GeneBe

HEATR1

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

Basic information

Region (hg38): 1:236549005-236604516

Links

ENSG00000119285 ∙ NCBI:55127 ∙ ∙ HGNC:25517 ∙ Uniprot:Q9H583 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HEATR1 gene.

  • not_specified (267 variants)
  • not_provided (18 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HEATR1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018072.6. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
6
clinvar
3
clinvar
 9
missense
250
clinvar
18
clinvar
5
clinvar
 273
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 250 24 8
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
HEATR1protein_codingprotein_codingENST00000366582 4455500
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.006.41e-121257320161257480.0000636
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.087110731.08e+30.9930.000054414023
Missense in Polyphen248293.90.843813931
Synonymous-0.3294314221.020.00002384063
Loss of Function8.8181060.07570.000005121406

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001530.000152
Ashkenazi Jewish0.00009920.0000992
East Asian0.00005440.0000544
Finnish0.00004620.0000462
European (Non-Finnish)0.00005320.0000527
Middle Eastern0.00005440.0000544
South Asian0.0001800.000131
Other0.000.00

dbNSFP

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}.;
Pathway
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 (Consensus)

Recessive Scores

pRec
0.0898

Intolerance Scores

loftool
0.195
rvis_EVS
2.32
rvis_percentile_EVS
98.37

Haploinsufficiency Scores

pHI
0.0975
hipred
Y
hipred_score
0.689
ghis
0.552

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.826

Gene Damage Prediction

AllRecessiveDominant
MendelianHighHighHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh

Mouse Genome Informatics

Gene name
Heatr1
Phenotype

Zebrafish Information Network

Gene name
heatr1
Affected structure
erythroblast
Phenotype tag
abnormal
Phenotype quality
decreased amount

Gene ontology

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
Cellular component
fibrillar center;nucleoplasm;nucleolus;mitochondrion;membrane;90S preribosome;small-subunit processome;t-UTP complex
Molecular function
RNA binding;protein binding