ACSS2

acyl-CoA synthetase short chain family member 2, the group of Acyl-CoA synthetase family

Basic information

Region (hg38): 20:34872146-34927962

Previous symbols: [ "ACAS2" ]

Links

ENSG00000131069 ∙ NCBI:55902 ∙ OMIM:605832 ∙ HGNC:15814 ∙ Uniprot:Q9NR19 ∙ 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 ACSS2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACSS2 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				8	1	9
missense			38	2	3	43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1		2	3
Total	0	0	39	10	6

Variants in ACSS2

This is a list of pathogenic ClinVar variants found in the ACSS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-34872671-C-T		not specified	Uncertain significance (Oct 26, 2022)
20-34872677-C-T		not specified	Uncertain significance (Dec 28, 2023)
20-34872800-C-G		not specified	Uncertain significance (Nov 10, 2022)
20-34876675-C-G		not specified	Uncertain significance (Feb 17, 2024)
20-34876725-G-C		not specified	Uncertain significance (May 23, 2023)
20-34876726-G-A			Likely benign (Aug 01, 2024)
20-34876731-G-C		not specified	Uncertain significance (Aug 01, 2022)
20-34876766-G-A		not specified	Uncertain significance (Jan 03, 2024)
20-34876769-C-A			Benign (Nov 06, 2018)
20-34876779-A-G		not specified	Uncertain significance (Jan 09, 2024)
20-34876800-G-C		not specified	Uncertain significance (Jul 26, 2022)
20-34876808-G-C		not specified	Uncertain significance (Mar 15, 2024)
20-34882856-C-T		not specified	Uncertain significance (Aug 13, 2021)
20-34882857-G-A		not specified	Likely benign (Oct 20, 2021)
20-34882860-A-T		not specified	Uncertain significance (Dec 16, 2023)
20-34882895-G-A		not specified	Uncertain significance (Oct 25, 2023)
20-34882934-G-C		ACSS2-related disorder	Likely benign (Aug 29, 2024)
20-34913132-A-G		ACSS2-related disorder	Likely benign (Feb 24, 2023)
20-34913166-A-G		not specified	Uncertain significance (Dec 06, 2022)
20-34913179-G-A		ACSS2-related disorder	Uncertain significance (Mar 23, 2024)
20-34913427-G-A		not specified	Uncertain significance (Dec 02, 2022)
20-34913468-C-T		not specified • ACSS2-related disorder	Uncertain significance (Jun 11, 2021)
20-34913780-T-C		not specified	Uncertain significance (Mar 01, 2023)
20-34914143-G-C		not specified	Uncertain significance (Oct 26, 2022)
20-34914359-C-T		ACSS2-related disorder	Benign (Mar 16, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACSS2	protein_coding	protein_coding	ENST00000253382	19	55821

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.14e-13	0.897	125682	0	66	125748	0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	333	393	0.846	0.0000213	4651
Missense in Polyphen		166	202.51	0.81972		2380
Synonymous	2.25	108	142	0.760	0.00000738	1379
Loss of Function	2.05	27	41.2	0.655	0.00000208	473

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000424	0.000424
Ashkenazi Jewish	0.000300	0.000298
East Asian	0.000109	0.000109
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000274	0.000273
Middle Eastern	0.000109	0.000109
South Asian	0.000523	0.000523
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Activates acetate so that it can be used for lipid synthesis or for energy generation.
• Pathway: Pyruvate metabolism - Homo sapiens (human);Glycolysis / Gluconeogenesis - Homo sapiens (human);Propanoate metabolism - Homo sapiens (human);Pyruvate Dehydrogenase Complex Deficiency;Disulfiram Action Pathway;Primary hyperoxaluria II, PH2;Pyruvate kinase deficiency;Leigh Syndrome;Ethanol Degradation;Pyruvate Metabolism;Pyruvate Decarboxylase E1 Component Deficiency (PDHE1 Deficiency);Fatty Acid Beta Oxidation;Fatty Acid Biosynthesis;Lipid Metabolism Pathway;Ethanol effects on histone modifications;Liver steatosis AOP;Amino acid conjugation of benzoic acid;Phase I - Functionalization of compounds;Butanoate metabolism;ethanol degradation II;acetate conversion to acetyl-CoA;Ethanol oxidation;Biological oxidations;Metabolism;oxidative ethanol degradation III;ethanol degradation IV;Propanoate metabolism;Pyruvate metabolism;Transcriptional activation of mitochondrial biogenesis;Mitochondrial biogenesis;Signaling events mediated by HDAC Class III;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.457

Intolerance Scores

• loftool: 0.962
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.7

Haploinsufficiency Scores

• pHI: 0.379
• hipred: Y
• hipred_score: 0.516
• ghis: 0.455

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.859

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Acss2

Gene ontology

• Biological process: ethanol oxidation;lipid biosynthetic process;acetate biosynthetic process;acetyl-CoA biosynthetic process from acetate;propionate biosynthetic process
• Cellular component: nucleoplasm;cytoplasm;mitochondrial matrix;cytosol;intracellular membrane-bounded organelle
• Molecular function: acetate-CoA ligase activity;ATP binding;AMP binding