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.

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.

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					2	2
missense			57	6	4	67
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region				1	1	2
non coding						0
Total	0	0	57	7	7

Variants in EPX

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

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

Position	Type	Phenotype	Significance	ClinVar
17-58192860-C-T		not specified	Likely benign (Mar 04, 2024)
17-58193064-G-A			Benign (May 08, 2018)
17-58193077-G-A			Benign (Mar 29, 2018)
17-58193093-G-C		not specified	Uncertain significance (Feb 11, 2022)
17-58193110-C-T		not specified	Uncertain significance (May 09, 2024)
17-58193136-A-G			Likely benign (Dec 31, 2019)
17-58193388-G-A		not specified	Uncertain significance (Nov 20, 2023)
17-58193393-G-A		not specified	Uncertain significance (May 30, 2024)
17-58193513-C-A		not specified	Uncertain significance (Dec 28, 2022)
17-58193528-G-A		not specified	Likely benign (Dec 12, 2022)
17-58193537-A-C		not specified	Uncertain significance (Jun 22, 2024)
17-58193737-C-T		not specified	Uncertain significance (Jan 16, 2024)
17-58193776-C-G		not specified	Uncertain significance (Sep 12, 2023)
17-58193807-C-G		not specified	Uncertain significance (Aug 17, 2022)
17-58193818-C-T		not specified	Uncertain significance (Nov 17, 2022)
17-58193839-C-T			Benign (May 14, 2018)
17-58193980-G-A		not specified	Uncertain significance (Apr 09, 2024)
17-58194968-G-A		not specified	Uncertain significance (May 31, 2022)
17-58194982-C-A		not specified	Uncertain significance (Mar 01, 2023)
17-58195001-A-G		not specified	Likely benign (Aug 16, 2021)
17-58195022-G-A		not specified	Uncertain significance (Aug 09, 2021)
17-58195028-G-A		not specified	Uncertain significance (Jul 14, 2022)
17-58195037-T-C		not specified	Uncertain significance (Feb 10, 2022)
17-58195094-C-T		not specified	Uncertain significance (Dec 06, 2021)
17-58195111-A-G		not specified	Uncertain significance (Dec 28, 2022)

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

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