PRDX1

peroxiredoxin 1, the group of Peroxiredoxins

Basic information

Region (hg38): 1:45510914-45542732

Previous symbols: [ "PAGA" ]

Links

ENSG00000117450 ∙ NCBI:5052 ∙ OMIM:176763 ∙ HGNC:9352 ∙ Uniprot:Q06830 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• methylmalonic aciduria and homocystinuria type cblC (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Methylmalonic aciduria and homocystinuria, cblC type, digenic	AR/Digenic	Biochemical	While no treatment is completely effective, specific dietary (eg, high-calorie, low protein diet and avoidance of fasting, with measures taken to avoid/treat decompensation) and other medical measures (eg, cofactor therapy) may be beneficial to treat and prevent sequelae in the acute and chronic states	Biochemical; Cardiovascular; Dermatologic; Hematologic; Neurologic; Ophthalmologic; Renal	29302025
Compound heterozygosity and digenic inheritance (with MMACHC) has been described

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PRDX1 gene.

• METHYLMALONIC ACIDURIA AND HOMOCYSTINURIA, cblC TYPE, DIGENIC (1 variants)
• Cobalamin C disease (1 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRDX1 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	10		11
missense			16			16
nonsense			1			1
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)	1					1
splice region				1	1	2
non coding			2	3	10	15
Total	1	0	22	13	10

Variants in PRDX1

This is a list of pathogenic ClinVar variants found in the PRDX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-45510915-A-G		Disorders of Intracellular Cobalamin Metabolism	Benign (Jan 13, 2018)
1-45510916-T-A		Disorders of Intracellular Cobalamin Metabolism	Uncertain significance (Jan 13, 2018)
1-45510929-A-G		Disorders of Intracellular Cobalamin Metabolism	Uncertain significance (Jan 13, 2018)
1-45510958-C-T		Disorders of Intracellular Cobalamin Metabolism	Uncertain significance (Jan 13, 2018)
1-45511371-A-G			Likely benign (Sep 15, 2021)
1-45511375-T-G			Uncertain significance (Jan 26, 2022)
1-45511377-GA-G			Uncertain significance (Dec 09, 2023)
1-45511406-C-A			Uncertain significance (Nov 20, 2023)
1-45511415-C-A		METHYLMALONIC ACIDURIA AND HOMOCYSTINURIA, cblC TYPE, DIGENIC • Cobalamin C disease	Pathogenic (Apr 11, 2023)
1-45511416-T-A		METHYLMALONIC ACIDURIA AND HOMOCYSTINURIA, cblC TYPE, DIGENIC	Pathogenic (Apr 04, 2023)
1-45511583-CAT-C			Benign (May 22, 2021)
1-45514499-T-C			Likely benign (Jan 02, 2024)
1-45514518-T-C		Inborn genetic diseases	Uncertain significance (May 04, 2023)
1-45514564-C-G			Uncertain significance (Apr 21, 2022)
1-45514580-G-A			Likely benign (Sep 10, 2023)
1-45514647-G-T			Likely benign (Dec 21, 2023)
1-45514651-TGAAAG-T			Likely benign (Aug 14, 2023)
1-45514864-A-T			Likely benign (Dec 28, 2023)
1-45514913-C-G		Inborn genetic diseases	Uncertain significance (Jan 18, 2022)
1-45514916-G-A			Uncertain significance (Jul 14, 2022)
1-45514924-G-C		Inborn genetic diseases	Uncertain significance (Feb 05, 2024)
1-45514954-T-C		Inborn genetic diseases	Uncertain significance (Nov 08, 2022)
1-45514958-T-C			Uncertain significance (May 03, 2022)
1-45514959-G-A			Likely benign (Aug 22, 2022)
1-45514967-G-A		PRDX1-related disorder	Benign (Nov 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRDX1	protein_coding	protein_coding	ENST00000262746	5	12012

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.70e-10	0.0218	125687	0	60	125747	0.000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.200	103	109	0.946	0.00000536	1320
Missense in Polyphen		35	41.196	0.8496		513
Synonymous	-0.129	40	39.0	1.03	0.00000193	373
Loss of Function	-1.08	12	8.59	1.40	3.63e-7	107

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000549	0.000547
Ashkenazi Jewish	0.000702	0.000695
East Asian	0.000279	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000297	0.000290
Middle Eastern	0.000279	0.000272
South Asian	0.0000653	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) (PubMed:9497357). Reduces an intramolecular disulfide bond in GDPD5 that gates the ability to GDPD5 to drive postmitotic motor neuron differentiation (By similarity). {ECO:0000250|UniProtKB:P0CB50, ECO:0000269|PubMed:9497357}.
• Pathway: Peroxisome - Homo sapiens (human);Androgen receptor signaling pathway;Selenium Micronutrient Network;Nuclear Receptors Meta-Pathway;NRF2 pathway;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;AndrogenReceptor;TP53 Regulates Metabolic Genes;Cellular responses to external stimuli;Coregulation of Androgen receptor activity;Transcriptional Regulation by TP53 (Consensus)

Recessive Scores

• pRec: 0.732

Intolerance Scores

• loftool: 0.944
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.42

Haploinsufficiency Scores

• pHI: 0.843
• hipred: Y
• hipred_score: 0.734
• ghis: 0.620

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• 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: Prdx1
• Phenotype: hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); neoplasm; immune system phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: skeletal system development;retina homeostasis;response to oxidative stress;cell population proliferation;removal of superoxide radicals;natural killer cell activation;regulation of stress-activated MAPK cascade;erythrocyte homeostasis;cellular response to oxidative stress;natural killer cell mediated cytotoxicity;hydrogen peroxide catabolic process;leukocyte activation;cell redox homeostasis;oxidation-reduction process;regulation of NIK/NF-kappaB signaling
• Cellular component: extracellular space;nucleus;cytoplasm;cytosol;melanosome;myelin sheath;extracellular exosome
• Molecular function: RNA binding;peroxidase activity;protein binding;thioredoxin peroxidase activity;identical protein binding;cadherin binding