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.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				6	3	9
missense			108	8	5	121
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding					1	1
Total	0	0	108	14	9

Variants in HEATR1

This is a list of pathogenic ClinVar variants found in the HEATR1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-236550909-T-C		not specified	Uncertain significance (Jul 20, 2021)
1-236550954-G-T		not specified	Uncertain significance (Jan 04, 2024)
1-236550992-T-TA		not specified	Benign (Mar 29, 2016)
1-236552116-G-A			Benign (May 08, 2018)
1-236553634-A-G		not specified	Uncertain significance (Aug 08, 2023)
1-236553639-G-C		not specified	Uncertain significance (Mar 30, 2024)
1-236553646-C-T		not specified	Uncertain significance (Aug 02, 2023)
1-236553666-T-C		not specified	Uncertain significance (May 31, 2023)
1-236553699-C-T		not specified	Uncertain significance (Jun 13, 2024)
1-236553718-C-G		not specified	Uncertain significance (Dec 05, 2022)
1-236553723-C-G		not specified	Uncertain significance (May 15, 2023)
1-236554641-C-T		not specified	Uncertain significance (May 20, 2024)
1-236554712-G-A			Likely benign (May 25, 2018)
1-236554735-A-C		not specified	Uncertain significance (May 09, 2023)
1-236555331-G-A		not specified	Uncertain significance (Jun 09, 2022)
1-236555400-G-A		not specified	Uncertain significance (May 07, 2024)
1-236555440-C-G		not specified	Uncertain significance (Apr 07, 2022)
1-236555545-C-G			Benign (Feb 20, 2018)
1-236555581-G-A			Likely benign (Jun 01, 2018)
1-236555587-T-A		not specified	Uncertain significance (Oct 27, 2021)
1-236555588-T-C		not specified	Uncertain significance (Feb 07, 2023)
1-236555618-A-G		not specified	Uncertain significance (Apr 24, 2024)
1-236555625-T-C		not specified	Uncertain significance (Jul 20, 2022)
1-236555630-G-A		not specified	Uncertain significance (Feb 06, 2023)
1-236555652-C-G		not specified	Uncertain significance (Feb 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HEATR1	protein_coding	protein_coding	ENST00000366582	44	55500

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	6.41e-12	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0871	1073	1.08e+3	0.993	0.0000544	14023
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000153	0.000152
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000532	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.000180	0.000131
Other	0.00	0.00

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

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

Mouse Genome Informatics

• Gene name: Heatr1

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