ACSM1

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

Basic information

Region (hg38): 16:20623234-20698890

Previous symbols: [ "BUCS1" ]

Links

ENSG00000166743 ∙ NCBI:116285 ∙ OMIM:614357 ∙ HGNC:18049 ∙ Uniprot:Q08AH1 ∙ 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 ACSM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACSM1 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				2		2
missense			33	4	1	38
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	33	6	2

Variants in ACSM1

This is a list of pathogenic ClinVar variants found in the ACSM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-20623511-C-T		not specified	Uncertain significance (Apr 24, 2023)
16-20623529-A-G		not specified	Uncertain significance (Feb 06, 2024)
16-20623556-T-C		not specified	Uncertain significance (Dec 12, 2023)
16-20624112-T-C		not specified	Likely benign (Sep 14, 2023)
16-20624155-T-A		not specified	Uncertain significance (Jul 12, 2023)
16-20624188-G-A		not specified	Uncertain significance (Dec 03, 2021)
16-20625481-T-G		not specified	Uncertain significance (Jun 10, 2024)
16-20627192-G-A		not specified	Uncertain significance (Apr 06, 2022)
16-20627270-T-C		not specified	Uncertain significance (Aug 02, 2021)
16-20636754-G-T			Likely benign (Mar 01, 2022)
16-20636755-A-G		not specified	Uncertain significance (Apr 18, 2023)
16-20636767-C-T		not specified	Likely benign (Feb 06, 2023)
16-20636776-T-C		not specified	Uncertain significance (Oct 27, 2021)
16-20636813-G-A		not specified	Uncertain significance (May 30, 2023)
16-20636840-C-T		not specified	Likely benign (Apr 23, 2024)
16-20637441-C-A		not specified	Uncertain significance (Dec 06, 2023)
16-20637445-T-G		not specified	Uncertain significance (Mar 20, 2023)
16-20637447-A-G		not specified	Uncertain significance (Apr 15, 2024)
16-20640468-G-A		not specified	Uncertain significance (Dec 19, 2023)
16-20640516-T-A		not specified	Uncertain significance (Nov 03, 2023)
16-20640532-G-A		not specified	Uncertain significance (May 05, 2023)
16-20640534-A-G		not specified	Uncertain significance (Apr 27, 2022)
16-20640570-G-A		not specified	Uncertain significance (Aug 13, 2021)
16-20661846-A-C		not specified	Uncertain significance (Sep 12, 2023)
16-20661849-G-T		not specified	Uncertain significance (Feb 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACSM1	protein_coding	protein_coding	ENST00000307493	13	75654

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.28e-15	0.207	125497	0	251	125748	0.000999

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.204	320	330	0.968	0.0000182	3740
Missense in Polyphen		120	130.81	0.91733		1552
Synonymous	0.640	116	125	0.927	0.00000684	1116
Loss of Function	1.21	27	34.7	0.779	0.00000189	358

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00302	0.00302
Ashkenazi Jewish	0.00	0.00
East Asian	0.000925	0.000925
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.00106	0.00106
Middle Eastern	0.000925	0.000925
South Asian	0.000361	0.000359
Other	0.00147	0.00147

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has medium-chain fatty acid:CoA ligase activity with broad substrate specificity (in vitro). Acts on acids from C(4) to C(11) and on the corresponding 3-hydroxy- and 2,3- or 3,4- unsaturated acids (in vitro). Functions as GTP-dependent lipoate- activating enzyme that generates the substrate for lipoyltransferase (By similarity). {ECO:0000250}.
• Pathway: Butanoate metabolism - Homo sapiens (human);Valproic Acid Pathway, Pharmacokinetics;Phenylacetate Metabolism;Valproic Acid Metabolism Pathway;Mitochondrial Beta-Oxidation of Medium Chain Saturated Fatty Acids;Butyrate Metabolism;Valproic acid pathway;chrebp regulation by carbohydrates and camp;Butanoate metabolism;Conjugation of benzoate with glycine;Conjugation of phenylacetate with glutamine;Conjugation of carboxylic acids;Amino Acid conjugation;Phase II - Conjugation of compounds;Biological oxidations;Metabolism;γ-linolenate biosynthesis;Butanoate metabolism;icosapentaenoate biosynthesis II (metazoa) (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.973
• rvis_EVS: 0.12
• rvis_percentile_EVS: 62.17

Haploinsufficiency Scores

• pHI: 0.0238
• hipred: N
• hipred_score: 0.145

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.541

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Acsm1

Gene ontology

• Biological process: fatty acid biosynthetic process;acyl-CoA metabolic process;xenobiotic metabolic process;energy derivation by oxidation of organic compounds;benzoate metabolic process;fatty acid oxidation;butyrate metabolic process;cholesterol homeostasis
• Cellular component: mitochondrial matrix;extracellular exosome;blood microparticle
• Molecular function: acyl-CoA ligase activity;fatty-acyl-CoA synthase activity;ATP binding;GTP binding;fatty acid ligase activity;CoA-ligase activity;metal ion binding;butyrate-CoA ligase activity