ACOX3

acyl-CoA oxidase 3, pristanoyl

Basic information

Region (hg38): 4:8366282-8440723

Links

ENSG00000087008 ∙ NCBI:8310 ∙ OMIM:603402 ∙ HGNC:121 ∙ Uniprot:O15254 ∙ 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 ACOX3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACOX3 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				7	4	11
missense			89	7	4	100
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					3	3
non coding					1	1
Total	0	0	89	14	9

Variants in ACOX3

This is a list of pathogenic ClinVar variants found in the ACOX3 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-8367004-G-A		not specified	Uncertain significance (Aug 02, 2021)
4-8367028-C-T		not specified	Uncertain significance (Dec 08, 2023)
4-8367029-G-A		not specified	Uncertain significance (Mar 29, 2022)
4-8367038-C-G		not specified	Uncertain significance (Aug 29, 2024)
4-8367062-C-T		not specified	Uncertain significance (Jan 05, 2022)
4-8370910-C-T		not specified	Uncertain significance (Jun 02, 2023)
4-8370958-C-T		not specified	Uncertain significance (May 16, 2024)
4-8370966-T-G		not specified	Uncertain significance (Jul 30, 2023)
4-8370974-G-A		not specified	Likely benign (Aug 31, 2023)
4-8371000-G-A			Benign (-)
4-8373581-C-T		not specified	Likely benign (Feb 23, 2023)
4-8373609-C-T			Likely benign (Nov 01, 2022)
4-8373615-G-A			Benign (-)
4-8373620-A-T		not specified	Uncertain significance (Mar 20, 2024)
4-8374992-G-A			Uncertain significance (Mar 03, 2020)
4-8374996-C-A		not specified	Uncertain significance (Apr 25, 2023)
4-8375037-C-T		not specified	Uncertain significance (Jun 13, 2022)
4-8375052-C-T		not specified	Uncertain significance (Apr 29, 2024)
4-8375053-G-A		not specified	Uncertain significance (May 03, 2023)
4-8375059-A-C		not specified	Uncertain significance (Mar 23, 2023)
4-8375083-C-T		not specified	Uncertain significance (Sep 26, 2024)
4-8375092-G-A		not specified	Uncertain significance (Oct 02, 2023)
4-8375108-C-G			Benign (-)
4-8375130-G-A		not specified	Uncertain significance (Dec 21, 2023)
4-8375131-C-G		not specified	Uncertain significance (Mar 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACOX3	protein_coding	protein_coding	ENST00000356406	17	74442

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.60e-16	0.208	125484	1	263	125748	0.00105

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.445	469	443	1.06	0.0000289	4483
Missense in Polyphen		133	125.42	1.0604		1275
Synonymous	-0.941	205	189	1.09	0.0000135	1433
Loss of Function	1.25	28	36.1	0.775	0.00000186	410

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00163	0.00163
Ashkenazi Jewish	0.00	0.00
East Asian	0.00906	0.00759
Finnish	0.000324	0.000323
European (Non-Finnish)	0.000609	0.000598
Middle Eastern	0.00906	0.00759
South Asian	0.000338	0.000327
Other	0.000930	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Oxidizes the CoA-esters of 2-methyl-branched fatty acids. {ECO:0000250, ECO:0000269|PubMed:9271077}.
• Pathway: Peroxisome - Homo sapiens (human);Biosynthesis of unsaturated fatty acids - Homo sapiens (human);Fatty acid degradation - Homo sapiens (human);cAMP signaling pathway - Homo sapiens (human);alpha-Linolenic acid metabolism - Homo sapiens (human);PPAR signaling pathway - Homo sapiens (human);PPAR signaling pathway;Metabolism of lipids;Metabolism of proteins;Tyrosine metabolism;Leukotriene metabolism;Beta-oxidation of pristanoyl-CoA;Omega-3 fatty acid metabolism;Saturated fatty acids beta-oxidation;Trihydroxycoprostanoyl-CoA beta-oxidation;Peroxisomal lipid metabolism;Metabolism;Peroxisomal protein import;Fatty acid metabolism;Mono-unsaturated fatty acid beta-oxidation;Omega-6 fatty acid metabolism;Bile acid biosynthesis;Di-unsaturated fatty acid beta-oxidation;Phytanic acid peroxisomal oxidation (Consensus)

Recessive Scores

• pRec: 0.634

Intolerance Scores

• loftool: 0.188
• rvis_EVS: -0.79
• rvis_percentile_EVS: 12.63

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.170
• ghis: 0.506

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.828

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Acox3

Gene ontology

• Biological process: protein targeting to peroxisome;fatty acid beta-oxidation using acyl-CoA oxidase;lipid homeostasis
• Cellular component: peroxisome;peroxisomal matrix;cytosol;membrane
• Molecular function: acyl-CoA oxidase activity;signaling receptor binding;fatty acid binding;pristanoyl-CoA oxidase activity;flavin adenine dinucleotide binding;FAD binding