PCYOX1

protein-coding

prenylcysteine oxidase 1

Gene summary

Prenylcysteine is released during the degradation of prenylated proteins. PCYOX1 catalyzes the degradation of prenylcysteine to yield free cysteines and a hydrophobic isoprenoid product (Tschantz et al., 1999 [PubMed 10585463]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_016297.4

Inheritance

—

ClinVar variants

U:78B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.04

Max pathogenic AF

—

Genomic locus

chr2:70,257,386-70,281,185

External References & Databases

Ensembl (ENSG00000116005)

Transcript & Mutation Effects

hg38 • Region Span ~23.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PCYOX1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 75

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016297.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			76 clinvar	5 clinvar	1 clinvar	82
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	78	5	1	84

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016297.4	RefSeq	NP_057381.3	6	MANE Select
ENST00000433351.7	Ensembl	ENSP00000387654.2	6	MANE Select
ENST00000264441.10	Ensembl	ENSP00000264441.5	6	Standard
ENST00000264441.9	Ensembl	ENSP00000264441.5	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Terpenoid backbone biosynthesis - Homo sapiens (human)

Biological Process

prenylated protein catabolic process
prenylcysteine catabolic process
prenylcysteine metabolic process
oxidation-reduction process
ATP hydrolysis coupled anion transmembrane transport

Molecular Function

prenylcysteine oxidase activity
chloride-transporting ATPase activity

Cellular Component

lysosome
plasma membrane
very-low-density lipoprotein particle
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000433351
Coding exons: 6
Length: 23806
Individuals with no LoFs: 125593
Homozygous LoFs: 0
Heterozygous LoFs: 155
Defined: 125748
p: 0.000616

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0672	290	287	1.01	0.0000154	3299
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00074	0.00074	rare
Latino/Admixed American	0.00041	0.00040	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.00023	0.00023	rare
European (Non-Finnish)	0.00089	0.00089	rare
South Asian	0.00065	0.00065	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in the degradation of prenylated proteins. Cleaves the thioether bond of prenyl-L-cysteines, such as farnesylcysteine and geranylgeranylcysteine.;

Recessive Scores

pRec: 0.133

Intolerance Scores

LoFtool: 0.902
RVIS EVS: -0.2
RVIS percentile EVS: 39.11

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.359

Gene Damage Prediction

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