PCYOX1L

protein-coding

prenylcysteine oxidase 1 like

Gene summary

Enables prenylcysteine oxidase activity. Predicted to be involved in neutrophil-mediated killing of bacterium and prenylated protein catabolic process. Located in membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_024028.4

Inheritance

—

ClinVar variants

U:84B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.88

Max pathogenic AF

—

Genomic locus

chr5:149,358,037-149,369,653

External References & Databases

Ensembl (ENSG00000145882)

Transcript & Mutation Effects

hg38 • Region Span ~11.6 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 PCYOX1L variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 80

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024028.4. 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				1 clinvar		1
missense			83 clinvar			83
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	84	1	0	85

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024028.4	RefSeq	NP_076933.3	6	MANE Select
ENST00000274569.9	Ensembl	ENSP00000274569.4	6	MANE Select
NM_001301054.2	RefSeq	NP_001287983.1	6	Standard
NM_001301057.2	RefSeq	NP_001287986.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Platelet degranulation
Response to elevated platelet cytosolic Ca2+
Platelet activation, signaling and aggregation
Hemostasis

Biological Process

platelet degranulation
prenylated protein catabolic process
prenylcysteine catabolic process
oxidation-reduction process

Molecular Function

prenylcysteine oxidase activity

Cellular Component

extracellular region
membrane
platelet alpha granule lumen

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000274569
Coding exons: 6
Length: 11647
Individuals with no LoFs: 125711
Homozygous LoFs: 0
Heterozygous LoFs: 37
Defined: 125748
p: 0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.542	261	287	0.910	0.0000176	3189
Missense (PolyPhen)		111	135	0.82224		1484
Synonymous	0.126	127	129	0.986	0.00000850	1025
Loss of Function	0.483	17	19.3	0.881	0.00000101	206

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00033	0.00033	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0.00023	0.00023	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable oxidoreductase. {ECO:0000250}.;

Intolerance Scores

LoFtool: 0.638
RVIS EVS: 0.6
RVIS percentile EVS: 82.74

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.141

Gene Damage Prediction

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