HMGA2 Gene (Protein Coding)

High Mobility Group AT-Hook 2

GC12P065824
GIFtS:
46
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 ... See more...

Aliases for HMGA2 Gene

Aliases for HMGA2 Gene

  • High Mobility Group AT-Hook 2 2 3 5
  • High-Mobility Group (Nonhistone Chromosomal) Protein Isoform I-C 2 3
  • High Mobility Group Protein HMGI-C 3 4
  • HMGIC 3 4
  • High Mobility Group AT-Hook Protein 2 4
  • HMGA2/KRT121P Fusion 3
  • HMGI-C 3
  • STQTL9 3
  • BABL 3
  • LIPO 3

External Ids for HMGA2 Gene

Previous HGNC Symbols for HMGA2 Gene

  • HMGIC

Previous GeneCards Identifiers for HMGA2 Gene

  • GC12P065624
  • GC12P066105
  • GC12P065934
  • GC12P064504
  • GC12P066218
  • GC12P063271

Summaries for HMGA2 Gene

Entrez Gene Summary for HMGA2 Gene

  • 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]

GeneCards Summary for HMGA2 Gene

HMGA2 (High Mobility Group AT-Hook 2) is a Protein Coding gene. Diseases associated with HMGA2 include Salivary Gland Adenoma, Pleomorphic and Silver-Russell Syndrome. Among its related pathways are Cellular Senescence (REACTOME) and DNA Damage/Telomere Stress Induced Senescence. Gene Ontology (GO) annotations related to this gene include enzyme binding and proximal promoter DNA-binding transcription activator activity, RNA polymerase II-specific. An important paralog of this gene is LYRM4.

UniProtKB/Swiss-Prot Summary for HMGA2 Gene

  • Functions as a transcriptional regulator. Functions in cell cycle regulation through CCNA2. Plays an important role in chromosome condensation during the meiotic G2/M transition of spermatocytes. Plays a role in postnatal myogenesis, is involved in satellite cell activation (By similarity).

Gene Wiki entry for HMGA2 Gene

Additional gene information for HMGA2 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for HMGA2 Gene

Genomics for HMGA2 Gene

GeneHancer (GH) Regulatory Elements for HMGA2 Gene

Promoters and enhancers for HMGA2 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HMGA2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HMGA2 gene promoter:
  • PPAR-gamma1
  • TBP
  • TFIID

Genomic Locations for HMGA2 Gene

Genomic Locations for HMGA2 Gene
chr12:65,824,131-65,966,295
(GRCh38/hg38)
Size:
142,165 bases
Orientation:
Plus strand
chr12:66,217,911-66,360,075
(GRCh37/hg19)
Size:
142,165 bases
Orientation:
Plus strand

Genomic View for HMGA2 Gene

Genes around HMGA2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HMGA2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HMGA2 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for HMGA2 Gene

Proteins for HMGA2 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for HMGA2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P52926-HMGA2_HUMAN
    Recommended name:
    High mobility group protein HMGI-C
    Protein Accession:
    P52926
    Secondary Accessions:
    • E7EP85
    • E7EWA2
    • Q1M182
    • Q1M185
    • Q1M186
    • Q1M187
    • Q1M188

    Protein attributes for HMGA2 Gene

    Size:
    109 amino acids
    Molecular mass:
    11832 Da
    Quaternary structure:
    • Interacts with E4F1 (PubMed:14645522). Interacts with NEK2 (By similarity).

    Alternative splice isoforms for HMGA2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for HMGA2 Gene

Protein Expression for HMGA2 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for HMGA2 Gene

  • Regulated by cell cycle-dependent phosphorylation which alters its DNA binding affinity. Phosphorylated by NEK2 (By similarity).
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HMGA2 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Abcam antibodies for HMGA2
  • Boster Bio Antibodies for HMGA2

No data available for DME Specific Peptides for HMGA2 Gene

Domains & Families for HMGA2 Gene

Gene Families for HMGA2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for HMGA2 Gene

Blocks:
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for HMGA2 Gene

GenScript: Design optimal peptide antigens:
  • High mobility group AT-hook protein 2 (HMGA2_HUMAN)
  • HMGA2e' (Q1M183_HUMAN)
  • High-mobility group protein isoform C (Q8IZX8_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P52926

UniProtKB/Swiss-Prot:

HMGA2_HUMAN :
  • Belongs to the HMGA family.
Family:
  • Belongs to the HMGA family.
genes like me logo Genes that share domains with HMGA2: view

Function for HMGA2 Gene

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  2. CRISPR
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Molecular function for HMGA2 Gene

UniProtKB/Swiss-Prot Function:
Functions as a transcriptional regulator. Functions in cell cycle regulation through CCNA2. Plays an important role in chromosome condensation during the meiotic G2/M transition of spermatocytes. Plays a role in postnatal myogenesis, is involved in satellite cell activation (By similarity).

