ACAA1

acetyl-CoA acyltransferase 1

Basic information

Region (hg38): 3:38103129-38137242

Links

ENSG00000060971 ∙ NCBI:30 ∙ OMIM:604054 ∙ HGNC:82 ∙ Uniprot:P09110 ∙ 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 ACAA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACAA1 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			32	2	1	35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	2	1

Variants in ACAA1

This is a list of pathogenic ClinVar variants found in the ACAA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-38107585-T-C		not specified	Uncertain significance (Jun 13, 2022)
3-38107606-G-T		not specified	Uncertain significance (Nov 03, 2023)
3-38107664-T-G		not specified	Uncertain significance (Aug 13, 2021)
3-38107708-C-T		not specified	Uncertain significance (Nov 15, 2024)
3-38108411-G-A		not specified	Uncertain significance (Apr 26, 2024)
3-38108452-A-T			Benign (Aug 17, 2018)
3-38108478-A-T		not specified	Uncertain significance (Jul 16, 2024)
3-38108504-G-A		not specified	Uncertain significance (Sep 01, 2021)
3-38108514-A-G		not specified	Uncertain significance (Jan 29, 2024)
3-38110166-A-G		not specified	Uncertain significance (Nov 10, 2024)
3-38110169-C-T			Likely benign (May 01, 2022)
3-38110170-G-A		not specified	Uncertain significance (Sep 11, 2024)
3-38110179-G-A		not specified	Uncertain significance (Sep 09, 2024)
3-38110199-C-T		not specified	Likely benign (Aug 21, 2024)
3-38110211-C-T		not specified	Uncertain significance (Sep 09, 2021)
3-38110217-C-T		not specified	Uncertain significance (May 13, 2024)
3-38110223-T-C		not specified	Uncertain significance (Jul 10, 2024)
3-38110235-G-C		not specified	Uncertain significance (Sep 10, 2024)
3-38110244-G-A		not specified	Uncertain significance (Mar 29, 2022)
3-38111681-A-G			Benign (Apr 03, 2018)
3-38112270-A-G		not specified	Uncertain significance (Oct 06, 2021)
3-38112275-A-G		not specified	Uncertain significance (May 30, 2023)
3-38112335-G-A		not specified	Uncertain significance (Dec 15, 2022)
3-38112352-C-A			Likely benign (Sep 01, 2022)
3-38112369-T-C			Benign (Apr 03, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACAA1	protein_coding	protein_coding	ENST00000333167	12	34114

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.59e-9	0.544	125667	0	81	125748	0.000322

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.22	195	249	0.783	0.0000134	2703
Missense in Polyphen		73	98.717	0.73948		1025
Synonymous	-0.646	108	99.8	1.08	0.00000555	899
Loss of Function	1.14	16	21.7	0.736	0.00000121	232

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000238	0.000238
Ashkenazi Jewish	0.00	0.00
East Asian	0.000710	0.000707
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000192	0.000185
Middle Eastern	0.000710	0.000707
South Asian	0.00114	0.00108
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Pathway: Peroxisome - Homo sapiens (human);Biosynthesis of unsaturated fatty acids - Homo sapiens (human);Fatty acid degradation - Homo sapiens (human);alpha-Linolenic acid metabolism - Homo sapiens (human);PPAR signaling pathway - Homo sapiens (human);Valine, leucine and isoleucine degradation - Homo sapiens (human);PPAR Alpha Pathway;Nuclear Receptors Meta-Pathway;Amino Acid metabolism;PPAR signaling pathway;Neutrophil degranulation;Metabolism of lipids;alpha-linolenic acid (ALA) metabolism;Metabolism of proteins;alpha-linolenic (omega3) and linoleic (omega6) acid metabolism;Tyrosine metabolism;Leukotriene metabolism;Omega-3 fatty acid metabolism;Saturated fatty acids beta-oxidation;Trihydroxycoprostanoyl-CoA beta-oxidation;Beta-oxidation of very long chain fatty acids;Peroxisomal lipid metabolism;Innate Immune System;Immune System;Metabolism;Peroxisomal protein import;Fatty acid metabolism;Propanoate 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;fatty acid β-oxidation (peroxisome);TYSND1 cleaves peroxisomal proteins;fatty acid β-oxidation;Valine Leucine Isoleucine degradation (Consensus)

Recessive Scores

• pRec: 0.695

Intolerance Scores

• loftool: 0.134
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.85

Haploinsufficiency Scores

• pHI: 0.0713
• hipred: N
• hipred_score: 0.338
• ghis: 0.535

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.667

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Acaa1b
• Phenotype: normal phenotype

Gene ontology

• Biological process: very long-chain fatty acid metabolic process;protein targeting to peroxisome;fatty acid beta-oxidation;bile acid metabolic process;phenylacetate catabolic process;fatty acid beta-oxidation using acyl-CoA oxidase;alpha-linolenic acid metabolic process;neutrophil degranulation
• Cellular component: extracellular region;peroxisome;peroxisomal matrix;cytosol;membrane;specific granule lumen;intracellular membrane-bounded organelle
• Molecular function: acetyl-CoA C-acyltransferase activity;protein binding;acetate CoA-transferase activity;palmitoyl-CoA oxidase activity