ACAA2

acetyl-CoA acyltransferase 2

Basic information

Region (hg38): 18:49782164-49813953

Links

ENSG00000167315 ∙ NCBI:10449 ∙ OMIM:604770 ∙ HGNC:83 ∙ Uniprot:P42765 ∙ 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 ACAA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACAA2 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			22	2	1	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	22	3	1

Variants in ACAA2

This is a list of pathogenic ClinVar variants found in the ACAA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-49783909-C-G		not specified	Uncertain significance (Nov 07, 2022)
18-49783909-C-T		not specified	Likely benign (Jun 21, 2022)
18-49783920-C-G		not specified	Uncertain significance (Jan 10, 2023)
18-49783926-C-A		not specified	Uncertain significance (Jul 20, 2021)
18-49783930-G-A		not specified	Uncertain significance (Nov 15, 2023)
18-49785204-C-T		not specified	Uncertain significance (Dec 21, 2022)
18-49785245-A-T		not specified	Uncertain significance (Jul 07, 2022)
18-49787272-A-AC			Likely benign (Dec 30, 2023)
18-49787302-C-A		not specified	Uncertain significance (Apr 01, 2024)
18-49787309-C-G		not specified	Uncertain significance (Apr 28, 2022)
18-49791473-T-C		not specified	Uncertain significance (Jul 14, 2023)
18-49791553-G-C		not specified	Uncertain significance (Sep 17, 2021)
18-49791586-C-T		not specified	Uncertain significance (Mar 19, 2024)
18-49791596-C-T		not specified	Likely benign (Mar 05, 2024)
18-49792157-C-T		not specified	Uncertain significance (May 02, 2024)
18-49792193-C-T		not specified	Uncertain significance (May 04, 2022)
18-49792255-A-G		not specified	Uncertain significance (Sep 22, 2022)
18-49792289-T-C		not specified	Uncertain significance (May 31, 2022)
18-49792313-A-T			Benign (Oct 17, 2017)
18-49794310-C-T		not specified	Uncertain significance (May 31, 2023)
18-49794412-A-G		not specified	Uncertain significance (Mar 17, 2023)
18-49795784-T-G		not specified	Uncertain significance (May 03, 2023)
18-49795809-C-T		not specified	Uncertain significance (Jul 28, 2021)
18-49795814-T-C		not specified	Uncertain significance (Oct 26, 2022)
18-49795868-T-C		not specified	Uncertain significance (Jan 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACAA2	protein_coding	protein_coding	ENST00000285093	10	30462

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.71e-10	0.181	125661	0	87	125748	0.000346

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.271	220	209	1.05	0.0000104	2551
Missense in Polyphen		92	84.824	1.0846		988
Synonymous	0.897	63	72.7	0.866	0.00000375	805
Loss of Function	0.559	16	18.6	0.860	9.33e-7	248

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00227	0.00228
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000163	0.000163
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000221	0.000220
Middle Eastern	0.000163	0.000163
South Asian	0.000262	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Abolishes BNIP3-mediated apoptosis and mitochondrial damage. {ECO:0000269|PubMed:18371312}.
• Pathway: Fatty acid degradation - Homo sapiens (human);Fatty acid elongation - Homo sapiens (human);Valine, leucine and isoleucine degradation - Homo sapiens (human);Long chain acyl-CoA dehydrogenase deficiency (LCAD);3-Methylglutaconic Aciduria Type I;Valine, Leucine and Isoleucine Degradation;2-Methyl-3-Hydroxybutryl CoA Dehydrogenase Deficiency;Trifunctional protein deficiency;Long-chain-3-hydroxyacyl-coa dehydrogenase deficiency (LCHAD);Carnitine palmitoyl transferase deficiency (II);Very-long-chain acyl coa dehydrogenase deficiency (VLCAD);Medium chain acyl-coa dehydrogenase deficiency (MCAD);Fatty Acid Elongation In Mitochondria;Isovaleric Aciduria;3-Methylcrotonyl Coa Carboxylase Deficiency Type I;Propionic Acidemia;Short Chain Acyl CoA Dehydrogenase Deficiency (SCAD Deficiency);Fatty acid Metabolism;Maple Syrup Urine Disease;3-Hydroxy-3-Methylglutaryl-CoA Lyase Deficiency;Isobutyryl-coa dehydrogenase deficiency;3-hydroxyisobutyric aciduria;3-hydroxyisobutyric acid dehydrogenase deficiency;Isovaleric acidemia;Glutaric Aciduria Type I;Ethylmalonic Encephalopathy;Methylmalonate Semialdehyde Dehydrogenase Deficiency;Mitochondrial Beta-Oxidation of Short Chain Saturated Fatty Acids;Mitochondrial Beta-Oxidation of Medium Chain Saturated Fatty Acids;Mitochondrial Beta-Oxidation of Long Chain Saturated Fatty Acids;Short-chain 3-hydroxyacyl-CoA dehydrogenase deficiency (SCHAD);Methylmalonic Aciduria;3-Methylglutaconic Aciduria Type IV;3-Methylglutaconic Aciduria Type III;Beta-Ketothiolase Deficiency;Carnitine palmitoyl transferase deficiency (I);miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Fatty Acid Biosynthesis;Liver steatosis AOP;Metabolism of lipids;Mitochondrial Fatty Acid Beta-Oxidation;3-oxo-10R-octadecatrienoate beta-oxidation;Leukotriene metabolism;Saturated fatty acids beta-oxidation;Metabolism;Fatty acid metabolism;Propanoate metabolism;Mono-unsaturated fatty acid beta-oxidation;Omega-6 fatty acid metabolism;Valine, leucine and isoleucine degradation;Dimethyl-branched-chain fatty acid mitochondrial beta-oxidation;Di-unsaturated fatty acid beta-oxidation;Vitamin E metabolism;fatty acid β-oxidation (peroxisome);fatty acid β-oxidation;bile acid biosynthesis, neutral pathway;Valine Leucine Isoleucine degradation (Consensus)

Recessive Scores

• pRec: 0.366

Intolerance Scores

• loftool: 0.307
• rvis_EVS: -0.58
• rvis_percentile_EVS: 18.72

Haploinsufficiency Scores

• pHI: 0.175
• hipred: N
• hipred_score: 0.319
• ghis: 0.543

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0135

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Acaa2

Gene ontology

• Biological process: fatty acid beta-oxidation;cholesterol biosynthetic process;cellular response to hypoxia;negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway;negative regulation of mitochondrial membrane permeability involved in apoptotic process
• Cellular component: mitochondrion;mitochondrial matrix
• Molecular function: RNA binding;acetyl-CoA C-acetyltransferase activity;acetyl-CoA C-acyltransferase activity;protein binding