ACSS3

acyl-CoA synthetase short chain family member 3, the group of MicroRNA protein coding host genes|Acyl-CoA synthetase family

Basic information

Region (hg38): 12:80936413-81261210

Links

ENSG00000111058 ∙ NCBI:79611 ∙ OMIM:614356 ∙ HGNC:24723 ∙ Uniprot:Q9H6R3 ∙ 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 ACSS3 gene.

• Inborn genetic diseases (28 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACSS3 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			27	1		28
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	1	0

Variants in ACSS3

This is a list of pathogenic ClinVar variants found in the ACSS3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-80937665-C-T		not specified	Uncertain significance (Aug 02, 2021)
12-80937695-G-A		not specified	Uncertain significance (Oct 30, 2023)
12-81078203-G-T		not specified	Uncertain significance (Oct 20, 2023)
12-81078220-C-T		not specified	Uncertain significance (Jan 29, 2024)
12-81078289-G-A		not specified	Uncertain significance (Aug 13, 2021)
12-81078292-A-G		not specified	Likely benign (Dec 01, 2022)
12-81078359-C-T		not specified	Uncertain significance (Nov 30, 2022)
12-81109574-T-G		not specified	Uncertain significance (Aug 21, 2023)
12-81109591-A-G		not specified	Uncertain significance (Nov 17, 2023)
12-81109624-G-A		not specified	Uncertain significance (Jul 19, 2022)
12-81109654-C-G		not specified	Uncertain significance (Jul 14, 2023)
12-81134823-A-G		not specified	Uncertain significance (Jan 16, 2024)
12-81134850-G-A		not specified	Uncertain significance (Jun 30, 2022)
12-81134865-A-T		not specified	Uncertain significance (Jan 05, 2022)
12-81134885-C-T		not specified	Uncertain significance (Mar 01, 2024)
12-81134945-A-G		not specified	Uncertain significance (May 03, 2023)
12-81139137-G-A		not specified	Uncertain significance (Dec 20, 2021)
12-81139174-G-A		not specified	Uncertain significance (May 23, 2023)
12-81139188-G-A		not specified	Likely benign (Feb 05, 2024)
12-81139240-T-C		not specified	Uncertain significance (Jun 27, 2022)
12-81139252-A-G		not specified	Uncertain significance (Dec 21, 2023)
12-81143111-C-A		not specified	Uncertain significance (Jul 12, 2023)
12-81143131-C-T		not specified	Uncertain significance (Jun 22, 2023)
12-81143176-G-A		not specified	Uncertain significance (Aug 17, 2022)
12-81143202-C-G		not specified	Uncertain significance (Jun 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACSS3	protein_coding	protein_coding	ENST00000548058	16	318940

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.05e-13	0.785	125670	0	78	125748	0.000310

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.146	375	383	0.979	0.0000195	4396
Missense in Polyphen		144	149.34	0.96425		1756
Synonymous	-1.39	160	139	1.15	0.00000740	1374
Loss of Function	1.79	25	36.7	0.681	0.00000177	452

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000334	0.000330
Ashkenazi Jewish	0.000104	0.0000992
East Asian	0.000230	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000416	0.000413
Middle Eastern	0.000230	0.000217
South Asian	0.000619	0.000523
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Activates acetate so that it can be used for lipid synthesis or for energy generation. {ECO:0000250}.
• Pathway: Propanoate metabolism - Homo sapiens (human);Malonyl-coa decarboxylase deficiency;Malonic Aciduria;Propanoate Metabolism;Mitochondrial Beta-Oxidation of Short Chain Saturated Fatty Acids;Short-chain 3-hydroxyacyl-CoA dehydrogenase deficiency (SCHAD);Methylmalonic Aciduria Due to Cobalamin-Related Disorders;Metabolism of lipids;ethanol degradation II;acetate conversion to acetyl-CoA;Metabolism;oxidative ethanol degradation III;ethanol degradation IV;Synthesis of Ketone Bodies;Ketone body metabolism (Consensus)

Recessive Scores

• pRec: 0.0919

Intolerance Scores

• loftool: 0.908
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.64

Haploinsufficiency Scores

• pHI: 0.122
• hipred: N
• hipred_score: 0.290
• ghis: 0.521

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.291

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Acss3

Gene ontology

• Biological process: ketone body biosynthetic process
• Cellular component: mitochondrial matrix
• Molecular function: acetate-CoA ligase activity;ATP binding