HMGA1

Chr 6

high mobility group AT-hook 1

Also known as: HMG-R, HMGA1A, HMGIY

NCBI Gene: 3159ENSG00000137309UniProt: P17096

This gene encodes a chromatin-associated protein involved in the regulation of gene transcription, integration of retroviruses into chromosomes, and the metastatic progression of cancer cells. The encoded protein preferentially binds to the minor groove of AT-rich regions in double-stranded DNA. Multiple transcript variants encoding different isoforms have been found for this gene. Pseudogenes of this gene have been identified on multiple chromosomes. [provided by RefSeq, Jan 2016]

ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant
This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.
1
Active trials
120
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.51
LOEUF
Multiple*
Mechanism· predicted
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint?
0.51LOEUF
pLI 0.832
Z-score 2.25
OE 0.00 (0.00–0.51)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?
1.81Z-score
OE missense 0.38 (0.27–0.53)
25 obs / 66.5 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.00 (0.00–0.51)
0≤0.351.4
Missense OE?0.38 (0.27–0.53)
0≤0.61.4
Synonymous OE?0.99
0≤1.21.6
LoF obs/exp: 0 / 5.9Missense obs/exp: 25 / 66.5Syn Z: 0.04

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

HMGA1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients