ACSL3

acyl-CoA synthetase long chain family member 3, the group of Acyl-CoA synthetase family

Basic information

Region (hg38): 2:222860942-222944639

Previous symbols: [ "FACL3" ]

Links

ENSG00000123983 ∙ NCBI:2181 ∙ OMIM:602371 ∙ HGNC:3570 ∙ Uniprot:O95573 ∙ 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 ACSL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACSL3 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				1	2	3
missense			17	2		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	3	2

Variants in ACSL3

This is a list of pathogenic ClinVar variants found in the ACSL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-222908805-C-T			Benign/Likely benign (Mar 01, 2023)
2-222908851-C-T		not specified	Uncertain significance (Jun 16, 2023)
2-222908870-A-G		not specified	Uncertain significance (Mar 20, 2023)
2-222908890-C-G		not specified	Uncertain significance (Aug 12, 2021)
2-222916424-A-G		not specified	Uncertain significance (Oct 25, 2023)
2-222916427-G-T		not specified	Uncertain significance (Aug 01, 2022)
2-222916430-A-G		not specified	Uncertain significance (Mar 19, 2024)
2-222916468-A-G			Benign (May 04, 2018)
2-222919158-A-T		not specified	Uncertain significance (May 01, 2024)
2-222919191-A-G			Likely benign (May 30, 2018)
2-222919199-A-G		not specified	Likely benign (Jun 27, 2023)
2-222921325-T-C		not specified	Uncertain significance (May 26, 2022)
2-222922760-A-G		not specified	Uncertain significance (Dec 01, 2022)
2-222922811-C-T		not specified	Uncertain significance (Feb 22, 2023)
2-222922829-C-G		not specified	Uncertain significance (Dec 15, 2022)
2-222922830-A-G		not specified	Uncertain significance (Nov 08, 2022)
2-222923079-C-A		not specified	Uncertain significance (May 30, 2023)
2-222927019-T-C		not specified	Uncertain significance (Jan 04, 2022)
2-222927027-C-T		not specified	Uncertain significance (Dec 07, 2021)
2-222927117-A-G		not specified	Uncertain significance (Aug 02, 2021)
2-222930750-A-G		not specified	Uncertain significance (Nov 15, 2021)
2-222933168-C-G		not specified	Uncertain significance (Oct 03, 2022)
2-222934531-T-C		not specified	Uncertain significance (Nov 12, 2021)
2-222934572-G-A			Benign (Aug 24, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACSL3	protein_coding	protein_coding	ENST00000357430	14	83706

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000348	1.00	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.01	283	396	0.715	0.0000211	4711
Missense in Polyphen		97	176.49	0.5496		2050
Synonymous	-0.960	154	140	1.10	0.00000755	1377
Loss of Function	3.72	13	37.6	0.346	0.00000204	468

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000590	0.0000590
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000882	0.0000879
Middle Eastern	0.000110	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acyl-CoA synthetases (ACSL) activates long-chain fatty acids for both synthesis of cellular lipids, and degradation via beta-oxidation. ACSL3 mediates hepatic lipogenesis (By similarity). Preferentially uses myristate, laurate, arachidonate and eicosapentaenoate as substrates (By similarity). Has mainly an anabolic role in energy metabolism. Required for the incorporation of fatty acids into phosphatidylcholine, the major phospholipid located on the surface of VLDL (very low density lipoproteins). {ECO:0000250, ECO:0000269|PubMed:18003621}.
• Pathway: Adipocytokine signaling pathway - Homo sapiens (human);Peroxisome - Homo sapiens (human);Thermogenesis - Homo sapiens (human);Fatty acid degradation - Homo sapiens (human);Fatty acid biosynthesis - Homo sapiens (human);PPAR signaling pathway - Homo sapiens (human);Ferroptosis - Homo sapiens (human);Fatty Acid Beta Oxidation;Fatty Acid Biosynthesis;Mitochondrial LC-Fatty Acid Beta-Oxidation;PPAR signaling pathway;Liver steatosis AOP;stearate biosynthesis;Metabolism of lipids;Fatty acyl-CoA biosynthesis;fatty acid activation;Leukotriene metabolism;Omega-3 fatty acid metabolism;Metabolism;Fatty acid metabolism;γ-linolenate biosynthesis;Mono-unsaturated fatty acid beta-oxidation;Omega-6 fatty acid metabolism;Di-unsaturated fatty acid beta-oxidation;Phytanic acid peroxisomal oxidation;fatty acid β-oxidation (peroxisome);icosapentaenoate biosynthesis II (metazoa);fatty acid β-oxidation;Synthesis of very long-chain fatty acyl-CoAs (Consensus)

Recessive Scores

• pRec: 0.186

Intolerance Scores

• loftool: 0.500
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.49

Haploinsufficiency Scores

• pHI: 0.827
• hipred: Y
• hipred_score: 0.554
• ghis: 0.512

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.997

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Acsl3
• Phenotype: growth/size/body region phenotype; immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: long-chain fatty acid metabolic process;fatty acid biosynthetic process;brain development;response to nutrient;response to organic cyclic compound;very-low-density lipoprotein particle assembly;long-chain fatty-acyl-CoA biosynthetic process;positive regulation of Golgi to plasma membrane protein transport;long-chain fatty acid import;positive regulation of secretion;positive regulation of phosphatidylcholine biosynthetic process
• Cellular component: mitochondrial outer membrane;peroxisomal membrane;endoplasmic reticulum;endoplasmic reticulum membrane;Golgi apparatus;lipid droplet;membrane;integral component of membrane;perinuclear region of cytoplasm
• Molecular function: long-chain fatty acid-CoA ligase activity;ATP binding;protein kinase binding;protein domain specific binding;decanoate-CoA ligase activity