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    HMGA2 high mobility group AT-hook 2 [ Homo sapiens (human) ]

    Gene ID: 8091, updated on 16-Apr-2017
    Official Symbol
    HMGA2provided by HGNC
    Official Full Name
    high mobility group AT-hook 2provided by HGNC
    Primary source
    HGNC:HGNC:5009
    See related
    Ensembl:ENSG00000149948 MIM:600698; Vega:OTTHUMG00000168936
    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
    BABL; LIPO; HMGIC; HMGI-C; STQTL9
    Summary
    This gene encodes a protein that belongs to the non-histone chromosomal high mobility group (HMG) protein family. HMG proteins function as architectural factors and are essential components of the enhancesome. This protein contains structural DNA-binding domains and may act as a transcriptional regulating factor. Identification of the deletion, amplification, and rearrangement of this gene that are associated with myxoid liposarcoma suggests a role in adipogenesis and mesenchymal differentiation. A gene knock out study of the mouse counterpart demonstrated that this gene is involved in diet-induced obesity. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]
    Orthologs
    Location:
    12q14.3
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 12 NC_000012.12 (65824460..65966291)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (66218240..66360071)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100507065 Neighboring gene uncharacterized LOC105369806 Neighboring gene PEST containing nuclear protein pseudogene 3 Neighboring gene ribosomal protein SA pseudogene 52 Neighboring gene uncharacterized LOC100129940 Neighboring gene long intergenic non-protein coding RNA 2425 Neighboring gene microRNA 6074

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Uterine leiomyoma
    MedGen: C0042133 OMIM: 150699 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated (2017-02-02)

    ClinGen Genome Curation Page
    Haploinsufficency

    Some evidence for dosage pathogenicity (Last evaluated (2017-02-02)

    ClinGen Genome Curation PagePubMed

    NHGRI GWAS Catalog

    Description
    A common variant of HMGA2 is associated with adult and childhood height in the general population.
    NHGRI GWA Catalog
    A genome-wide association study for diabetic nephropathy genes in African Americans.
    NHGRI GWA Catalog
    A novel common variant in DCST2 is associated with length in early life and height in adulthood.
    NHGRI GWA Catalog
    Common variants at 12q15 and 12q24 are associated with infant head circumference.
    NHGRI GWA Catalog
    Genetic variants associated with cardiac structure and function: a meta-analysis and replication of genome-wide association data.
    NHGRI GWA Catalog
    Genome-wide association analysis identifies 20 loci that influence adult height.
    NHGRI GWA Catalog
    Genome-wide association study identifies eight new risk loci for polycystic ovary syndrome.
    NHGRI GWA Catalog
    Genome-wide association study identifies four loci associated with eruption of permanent teeth.
    NHGRI GWA Catalog
    Genome-wide association study of body height in African Americans: the Women's Health Initiative SNP Health Association Resource (SHARe).
    NHGRI GWA Catalog
    Genome-wide association study of height and body mass index in Australian twin families.
    NHGRI GWA Catalog
    Genome-wide association study of primary tooth eruption identifies pleiotropic loci associated with height and craniofacial distances.
    NHGRI GWA Catalog
    Genome-wide association study reveals multiple loci associated with primary tooth development during infancy.
    NHGRI GWA Catalog
    Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
    NHGRI GWA Catalog
    Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.
    NHGRI GWA Catalog
    Hundreds of variants clustered in genomic loci and biological pathways affect human height.
    NHGRI GWA Catalog
    Identification of common variants associated with human hippocampal and intracranial volumes.
    NHGRI GWA Catalog
    Identification of ten loci associated with height highlights new biological pathways in human growth.
    NHGRI GWA Catalog
    Identification, replication, and fine-mapping of Loci associated with adult height in individuals of african ancestry.
    NHGRI GWA Catalog
    Many sequence variants affecting diversity of adult human height.
    NHGRI GWA Catalog
    Meta-analysis of genome-wide association studies in african americans provides insights into the genetic architecture of type 2 diabetes.
    NHGRI GWA Catalog
    Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
    NHGRI GWA Catalog
    Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size.
    NHGRI GWA Catalog
    New loci associated with birth weight identify genetic links between intrauterine growth and adult height and metabolism.
    NHGRI GWA Catalog
    Nine loci for ocular axial length identified through genome-wide association studies, including shared loci with refractive error.
    NHGRI GWA Catalog
    Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis.
    NHGRI GWA Catalog

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat Interaction of HIV-1 Tat with HMGA2 in T-cells is identified by a proteomic strategy based on affinity chromatography coupled with mass spectrometry PubMed

