ACAT2

acetyl-CoA acetyltransferase 2

Basic information

Region (hg38): 6:159762045-159779112

Links

ENSG00000120437 ∙ NCBI:39 ∙ OMIM:100678 ∙ HGNC:94 ∙ Uniprot:Q9BWD1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• acetyl-CoA acetyltransferase-2 deficiency (Limited), mode of inheritance: AR
• acetyl-CoA acetyltransferase-2 deficiency (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ACAT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACAT2 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				3	1	4
missense			21	3	1	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			1	2		3
Total	0	0	22	8	2

Variants in ACAT2

This is a list of pathogenic ClinVar variants found in the ACAT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-159762730-G-A			Likely benign (Jun 13, 2018)
6-159762928-A-C		not specified	Uncertain significance (Feb 15, 2023)
6-159762928-A-G		not specified	Uncertain significance (Dec 20, 2023)
6-159767007-T-G		not specified	Uncertain significance (Jan 18, 2023)
6-159767158-T-A		not specified	Uncertain significance (Apr 17, 2024)
6-159768557-T-A		not specified	Uncertain significance (Aug 08, 2022)
6-159768558-G-A		not specified	Uncertain significance (May 02, 2024)
6-159768591-T-G			Likely benign (Oct 05, 2017)
6-159768609-C-T			Likely benign (Feb 13, 2018)
6-159768610-T-C		not specified	Uncertain significance (Dec 27, 2023)
6-159768640-A-G		not specified	Likely benign (Oct 20, 2023)
6-159775205-G-A		Acetyl-CoA acetyltransferase-2 deficiency	Uncertain significance (Mar 05, 2018)
6-159775252-T-G		not specified	Uncertain significance (Jan 03, 2024)
6-159775264-T-G			Benign (Aug 05, 2018)
6-159776157-T-C			Likely benign (May 15, 2018)
6-159776187-T-A		not specified	Uncertain significance (Dec 20, 2022)
6-159776234-C-G		not specified	Uncertain significance (Oct 10, 2023)
6-159777328-G-A		not specified	Uncertain significance (Oct 29, 2021)
6-159777334-A-C		not specified	Uncertain significance (Jul 30, 2023)
6-159777342-G-C		not specified	Uncertain significance (Oct 13, 2023)
6-159777395-C-G			Benign (Jun 13, 2018)
6-159777401-T-C		not specified	Likely benign (Nov 09, 2022)
6-159777403-G-A		not specified	Uncertain significance (Sep 23, 2023)
6-159777411-G-T		not specified	Uncertain significance (Apr 17, 2023)
6-159777412-C-T		not specified	Uncertain significance (Mar 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACAT2	protein_coding	protein_coding	ENST00000367048	9	18785

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.53e-7	0.671	125709	0	39	125748	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.699	190	219	0.867	0.0000104	2561
Missense in Polyphen		57	87.792	0.64926		1046
Synonymous	0.418	68	72.5	0.938	0.00000331	817
Loss of Function	1.12	12	17.0	0.706	7.82e-7	218

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000582	0.0000582
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000250	0.000246
Middle Eastern	0.000164	0.000163
South Asian	0.000199	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Mevalonate pathway;Tryptophan metabolism - Homo sapiens (human);Pyruvate metabolism - Homo sapiens (human);Butanoate metabolism - Homo sapiens (human);Fat digestion and absorption - Homo sapiens (human);Lysine degradation - Homo sapiens (human);Propanoate metabolism - Homo sapiens (human);Fatty acid degradation - Homo sapiens (human);Synthesis and degradation of ketone bodies - Homo sapiens (human);Terpenoid backbone biosynthesis - Homo sapiens (human);Valine, leucine and isoleucine degradation - Homo sapiens (human);Glyoxylate and dicarboxylate metabolism - Homo sapiens (human);Simvastatin Action Pathway;Pravastatin Action Pathway;Atorvastatin Action Pathway;Hyper-IgD syndrome;Cholesteryl ester storage disease;Lysosomal Acid Lipase Deficiency (Wolman Disease);Alendronate Action Pathway;Rosuvastatin Action Pathway;Lovastatin Action Pathway;Mevalonic aciduria;Wolman disease;Risedronate Action Pathway;Cerivastatin Action Pathway;Pamidronate Action Pathway;Fluvastatin Action Pathway;Smith-Lemli-Opitz Syndrome (SLOS);Chondrodysplasia Punctata II, X Linked Dominant (CDPX2);CHILD Syndrome;Desmosterolosis;Hypercholesterolemia;Steroid Biosynthesis;Zoledronate Action Pathway;Ibandronate Action Pathway;ketogenesis;ketolysis;Butanoate metabolism;Metabolism of lipids;Citrate cycle;Metabolism;Lysine degradation;superpathway of cholesterol biosynthesis;Metabolism of steroids;isoleucine degradation;Pyruvate metabolism;glutaryl-CoA degradation;Tryptophan degradation;Cholesterol biosynthesis;mevalonate pathway;superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate) (Consensus)

Recessive Scores

• pRec: 0.259

Intolerance Scores

• loftool: 0.537
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.93

Haploinsufficiency Scores

• pHI: 0.114
• hipred: N
• hipred_score: 0.272
• ghis: 0.605

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.348

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Acat3

Gene ontology

• Biological process: lipid metabolic process;fatty acid beta-oxidation;cholesterol biosynthetic process
• Cellular component: nucleus;nucleolus;cytoplasm;mitochondrion;cytosol;extracellular exosome
• Molecular function: acetyl-CoA C-acetyltransferase activity;acetyl-CoA C-acyltransferase activity;protein binding