U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from MedGen

    • Showing Current items.

    RUNX2 RUNX family transcription factor 2 [ Homo sapiens (human) ]

    Gene ID: 860, updated on 22-Feb-2024

    Summary

    Official Symbol
    RUNX2provided by HGNC
    Official Full Name
    RUNX family transcription factor 2provided by HGNC
    Primary source
    HGNC:HGNC:10472
    See related
    Ensembl:ENSG00000124813 MIM:600211; AllianceGenome:HGNC:10472
    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
    CCD; AML3; CCD1; CLCD; OSF2; CBFA1; OSF-2; PEA2aA; PEBP2aA; CBF-alpha-1
    Summary
    This gene is a member of the RUNX family of transcription factors and encodes a nuclear protein with an Runt DNA-binding domain. This protein is essential for osteoblastic differentiation and skeletal morphogenesis and acts as a scaffold for nucleic acids and regulatory factors involved in skeletal gene expression. The protein can bind DNA both as a monomer or, with more affinity, as a subunit of a heterodimeric complex. Two regions of potential trinucleotide repeat expansions are present in the N-terminal region of the encoded protein, and these and other mutations in this gene have been associated with the bone development disorder cleidocranial dysplasia (CCD). Transcript variants that encode different protein isoforms result from the use of alternate promoters as well as alternate splicing. [provided by RefSeq, Jul 2016]
    Expression
    Broad expression in bone marrow (RPKM 1.9), appendix (RPKM 1.3) and 23 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See RUNX2 in Genome Data Viewer
    Location:
    6p21.1
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (45328330..45551082)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (45163134..45385899)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (45296067..45518819)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene SPT3 homolog, SAGA and STAGA complex component Neighboring gene poly(rC) binding protein 2 pseudogene Neighboring gene MPRA-validated peak5821 silencer Neighboring gene microRNA 586 Neighboring gene MPRA-validated peak5822 silencer Neighboring gene RUNX2 P1 promoter region Neighboring gene MPRA-validated peak5825 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:45345603-45346146 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17265 Neighboring gene uncharacterized LOC124901324 Neighboring gene runt related transcription factor 2 polyalanine expansion region Neighboring gene NANOG hESC enhancer GRCh37_chr6:45413685-45414186 Neighboring gene Sharpr-MPRA regulatory region 695 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:45487956-45488510 Neighboring gene Sharpr-MPRA regulatory region 12811 Neighboring gene RUNX2 antisense RNA 1 Neighboring gene U6 spliceosomal RNA

    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

    EBI GWAS Catalog

    Description
    Genome-wide association study of periodontal pathogen colonization.
    EBI GWAS Catalog
    Many sequence variants affecting diversity of adult human height.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env In human osteoblast (hOB) cell lines, HIV-1 Gag and gp120 reduce RUNX-2 and PPAR-gamma mRNA expression and activity PubMed
    Nef nef HIV-1 Nef downregulates the expression of RUNX2 protein in human mesenchymal stem cells PubMed
    Pr55(Gag) gag In human osteoblast (hOB) cell lines, HIV-1 Gag and gp120 reduce RUNX-2 and PPAR-gamma mRNA expression and activity PubMed
    Tat tat HIV-1 Tat downregulates the expression of RUNX2 protein in human mesenchymal stem cells PubMed
    Vif vif The binding of HIV-1 Vif to CBF-beta is mutually exclusive of endogenous RUNX transcriptional factors in cells. Vif inhibits transcription of a RUNX1 reporter gene by competition with CBF-beta PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC120022, MGC120023

