HBP1

Chr 7

HMG-box transcription factor 1

NCBI Gene: 26959ENSG00000105856UniProt: O60381

Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of lipid transport; negative regulation of reactive oxygen species biosynthetic process; and negative regulation of transcription by RNA polymerase II. Located in nuclear speck. Biomarker of osteoarthritis. [provided by Alliance of Genome Resources, Jul 2025]

0
ClinVar variants
0
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— HBP1
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.34) despite low pLI — interpret in context.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.59LOEUF
pLI 0.004
Z-score 3.17
OE 0.34 (0.20–0.59)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
1.64Z-score
OE missense 0.72 (0.64–0.81)
197 obs / 273.3 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.34 (0.20–0.59)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.72 (0.64–0.81)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.13
0≤1.21.6
LoF obs/exp: 9 / 26.6Missense obs/exp: 197 / 273.3Syn Z: -0.99

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

HBP1 · protein map & ClinVar variants

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

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
The HBP1 transcriptional repressor and the p38 MAP kinase: unlikely partners in G1 regulation and tumor suppression.
Yee AS et al.·Gene
2004Review
HBP1 enhances progesterone receptor activity and IGFBP1 expression driving endometrial decidualization.
Guo Y et al.·Commun Biol
2026
Circ-0044539 promotes lymph node metastasis of hepatocellular carcinoma through exosomal-miR-29a-3p.
Yang Y et al.·Cell Death Dis
2024
HBP1-mediated transcriptional repression of AFP inhibits hepatoma progression.
Cao Z et al.·J Exp Clin Cancer Res
2021
HBP1 promoter methylation augments the oncogenic β-catenin to correlate with prognosis in NSCLC.
Tseng RC et al.·J Cell Mol Med
2014
Transcription Factor HBP1 Enhances Radiosensitivity by Inducing Apoptosis in Prostate Cancer Cell Lines.
Chen Y et al.·Anal Cell Pathol (Amst)
2016
Alterations of the HBP1 transcriptional repressor are associated with invasive breast cancer.
Paulson KE et al.·Cancer Res
2007
Identification and validation of prognostic biomarkers in ccRCC: immune-stromal score and survival prediction.
Lyu F et al.·BMC Cancer
2025
Diagnosis and treatment of severe hypertriglyceridemia.
Viljoen A et al.·Expert Rev Cardiovasc Ther
2012Review
The HBP1 transcriptional repressor participates in RAS-induced premature senescence.
Zhang X et al.·Mol Cell Biol
2006
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

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External Resources

Links to major genomics databases and tools