ACSS1

acyl-CoA synthetase short chain family member 1, the group of Acyl-CoA synthetase family

Basic information

Region (hg38): 20:25006229-25058980

Previous symbols: [ "ACAS2L" ]

Links

ENSG00000154930 ∙ NCBI:84532 ∙ OMIM:614355 ∙ HGNC:16091 ∙ Uniprot:Q9NUB1 ∙ 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 ACSS1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACSS1 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					1	1
missense			28	3	1	32
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	28	4	2

Variants in ACSS1

This is a list of pathogenic ClinVar variants found in the ACSS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-25007785-C-T		not specified	Uncertain significance (Jun 16, 2024)
20-25007818-C-T		not specified	Likely benign (Oct 20, 2021)
20-25007826-C-G		not specified	Uncertain significance (Aug 05, 2023)
20-25007830-G-A		not specified	Uncertain significance (Aug 02, 2022)
20-25007847-G-A		not specified	Uncertain significance (Jun 24, 2022)
20-25007871-C-A		not specified	Uncertain significance (Nov 27, 2023)
20-25009322-T-C		not specified	Likely benign (Jan 23, 2024)
20-25009355-G-A		not specified	Uncertain significance (Aug 05, 2023)
20-25009370-A-C		not specified	Uncertain significance (Oct 26, 2022)
20-25012602-T-A		not specified	Uncertain significance (Nov 15, 2023)
20-25012634-C-T		not specified	Uncertain significance (Jun 02, 2024)
20-25012844-G-A		not specified	Uncertain significance (Nov 12, 2021)
20-25012924-C-T		not specified	Uncertain significance (Oct 17, 2023)
20-25013559-T-C		not specified	Uncertain significance (Dec 08, 2023)
20-25013568-C-A		not specified	Uncertain significance (Jun 09, 2022)
20-25013638-C-T		not specified	Uncertain significance (Mar 06, 2023)
20-25013978-C-T			Benign (Mar 03, 2015)
20-25014053-C-T		not specified	Uncertain significance (Jan 16, 2024)
20-25020034-A-T		not specified	Uncertain significance (Mar 31, 2024)
20-25020043-A-G		not specified	Uncertain significance (May 09, 2023)
20-25020047-C-T			Benign (Feb 01, 2023)
20-25020081-C-T		not specified	Uncertain significance (Dec 16, 2023)
20-25021446-G-A		not specified	Uncertain significance (Mar 25, 2024)
20-25021451-C-G		not specified	Uncertain significance (Feb 01, 2023)
20-25022954-C-T		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACSS1	protein_coding	protein_coding	ENST00000323482	14	52749

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.08e-7	0.997	125715	0	33	125748	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.83	313	419	0.748	0.0000248	4447
Missense in Polyphen		109	179.84	0.60608		1788
Synonymous	-0.624	184	174	1.06	0.0000111	1410
Loss of Function	2.62	16	32.0	0.500	0.00000163	348

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000140	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000186	0.000185
Middle Eastern	0.000163	0.000163
South Asian	0.0000984	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Important for maintaining normal body temperature during fasting and for energy homeostasis. Essential for energy expenditure under ketogenic conditions (By similarity). Converts acetate to acetyl-CoA so that it can be used for oxidation through the tricarboxylic cycle to produce ATP and CO(2). {ECO:0000250, ECO:0000269|PubMed:16788062}.
• Pathway: Pyruvate metabolism - Homo sapiens (human);Glycolysis / Gluconeogenesis - Homo sapiens (human);Propanoate metabolism - Homo sapiens (human);Disulfiram Action Pathway;Malonyl-coa decarboxylase deficiency;Malonic Aciduria;Propanoate Metabolism;Ethanol Degradation;Methylmalonic Aciduria Due to Cobalamin-Related Disorders;Sterol Regulatory Element-Binding Proteins (SREBP) signalling;Amino Acid metabolism;Statin Pathway;Phase I - Functionalization of compounds;ethanol degradation II;acetate conversion to acetyl-CoA;Glycolysis and Gluconeogenesis;Ethanol oxidation;Biological oxidations;Metabolism;oxidative ethanol degradation III;ethanol degradation IV;Propanoate metabolism;Signaling events mediated by HDAC Class III (Consensus)

Recessive Scores

• pRec: 0.195

Intolerance Scores

• loftool: 0.669
• rvis_EVS: -0.95
• rvis_percentile_EVS: 9.32

Haploinsufficiency Scores

• pHI: 0.137
• hipred: Y
• hipred_score: 0.603
• ghis: 0.517

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.561

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Acss1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: ethanol oxidation;acetyl-CoA biosynthetic process;acetate biosynthetic process;acetyl-CoA biosynthetic process from acetate;propionate biosynthetic process
• Cellular component: mitochondrial matrix
• Molecular function: acetate-CoA ligase activity;protein binding;ATP binding;AMP binding