HEATR1

protein-coding

HEAT repeat containing 1, the group of UTPa subcomplex|Minor histocompatibility antigens|Armadillo like helical domain containing

Gene summary

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]

MANE transcript

NM_018072.6

Inheritance

—

ClinVar variants

U:322B:34

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.08

Max pathogenic AF

—

Genomic locus

chr1:236,549,005-236,604,516

External References & Databases

Ensembl (ENSG00000119285)

Transcript & Mutation Effects

hg38 • Region Span ~55.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to HEATR1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 301

not providedTotal: 22

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018072.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	6 clinvar	3 clinvar	11
missense			304 clinvar	20 clinvar	5 clinvar	329
nonsense			2 clinvar			2
start loss						0
frameshift			5 clinvar			5
splice donor/acceptor (+/-2bp)			9 clinvar			9
Total	0	0	322	26	8	356

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018072.6	RefSeq	NP_060542.4	44	MANE Select
ENST00000366582.8	Ensembl	ENSP00000355541.3	44	MANE Select
ENST00000366579.1	Ensembl	ENSP00000355538.1	2	Standard
ENST00000366579.2	Ensembl	ENSP00000355538.1	2	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
heatr1	Danio rerio	Structure: erythroblast Quality: decreased amount abnormal

Gene / Model

Organism

Observed Phenotype

heatr1

Danio rerio

Structure: erythroblast

Quality: decreased amount

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ribosome biogenesis in eukaryotes - Homo sapiens (human)
rRNA processing
Metabolism of RNA
rRNA modification in the nucleus and cytosol
rRNA processing in the nucleus and cytosol

Biological Process

maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
rRNA processing
positive regulation of transcription by RNA polymerase I
positive regulation of rRNA processing

Molecular Function

RNA binding
protein binding

Cellular Component

fibrillar center
nucleoplasm
nucleolus
mitochondrion
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000366582
Coding exons: 44
Length: 55500
Individuals with no LoFs: 125732
Homozygous LoFs: 0
Heterozygous LoFs: 16
Defined: 125748
p: 0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0871	1073	1.08e+3	0.993	0.0000544	14023
Missense (PolyPhen)		248	293.9	0.84381		3931
Synonymous	-0.329	431	422	1.02	0.0000238	4063
Loss of Function	8.81	8	106	0.0757	0.00000512	1406

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000053	0.000053	rare
South Asian	0.00018	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Ribosome biogenesis factor. Involved in nucleolar processing of pre-18S ribosomal RNA. Required for optimal pre- ribosomal RNA transcription by RNA polymerase I. {ECO:0000269|PubMed:17699751}.;

Recessive Scores

pRec: 0.0898

Intolerance Scores

LoFtool: 0.195
RVIS EVS: 2.32
RVIS percentile EVS: 98.37

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.826

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High