HEBP1

heme binding protein 1, the group of Receptor ligands

Basic information

Region (hg38): 12:12974870-13000265

Links

ENSG00000013583 ∙ NCBI:50865 ∙ OMIM:605826 ∙ HGNC:17176 ∙ Uniprot:Q9NRV9 ∙ 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 HEBP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HEBP1 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			17
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	0	0

Variants in HEBP1

This is a list of pathogenic ClinVar variants found in the HEBP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-12975316-T-G		not specified	Uncertain significance (May 16, 2023)
12-12975379-A-G		not specified	Uncertain significance (Jan 09, 2024)
12-12975388-C-T		not specified	Uncertain significance (Apr 22, 2022)
12-12975429-C-T		not specified	Uncertain significance (Nov 09, 2021)
12-12975445-C-T		not specified	Uncertain significance (Sep 30, 2024)
12-12987176-C-T		not specified	Uncertain significance (Nov 25, 2024)
12-12987177-G-A		not specified	Uncertain significance (Jun 16, 2023)
12-12987185-A-G		not specified	Uncertain significance (Dec 21, 2021)
12-12987323-A-T		not specified	Uncertain significance (Jun 28, 2022)
12-12989283-C-A		not specified	Uncertain significance (Aug 11, 2022)
12-12989300-T-C		not specified	Uncertain significance (Aug 02, 2021)
12-12989306-G-T		not specified	Uncertain significance (Jun 03, 2022)
12-12989327-C-T		not specified	Uncertain significance (Jun 25, 2024)
12-12989352-C-G		not specified	Uncertain significance (Dec 08, 2023)
12-12989363-A-G		not specified	Uncertain significance (Oct 20, 2024)
12-13000042-C-T		not specified	Uncertain significance (Nov 27, 2023)
12-13000056-A-C		not specified	Uncertain significance (Aug 02, 2021)
12-13000061-C-A		not specified	Uncertain significance (Feb 07, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HEBP1	protein_coding	protein_coding	ENST00000014930	4	25410

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000418	0.228	125706	0	42	125748	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0938	115	118	0.976	0.00000708	1232
Missense in Polyphen		42	47.624	0.88192		489
Synonymous	-0.803	51	44.2	1.15	0.00000261	371
Loss of Function	-0.112	8	7.66	1.04	3.23e-7	97

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000947	0.0000916
Ashkenazi Jewish	0.00	0.00
East Asian	0.000442	0.000435
Finnish	0.00	0.00
European (Non-Finnish)	0.0000449	0.0000439
Middle Eastern	0.000442	0.000435
South Asian	0.000892	0.000882
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May bind free porphyrinogens that may be present in the cell and thus facilitate removal of these potentially toxic compound. Binds with a high affinity to one molecule of heme or porphyrins. It binds metalloporphyrins, free porphyrins and N- methylprotoporphyrin with similar affinities. {ECO:0000269|PubMed:12413491}.
• Pathway: Signaling by GPCR;Signal Transduction;Formyl peptide receptors bind formyl peptides and many other ligands;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (i) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.135

Intolerance Scores

• loftool: 0.670
• rvis_EVS: -0.18
• rvis_percentile_EVS: 39.95

Haploinsufficiency Scores

• pHI: 0.142
• hipred: N
• hipred_score: 0.248
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hebp1

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;circadian rhythm
• Cellular component: extracellular region;extracellular exosome
• Molecular function: heme binding