HMG20A

Chr 15

high mobility group 20A

Also known as: HMGX1, HMGXB1

NCBI Gene: 10363 ENSG00000140382 UniProt: Q9NP66

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, Jul 2025]

Research

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.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.43

LOEUF

—

Mechanism

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?

0.43LOEUF

pLI 0.678

Z-score 3.46

OE 0.19 (0.09–0.43)

Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?

1.41Z-score

OE missense 0.72 (0.63–0.83)

148 obs / 204.9 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.19 (0.09–0.43)

0≤0.351.4

Missense OE?0.72 (0.63–0.83)

0≤0.61.4

Synonymous OE?1.03

0≤1.21.6

LoF obs/exp: 4 / 21.2Missense obs/exp: 148 / 204.9Syn Z: -0.17

Background carrier burden — how many people carry a rare variant somewhere in HMG20A?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 230

362 rare PASS variants

Rare truncating (LoF)

1 in 4,600

50 rare PASS variants

Rare synonymous (reference)

1 in 630

143 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for HMG20A. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 270	1 in 4,100
South Asian	~43k	1 in 150	1 in 4,300
Remaining (unassigned)	~30k	1 in 160	≈ 1 in 7,500
European (Finnish)	~27k	1 in 300	≈ 1 in 27,000
Admixed American	~22k	1 in 200	≈ 1 in 7,400
African / African American	~21k	1 in 150	≈ 1 in 9,200
East Asian	~20k	1 in 250	≈ 1 in 20,000
Ashkenazi Jewish	~13k	1 in 970	1 in 1,900
Middle Eastern	~2,884	1 in 230	none seen

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 7 of 8 coding exons well covered in gnomAD exomes; exon 6 marginal. Genomes: all 8.? see exons ↓