247
      Consensus CDS
      CCDS54950.1
      UniProtKB/Swiss-Prot
      P52952
      UniProtKB/TrEMBL
      A0A0S2Z3K2
      Related
      ENSP00000395378.2, ENST00000424406.2
    2. NM_001166176.2NP_001159648.1  homeobox protein Nkx-2.5 isoform 3

      See identical proteins and their annotated locations for NP_001159648.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (3) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AI609745, AK290615, AK297844
      Consensus CDS
      CCDS54949.1
      UniProtKB/Swiss-Prot
      P52952
      Related
      ENSP00000427906.1, ENST00000521848.1
    3. NM_004387.4NP_004378.1  homeobox protein Nkx-2.5 isoform 1

      See identical proteins and their annotated locations for NP_004378.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the shortest transcript but encodes the longest isoform (1).
      Source sequence(s)
      BC025711, DA559427
      Consensus CDS
      CCDS4387.1
      UniProtKB/Swiss-Prot
      P52952
      UniProtKB/TrEMBL
      A0A0S2Z383
      Related
      ENSP00000327758.4, ENST00000329198.5
      Conserved Domains (1) summary
      pfam00046
      Location:145194
      Homeobox; Homeobox domain

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

      Range
      173232109..173235321 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017009071.2XP_016864560.1  homeobox protein Nkx-2.5 isoform X1

      UniProtKB/TrEMBL
      E5RH49
      Related
      ENSP00000429905.1, ENST00000517440.1
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