PRDX6

peroxiredoxin 6, the group of Peroxiredoxins

Basic information

Region (hg38): 1:173477329-173488815

Links

ENSG00000117592 ∙ NCBI:9588 ∙ OMIM:602316 ∙ HGNC:16753 ∙ Uniprot:P30041 ∙ 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 PRDX6 gene.

• Inborn genetic diseases (6 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRDX6 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	6	0	0

Variants in PRDX6

This is a list of pathogenic ClinVar variants found in the PRDX6 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-173477402-C-T		not specified	Uncertain significance (Feb 03, 2022)
1-173477439-T-G		not specified	Uncertain significance (Aug 30, 2021)
1-173481318-C-G			Benign (May 18, 2018)
1-173481351-C-G		not specified	Uncertain significance (May 09, 2023)
1-173481352-G-A		not specified	Uncertain significance (Jan 23, 2024)
1-173481421-G-A		not specified	Uncertain significance (Jul 09, 2021)
1-173485389-C-T		not specified	Uncertain significance (Dec 15, 2023)
1-173485421-G-C		not specified	Uncertain significance (Jan 11, 2023)
1-173486377-G-T		not specified	Uncertain significance (Dec 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRDX6	protein_coding	protein_coding	ENST00000340385	5	11542

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000482	0.439	125717	0	31	125748	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.47	78	124	0.630	0.00000602	1465
Missense in Polyphen		20	45.269	0.4418		572
Synonymous	0.134	44	45.1	0.975	0.00000209	455
Loss of Function	0.341	7	8.04	0.870	3.46e-7	104

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000300	0.000277
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000205	0.000202
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
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. Can reduce H(2)O(2) and short chain organic, fatty acid, and phospholipid hydroperoxides. Also has phospholipase activity, and can therefore either reduce the oxidized sn-2 fatty acyl grup of phospholipids (peroxidase activity) or hydrolyze the sn-2 ester bond of phospholipids (phospholipase activity). These activities are dependent on binding to phospholipids at acidic pH and to oxidized phospholipds at cytosolic pH. Plays a role in cell protection against oxidative stress by detoxifying peroxides and in phospholipid homeostasis. {ECO:0000269|PubMed:10893423, ECO:0000269|PubMed:9497358}.
• Pathway: Nuclear Receptors Meta-Pathway;NRF2 pathway;Neutrophil degranulation;Detoxification of Reactive Oxygen Species;Cellular responses to stress;Tyrosine metabolism;Androgen and estrogen biosynthesis and metabolism;Purine metabolism;Innate Immune System;Immune System;Cellular responses to external stimuli;Arachidonic acid metabolism (Consensus)

Recessive Scores

• pRec: 0.519

Intolerance Scores

• loftool: 0.589
• rvis_EVS: -0.27
• rvis_percentile_EVS: 33.97

Haploinsufficiency Scores

• pHI: 0.423
• hipred: N
• hipred_score: 0.456
• ghis: 0.584

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.998

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prdx6
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; renal/urinary system phenotype; normal phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); liver/biliary system phenotype; respiratory system phenotype

Gene ontology

• Biological process: response to oxidative stress;cellular response to oxidative stress;hydrogen peroxide catabolic process;neutrophil degranulation;cell redox homeostasis;glycerophospholipid catabolic process;positive regulation of mRNA splicing, via spliceosome;oxidation-reduction process;cellular oxidant detoxification
• Cellular component: extracellular region;extracellular space;nucleus;cytoplasm;cytosol;membrane;azurophil granule lumen;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: peroxidase activity;glutathione peroxidase activity;protein binding;ubiquitin protein ligase binding;protein homodimerization activity;cadherin binding;calcium-independent phospholipase A2 activity;peroxiredoxin activity;phospholipase A2 activity (consuming 1,2-dipalmitoylphosphatidylcholine);phospholipase A2 activity consuming 1,2-dioleoylphosphatidylethanolamine)