HMGA1

high mobility group AT-hook 1, the group of Canonical high mobility group|MicroRNA protein coding host genes

Basic information

Region (hg38): 6:34236872-34246231

Previous symbols: [ "HMGIY" ]

Links

ENSG00000137309 ∙ NCBI:3159 ∙ OMIM:600701 ∙ HGNC:5010 ∙ Uniprot:P17096 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• type 2 diabetes mellitus (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HMGA1 gene.

• not provided (2 variants)
• Inborn genetic diseases (2 variants)
• Diabetes mellitus type 2, susceptibility to (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HMGA1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	2	0	2

Variants in HMGA1

This is a list of pathogenic ClinVar variants found in the HMGA1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
6-34240791-C-T		not specified	Uncertain significance (Jun 22, 2021)
6-34240809-A-G		not specified	Uncertain significance (Oct 29, 2021)
6-34240837-C-T			Benign (Dec 31, 2019)
6-34240882-G-A		not specified	Likely benign (Sep 19, 2023)
6-34242693-A-AC		Diabetes mellitus type 2, susceptibility to	Benign (Apr 19, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HMGA1	protein_coding	protein_coding	ENST00000447654	4	9359

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.832	0.165	124928	0	1	124929	0.00000400

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.81	25	66.5	0.376	0.00000451	670
Missense in Polyphen		0	5.7641	0		31
Synonymous	0.0383	27	27.3	0.991	0.00000193	211
Loss of Function	2.25	0	5.88	0.00	3.37e-7	67

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000890	0.00000890
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: HMG-I/Y bind preferentially to the minor groove of A+T rich regions in double-stranded DNA. It is suggested that these proteins could function in nucleosome phasing and in the 3'-end processing of mRNA transcripts. They are also involved in the transcription regulation of genes containing, or in close proximity to A+T-rich regions.
• Disease: DISEASE: Note=A chromosomal aberration involving HMGA1 is found in pulmonary chondroid hamartoma. Translocation t(6;14)(p21;q23-24) with RAD51B. {ECO:0000269|PubMed:11978964}.
• Pathway: miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Adipogenesis;Preimplantation Embryo;Senescence and Autophagy in Cancer;Disease;il 4 signaling pathway;HIV Life Cycle;Host Interactions of HIV factors;HIV Infection;Formation of Senescence-Associated Heterochromatin Foci (SAHF);DNA Damage/Telomere Stress Induced Senescence;Vpr-mediated nuclear import of PICs;2-LTR circle formation;Cellular Senescence;Cellular responses to stress;Infectious disease;APOBEC3G mediated resistance to HIV-1 infection;Cellular responses to external stimuli;Interactions of Vpr with host cellular proteins;Validated targets of C-MYC transcriptional activation;IL4-mediated signaling events;Integration of viral DNA into host genomic DNA;Autointegration results in viral DNA circles;Integration of provirus;Early Phase of HIV Life Cycle (Consensus)

Recessive Scores

• pRec: 0.535

Intolerance Scores

• loftool: 0.467
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• pHI: 0.994
• hipred: Y
• hipred_score: 0.711
• ghis: 0.654

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.959

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Hmga1
• Phenotype: hearing/vestibular/ear phenotype; limbs/digits/tail phenotype; skeleton phenotype; immune system phenotype; neoplasm; endocrine/exocrine gland phenotype; growth/size/body region phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: DNA unwinding involved in DNA replication;base-excision repair;nucleosome disassembly;regulation of transcription, DNA-templated;negative regulation of cell population proliferation;response to virus;negative regulation of chromatin silencing;senescence-associated heterochromatin focus assembly;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;nuclear transport;protein-containing complex assembly;establishment of integrated proviral latency;oncogene-induced cell senescence;positive regulation of cellular senescence
• Cellular component: nucleus;nucleoplasm;transcription factor complex;cytosol;focal adhesion;senescence-associated heterochromatin focus;RNA polymerase II transcription factor complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;enhancer sequence-specific DNA binding;DNA binding;AT DNA binding;chromatin binding;transcription coactivator activity;DNA-(apurinic or apyrimidinic site) endonuclease activity;protein binding;transcription factor binding;enzyme binding;nuclear receptor transcription coactivator activity;structural constituent of chromatin;retinoic acid receptor binding;peroxisome proliferator activated receptor binding;retinoid X receptor binding