U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from MedGen

    • Showing Current items.

    RUNX1 RUNX family transcription factor 1 [ Homo sapiens (human) ]

    Gene ID: 861, updated on 4-Mar-2024

    Summary

    Official Symbol
    RUNX1provided by HGNC
    Official Full Name
    RUNX family transcription factor 1provided by HGNC
    Primary source
    HGNC:HGNC:10471
    See related
    Ensembl:ENSG00000159216 MIM:151385; AllianceGenome:HGNC:10471
    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
    AML1; CBFA2; EVI-1; AMLCR1; PEBP2aB; CBF2alpha; AML1-EVI-1; PEBP2alpha
    Summary
    Core binding factor (CBF) is a heterodimeric transcription factor that binds to the core element of many enhancers and promoters. The protein encoded by this gene represents the alpha subunit of CBF and is thought to be involved in the development of normal hematopoiesis. Chromosomal translocations involving this gene are well-documented and have been associated with several types of leukemia. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in appendix (RPKM 7.9), bone marrow (RPKM 7.3) and 24 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See RUNX1 in Genome Data Viewer
    Location:
    21q22.12
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (34787801..35049302, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (33170406..33432142, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (36160098..36421599, complement)

    Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985515 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:36118001-36118502 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:36118503-36119002 Neighboring gene Sharpr-MPRA regulatory region 10169 Neighboring gene long intergenic non-protein coding RNA 160 Neighboring gene long intergenic non-protein coding RNA 1426 Neighboring gene RUNX1 element RE2 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr21:36208094-36209293 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr21:36237597-36238796 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:36239537-36240204 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:36240205-36240870 Neighboring gene RUNX1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13274 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:36258923-36259694 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:36258151-36258922 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18407 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18408 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13275 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13276 Neighboring gene Sharpr-MPRA regulatory region 10978 Neighboring gene NANOG hESC enhancer GRCh37_chr21:36332885-36333440 Neighboring gene Sharpr-MPRA regulatory region 10330 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18410 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18411 Neighboring gene Sharpr-MPRA regulatory region 3099 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18412 Neighboring gene Sharpr-MPRA regulatory region 4684 Neighboring gene RUNX1 enhancer RE1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18413 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18414 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13277 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18415 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18416 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18417 Neighboring gene RUNX1 intronic transcript 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:36466332-36466488 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:36477528-36477706 Neighboring gene Sharpr-MPRA regulatory region 12281 Neighboring gene uncharacterized LOC124905015 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:36589399-36590598 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr21:36604354-36605553 Neighboring gene enhancer 4 sub-fragment of super-enhancer upstream of RUNX1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:36646465-36646966 Neighboring gene NANOG hESC enhancer GRCh37_chr21:36743463-36743964 Neighboring gene uncharacterized LOC100506403 Neighboring gene Sharpr-MPRA regulatory region 14404 Neighboring gene Sharpr-MPRA regulatory region 5568 Neighboring gene NANOG hESC enhancer GRCh37_chr21:36786783-36787398 Neighboring gene ribosomal protein L34 pseudogene 3

    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

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2023-06-14)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2023-06-14)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    Genetic loci associated with plasma phospholipid n-3 fatty acids: a meta-analysis of genome-wide association studies from the CHARGE Consortium.
    EBI GWAS Catalog
    Genetics of rheumatoid arthritis contributes to biology and drug discovery.
    EBI GWAS Catalog
    Genome-wide association study identifies three new susceptibility loci for esophageal squamous-cell carcinoma in Chinese populations.
    EBI GWAS Catalog
    Genome-wide association study of antibody response to smallpox vaccine.
    EBI GWAS Catalog
    Genome-wide association study of pre-eclampsia detects novel maternal single nucleotide polymorphisms and copy-number variants in subsets of the Hyperglycemia and Adverse Pregnancy Outcome (HAPO) study cohort.
    EBI GWAS Catalog
    Joint analysis of three genome-wide association studies of esophageal squamous cell carcinoma in Chinese populations.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Vif vif HIV-1 Vif inhibits RUNX1 transcriptional activator by binding CBFB, which can be disrupted by mutating residue F68 in CBFB PubMed
    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
    vif HIV-1 Vif modulates cellular gene expression with RUNX1-associated regulatory domains PubMed
    vif The C-terminal tail (residues 131-182) of CBFbeta is dispensable for both Vif-induced A3G degradation and RUNX1-mediated gene transcription PubMed
    vif CBFbeta1-130, but not CBFbeta1-126, can fully support RUNX1-mediated gene transcription, indicating CBFbeta acts through different domains in its interaction with Vif and RUNX1 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

