HEATR5B

HEAT repeat containing 5B, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 2:36968383-37084372

Links

ENSG00000008869 ∙ NCBI:54497 ∙ OMIM:619627 ∙ HGNC:29273 ∙ Uniprot:Q9P2D3 ∙ 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 HEATR5B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HEATR5B 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				3		3
missense			85			85
nonsense		1				1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region		1				1
non coding						0
Total	0	2	85	3	0

Variants in HEATR5B

This is a list of pathogenic ClinVar variants found in the HEATR5B region.

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

Position	Type	Phenotype	Significance	ClinVar
2-36981546-G-A		not specified	Uncertain significance (Dec 28, 2022)
2-36981551-C-T		not specified	Uncertain significance (Jan 31, 2024)
2-36981576-C-T		not specified	Uncertain significance (Sep 10, 2024)
2-36981591-C-T		not specified	Uncertain significance (Oct 26, 2021)
2-36981596-G-A		not specified	Uncertain significance (Jul 12, 2023)
2-36981626-G-A		not specified	Uncertain significance (Jul 26, 2022)
2-36981671-T-C		not specified	Uncertain significance (May 28, 2024)
2-36981780-C-T		not specified	Uncertain significance (Dec 04, 2024)
2-36988670-C-T		not specified	Uncertain significance (May 17, 2023)
2-36988705-G-A		not specified	Uncertain significance (May 02, 2024)
2-36988718-T-C		not specified	Uncertain significance (Apr 09, 2024)
2-36988747-G-C		not specified	Uncertain significance (Oct 16, 2024)
2-36988763-C-A		not specified	Uncertain significance (May 17, 2023)
2-36988769-T-C		not specified	Uncertain significance (Mar 24, 2023)
2-36988775-C-A		not specified	Uncertain significance (Dec 15, 2021)
2-36988807-C-T		not specified	Uncertain significance (Aug 02, 2023)
2-36988844-A-T		not specified	Uncertain significance (Dec 15, 2022)
2-36990686-T-A		not specified	Uncertain significance (Jun 26, 2024)
2-36990709-T-A		not specified	Uncertain significance (Jun 21, 2023)
2-36990751-G-A		not specified	Uncertain significance (Mar 06, 2023)
2-36990763-A-G		not specified	Uncertain significance (May 23, 2024)
2-36990766-A-T		not specified	Uncertain significance (May 20, 2024)
2-36990768-G-T		not specified	Uncertain significance (Aug 05, 2024)
2-37000640-A-C		not specified	Uncertain significance (May 24, 2023)
2-37000670-C-T		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HEATR5B	protein_coding	protein_coding	ENST00000233099	35	115960

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.07e-22	1.00	125573	0	175	125748	0.000696

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.14	933	1.14e+3	0.821	0.0000616	13351
Missense in Polyphen		147	275.37	0.53383		3275
Synonymous	-2.93	477	402	1.19	0.0000216	4290
Loss of Function	4.76	54	107	0.504	0.00000684	1184

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000783	0.000779
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000545	0.000544
Finnish	0.00337	0.00338
European (Non-Finnish)	0.000519	0.000501
Middle Eastern	0.000545	0.000544
South Asian	0.000303	0.000294
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.834
• rvis_EVS: -2.51
• rvis_percentile_EVS: 0.91

Haploinsufficiency Scores

• pHI: 0.253
• hipred: Y
• hipred_score: 0.685
• ghis: 0.623

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.600

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Heatr5b

Gene ontology

• Biological process: endocytosis;protein localization;retrograde transport, endosome to Golgi
• Cellular component: cytosol;membrane;endocytic vesicle
• Molecular function: protein binding