Phenotypes From GWAS Catalog for HMGA2 Gene

Gene Ontology (GO) - Molecular Function for HMGA2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IDA 14627817
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISA --
GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific IDA 14627817
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific IDA 18832382
GO:0003677 DNA binding NAS,IEA 8198613
genes like me logo Genes that share ontologies with HMGA2: view
genes like me logo Genes that share phenotypes with HMGA2: view

Human Phenotype Ontology for HMGA2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

miRNA for HMGA2 Gene

miRTarBase miRNAs that target HMGA2

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HMGA2

Clone Products

  • Addgene plasmids for HMGA2

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for HMGA2 Gene

Localization for HMGA2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HMGA2 Gene

Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HMGA2 gene
Compartment Confidence
nucleus 5
extracellular 2
plasma membrane 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (3)
  • Nucleus (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for HMGA2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000228 nuclear chromosome ISS --
GO:0000785 chromatin IEA --
GO:0005634 nucleus IDA,IEA 16901784
GO:0005654 nucleoplasm TAS --
GO:0032993 protein-DNA complex IDA 19465398
genes like me logo Genes that share ontologies with HMGA2: view

Pathways & Interactions for HMGA2 Gene

genes like me logo Genes that share pathways with HMGA2: view

Pathways by source for HMGA2 Gene

1 BioSystems pathway for HMGA2 Gene
1 Cell Signaling Technology pathway for HMGA2 Gene
1 GeneTex pathway for HMGA2 Gene

SIGNOR curated interactions for HMGA2 Gene

Activates:
Inactivates:
Is inactivated by:

Gene Ontology (GO) - Biological Process for HMGA2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IDA 14627817
GO:0001837 epithelial to mesenchymal transition IMP 18832382
GO:0002062 chondrocyte differentiation IDA 21484705
GO:0003131 mesodermal-endodermal cell signaling IMP 17624332
GO:0006284 base-excision repair IBA,IDA 19465398
genes like me logo Genes that share ontologies with HMGA2: view

Drugs & Compounds for HMGA2 Gene

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  1. Drug

(3) Drugs for HMGA2 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(4) Additional Compounds for HMGA2 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with HMGA2: view

Transcripts for HMGA2 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for HMGA2 Gene

(6) REFSEQ mRNAs :
(28) Additional mRNA sequences :
(175) Selected AceView cDNA sequences:
(11) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HMGA2

Clone Products

  • Addgene plasmids for HMGA2

Alternative Splicing Database (ASD) splice patterns (SP) for HMGA2 Gene

No ASD Table

Relevant External Links for HMGA2 Gene

GeneLoc Exon Structure for
HMGA2
ECgene alternative splicing isoforms for
HMGA2

Expression for HMGA2 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HMGA2 Gene

mRNA expression in normal human tissues for HMGA2 Gene
mRNA expression by GTEx for HMGA2 GenemRNA expression by BioGPS for HMGA2 Gene

Protein differential expression in normal tissues from HIPED for HMGA2 Gene

This gene is overexpressed in Amniocyte (48.6) and Fetal ovary (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for HMGA2 Gene



Protein tissue co-expression partners for HMGA2 Gene

NURSA nuclear receptor signaling pathways regulating expression of HMGA2 Gene:

HMGA2

SOURCE GeneReport for Unigene cluster for HMGA2 Gene:

Hs.505924

Evidence on tissue expression from TISSUES for HMGA2 Gene

  • Liver(2.5)
  • Lung(2.5)
  • Nervous system(2.4)
  • Skin(2.3)
  • Spleen(2.3)
  • Blood(2.2)
  • Intestine(2.2)
  • Thyroid gland(2.2)
  • Bone marrow(2.1)
  • Kidney(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for HMGA2 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • integumentary
  • nervous
  • reproductive
  • skeleton
Regions:
Head and neck:
  • brain
  • head
Pelvis:
  • uterus
General:
  • skin
genes like me logo Genes that share expression patterns with HMGA2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for HMGA2 Gene

Orthologs for HMGA2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for HMGA2 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
 Mammalia HMGA2 33 32
  • 96.94 (n)
 OneToOne
mouse
(Mus musculus)
 Mammalia Hmga2 33
  • 96 (a)
 OneToOne
chimpanzee
(Pan troglodytes)
 Mammalia HMGA2 33
  • 48 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves HMGI-C 33
  • 100 (a)
 OneToOne
HMGA2 32
  • 82.87 (n)
lizard
(Anolis carolinensis)
 Reptilia HMGA2 33
  • 93 (a)
 OneToOne
African clawed frog
(Xenopus laevis)
 Amphibia Xl.33871 32
tropical clawed frog
(Silurana tropicalis)
 Amphibia Str.8936 32
zebrafish
(Danio rerio)
 Actinopterygii hmga2 33
  • 48 (a)
 OneToOne
Species where no ortholog for HMGA2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for HMGA2 Gene

