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

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: mouse all
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Genomic context

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_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Beneath HMGA2 alterations in pleomorphic adenomas: Pathological, immunohistochemical, and molecular insights.
Title: Beneath HMGA2 alterations in pleomorphic adenomas: Pathological, immunohistochemical, and molecular insights.
HMGA2-mediated glutamine metabolism is required for Cd-induced cell growth and cell migration.
Title: HMGA2-mediated glutamine metabolism is required for Cd-induced cell growth and cell migration.
Peculiar nuclear atypia associated with MDM2 gene amplification in carcinoma ex-pleomorphic adenoma harbouring an alteration of HMGA2.
Title: Peculiar nuclear atypia associated with MDM2 gene amplification in carcinoma ex-pleomorphic adenoma harbouring an alteration of HMGA2.
Chromatin modifier Hmga2 promotes adult hematopoietic stem cell function and blood regeneration in stress conditions.
Title: Chromatin modifier Hmga2 promotes adult hematopoietic stem cell function and blood regeneration in stress conditions.
Effects of HMGA2 on the biological characteristics and stemness acquisition of gastric cancer cells.
Title: Effects of HMGA2 on the biological characteristics and stemness acquisition of gastric cancer cells.
Association of deletion polymorphism rs10573247 in the HMGA2 gene with the risk of breast cancer: bioinformatic and experimental analyses.
Title: Association of deletion polymorphism rs10573247 in the HMGA2 gene with the risk of breast cancer: bioinformatic and experimental analyses.
Exosomal circFAM63Bsuppresses bone regeneration of postmenopausal osteoporosis via regulating miR-578/HMGA2 axis.
Title: Exosomal circFAM63Bsuppresses bone regeneration of postmenopausal osteoporosis via regulating miR-578/HMGA2 axis.
Keratin-Positive Giant Cell-Rich Tumor of Bone Harboring an HMGA2::NCOR2 Fusion: Two Cases, Including a Patient With Metastatic Disease, and Review of the Literature.
Title: Keratin-Positive Giant Cell-Rich Tumor of Bone Harboring an HMGA2::NCOR2 Fusion: Two Cases, Including a Patient With Metastatic Disease, and Review of the Literature.
Characterization of HMGA2 variants expands the spectrum of Silver-Russell syndrome.
Title: Characterization of HMGA2 variants expands the spectrum of Silver-Russell syndrome.
SOX10-Internal Tandem Duplications and PLAG1 or HMGA2 Fusions Segregate Eccrine-Type and Apocrine-Type Cutaneous Mixed Tumors.
Title: SOX10-Internal Tandem Duplications and PLAG1 or HMGA2 Fusions Segregate Eccrine-Type and Apocrine-Type Cutaneous Mixed Tumors.

Submit: New GeneRIF Correction See all GeneRIFs (426)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D12S1521 (e-PCR)
- UniSTS:18688

NoName (e-PCR)
- UniSTS:483861

SHGC-146271 (e-PCR)
- UniSTS:172576

D12S1523 (e-PCR)
- UniSTS:67882

RH69419 (e-PCR)
- UniSTS:77611

D8S2279 (e-PCR)
- UniSTS:473907

Hmga2 (e-PCR), detects polymorphism
- UniSTS:498761

SHGC-146550 (e-PCR)
- UniSTS:172633

D12S1511 (e-PCR)
- UniSTS:610

D12S1509 (e-PCR)
- UniSTS:53895

HMGA2_3902 (e-PCR)
- UniSTS:462248

STS-L44578 (e-PCR)
- UniSTS:49091

D12S1549 (e-PCR)
- UniSTS:154091

D12S1550 (e-PCR)
- UniSTS:154092

D12S1552 (e-PCR)
- UniSTS:154094

D12S1555 (e-PCR)
- UniSTS:154097

D12S1556 (e-PCR)
- UniSTS:154098

D12S1557 (e-PCR)
- UniSTS:154099

RH48124 (e-PCR)
- UniSTS:2292

D12S1561 (e-PCR)
- UniSTS:154103

D12S1562 (e-PCR)
- UniSTS:154104

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 more info	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

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Preferred Names: high mobility group protein HMGI-C

Names: HMGA2/KRT121P fusion

NCBI Reference Sequences (RefSeq)

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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

NG_016296.1 RefSeqGene

Range

5024..146832

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001300918.1 → NP_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:3 → 75

RNB; RNB domain
NM_001300919.1 → NP_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:84 → 128

GVQW; Putative domain of unknown function
NM_001330190.1 → NP_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:3 → 75

RNB; RNB domain
NM_003483.6 → NP_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:3 → 75

RNB; RNB domain
NM_003484.1 → NP_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:3 → 75

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

NC_000012.12 Reference GRCh38.p14 Primary Assembly

Range

65824460..65966291

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

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

NM_001015886.1: Suppressed sequence

Description

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