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

Gene ID: 8091, updated on 12-Aug-2018

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; 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]
Expression
Low expression observed in reference dataset See more
Orthologs

Genomic context

See HMGA2 in Genome Data Viewer
Location:
12q14.3
Exon count:
8
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 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 HNF4 motif-containing MPRA enhancer 102 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

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

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 BioSystems

  • 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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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) endonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-(apurinic or apyrimidinic site) endonuclease activity IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
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 
RNA polymerase II proximal promoter sequence-specific DNA 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 
nucleosomal DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
proximal promoter DNA-binding transcription activator activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
PubMed 
proximal promoter DNA-binding transcription repressor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
PubMed 
transcription coregulator activity IDA
Inferred from Direct Assay
more info
PubMed 
transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription regulatory region DNA 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 IBA
Inferred from Biological aspect of Ancestor
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 cellular senescence ISS
Inferred from Sequence or Structural Similarity
more info
 
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 by RNA polymerase II 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 angiogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
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 cell proliferation in bone marrow ISS
Inferred from Sequence or Structural Similarity
more info
 
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 by RNA polymerase II 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 IBA
Inferred from Biological aspect of Ancestor
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 by RNA polymerase II 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 HDA PubMed 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 

General protein information

Preferred Names
high mobility group protein HMGI-C
Names
HMGA2/KRT121P fusion
high-mobility group (nonhistone chromosomal) protein isoform I-C

NCBI Reference Sequences (RefSeq)

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
    cl26247
    Location:393
    DNA_pol3_delta2; DNA polymerase III, delta subunit
  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
    Related
    ENSP00000377206.3, ENST00000393578.7
  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
    cl25438
    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, OTTHUMP00000239776, ENST00000354636.7, OTTHUMT00000401660
    Conserved Domains (1) summary
    cl25948
    Location:1499
    PulA; Pullulanase/glycogen debranching enzyme [Carbohydrate transport and metabolism]

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p12 Primary Assembly

    Range
    65824460..65966291
    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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