PRDX3

peroxiredoxin 3, the group of Peroxiredoxins

Basic information

Region (hg38): 10:119167719-119178812

Previous symbols: [ "AOP1" ]

Links

ENSG00000165672 ∙ NCBI:10935 ∙ OMIM:604769 ∙ HGNC:9354 ∙ Uniprot:P30048 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spinocerebellar ataxia, autosomal recessive 32 (Moderate), mode of inheritance: AR
• spinocerebellar ataxia, autosomal recessive 32 (Strong), mode of inheritance: AR
• corneal dystrophy, punctiform and polychromatic pre-descemet (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Corneal dystrophy, punctiform and polychromatic pre-Descemet; Spinocerebellar ataxia, autosomal recessive 32	AD/AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic; Ophthalmologic	31782998; 33889951; 34369396; 35792670

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PRDX3 gene.

• Inborn genetic diseases (13 variants)
• not provided (5 variants)
• Spinocerebellar ataxia, autosomal recessive 32 (3 variants)
• Autosomal recessive cerebellar ataxia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRDX3 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				1		1
missense			16	1		17
nonsense		2				2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	2	16	2	0

Highest pathogenic variant AF is 0.00000657

Variants in PRDX3

This is a list of pathogenic ClinVar variants found in the PRDX3 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-119168521-G-T		Inborn genetic diseases	Uncertain significance (Feb 07, 2023)
10-119168531-G-C		Inborn genetic diseases	Uncertain significance (Aug 23, 2021)
10-119169176-C-T			Likely pathogenic (Feb 01, 2024)
10-119169178-G-A		Inborn genetic diseases	Uncertain significance (Aug 13, 2021)
10-119169190-G-A		Inborn genetic diseases	Uncertain significance (Mar 08, 2024)
10-119169202-G-A		Inborn genetic diseases	Uncertain significance (May 05, 2023)
10-119169236-G-A		Spinocerebellar ataxia, autosomal recessive 32	Pathogenic (Jan 26, 2023)
10-119169269-C-T		Inborn genetic diseases	Uncertain significance (Jul 13, 2021)
10-119169290-C-T		Spinocerebellar ataxia, autosomal recessive 32	Pathogenic (May 16, 2022)
10-119169326-C-G		Corneal dystrophy, punctiform and polychromatic pre-descemet	Pathogenic (May 16, 2022)
10-119172394-C-T		Inborn genetic diseases	Uncertain significance (Jan 10, 2024)
10-119172413-C-A		Inborn genetic diseases	Uncertain significance (Mar 11, 2024)
10-119172416-C-A			Likely benign (Jun 01, 2023)
10-119172418-T-C		Inborn genetic diseases	Uncertain significance (Feb 16, 2023)
10-119172425-G-A		Spinocerebellar ataxia, autosomal recessive 32	Likely pathogenic (Sep 01, 2022)
10-119172444-G-C		Spinocerebellar ataxia, autosomal recessive 32	Pathogenic (Mar 31, 2023)
10-119172461-T-A		Inborn genetic diseases	Uncertain significance (Jan 04, 2024)
10-119172482-C-T		Spinocerebellar ataxia, autosomal recessive 32	Uncertain significance (Sep 01, 2022)
10-119173759-G-C		Spinocerebellar ataxia, autosomal recessive 32	Pathogenic (May 16, 2022)
10-119173793-C-T		Inborn genetic diseases	Uncertain significance (Nov 10, 2022)
10-119173797-A-G			Likely benign (Jan 01, 2023)
10-119173798-A-G		Inborn genetic diseases	Uncertain significance (Oct 26, 2021)
10-119173843-G-C		Inborn genetic diseases	Uncertain significance (Feb 05, 2024)
10-119173843-G-GC		Spinocerebellar ataxia, autosomal recessive 32	Pathogenic (May 16, 2022)
10-119173865-C-T			Uncertain significance (Aug 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRDX3	protein_coding	protein_coding	ENST00000298510	7	11131

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00424	0.965	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0584	145	147	0.986	0.00000785	1660
Missense in Polyphen		44	52.458	0.83876		649
Synonymous	0.627	52	58.1	0.895	0.00000360	508
Loss of Function	1.89	6	13.5	0.445	8.26e-7	150

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000580	0.0000580
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000158	0.000158
Middle Eastern	0.000163	0.000163
South Asian	0.000138	0.000131
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 (PubMed:7733872, PubMed:17707404). Acts synergistically with MAP3K13 to regulate the activation of NF-kappa-B in the cytosol (PubMed:12492477). {ECO:0000269|PubMed:12492477, ECO:0000269|PubMed:17707404, ECO:0000269|PubMed:7733872}.
• Pathway: Selenium Micronutrient Network;Detoxification of Reactive Oxygen Species;Cellular responses to stress;Cellular responses to external stimuli;Validated targets of C-MYC transcriptional activation (Consensus)

Recessive Scores

• pRec: 0.338

Intolerance Scores

• loftool: 0.844
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.18

Haploinsufficiency Scores

• pHI: 0.414
• hipred: Y
• hipred_score: 0.783
• ghis: 0.538

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.886

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prdx3
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype; immune system phenotype; cellular phenotype; respiratory system phenotype

Gene ontology

• Biological process: maternal placenta development;apoptotic process;response to oxidative stress;mitochondrion organization;positive regulation of cell population proliferation;peptidyl-cysteine oxidation;myeloid cell differentiation;response to lipopolysaccharide;negative regulation of kinase activity;cellular response to oxidative stress;cellular response to reactive oxygen species;response to hydrogen peroxide;hydrogen peroxide catabolic process;negative regulation of apoptotic process;negative regulation of cysteine-type endopeptidase activity involved in apoptotic process;cell redox homeostasis;positive regulation of NF-kappaB transcription factor activity;regulation of mitochondrial membrane potential;cellular oxidant detoxification
• Cellular component: cytoplasm;mitochondrion;mitochondrial matrix;early endosome;cytosol;protein-containing complex;myelin sheath
• Molecular function: protein binding;protein C-terminus binding;thioredoxin peroxidase activity;alkyl hydroperoxide reductase activity;kinase binding;protein kinase binding;identical protein binding;cysteine-type endopeptidase inhibitor activity involved in apoptotic process