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in cardiac muscle tissue regeneration ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in chondrocyte differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in hematopoietic stem cell proliferation TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in hemopoiesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in hemopoiesis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in myeloid leukocyte differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of CD4-positive, alpha-beta T cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in neuron differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in ossification IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in peripheral nervous system neuron development TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in positive regulation of CD8-positive, alpha-beta T cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of angiogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of collagen biosynthetic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of extracellular matrix organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of granulocyte differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of interleukin-2 production IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of regulation of cardiac muscle cell proliferation 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 connective tissue replacement ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within regulation of plasminogen activation 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
     
    Component Evidence Code Pubs
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    part_of core-binding factor complex TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    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 

    General protein information

    Preferred Names
    runt-related transcription factor 1
    Names
    AML1-ETO fusion
    AML1-ETO fusion protein
    AML1-EVI-1 fusion protein
    PEA2-alpha B
    PEBP2-alpha B
    SL3-3 enhancer factor 1 alpha B subunit
    SL3/AKV core-binding factor alpha B subunit
    acute myeloid leukemia 1 protein
    core-binding factor, runt domain, alpha subunit 2
    mutant RUNX1
    oncogene AML-1
    polyomavirus enhancer-binding protein 2 alpha B subunit
    runt related transcription factor 1

    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_011402.2 RefSeqGene

      Range
      940414..1201911
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_482

    mRNA and Protein(s)

    1. NM_001001890.3NP_001001890.1  runt-related transcription factor 1 isoform AML1b

      See identical proteins and their annotated locations for NP_001001890.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding region compared to variant 1. The resulting isoform (AML1b) is shorter and has a distinct N-terminus compared to isoform AML1c.
      Source sequence(s)
      AP000330, AP000331, D43968
      Consensus CDS
      CCDS42922.1
      UniProtKB/Swiss-Prot
      A8MV94, B2RMS4, D3DSG1, O60472, O60473, O76047, O76089, Q01196, Q13081, Q13755, Q13756, Q13757, Q13758, Q13759, Q15341, Q15343, Q16284, Q16285, Q16286
      UniProtKB/TrEMBL
      H9KVB1
      Related
      ENSP00000340690.4, ENST00000344691.8
      Conserved Domains (2) summary
      pfam00853
      Location:58179
      Runt; Runt domain
      pfam08504
      Location:362453
      RunxI; Runx inhibition domain
    2. NM_001122607.2NP_001116079.1  runt-related transcription factor 1 isoform AML1a

      See identical proteins and their annotated locations for NP_001116079.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding region as well as the 3' UTR and coding region compared to variant 1. The resulting isoform (AML1a) is shorter and has distinct N- and C-termini compared to isoform AML1c.
      Source sequence(s)
      AP000331, D43967
      Consensus CDS
      CCDS46646.1
      UniProtKB/TrEMBL
      A8MZI9
      Related
      ENSP00000351123.5, ENST00000358356.9
      Conserved Domains (1) summary
      pfam00853
      Location:58179
      Runt; Runt domain
    3. NM_001754.5NP_001745.2  runt-related transcription factor 1 isoform AML1c

      See identical proteins and their annotated locations for NP_001745.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest isoform (AML1c).
      Source sequence(s)
      AF015262, AP000330, U19601
      Consensus CDS
      CCDS13639.1
      UniProtKB/TrEMBL
      H9KVB1
      Related
      ENSP00000501943.1, ENST00000675419.1
      Conserved Domains (2) summary
      pfam00853
      Location:81207
      Runt; Runt domain
      pfam08504
      Location:389480
      RunxI; Runx inhibition 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_000021.9 Reference GRCh38.p14 Primary Assembly

      Range
      34787801..35049302 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011529768.3XP_011528070.1  runt-related transcription factor 1 isoform X6

      UniProtKB/TrEMBL
      H9KVB1
      Conserved Domains (2) summary
      pfam00853
      Location:72192
      Runt; Runt domain
      pfam08504
      Location:312403
      RunxI; Runx inhibition domain
    2. XM_011529767.3XP_011528069.1  runt-related transcription factor 1 isoform X3

      See identical proteins and their annotated locations for XP_011528069.1

      UniProtKB/TrEMBL
      H9KVB1
      Conserved Domains (2) summary
      pfam00853
      Location:68194
      Runt; Runt domain
      pfam08504
      Location:376467
      RunxI; Runx inhibition domain
    3. XM_005261069.5XP_005261126.1  runt-related transcription factor 1 isoform X4

      UniProtKB/TrEMBL
      H9KVB1
      Conserved Domains (2) summary
      pfam00853
      Location:81207
      Runt; Runt domain
      pfam08504
      Location:325416
      RunxI; Runx inhibition domain
    4. XM_047441015.1XP_047296971.1  runt-related transcription factor 1 isoform X6

