HEBP2

heme binding protein 2

Basic information

Region (hg38): 6:138403531-138422197

Previous symbols: [ "C6orf34" ]

Links

ENSG00000051620 ∙ NCBI:23593 ∙ OMIM:605825 ∙ HGNC:15716 ∙ Uniprot:Q9Y5Z4 ∙ 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 HEBP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HEBP2 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			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	0

Variants in HEBP2

This is a list of pathogenic ClinVar variants found in the HEBP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-138404515-C-T		not specified	Uncertain significance (Aug 08, 2023)
6-138404538-G-A		not specified	Uncertain significance (Mar 15, 2024)
6-138404572-A-T		not specified	Uncertain significance (Nov 18, 2022)
6-138404589-G-C		not specified	Uncertain significance (Jun 09, 2022)
6-138404593-C-T		not specified	Uncertain significance (Aug 28, 2024)
6-138405167-A-G		Malignant tumor of prostate	Uncertain significance (-)
6-138405191-G-T		not specified	Uncertain significance (Jul 09, 2021)
6-138405985-A-G		not specified	Uncertain significance (Feb 21, 2024)
6-138405992-C-T		not specified	Uncertain significance (Jan 29, 2024)
6-138405997-G-A		not specified	Uncertain significance (Oct 16, 2023)
6-138406042-A-G		not specified	Uncertain significance (Apr 26, 2023)
6-138406045-A-G		not specified	Uncertain significance (Jan 03, 2024)
6-138406049-C-T		not specified	Uncertain significance (Feb 23, 2023)
6-138406118-T-C		not specified	Uncertain significance (Dec 27, 2023)
6-138406132-G-C		not specified	Uncertain significance (Jun 16, 2024)
6-138406150-C-T		not specified	Uncertain significance (Apr 07, 2022)
6-138412887-G-A			Likely benign (Jan 01, 2023)
6-138412977-G-A		not specified	Uncertain significance (Aug 05, 2024)
6-138412993-G-A		not specified	Uncertain significance (Oct 01, 2024)
6-138413001-A-G		not specified	Uncertain significance (Dec 17, 2023)
6-138413021-T-A		not specified	Uncertain significance (Mar 14, 2023)
6-138413069-A-C		not specified	Uncertain significance (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HEBP2	protein_coding	protein_coding	ENST00000607197	4	18667

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000608	0.485	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.109	95	98.1	0.969	0.00000486	1340
Missense in Polyphen		36	35.111	1.0253		447
Synonymous	0.116	37	37.9	0.976	0.00000226	373
Loss of Function	0.446	7	8.39	0.834	3.59e-7	116

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000503	0.000503
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.0000442	0.0000439
Middle Eastern	0.000272	0.000272
South Asian	0.000165	0.000163
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Can promote mitochondrial permeability transition and facilitate necrotic cell death under different types of stress conditions. {ECO:0000269|PubMed:17098234}.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.842
• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.49

Haploinsufficiency Scores

• pHI: 0.101
• hipred: N
• hipred_score: 0.170
• ghis: 0.469

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.499

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hebp2

Gene ontology

• Biological process: negative regulation of mitochondrial membrane potential;positive regulation of necrotic cell death;positive regulation of mitochondrial membrane permeability;neutrophil degranulation;regulation of response to reactive oxygen species
• Cellular component: extracellular region;cytoplasm;mitochondrion;azurophil granule lumen;extracellular exosome
• Molecular function: protein binding;heme binding