HMG20A high mobility group 20A [Homo sapiens (human)] - Gene

Summary

Official Symbol: HMG20Aprovided by HGNC
Official Full Name: high mobility group 20Aprovided by HGNC
Primary source: HGNC:HGNC:5001
See related: Ensembl:ENSG00000140382 MIM:605534; AllianceGenome:HGNC:5001
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: HMGX1; HMGXB1
Summary: Enables identical protein binding activity. Predicted to be involved in regulation of gene expression. Predicted to act upstream of or within negative regulation of neuron differentiation; negative regulation of protein sumoylation; and negative regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in spleen (RPKM 13.0), testis (RPKM 10.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 15q24.3

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (77420888..77520050)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (75281332..75380959)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (77713230..77777945)

Chromosome 15 - NC_000015.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HMG20A was identified as a key enhancer driver associated with DNA damage repair in oral squamous cell carcinomas.
Title: HMG20A was identified as a key enhancer driver associated with DNA damage repair in oral squamous cell carcinomas.
The high mobility group protein HMG20A cooperates with the histone reader PHF14 to modulate TGFbeta and Hippo pathways.
Title: The high mobility group protein HMG20A cooperates with the histone reader PHF14 to modulate TGFβ and Hippo pathways.
Identification and Biochemical Characterization of High Mobility Group Protein 20A as a Novel Ca(2+)/S100A6 Target.
Title: Identification and Biochemical Characterization of High Mobility Group Protein 20A as a Novel Ca(2+)/S100A6 Target.
Influence of IGF2BP2, HMG20A, and HNF1B genetic polymorphisms on the susceptibility to Type 2 diabetes mellitus in Chinese Han population.
Title: Influence of IGF2BP2, HMG20A, and HNF1B genetic polymorphisms on the susceptibility to Type 2 diabetes mellitus in Chinese Han population.
rs7178572 at HMG 20A , previously associated with GDM in South Indian and European women, was replicated in North Indian women.
Title: Phenotypic and genotypic differences between Indian and Scandinavian women with gestational diabetes mellitus.
HMG20A is a key regulator of mature beta cell function in type 2 diabetes mellitus.
Title: The type 2 diabetes-associated HMG20A gene is mandatory for islet beta cell functional maturity.
HMG20A together with LSD1 are required for SNAI1-dependent repression of epithelial genes.
Title: HMG20A is required for SNAI1-mediated epithelial to mesenchymal transition.
ectopic expression of BRAP2 inhibits nuclear localization of HMG20A and NuMA1, and prevents nuclear envelope accumulation of SYNE2.
Title: The BRCA1-binding protein BRAP2 can act as a cytoplasmic retention factor for nuclear and nuclear envelope-localizing testicular proteins.
HMG20A/iBRAF forms heterodimers with HMG20B/BRAF35. Heterodimerization impairs HMG20B/BRAF35 sumoylation and interaction with the LSD1-CoREST complex.
Title: Control of neuronal differentiation by sumoylation of BRAF35, a subunit of the LSD1-CoREST histone demethylase complex.
we report associations with the LAMA1 and HMG20A (not previously associated at genome-wide significance in Europeans) gene regions with type 2 diabetes risk
Title: Stratifying type 2 diabetes cases by BMI identifies genetic risk variants in LAMA1 and enrichment for risk variants in lean compared to obese cases.

Submit: New GeneRIF Correction See all GeneRIFs (11)

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

EBI GWAS Catalog

Description
Genome-wide association study in individuals of South Asian ancestry identifies six new type 2 diabetes susceptibility loci. 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
Stratifying type 2 diabetes cases by BMI identifies genetic risk variants in LAMA1 and enrichment for risk variants in lean compared to obese cases. EBI GWAS Catalog EBI GWAS CatalogPubMed
Transferability of type 2 diabetes implicated loci in multi-ethnic cohorts from Southeast Asia. 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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-147252 (e-PCR)
- UniSTS:175700

SGC32715 (e-PCR)
- UniSTS:67679

D15S739 (e-PCR)
- UniSTS:31414

HMG20A_9095 (e-PCR)
- UniSTS:468462

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in chromatin organization	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of neuron differentiation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of protein sumoylation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in regulation of DNA-templated transcription	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	NAS Non-traceable Author Statement more info	PubMed

General protein information

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Preferred Names: high mobility group protein 20A

Names: HMG box domain containing 1; HMG box-containing protein 20A; HMG domain-containing protein 1; HMG domain-containing protein HMGX1

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.

mRNA and Protein(s)

NM_001304504.2 → NP_001291433.1 high mobility group protein 20A isoform a

See identical proteins and their annotated locations for NP_001291433.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an exon in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform (a).

Source sequence(s)

AA233289, AK001601, AK096546

Consensus CDS

CCDS10295.1

UniProtKB/Swiss-Prot

A6NHY3, D3DW78, Q53G31, Q9NP66, Q9NSF6

Related

ENSP00000336856.4, ENST00000336216.9

Conserved Domains (2) summary

cd01390
Location:103 → 168

HMGB-UBF_HMG-box; class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal ...

pfam17380
Location:59 → 313

DUF5401; Family of unknown function (DUF5401)
NM_001304505.2 → NP_001291434.1 high mobility group protein 20A isoform b

See identical proteins and their annotated locations for NP_001291434.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks an exon and uses an alternate splice site in the 5' region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (b) has a shorter N-terminus than isoform a.

Source sequence(s)

AA233289, AK001601, AK096546, DB068283, DB213761

UniProtKB/TrEMBL

B4DMG1

Conserved Domains (1) summary

cd01390
Location:1 → 55

HMGB-UBF_HMG-box; class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal ...
NM_018200.4 → NP_060670.1 high mobility group protein 20A isoform a

See identical proteins and their annotated locations for NP_060670.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1 and 2 encode the same isoform (a).

Source sequence(s)

AA233289, AK001601, AK096546, BC021959, DB213761

Consensus CDS

CCDS10295.1

UniProtKB/Swiss-Prot

A6NHY3, D3DW78, Q53G31, Q9NP66, Q9NSF6

Related

ENSP00000371133.3, ENST00000381714.7

Conserved Domains (2) summary

cd01390
Location:103 → 168

HMGB-UBF_HMG-box; class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal ...

pfam17380
Location:59 → 313

DUF5401; Family of unknown function (DUF5401)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000015.10 Reference GRCh38.p14 Primary Assembly

Range

77420888..77520050

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011521158.4 → XP_011519460.1 high mobility group protein 20A isoform X1

See identical proteins and their annotated locations for XP_011519460.1

UniProtKB/Swiss-Prot

A6NHY3, D3DW78, Q53G31, Q9NP66, Q9NSF6

Conserved Domains (2) summary

cd01390
Location:103 → 168

HMGB-UBF_HMG-box; class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal ...

pfam17380
Location:59 → 313

DUF5401; Family of unknown function (DUF5401)
XM_047432109.1 → XP_047288065.1 high mobility group protein 20A isoform X1

UniProtKB/Swiss-Prot

A6NHY3, D3DW78, Q53G31, Q9NP66, Q9NSF6
XM_047432108.1 → XP_047288064.1 high mobility group protein 20A isoform X1

UniProtKB/Swiss-Prot

A6NHY3, D3DW78, Q53G31, Q9NP66, Q9NSF6