      UniProtKB/TrEMBL
      H9KVB1
    5. XM_047441010.1XP_047296966.1  runt-related transcription factor 1 isoform X3

      UniProtKB/TrEMBL
      H9KVB1
    6. XM_047441012.1XP_047296968.1  runt-related transcription factor 1 isoform X4

      UniProtKB/TrEMBL
      H9KVB1
    7. XM_011529766.3XP_011528068.1  runt-related transcription factor 1 isoform X1

      See identical proteins and their annotated locations for XP_011528068.1

      UniProtKB/TrEMBL
      H9KVB1
      Conserved Domains (2) summary
      pfam00853
      Location:81207
      Runt; Runt domain
      pfam08504
      Location:389480
      RunxI; Runx inhibition domain
    8. XM_047441014.1XP_047296970.1  runt-related transcription factor 1 isoform X6

      UniProtKB/TrEMBL
      H9KVB1
    9. XM_047441009.1XP_047296965.1  runt-related transcription factor 1 isoform X3

      UniProtKB/TrEMBL
      H9KVB1
    10. XM_047441011.1XP_047296967.1  runt-related transcription factor 1 isoform X4

      UniProtKB/TrEMBL
      H9KVB1
    11. XM_047441007.1XP_047296963.1  runt-related transcription factor 1 isoform X1

      UniProtKB/TrEMBL
      H9KVB1
      Related
      ENSP00000300305.3, ENST00000300305.7
    12. XM_047441013.1XP_047296969.1  runt-related transcription factor 1 isoform X5

      UniProtKB/TrEMBL
      H9KVB1
      Related
      ENSP00000382184.1, ENST00000399240.5
    13. XM_005261068.4XP_005261125.1  runt-related transcription factor 1 isoform X2

      See identical proteins and their annotated locations for XP_005261125.1

      UniProtKB/TrEMBL
      H9KVB1
      Conserved Domains (2) summary
      pfam00853
      Location:73194
      Runt; Runt domain
      pfam08504
      Location:377468
      RunxI; Runx inhibition domain
    14. XM_011529770.3XP_011528072.1  runt-related transcription factor 1 isoform X8

      UniProtKB/TrEMBL
      A8MZI9
      Conserved Domains (1) summary
      pfam00853
      Location:85206
      Runt; Runt domain
    15. XM_047441016.1XP_047296972.1  runt-related transcription factor 1 isoform X7

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060945.1 Alternate T2T-CHM13v2.0

      Range
      33170406..33432142 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054324898.1XP_054180873.1  runt-related transcription factor 1 isoform X3

      UniProtKB/TrEMBL
      H9KVB1
    2. XM_054324899.1XP_054180874.1  runt-related transcription factor 1 isoform X3

      UniProtKB/TrEMBL
      H9KVB1
    3. XM_054324901.1XP_054180876.1  runt-related transcription factor 1 isoform X4

      UniProtKB/TrEMBL
      H9KVB1
    4. XM_054324894.1XP_054180869.1  runt-related transcription factor 1 isoform X1

      UniProtKB/TrEMBL
      H9KVB1
    5. XM_054324905.1XP_054180880.1  runt-related transcription factor 1 isoform X6

      UniProtKB/TrEMBL
      H9KVB1
    6. XM_054324902.1XP_054180877.1  runt-related transcription factor 1 isoform X4

      UniProtKB/TrEMBL
      H9KVB1
    7. XM_054324895.1XP_054180870.1  runt-related transcription factor 1 isoform X1

      UniProtKB/TrEMBL
      H9KVB1
    8. XM_054324904.1XP_054180879.1  runt-related transcription factor 1 isoform X6

      UniProtKB/TrEMBL
      H9KVB1
    9. XM_054324897.1XP_054180872.1  runt-related transcription factor 1 isoform X3

      UniProtKB/TrEMBL
      H9KVB1
    10. XM_054324900.1XP_054180875.1  runt-related transcription factor 1 isoform X4

      UniProtKB/TrEMBL
      H9KVB1
    11. XM_054324903.1XP_054180878.1  runt-related transcription factor 1 isoform X5

      UniProtKB/TrEMBL
      H9KVB1
    12. XM_054324896.1XP_054180871.1  runt-related transcription factor 1 isoform X2

      UniProtKB/TrEMBL
      H9KVB1
    13. XM_054324907.1XP_054180882.1  runt-related transcription factor 1 isoform X8

      UniProtKB/TrEMBL
      A8MZI9
    14. XM_054324906.1XP_054180881.1  runt-related transcription factor 1 isoform X9