HEATR4

HEAT repeat containing 4, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 14:73478484-73558947

Links

ENSG00000187105 ∙ NCBI:399671 ∙ ∙ HGNC:16761 ∙ Uniprot:Q86WZ0 ∙ 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 HEATR4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HEATR4 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				1		1
missense			67	9		76
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			24	7	5	36
Total	0	0	92	17	5

Variants in HEATR4

This is a list of pathogenic ClinVar variants found in the HEATR4 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-73478611-G-A		not specified	Likely benign (Feb 27, 2023)
14-73478641-A-G		not specified	Uncertain significance (Dec 01, 2022)
14-73478694-G-C		not specified	Uncertain significance (Feb 06, 2023)
14-73478701-C-T		not specified	Uncertain significance (Dec 10, 2024)
14-73478769-C-T		not specified	Likely benign (Oct 05, 2023)
14-73478819-A-T		not specified	Uncertain significance (May 04, 2023)
14-73491097-G-A		not specified	Uncertain significance (Aug 09, 2021)
14-73491111-C-A			Benign (Dec 31, 2019)
14-73492604-C-G			Benign/Likely benign (Sep 01, 2022)
14-73495282-T-C		not specified	Uncertain significance (Mar 01, 2024)
14-73495300-G-A		not specified	Uncertain significance (Jun 01, 2023)
14-73495318-C-G		not specified	Uncertain significance (Jan 03, 2024)
14-73495324-C-T		not specified	Likely benign (Aug 12, 2021)
14-73495332-A-G		not specified	Uncertain significance (Sep 02, 2024)
14-73496615-C-G		not specified	Uncertain significance (Dec 15, 2023)
14-73496636-C-T		not specified	Uncertain significance (Dec 28, 2022)
14-73496651-T-C		not specified	Uncertain significance (Jun 06, 2023)
14-73498165-C-T		not specified	Uncertain significance (Oct 06, 2022)
14-73498168-C-T		not specified	Uncertain significance (Oct 16, 2024)
14-73498189-C-T		not specified	Uncertain significance (Jan 23, 2024)
14-73498198-A-G		not specified	Uncertain significance (Nov 21, 2022)
14-73498212-C-G		not specified	Uncertain significance (Jul 27, 2024)
14-73498212-C-T		not specified	Likely benign (Jan 03, 2024)
14-73498221-T-A		not specified	Uncertain significance (Jul 30, 2023)
14-73498245-C-T		not specified	Uncertain significance (Sep 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HEATR4	protein_coding	protein_coding	ENST00000553558	16	80463

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.37e-29	0.000243	124776	10	962	125748	0.00387

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.329	554	576	0.961	0.0000322	6679
Missense in Polyphen		138	150.52	0.91679		1887
Synonymous	0.786	197	212	0.931	0.0000109	2027
Loss of Function	0.388	46	48.9	0.940	0.00000251	550

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0380	0.0379
Ashkenazi Jewish	0.00919	0.00917
East Asian	0.00224	0.00223
Finnish	0.000140	0.000139
European (Non-Finnish)	0.00117	0.00116
Middle Eastern	0.00224	0.00223
South Asian	0.00153	0.00108
Other	0.00261	0.00261

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0751

Intolerance Scores

• loftool: 0.988
• rvis_EVS: -0.01
• rvis_percentile_EVS: 52.38

Haploinsufficiency Scores

• pHI: 0.0788
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0864

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Heatr4