HEATR1

Chr 1

HEAT repeat containing 1

Also known as: BAP28, UTP10

NCBI Gene: 55127ENSG00000119285UniProt: Q9H583

Enables RNA binding activity. Involved in several processes, including positive regulation of RNA metabolic process; protein localization to nucleolus; and ribosomal small subunit biogenesis. Located in fibrillar center and mitochondrion. Part of small-subunit processome. Implicated in pancreatic ductal carcinoma. Biomarker of glioblastoma. [provided by Alliance of Genome Resources, Jul 2025]

0
Active trials
46
Pathogenic / LP
280
ClinVar variants
4
Pubs (1 yr)
0.1
Missense Z
0.14
LOEUF· LoF intolerant
Clinical Summary— HEATR1
⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.
📋
ClinVar Variants
46 Pathogenic / Likely Pathogenic· 205 VUS of 280 total submissions
Some data sources returned errors (1)

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint
0.14LOEUF
pLI 1.000
Z-score 8.81
OE 0.08 (0.04–0.14)
Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint
0.09Z-score
OE missense 0.99 (0.94–1.04)
1073 obs / 1081.1 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.08 (0.04–0.14)
0≤0.351.4
Missense OE0.99 (0.94–1.04)
0≤0.61.4
Synonymous OE1.02
0≤1.21.6
LoF obs/exp: 8 / 105.7Missense obs/exp: 1073 / 1081.1Syn Z: -0.33
LOF
DN
0.3594th %ile
GOF
0.3094th %ile
LOF
0.65top 25%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.14

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

280 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic45
Likely Pathogenic1
VUS205
Likely Benign18
Benign11
45
Pathogenic
1
Likely Pathogenic
205
VUS
18
Likely Benign
11
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
45
0
45
Likely Pathogenic
0
0
1
0
1
VUS
0
189
16
0
205
Likely Benign
0
12
1
5
18
Benign
0
5
3
3
11
Total0206668280

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

HEATR1 · protein map & ClinVar variants

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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Nucleolar HEAT Repeat Containing 1 Up-regulated by the Mechanistic Target of Rapamycin Complex 1 Signaling Promotes Hepatocellular Carcinoma Growth by Dominating Ribosome Biogenesis and Proteome Homeostasis.
Yang XM et al.·Gastroenterology
2023
Silencing HEATR1 Rescues Cisplatin Resistance of Non-small Cell Lung Cancer by Inducing Ferroptosis via the p53/SAT1/ALOX15 Axis.
Ma X et al.·Curr Cancer Drug Targets
2025
Identification of hub genes and pathways in cholangiocarcinoma by coexpression analysis.
Kong J et al.·Cancer Biomark
2020
Revealing the potential role of hub metabolism-related genes and their correlation with immune cells in acute ischemic stroke.
Zhang X et al.·IET Syst Biol
2024
Transcriptomics based multi-dimensional characterization and drug screen in esophageal squamous cell carcinoma.
Li Y et al.·EBioMedicine
2021
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

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