    Go to the HIV-1, Human Interaction Database

    • Cellular Senescence, organism-specific biosystem (from REACTOME)
      Cellular Senescence, organism-specific biosystemCellular senescence involves irreversible growth arrest accompanied by phenotypic changes such as enlarged morphology, reorganization of chromatin through formation of senescence-associated heterochr...
    • Cellular responses to stress, organism-specific biosystem (from REACTOME)
      Cellular responses to stress, organism-specific biosystemCells are subject to external molecular and physical stresses such as foreign molecules that perturb metabolic or signaling processes, and changes in temperature or pH. The ability of cells and tissu...
    • DNA Damage/Telomere Stress Induced Senescence, organism-specific biosystem (from REACTOME)
      DNA Damage/Telomere Stress Induced Senescence, organism-specific biosystemReactive oxygen species (ROS), whose concentration increases in senescent cells due to oncogenic RAS-induced mitochondrial dysfunction (Moiseeva et al. 2009) or due to environmental stress, cause DNA...
    • Formation of Senescence-Associated Heterochromatin Foci (SAHF), organism-specific biosystem (from REACTOME)
      Formation of Senescence-Associated Heterochromatin Foci (SAHF), organism-specific biosystemThe process of DNA damage/telomere stress induced senescence culminates in the formation of senescence associated heterochromatin foci (SAHF). These foci represent facultative heterochromatin that is...
    • Mesodermal Commitment Pathway, organism-specific biosystem (from WikiPathways)
      Mesodermal Commitment Pathway, organism-specific biosystemModel depicting mesodermal specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell l...
    • MicroRNAs in cancer, organism-specific biosystem (from KEGG)
      MicroRNAs in cancer, organism-specific biosystemMicroRNA (miRNA) is a cluster of small non-encoding RNA molecules of 21 - 23 nucleotides in length, which controls gene expression post-transcriptionally either via the degradation of target mRNAs or...
    • MicroRNAs in cancer, conserved biosystem (from KEGG)
      MicroRNAs in cancer, conserved biosystemMicroRNA (miRNA) is a cluster of small non-encoding RNA molecules of 21 - 23 nucleotides in length, which controls gene expression post-transcriptionally either via the degradation of target mRNAs or...
    • Transcriptional misregulation in cancer, organism-specific biosystem (from KEGG)
      Transcriptional misregulation in cancer, organism-specific biosystem
      Transcriptional misregulation in cancer
    • Transcriptional misregulation in cancer, conserved biosystem (from KEGG)
      Transcriptional misregulation in cancer, conserved biosystem
      Transcriptional misregulation in cancer
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    5'-deoxyribose-5-phosphate lyase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    AT DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    AT DNA binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    C2H2 zinc finger domain binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    DNA binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    DNA binding, bending IDA
    Inferred from Direct Assay
    more info
    PubMed 
    DNA binding, bending IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    DNA-(apurinic or apyrimidinic site) lyase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    DNA-dependent protein kinase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    MH1 domain binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    MH2 domain binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    SMAD binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    cAMP response element binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    core promoter binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleosomal DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    regulatory region DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    contributes_to transcription factor activity, transcription factor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    DNA damage response, detection of DNA damage IDA
    Inferred from Direct Assay
    more info
    PubMed 
    base-excision repair IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cell division IEA
    Inferred from Electronic Annotation
    more info
     
    chondrocyte differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    chondrocyte proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    chromatin organization TAS
    Traceable Author Statement
    more info
    PubMed 
    chromosome breakage IDA
    Inferred from Direct Assay
    more info
    PubMed 
    chromosome condensation IEA
    Inferred from Electronic Annotation
    more info
     
    endodermal cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    epithelial to mesenchymal transition IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    fat cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    heterochromatin assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    histone H2A-S139 phosphorylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    mesenchymal cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    mesodermal cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    mesodermal-endodermal cell signaling IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    mitotic G2 DNA damage checkpoint IDA
    Inferred from Direct Assay
    more info
    PubMed 
    multicellular organism development TAS
    Traceable Author Statement
    more info
    PubMed 
    negative regulation by host of viral transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of apoptotic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of double-strand break repair via nonhomologous end joining IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of single stranded viral RNA replication via double stranded DNA intermediate IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of transcription from RNA polymerase II promoter IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of transcription, DNA-templated IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    oncogene-induced cell senescence IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of apoptotic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of cell cycle arrest IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of cellular response to X-ray IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of cellular senescence IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of gene expression IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of response to DNA damage stimulus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of stem cell proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of stem cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of transcription from RNA polymerase II promoter IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of transcription regulatory region DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of transcription, DNA-templated IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of cell cycle process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of cellular response to drug IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of growth IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of stem cell population maintenance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of stem cell population maintenance TAS
    Traceable Author Statement
    more info
    PubMed 
    regulation of transcription, DNA-templated IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    response to virus IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    senescence-associated heterochromatin focus assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    stem cell differentiation IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    transcription from RNA polymerase II promoter IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    SMAD protein complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nuclear chromosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein-DNA complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    senescence-associated heterochromatin focus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    high mobility group protein HMGI-C
    Names
    high-mobility group (nonhistone chromosomal) protein isoform I-C

