PCYOX1

prenylcysteine oxidase 1

Basic information

Region (hg38): 2:70257386-70281185

Links

ENSG00000116005 ∙ NCBI:51449 ∙ OMIM:610995 ∙ HGNC:20588 ∙ Uniprot:Q9UHG3 ∙ 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 PCYOX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCYOX1 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			23	2	1	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	2	1

Variants in PCYOX1

This is a list of pathogenic ClinVar variants found in the PCYOX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-70258181-C-T		not specified	Uncertain significance (Oct 12, 2022)
2-70258193-C-T		not specified	Uncertain significance (Aug 20, 2024)
2-70258196-C-T		not specified	Uncertain significance (Jan 03, 2024)
2-70258219-C-G		not specified	Uncertain significance (Dec 05, 2022)
2-70258243-G-C		not specified	Uncertain significance (Mar 28, 2024)
2-70258259-C-G		not specified	Uncertain significance (Sep 01, 2021)
2-70259381-G-T		not specified	Uncertain significance (Sep 26, 2024)
2-70259398-T-C		not specified	Uncertain significance (Feb 23, 2023)
2-70259465-G-A		not specified	Uncertain significance (Oct 12, 2024)
2-70259484-G-T		not specified	Uncertain significance (Jan 04, 2024)
2-70259528-C-T		not specified	Uncertain significance (Sep 06, 2022)
2-70259536-C-G		not specified	Uncertain significance (Mar 03, 2022)
2-70261322-C-T		not specified	Uncertain significance (Jun 29, 2023)
2-70261343-C-T		not specified	Uncertain significance (Aug 23, 2021)
2-70261352-A-G		not specified	Uncertain significance (Sep 10, 2024)
2-70274964-A-T		not specified	Uncertain significance (Jul 17, 2024)
2-70275002-G-A		not specified	Uncertain significance (Jan 23, 2023)
2-70275030-A-G		not specified	Uncertain significance (Jun 13, 2022)
2-70275059-C-T		not specified	Uncertain significance (Aug 01, 2024)
2-70275150-C-T		not specified	Likely benign (Jul 19, 2022)
2-70275568-A-T		not specified	Uncertain significance (Nov 07, 2022)
2-70275588-C-T		not specified	Uncertain significance (May 20, 2024)
2-70275592-T-A		not specified	Uncertain significance (Oct 05, 2023)
2-70275597-G-A		not specified	Uncertain significance (Jul 25, 2024)
2-70275616-T-C		not specified	Uncertain significance (Jun 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCYOX1	protein_coding	protein_coding	ENST00000433351	6	23806

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.25e-15	0.00844	125593	0	155	125748	0.000616

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0672	290	287	1.01	0.0000154	3299
Missense in Polyphen		100	107.19	0.93293		1282
Synonymous	-0.0915	111	110	1.01	0.00000614	986
Loss of Function	-0.174	22	21.1	1.04	0.00000109	256

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00115	0.00115
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000892	0.000888
Middle Eastern	0.000111	0.000109
South Asian	0.000655	0.000653
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the degradation of prenylated proteins. Cleaves the thioether bond of prenyl-L-cysteines, such as farnesylcysteine and geranylgeranylcysteine.
• Pathway: Terpenoid backbone biosynthesis - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.133

Intolerance Scores

• loftool: 0.902
• rvis_EVS: -0.2
• rvis_percentile_EVS: 39.11

Haploinsufficiency Scores

• pHI: 0.0935
• hipred: N
• hipred_score: 0.197
• ghis: 0.567

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.359

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcyox1
• Phenotype: normal phenotype

Gene ontology

• Biological process: prenylated protein catabolic process;prenylcysteine catabolic process;prenylcysteine metabolic process;oxidation-reduction process;ATP hydrolysis coupled anion transmembrane transport;chloride transmembrane transport
• Cellular component: lysosome;plasma membrane;very-low-density lipoprotein particle;extracellular exosome
• Molecular function: prenylcysteine oxidase activity;chloride-transporting ATPase activity