PRDX2

peroxiredoxin 2, the group of Peroxiredoxins

Basic information

Region (hg38): 19:12796819-12801800

Previous symbols: [ "TDPX1" ]

Links

ENSG00000167815 ∙ NCBI:7001 ∙ OMIM:600538 ∙ HGNC:9353 ∙ Uniprot:P32119 ∙ 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 PRDX2 gene.

• Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRDX2 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in PRDX2

This is a list of pathogenic ClinVar variants found in the PRDX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-12799911-A-C		not specified	Uncertain significance (Feb 12, 2024)
19-12800229-G-A		not specified	Uncertain significance (May 18, 2022)
19-12800238-C-T		not specified	Uncertain significance (Aug 14, 2023)
19-12800920-C-A		not specified	Uncertain significance (Dec 15, 2023)
19-12800924-G-T		not specified	Uncertain significance (Jan 24, 2024)
19-12800991-C-T		not specified	Likely benign (Jan 03, 2024)
19-12801030-G-C		not specified	Uncertain significance (Oct 06, 2021)
19-12801037-C-T		not specified	Uncertain significance (Nov 14, 2023)
19-12801191-G-A		not specified	Uncertain significance (Aug 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRDX2	protein_coding	protein_coding	ENST00000301522	5	5061

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0865	0.875	125690	0	38	125728	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.05	91	124	0.735	0.00000714	1283
Missense in Polyphen		16	37.609	0.42543		462
Synonymous	-0.170	55	53.4	1.03	0.00000331	401
Loss of Function	1.77	3	8.59	0.349	3.64e-7	101

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00169	0.00169
Finnish	0.00	0.00
European (Non-Finnish)	0.0000443	0.0000440
Middle Eastern	0.00169	0.00169
South Asian	0.0000662	0.0000653
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. Might participate in the signaling cascades of growth factors and tumor necrosis factor-alpha by regulating the intracellular concentrations of H(2)O(2). {ECO:0000269|PubMed:9497357}.
• Pathway: Oxidative Stress Regulatory Pathway (Erythrocyte);Selenium Micronutrient Network;Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer,s disease models;Neurodegenerative Diseases;Disease;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;Transcriptional Regulation by TP53 (Consensus)

Recessive Scores

• pRec: 0.599

Intolerance Scores

• loftool: 0.427
• rvis_EVS: -0.41
• rvis_percentile_EVS: 26.23

Haploinsufficiency Scores

• pHI: 0.926
• hipred: N
• hipred_score: 0.497
• ghis: 0.647

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.993

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prdx2
• Phenotype: immune system phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: response to oxidative stress;removal of superoxide radicals;cellular response to oxidative stress;hydrogen peroxide catabolic process;regulation of apoptotic process;negative regulation of apoptotic process;leukocyte activation;cell redox homeostasis;oxidation-reduction process
• Cellular component: cytoplasm;cytosol;extracellular exosome
• Molecular function: protein binding;thioredoxin peroxidase activity;antioxidant activity