HEATR3

HEAT repeat containing 3, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 16:50065967-50107272

Links

ENSG00000155393 ∙ NCBI:55027 ∙ OMIM:614951 ∙ HGNC:26087 ∙ Uniprot:Q7Z4Q2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Diamond-Blackfan anemia 21 (Strong), mode of inheritance: AR
• Diamond-Blackfan anemia 21 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Diamond-Blackfan anemia 21	AR	Cardiovascular; Hematologic; Oncologic	The condition can include congenital cardiac anomalies, and awareness may allow early diagnosis and management; The condition may involve severe anemia, and interventions such as transfusions have been described; Individuals may be at an increased risk of certain types of cancer, and awareness may allow early diagnosis and management of oncologic manifestations	Cardiovascular; Craniofacial; Hematologic; Musculoskeletal; Neurologic; Oncologic	35213692

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HEATR3 gene.

• Diamond-Blackfan anemia 21 (2 variants)
• Diamond-Blackfan anemia 1 (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HEATR3 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						0
missense	1		54	4	2	61
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)	1					1
splice region						0
non coding						0
Total	2	0	54	4	2

Variants in HEATR3

This is a list of pathogenic ClinVar variants found in the HEATR3 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-50066160-A-G		not specified	Uncertain significance (Jan 20, 2025)
16-50066170-G-C		not specified	Uncertain significance (Nov 18, 2022)
16-50066178-C-T		not specified	Uncertain significance (Dec 12, 2023)
16-50066180-A-G		not specified	Uncertain significance (Dec 11, 2024)
16-50066204-G-C		not specified	Uncertain significance (Mar 05, 2025)
16-50066250-C-G		not specified	Uncertain significance (Aug 15, 2023)
16-50066371-A-G		not specified	Uncertain significance (Feb 16, 2023)
16-50066371-A-T		not specified	Uncertain significance (Apr 04, 2023)
16-50066387-G-C		not specified	Uncertain significance (Sep 23, 2023)
16-50066425-T-C		not specified	Uncertain significance (Jun 07, 2024)
16-50066439-G-T		not specified	Uncertain significance (Jan 01, 2025)
16-50066442-C-T		not specified	Uncertain significance (Jul 27, 2024)
16-50066449-G-T		not specified	Uncertain significance (Jan 04, 2025)
16-50066455-C-T		not specified	Uncertain significance (Oct 03, 2022)
16-50066464-A-G		not specified	Uncertain significance (Nov 20, 2024)
16-50066467-C-T		Diamond-Blackfan anemia 21	Uncertain significance (Nov 28, 2023)
16-50066473-G-A		not specified	Uncertain significance (Apr 22, 2022)
16-50066476-G-C		not specified	Uncertain significance (Oct 04, 2022)
16-50066517-G-A		not specified	Uncertain significance (Jan 17, 2025)
16-50066520-A-G		not specified	Uncertain significance (Mar 28, 2024)
16-50068819-C-G		not specified	Uncertain significance (Jul 10, 2024)
16-50068857-T-A		not specified	Uncertain significance (Feb 07, 2023)
16-50068868-G-T		Diamond-Blackfan anemia 1 • Diamond-Blackfan anemia 21	Pathogenic (Jan 13, 2022)
16-50070178-T-C		Diamond-Blackfan anemia 1 • Diamond-Blackfan anemia 21	Pathogenic (Oct 12, 2022)
16-50070187-G-A		not specified	Uncertain significance (Jun 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HEATR3	protein_coding	protein_coding	ENST00000299192	15	40447

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.52e-7	0.987	125701	0	46	125747	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.14	275	333	0.825	0.0000160	4429
Missense in Polyphen		37	64.493	0.57371		901
Synonymous	-0.187	131	128	1.02	0.00000692	1320
Loss of Function	2.28	15	28.0	0.536	0.00000118	389

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000421	0.000421
Ashkenazi Jewish	0.000198	0.0000992
East Asian	0.000109	0.000109
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000183	0.000176
Middle Eastern	0.000109	0.000109
South Asian	0.000164	0.000163
Other	0.000331	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.752
• rvis_EVS: 0.11
• rvis_percentile_EVS: 62

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.492
• ghis: 0.509

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.387

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Heatr3
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: protein import into nucleus;ribosomal large subunit biogenesis
• Cellular component: cell
• Molecular function: unfolded protein binding