ENSEMBL:
Gene Tree for HMGA2 (if available)
TreeFam:
Gene Tree for HMGA2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for HMGA2: view image

Paralogs for HMGA2 Gene

Paralogs for HMGA2 Gene

(45) SIMAP similar genes for HMGA2 Gene using alignment to 6 proteins:

  • HMGA2_HUMAN
  • F5H2A4_HUMAN
  • F5H2U8_HUMAN
  • F5H6H0_HUMAN
  • H0YFY4_HUMAN
  • Q1M183_HUMAN

Pseudogenes.org Pseudogenes for HMGA2 Gene

genes like me logo Genes that share paralogs with HMGA2: view

Variants for HMGA2 Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Polymorphic Variants from UniProtKB/Swiss-Prot for HMGA2 Gene

HMGA2_HUMAN-P52926
Genetic variations in HMGA2 define the stature quantitative trait locus 9 (STQTL9) [MIM:611547]. Human height is a classic, highly heritable quantitative trait.

Sequence variations from dbSNP and Humsavar for HMGA2 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1114167319 pathogenic, Russell-Silver syndrome 65,828,082(+) C/T coding_sequence_variant, stop_gained
rs1114167320 pathogenic, Russell-Silver syndrome 65,828,078(+) A/ coding_sequence_variant, frameshift
rs1000010497 -- 65,902,245(+) C/A/T genic_downstream_transcript_variant, intron_variant
rs1000036093 -- 65,861,071(+) A/G/T genic_downstream_transcript_variant, intron_variant
rs1000039239 -- 65,944,169(+) A/G genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for HMGA2 Gene

Variant ID Type Subtype PubMed ID
esv3629792 CNV loss 21293372
esv3629793 CNV loss 21293372
esv8071 CNV gain 19470904
nsv507649 OTHER sequence alteration 20534489

Variation tolerance for HMGA2 Gene

Residual Variation Intolerance Score: 57.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.28; 25.45% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HMGA2 Gene

Human Gene Mutation Database (HGMD)
HMGA2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
HMGA2

SNP Genotyping and Copy Number Assay Products

Disorders for HMGA2 Gene

MalaCards: The human disease database

(61) MalaCards diseases for HMGA2 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search HMGA2 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

HMGA2_HUMAN
  • Note=A chromosomal aberration involving HMGA2 is associated with a subclass of benign mesenchymal tumors known as lipomas. Translocation t(3;12)(q27-q28;q13-q15) with LPP is shown in lipomas. HMGA2 is also fused with a number of other genes in lipomas. {ECO:0000269 PubMed:8824803}.
  • Note=A chromosomal aberration involving HMGA2 is associated with pulmonary chondroid hamartomas. Translocation t(3;12)(q27-q28;q14-q15) with LPP is detected in pulmonary chondroid hamartomas. {ECO:0000269 PubMed:11066083}.
  • Note=A chromosomal aberration involving HMGA2 is associated with parosteal lipomas. Translocation t(3;12)(q28;q14) with LPP is also shown in one parosteal lipoma. {ECO:0000269 PubMed:9772904}.
  • Note=A chromosomal aberration involving HMGA2 is found in uterine leiomyoma. Translocation t(12;14)(q15;q23-24) with RAD51B. Chromosomal rearrangements involving HMGA2 do not seem to be the principle pathobiological mechanism in uterine leiomyoma. {ECO:0000269 PubMed:12649198, ECO:0000269 PubMed:9892177}.

Additional Disease Information for HMGA2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with HMGA2: view

No data available for Genatlas for HMGA2 Gene

Publications for HMGA2 Gene

  1. Genomic characterization of human HMGIC, a member of the accessory transcription factor family found at translocation breakpoints in lipomas. (PMID: 8824803) Ashar HR … Chada K (Genomics 1996) 2 3 4 23 56
  2. HMGA2 is confirmed to be associated with human adult height. (PMID: 19930247) Yang TL … Deng HW (Annals of human genetics 2010) 3 23 43 56
  3. Association of a high mobility group gene (HMGA2) variant with bone mineral density. (PMID: 19376282) Kuipers A … Zmuda JM (Bone 2009) 3 23 43 56
  4. Uterine leiomyomata and decreased height: a common HMGA2 predisposition allele. (PMID: 19132395) Hodge JC … Morton CC (Human genetics 2009) 3 23 43 56
  5. A common variant of HMGA2 is associated with adult and childhood height in the general population. (PMID: 17767157) Weedon MN … Frayling TM (Nature genetics 2007) 3 4 43 56

ExternalLinks

View latest publications for HMGA2 gene in Mastermind

Products for HMGA2 Gene

  • Addgene plasmids for HMGA2

Sources for HMGA2 Gene