HPX

hemopexin

Basic information

Region (hg38): 11:6431049-6442617

Links

ENSG00000110169 ∙ NCBI:3263 ∙ OMIM:142290 ∙ HGNC:5171 ∙ Uniprot:P02790 ∙ 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 HPX gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HPX 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					5	5
missense			27	4	5	36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	4	10

Variants in HPX

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

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

Position	Type	Phenotype	Significance	ClinVar
11-6431224-C-A		not specified	Uncertain significance (Apr 12, 2022)
11-6431302-A-G		not specified	Uncertain significance (Oct 14, 2023)
11-6431325-C-A		not specified	Uncertain significance (Dec 12, 2023)
11-6431337-A-T		not specified	Uncertain significance (Sep 01, 2021)
11-6431338-T-C		not specified	Uncertain significance (May 29, 2024)
11-6431359-C-A		not specified	Uncertain significance (Feb 21, 2024)
11-6431375-T-C		not specified	Likely benign (Mar 18, 2024)
11-6431388-G-A			Benign (Jun 19, 2018)
11-6431424-C-T			Benign (Apr 16, 2018)
11-6431437-C-T		not specified	Uncertain significance (Jan 10, 2023)
11-6431465-G-A		not specified	Uncertain significance (Mar 08, 2024)
11-6431468-G-A			Likely benign (Jun 19, 2018)
11-6431647-T-C		not specified	Uncertain significance (Feb 16, 2023)
11-6431659-G-A			Benign (Mar 02, 2018)
11-6431671-G-A		not specified	Uncertain significance (Aug 28, 2024)
11-6431719-T-A		not specified	Likely benign (Feb 05, 2024)
11-6431723-G-A			Benign (Jul 26, 2018)
11-6431752-C-T		not specified	Uncertain significance (Nov 22, 2023)
11-6431796-T-C		not specified	Uncertain significance (Jul 15, 2024)
11-6431964-T-C		not specified	Uncertain significance (Sep 25, 2024)
11-6437069-T-C		not specified	Uncertain significance (Jan 09, 2023)
11-6437069-T-G		not specified	Uncertain significance (Dec 22, 2023)
11-6437138-G-C		not specified	Uncertain significance (Apr 11, 2023)
11-6437144-T-C		not specified	Uncertain significance (Dec 16, 2023)
11-6437160-C-T		not specified	Likely benign (Aug 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HPX	protein_coding	protein_coding	ENST00000265983	10	11569

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.30e-11	0.321	125665	0	81	125746	0.000322

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.818	235	273	0.861	0.0000161	3001
Missense in Polyphen		69	81.629	0.84528		933
Synonymous	-0.862	113	102	1.11	0.00000562	906
Loss of Function	1.05	20	25.8	0.777	0.00000129	272

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00120	0.00120
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.0000942	0.0000924
European (Non-Finnish)	0.000319	0.000316
Middle Eastern	0.000218	0.000217
South Asian	0.000295	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds heme and transports it to the liver for breakdown and iron recovery, after which the free hemopexin returns to the circulation.
• Pathway: Vesicle-mediated transport;Scavenging of heme from plasma;Binding and Uptake of Ligands by Scavenger Receptors (Consensus)

Recessive Scores

• pRec: 0.543

Intolerance Scores

• loftool: 0.786
• rvis_EVS: 0.11
• rvis_percentile_EVS: 62.1

Haploinsufficiency Scores

• pHI: 0.278
• hipred: N
• hipred_score: 0.331
• ghis: 0.441

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.410

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hpx
• Phenotype: homeostasis/metabolism phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; liver/biliary system phenotype; immune system phenotype; renal/urinary system phenotype

Gene ontology

• Biological process: positive regulation of immunoglobulin production;positive regulation of humoral immune response mediated by circulating immunoglobulin;proteolysis;cellular iron ion homeostasis;receptor-mediated endocytosis;heme transport;viral process;heme metabolic process;positive regulation of tyrosine phosphorylation of STAT protein;positive regulation of interferon-gamma-mediated signaling pathway
• Cellular component: extracellular region;extracellular space;collagen-containing extracellular matrix;extracellular exosome;endocytic vesicle lumen;blood microparticle
• Molecular function: protein binding;heme transporter activity;metal ion binding