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

Gene ID: 8091, updated on 22-Jan-2023

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
110 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (65824460..65966291)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (65803963..65945820)
105.20220307 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 PEST containing nuclear protein pseudogene 3 Neighboring gene ribosomal protein SA pseudogene 52 Neighboring gene HMGA2 antisense RNA 1 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:66285256-66286168 Neighboring gene HNF4 motif-containing MPRA enhancer 102 Neighboring gene uncharacterized LOC124902955 Neighboring gene negCOR silencer S1 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

Homology

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
PubMed 
enables transcription corepressor activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
involved_in DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
involved_in base-excision repair IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cell cycle IEA
Inferred from Electronic Annotation
more info
 
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
PubMed 
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
PubMed 
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
    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
    P52926, 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: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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.