PRDX4

peroxiredoxin 4, the group of Peroxiredoxins

Basic information

Region (hg38): X:23664261-23686397

Links

ENSG00000123131 ∙ NCBI:10549 ∙ OMIM:300927 ∙ HGNC:17169 ∙ Uniprot:Q13162 ∙ 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 PRDX4 gene.

• Inborn genetic diseases (8 variants)
• not provided (1 variants)
• Neurodevelopmental delay (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRDX4 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			9		1	10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	1

Variants in PRDX4

This is a list of pathogenic ClinVar variants found in the PRDX4 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-23667598-A-G		not specified	Uncertain significance (Dec 09, 2023)
X-23667619-C-A		not specified	Uncertain significance (Oct 27, 2022)
X-23667754-G-A		not specified	Uncertain significance (Mar 07, 2024)
X-23671559-C-G		not specified	Uncertain significance (Apr 07, 2023)
X-23671600-G-A			Benign (Feb 25, 2018)
X-23671606-C-T		not specified	Uncertain significance (Nov 21, 2022)
X-23675006-A-T		not specified	Uncertain significance (Sep 26, 2022)
X-23675046-G-C		not specified	Uncertain significance (Apr 14, 2022)
X-23679223-G-C		not specified	Uncertain significance (Apr 25, 2022)
X-23682515-A-G		not specified	Uncertain significance (Mar 31, 2023)
X-23682520-G-A		Neurodevelopmental delay	Uncertain significance (Apr 03, 2017)
X-23686321-G-A		not specified	Uncertain significance (Jul 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRDX4	protein_coding	protein_coding	ENST00000379341	7	22138

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0268	0.925	125738	5	4	125747	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.04	68	96.8	0.703	0.00000682	1720
Missense in Polyphen		18	39.478	0.45595		706
Synonymous	-0.284	43	40.7	1.06	0.00000295	563
Loss of Function	1.70	4	9.71	0.412	6.72e-7	173

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000270	0.000253
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000748	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000250	0.0000176
Middle Eastern	0.0000748	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Thiol-specific peroxidase that catalyzes the reduction of hydrogen peroxide and organic hydroperoxides to water and alcohols, respectively. Plays a role in cell protection against oxidative stress by detoxifying peroxides and as sensor of hydrogen peroxide-mediated signaling events. Regulates the activation of NF-kappa-B in the cytosol by a modulation of I- kappa-B-alpha phosphorylation. {ECO:0000269|PubMed:9388242}.
• Pathway: Selenium Micronutrient Network;Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.302

Intolerance Scores

• loftool: 0.586
• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.28

Haploinsufficiency Scores

• pHI: 0.207
• hipred: Y
• hipred_score: 0.593
• ghis: 0.399

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.244

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prdx4
• Phenotype: reproductive system phenotype; endocrine/exocrine gland phenotype; cellular phenotype

Gene ontology

• Biological process: response to oxidative stress;I-kappaB phosphorylation;spermatogenesis;male gonad development;4-hydroxyproline metabolic process;protein maturation by protein folding;extracellular matrix organization;hydrogen peroxide catabolic process;neutrophil degranulation;cell redox homeostasis;oxidation-reduction process;cellular oxidant detoxification;negative regulation of male germ cell proliferation
• Cellular component: extracellular region;nucleus;cytoplasm;endoplasmic reticulum;smooth endoplasmic reticulum;cytosol;secretory granule lumen;extracellular exosome;ficolin-1-rich granule lumen
• Molecular function: protein binding;thioredoxin peroxidase activity;protein homodimerization activity