    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_016296.1 RefSeqGene

      Range
      5001..146832
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001300918.1NP_001287847.1  high mobility group protein HMGI-C isoform c

      See identical proteins and their annotated locations for NP_001287847.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternate 3' terminal exon, resulting in a novel 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (c) has a distinct C-terminus, and is longer, compared to isoform a.
      Source sequence(s)
      AC090673, AC107308
      Consensus CDS
      CCDS73492.1
      UniProtKB/TrEMBL
      F5H2A4
      Related
      ENSP00000377205.3, OTTHUMP00000239778, ENST00000393577.7, OTTHUMT00000401663
      Conserved Domains (1) summary
      PRK14965
      Location:393
      PRK14965; DNA polymerase III subunits gamma and tau; Provisional
    2. NM_001300919.1NP_001287848.1  high mobility group protein HMGI-C isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 3' structure, resulting in a novel 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (d) has a distinct C-terminus, and is longer, compared to isoform a.
      Source sequence(s)
      AC090673, AC107308, AY601865, CA422738
      Consensus CDS
      CCDS73491.1
      UniProtKB/TrEMBL
      F5H6H0, Q1M183
      Related
      ENSP00000437621.1, OTTHUMP00000239775, ENST00000536545.5, OTTHUMT00000401659
      Conserved Domains (1) summary
      pfam13900
      Location:84128
      GVQW; Putative domain of unknown function
    3. NM_001330190.1NP_001317119.1  high mobility group protein HMGI-C isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 3' structure, resulting in a novel 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (e) has a distinct C-terminus, and is shorter, compared to isoform a.
      Source sequence(s)
      AC107308, AF533651, AI073570, AY601861, CN334368, U28749
      Consensus CDS
      CCDS81709.1
      UniProtKB/Swiss-Prot
      P52926
    4. NM_003483.4NP_003474.1  high mobility group protein HMGI-C isoform a

      See identical proteins and their annotated locations for NP_003474.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes isoform a.
      Source sequence(s)
      AC090673, BM782659, CN334368, U28749, Z31595
      Consensus CDS
      CCDS44936.1
      UniProtKB/Swiss-Prot
      P52926
      Related
      ENSP00000384026.2, OTTHUMP00000239770, ENST00000403681.6, OTTHUMT00000401654
      Conserved Domains (1) summary
      pfam15782
      Location:981
      GREB1; Gene regulated by oestrogen in breast cancer
    5. NM_003484.1NP_003475.1  high mobility group protein HMGI-C isoform b

      See identical proteins and their annotated locations for NP_003475.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 3' structure, resulting in a novel 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (b) has a distinct C-terminus, and is shorter, compared to isoform a.
      Source sequence(s)
      AF533652, CA422738, CN334368, U28749
      Consensus CDS
      CCDS31854.1
      UniProtKB/Swiss-Prot
      P52926
      Related
      ENSP00000346658.3, OTTHUMP00000239776, ENST00000354636.7, OTTHUMT00000401660
      Conserved Domains (1) summary
      TIGR02102
      Location:1499
      pullulan_Gpos; pullulanase, extracellular, Gram-positive

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p7 Primary Assembly

      Range
      65824460..65966291
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017019989.1XP_016875478.1  high mobility group protein HMGI-C isoform X1

      Related
      ENSP00000377206.3, OTTHUMP00000239772, ENST00000393578.7, OTTHUMT00000401656
      Conserved Domains (1) summary
      pfam05918
      Location:746
      API5; Apoptosis inhibitory protein 5 (API5)

    Alternate CHM1_1.1

    Genomic

    1. NC_018923.2 Alternate CHM1_1.1

      Range
      66185507..66327350
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001015886.1: Suppressed sequence

      Description
      NM_001015886.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
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