ACSL1

acyl-CoA synthetase long chain family member 1, the group of Acyl-CoA synthetase family

Basic information

Region (hg38): 4:184755595-184826818

Previous symbols: [ "FACL2" ]

Links

ENSG00000151726 ∙ NCBI:2180 ∙ OMIM:152425 ∙ HGNC:3569 ∙ Uniprot:P33121 ∙ 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 ACSL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACSL1 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	3	4
missense			27	4		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	5	3

Variants in ACSL1

This is a list of pathogenic ClinVar variants found in the ACSL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-184757178-G-A		not specified	Uncertain significance (Nov 14, 2023)
4-184757667-C-G		not specified	Uncertain significance (Jan 09, 2024)
4-184757686-G-A			Benign (Jul 10, 2018)
4-184757857-C-T		not specified	Uncertain significance (Nov 09, 2021)
4-184760413-T-C		not specified	Uncertain significance (Dec 08, 2023)
4-184760421-A-G		not specified	Uncertain significance (Jan 07, 2022)
4-184760433-G-A		not specified	Uncertain significance (Jan 24, 2023)
4-184760437-T-C		not specified	Uncertain significance (Nov 12, 2021)
4-184762429-C-T		not specified	Uncertain significance (Jun 16, 2024)
4-184763170-G-A			Benign (Aug 09, 2017)
4-184763244-C-T		not specified	Uncertain significance (Dec 28, 2022)
4-184763255-C-G		not specified	Uncertain significance (Jun 07, 2024)
4-184764856-C-T		not specified	Uncertain significance (Apr 11, 2023)
4-184764889-C-T		not specified	Uncertain significance (Mar 25, 2024)
4-184764897-C-T		not specified	Uncertain significance (Jul 26, 2021)
4-184765907-G-A		not specified	Uncertain significance (Nov 10, 2022)
4-184765919-G-A		not specified	Uncertain significance (Aug 02, 2023)
4-184765940-G-A		not specified	Uncertain significance (Nov 27, 2024)
4-184765947-C-T		not specified	Uncertain significance (Dec 15, 2023)
4-184765965-G-A		not specified	Uncertain significance (Apr 20, 2024)
4-184765985-G-A		not specified	Uncertain significance (May 29, 2024)
4-184766634-G-C		not specified	Uncertain significance (Oct 06, 2024)
4-184766660-T-G		not specified	Uncertain significance (Feb 27, 2023)
4-184766735-T-C		not specified	Uncertain significance (May 23, 2024)
4-184768317-C-T		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACSL1	protein_coding	protein_coding	ENST00000515030	20	71224

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00153	0.998	125720	0	27	125747	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.40	330	410	0.805	0.0000234	4552
Missense in Polyphen		54	103.31	0.5227		1221
Synonymous	0.439	153	160	0.956	0.0000103	1350
Loss of Function	4.37	14	46.0	0.305	0.00000263	492

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000218	0.000218
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000552	0.0000544
Finnish	0.000385	0.000370
European (Non-Finnish)	0.0000709	0.0000703
Middle Eastern	0.0000552	0.0000544
South Asian	0.0000654	0.0000653
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Activation of long-chain fatty acids for both synthesis of cellular lipids, and degradation via beta-oxidation. Preferentially uses palmitoleate, oleate and linoleate.
• 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);Long chain acyl-CoA dehydrogenase deficiency (LCAD);Trifunctional protein deficiency;Carnitine palmitoyl transferase deficiency (II);Very-long-chain acyl coa dehydrogenase deficiency (VLCAD);Medium chain acyl-coa dehydrogenase deficiency (MCAD);Beta Oxidation of Very Long Chain Fatty Acids;Short Chain Acyl CoA Dehydrogenase Deficiency (SCAD Deficiency);Fatty acid Metabolism;Oxidation of Branched Chain Fatty Acids;Glutaric Aciduria Type I;Ethylmalonic Encephalopathy;Mitochondrial Beta-Oxidation of Long Chain Saturated Fatty Acids;Adrenoleukodystrophy, X-linked;Carnitine-acylcarnitine translocase deficiency;Carnitine palmitoyl transferase deficiency (I);Fatty Acid Beta Oxidation;Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha);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;alpha-linolenic acid (ALA) metabolism;Linoleic acid (LA) metabolism;alpha-linolenic (omega3) and linoleic (omega6) acid metabolism;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: 0.329

Intolerance Scores

• loftool: 0.636
• rvis_EVS: -0.84
• rvis_percentile_EVS: 11.36

Haploinsufficiency Scores

• pHI: 0.248
• hipred: Y
• hipred_score: 0.554
• ghis: 0.514

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.579

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Acsl1
• Phenotype: growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: long-chain fatty acid metabolic process;response to nutrient;lipid biosynthetic process;response to organic cyclic compound;regulation of lipid metabolic process;triglyceride biosynthetic process;adiponectin-activated signaling pathway;response to oleic acid;long-chain fatty-acyl-CoA biosynthetic process;alpha-linolenic acid metabolic process;xenobiotic catabolic process;response to drug;linoleic acid metabolic process;long-chain fatty acid import;positive regulation of protein serine/threonine kinase activity;positive regulation of cold-induced thermogenesis
• Cellular component: mitochondrion;mitochondrial outer membrane;peroxisomal membrane;endoplasmic reticulum membrane;plasma membrane;membrane;integral component of membrane
• Molecular function: long-chain fatty acid-CoA ligase activity;ATP binding;decanoate-CoA ligase activity