PRDX5

peroxiredoxin 5, the group of Peroxiredoxins

Basic information

Region (hg38): 11:64318120-64321811

Links

ENSG00000126432 ∙ NCBI:25824 ∙ OMIM:606583 ∙ HGNC:9355 ∙ Uniprot:P30044 ∙ 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 PRDX5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRDX5 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			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	0

Variants in PRDX5

This is a list of pathogenic ClinVar variants found in the PRDX5 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-64318264-C-A		not specified	Uncertain significance (May 04, 2023)
11-64318270-G-C		not specified	Likely benign (Jul 26, 2022)
11-64319836-G-C		not specified	Uncertain significance (Dec 21, 2022)
11-64320674-G-A		not specified	Uncertain significance (Feb 26, 2024)
11-64320895-T-G		not specified	Uncertain significance (Dec 27, 2022)
11-64321056-G-A		not specified	Uncertain significance (May 25, 2022)
11-64321595-G-A		not specified	Uncertain significance (May 17, 2023)
11-64321659-A-G		not specified	Uncertain significance (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRDX5	protein_coding	protein_coding	ENST00000265462	6	3724

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000179	0.717	125720	0	28	125748	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0820	119	122	0.979	0.00000594	1350
Missense in Polyphen		24	42.704	0.562		515
Synonymous	-1.08	61	51.2	1.19	0.00000252	476
Loss of Function	0.938	7	10.2	0.684	5.85e-7	113

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000182	0.000176
Middle Eastern	0.000163	0.000163
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

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. {ECO:0000269|PubMed:10514471, ECO:0000269|PubMed:10521424, ECO:0000269|PubMed:10751410}.
• Pathway: Peroxisome - Homo sapiens (human);Selenium Micronutrient Network;Detoxification of Reactive Oxygen Species;Gene expression (Transcription);Generic Transcription Pathway;Cellular responses to stress;RNA Polymerase II Transcription;TP53 Regulates Metabolic Genes;Cellular responses to external stimuli;thioredoxin pathway;Transcriptional Regulation by TP53 (Consensus)

Recessive Scores

• pRec: 0.551

Intolerance Scores

• loftool: 0.869
• rvis_EVS: 0.42
• rvis_percentile_EVS: 76.81

Haploinsufficiency Scores

• pHI: 0.410
• hipred: N
• hipred_score: 0.335
• ghis: 0.450

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.863

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prdx5

Gene ontology

• Biological process: apoptotic process;inflammatory response;response to oxidative stress;negative regulation of transcription by RNA polymerase III;cellular response to oxidative stress;cellular response to reactive oxygen species;hydrogen peroxide catabolic process;negative regulation of apoptotic process;negative regulation of cysteine-type endopeptidase activity involved in apoptotic process;cell redox homeostasis;oxidation-reduction process;cellular oxidant detoxification
• Cellular component: extracellular space;nucleus;cytoplasm;mitochondrion;mitochondrial matrix;peroxisome;peroxisomal matrix;cytosol;cytoplasmic vesicle;intracellular membrane-bounded organelle;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: RNA polymerase III regulatory region DNA binding;peroxidase activity;signaling receptor binding;protein binding;thioredoxin peroxidase activity;cysteine-type endopeptidase inhibitor activity involved in apoptotic process;protein dimerization activity