PCYOX1L

prenylcysteine oxidase 1 like

Basic information

Region (hg38): 5:149358036-149369653

Links

ENSG00000145882 ∙ NCBI:78991 ∙ ∙ HGNC:28477 ∙ Uniprot:Q8NBM8 ∙ 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 PCYOX1L gene.

• Inborn genetic diseases (20 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCYOX1L 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			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in PCYOX1L

This is a list of pathogenic ClinVar variants found in the PCYOX1L region.

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

Position	Type	Phenotype	Significance	ClinVar
5-149358079-C-T		not specified	Uncertain significance (May 31, 2023)
5-149358085-C-A		not specified	Uncertain significance (Sep 27, 2022)
5-149358088-T-A		not specified	Uncertain significance (Jul 20, 2022)
5-149358096-G-C		not specified	Uncertain significance (Feb 28, 2023)
5-149358117-G-A		not specified	Uncertain significance (Sep 21, 2023)
5-149358152-A-T		not specified	Uncertain significance (Mar 05, 2024)
5-149362637-C-T		not specified	Uncertain significance (May 25, 2022)
5-149364048-G-A		not specified	Uncertain significance (Mar 02, 2023)
5-149364071-G-A		not specified	Uncertain significance (Nov 21, 2023)
5-149364080-G-A		not specified	Uncertain significance (Feb 08, 2023)
5-149364150-A-C		not specified	Uncertain significance (Mar 22, 2023)
5-149366009-G-A		not specified	Uncertain significance (Jul 25, 2023)
5-149366111-C-T		not specified	Uncertain significance (Dec 26, 2023)
5-149367377-G-A		not specified	Uncertain significance (Oct 05, 2023)
5-149367423-T-C		not specified	Uncertain significance (Jan 17, 2023)
5-149368017-C-T		not specified	Uncertain significance (Aug 26, 2022)
5-149368057-C-G		not specified	Uncertain significance (Aug 17, 2022)
5-149368184-G-A		not specified	Uncertain significance (May 31, 2023)
5-149368319-C-T		not specified	Uncertain significance (Jun 02, 2023)
5-149368458-C-T		not specified	Uncertain significance (Jul 26, 2022)
5-149368461-G-T		not specified	Uncertain significance (Jan 23, 2023)
5-149368467-C-T		not specified	Uncertain significance (Jul 26, 2021)
5-149368477-G-T		not specified	Uncertain significance (Apr 21, 2022)
5-149368509-A-G		not specified	Uncertain significance (Apr 07, 2023)
5-149368614-A-T		not specified	Uncertain significance (Jul 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCYOX1L	protein_coding	protein_coding	ENST00000274569	6	11647

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.56e-11	0.129	125711	0	37	125748	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.542	261	287	0.910	0.0000176	3189
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000148	0.000148
Ashkenazi Jewish	0.00	0.00
East Asian	0.000327	0.000326
Finnish	0.0000474	0.0000462
European (Non-Finnish)	0.000168	0.000167
Middle Eastern	0.000327	0.000326
South Asian	0.000229	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable oxidoreductase. {ECO:0000250}.
• Pathway: Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Intolerance Scores

• loftool: 0.638
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.74

Haploinsufficiency Scores

• pHI: 0.213
• hipred: N
• hipred_score: 0.251
• ghis: 0.459

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.141

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcyox1l

Gene ontology

• Biological process: platelet degranulation;prenylated protein catabolic process;prenylcysteine catabolic process;oxidation-reduction process
• Cellular component: extracellular region;membrane;platelet alpha granule lumen
• Molecular function: prenylcysteine oxidase activity