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in BMP signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in SMAD protein signal transduction IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in T cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in bone mineralization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cell maturation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chondrocyte development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chondrocyte differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in embryonic cranial skeleton morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic forelimb morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in endochondral ossification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in epithelial cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in hemopoiesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in ligamentous ossification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of smoothened signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neuron differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in odontogenesis of dentin-containing tooth IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in ossification IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in ossification TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in osteoblast development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in osteoblast differentiation IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in osteoblast differentiation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in osteoblast differentiation TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in osteoblast fate commitment IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of chondrocyte differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of epithelial cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of osteoblast differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of stem cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    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
     
    involved_in regulation of cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of fibroblast growth factor receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of odontogenesis of dentin-containing tooth IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of ossification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in response to sodium phosphate IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in smoothened signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in stem cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in stem cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    part_of chromatin ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of transcription regulator complex IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    runt-related transcription factor 2
    Names
    PEA2-alpha A
    PEBP2-alpha A
    SL3-3 enhancer factor 1 alpha A subunit
    SL3/AKV core-binding factor alpha A subunit
    acute myeloid leukemia 3 protein
    core-binding factor, runt domain, alpha subunit 1
    oncogene AML-3
    osteoblast-specific transcription factor 2
    polyomavirus enhancer-binding protein 2 alpha A subunit
    runt related transcription factor 2

    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_008020.2 RefSeqGene

      Range
      5014..227766
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001015051.4NP_001015051.3  runt-related transcription factor 2 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (b, also known as OSF2/CBF1b) is shorter, compared to isoform a.
      Source sequence(s)
      AL096865, AL161907, AL358135
      Consensus CDS
      CCDS43468.2
      UniProtKB/Swiss-Prot
      Q13950
      Related
      ENSP00000360486.4, ENST00000371432.7
      Conserved Domains (3) summary
      pfam00853
      Location:109230
      Runt; Runt domain
      pfam08504
      Location:408499
      RunxI; Runx inhibition domain
      cl25496
      Location:266459
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    2. NM_001024630.4NP_001019801.3  runt-related transcription factor 2 isoform a

      See identical proteins and their annotated locations for NP_001019801.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a, also known as OSF2/CBFA1a).
      Source sequence(s)
      AL096865, AL161907, AL358135
      Consensus CDS
      CCDS43467.2
      UniProtKB/Swiss-Prot
      O14614, O14615, O95181, Q13950
      Related
      ENSP00000495497.1, ENST00000647337.2
      Conserved Domains (3) summary
      pfam00853
      Location:109230
      Runt; Runt domain
      pfam08504
      Location:430521
      RunxI; Runx inhibition domain
      cl25496
      Location:266481
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    3. NM_001278478.2NP_001265407.1  runt-related transcription factor 2 isoform d

      See identical proteins and their annotated locations for NP_001265407.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) contains an alternate 5'-most exon, lacks an in-frame exon in the 3' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (d) has a distinct and shorter N-terminus, compared to isoform a.
      Source sequence(s)
      AL096865, AL161907, AL358135
      Consensus CDS
      CCDS64443.1
      UniProtKB/TrEMBL
      A0A0D9SEN7
      Related
      ENSP00000485863.1, ENST00000625924.1
      Conserved Domains (3) summary
      pfam05109
      Location:252445
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      pfam00853
      Location:91217
      Runt; Runt domain
      pfam08504
      Location:394485
      RunxI; Runx inhibition domain
    4. NM_001369405.1NP_001356334.1  runt-related transcription factor 2 isoform e

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) contains an alternate 5'-most exon and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (e) has a distinct and shorter N-terminus, compared to isoform a.
      Source sequence(s)
      AL096865, AL161907, AL358135
      Consensus CDS
      CCDS4913.1
      Related
      ENSP00000352514.5, ENST00000359524.7
      Conserved Domains (3) summary
      pfam05109
      Location:252467
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      pfam00853
      Location:91217
      Runt; Runt domain
      pfam08504
      Location:416507
      RunxI; Runx inhibition domain

    RNA

    1. NR_103532.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses an alternate splice site in the 5'-terminal exon, lacks several exons, and contains an alternate 3'-terminal exon, compared to variant 1. This variant is represented as non-coding because it lacks a significant portion of the coding region and does not encode a supported protein.
      Source sequence(s)
      AL096865, BX108677
      Related
      ENST00000483243.5
    2. NR_103533.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) lacks several exons, and contains an alternate 3'-terminal exon, compared to variant 1. This variant is represented as non-coding because it lacks a significant portion of the coding region and does not encode a supported protein.
      Source sequence(s)
      AL096865, AW469546, BX108677

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      45328330..45551082
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      45163134..45385899
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)