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

    Gene ID: 8091, updated on 27-Nov-2024

    Summary

    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; AllianceGenome:HGNC:5009
    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; SRS5; 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]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See HMGA2 in Genome Data Viewer
    Location:
    12q14.3
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (65824460..65966291)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (65803963..65945820)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (66218240..66360071)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene MSRB3 antisense RNA 1 Neighboring gene uncharacterized LOC105369806 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:66050206-66051405 Neighboring gene PEST containing nuclear protein pseudogene 3 Neighboring gene Sharpr-MPRA regulatory region 9176 Neighboring gene MPRA-validated peak1767 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:66132196-66132696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:66135292-66135792 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:66135793-66136293 Neighboring gene MPRA-validated peak1768 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6609 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:66155026-66155586 Neighboring gene Sharpr-MPRA regulatory region 15140 Neighboring gene NANOG hESC enhancer GRCh37_chr12:66172695-66173196 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:66175547-66176083 Neighboring gene ribosomal protein SA pseudogene 52 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:66192736-66193237 Neighboring gene Sharpr-MPRA regulatory region 869 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:66219383-66219990 Neighboring gene MPRA-validated peak1769 silencer Neighboring gene MPRA-validated peak1770 silencer Neighboring gene HMGA2 antisense RNA 1 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:66285256-66286168 Neighboring gene hESC enhancers GRCh37_chr12:66289853-66290620 and GRCh37_chr12:66290621-66291388 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:66291389-66292155 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:66320206-66320716 Neighboring gene HNF4 motif-containing MPRA enhancer 102 Neighboring gene uncharacterized LOC124902955 Neighboring gene negCOR silencer S1 Neighboring gene long intergenic non-protein coding RNA 2425 Neighboring gene microRNA 6074

    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
    Silver-Russell syndrome 5
    MedGen: C5394456 OMIM: 618908 GeneReviews: Silver-Russell Syndrome
    not available

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    Little evidence for dosage pathogenicity (Last evaluated 2021-09-14)

    ClinGen Genome Curation PagePubMed
    Triplosensitivity

    No evidence available (Last evaluated 2021-09-14)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

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

    HIV-1 interactions

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 5'-deoxyribose-5-phosphate lyase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables C2H2 zinc finger domain binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables DNA binding, bending IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA binding, bending IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables DNA-(apurinic or apyrimidinic site) endonuclease activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables MH1 domain binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables MH2 domain binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables RNA polymerase II-specific DNA-binding transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables SMAD binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables cAMP response element binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables minor groove of adenine-thymine-rich DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables minor groove of adenine-thymine-rich DNA binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables nucleic acid binding EXP
    Inferred from Experiment
    more info
    PubMed 
    enables nucleosomal DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transcription cis-regulatory region binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables transcription coregulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables transcription corepressor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in base-excision repair IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cell division IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chondrocyte differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in chondrocyte proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in chromatin organization TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in chromosome condensation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in endodermal cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in epithelial to mesenchymal transition IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in fat cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in heterochromatin formation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in intracellular signal transduction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in mesenchymal cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in mesodermal cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in mesodermal-endodermal cell signaling IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation by host of viral transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of DNA binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of apoptotic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of cellular senescence ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of double-strand break repair via nonhomologous end joining IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of single stranded viral RNA replication via double stranded DNA intermediate IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in oncogene-induced cell senescence IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of angiogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of cell proliferation in bone marrow ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of gene expression IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of protein serine/threonine kinase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of stem cell proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of stem cell proliferation 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 regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of cell cycle process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of stem cell population maintenance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of stem cell population maintenance TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in response to virus IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in stem cell differentiation IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of SMAD protein complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nuclear chromosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus HDA 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 
    part_of protein-DNA complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in senescence-associated heterochromatin focus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    high mobility group protein HMGI-C
    Names
    HMGA2/KRT121P fusion

    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_016296.1 RefSeqGene

      Range
      5024..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, F5H2U8
      Related
      ENSP00000377205.3, ENST00000393577.7
      Conserved Domains (1) summary
      cl39058
      Location:375
      RNB; RNB domain
    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, ENST00000536545.5
      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
      Related
      ENSP00000377206.3, ENST00000393578.7
      Conserved Domains (1) summary
      cl39058
      Location:375
      RNB; RNB domain
    4. NM_003483.6NP_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, AC107308, BM782659, Z31595
      Consensus CDS
      CCDS44936.1
      UniProtKB/Swiss-Prot
      E7EP85, E7EWA2, P52926, Q1M182, Q1M185, Q1M186, Q1M187, Q1M188
      Related
      ENSP00000384026.2, ENST00000403681.7
      Conserved Domains (1) summary
      cl39058
      Location:375
      RNB; RNB domain
    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, ENST00000354636.7
      Conserved Domains (1) summary
      cl39058
      Location:375
      RNB; RNB 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

    1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      65803963..65945820
      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.