EPX

eosinophil peroxidase

Basic information

Region (hg38): 17:58192726-58205174

Links

ENSG00000121053

∙ NCBI:8288 ∙ OMIM:131399 ∙ HGNC:3423 ∙ Uniprot:P11678 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

eosinophil peroxidase deficiency (No Known Disease Relationship), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Eosinophil peroxidase deficiency	AR	General	The clinical relevance is unclear	General	7809065

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EPX gene.

not_specified (123 variants)
not_provided (14 variants)
Eosinophil_peroxidase_deficiency (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EPX gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000502.6. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous					2 clinvar	2
missense			122 clinvar	7 clinvar	4 clinvar	133
nonsense			1 clinvar		1 clinvar	2
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)				1 clinvar		1
Total	0	0	124	8	7

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EPX	protein_coding	protein_coding	ENST00000225371	12	12438

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.27e-20	0.00677	122463	33	3252	125748	0.0131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.957	503	446	1.13	0.0000321	4598
Missense in Polyphen		161	149.28	1.0785		1787
Synonymous	-0.00419	180	180	1.00	0.0000114	1541
Loss of Function	0.479	32	35.1	0.913	0.00000249	328

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0135	0.0135
Ashkenazi Jewish	0.0121	0.0122
East Asian	0.000381	0.000381
Finnish	0.00755	0.00747
European (Non-Finnish)	0.0150	0.0150
Middle Eastern	0.000381	0.000381
South Asian	0.0292	0.0286
Other	0.0155	0.0156

dbNSFP

Source: dbNSFP

Function: FUNCTION: Mediates tyrosine nitration of secondary granule proteins in mature resting eosinophils. Shows significant inhibitory activity towards Mycobacterium tuberculosis H37Rv by inducing bacterial fragmentation and lysis. {ECO:0000269|PubMed:12540536, ECO:0000269|PubMed:18694936}.;
Disease: DISEASE: Eosinophil peroxidase deficiency (EPXD) [MIM:261500]: A rare abnormality without clinical symptoms characterized by decreased or absent peroxidase activity and decreased volume of the granule matrix in eosinophils. {ECO:0000269|PubMed:7809065}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway: Asthma - Homo sapiens (human);Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

pRec: 0.279

Intolerance Scores

loftool: 0.861
rvis_EVS: 1.14
rvis_percentile_EVS: 92.39

Haploinsufficiency Scores

pHI: 0.117
hipred: N
hipred_score: 0.270
ghis

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.843

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Epx
Phenotype: immune system phenotype; hematopoietic system phenotype;

Gene ontology

Biological process: defense response to nematode;response to oxidative stress;negative regulation of interleukin-10 production;negative regulation of interleukin-5 production;positive regulation of interleukin-4 production;defense response to bacterium;hydrogen peroxide catabolic process;neutrophil degranulation;oxidation-reduction process;eosinophil migration;cellular oxidant detoxification
Cellular component: extracellular region;extracellular space;cytoplasm;secretory granule lumen;extracellular exosome
Molecular function: peroxidase activity;heme binding;metal ion binding