ACSM1
protein-codingacyl-CoA synthetase medium chain family member 1, the group of Acyl-CoA synthetase family
Gene summary
Enables benzoate-CoA ligase activity; decanoate-CoA ligase activity; and long-chain fatty acid-CoA ligase activity. Predicted to be involved in acyl-CoA metabolic process and fatty acid biosynthetic process. Located in mitochondrial matrix. [provided by Alliance of Genome Resources, Jul 2025]
- BUCS1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~75.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ACSM1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001318890.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 3 | 4 | |||
| missense | 85 | 8 | 1 | 94 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 88 | 11 | 1 | 100 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001305819.1 | 13 | MANE Select | |
| Ensembl | ENSP00000428047.1 | 13 | MANE Select | |
| RefSeq | NP_443188.2 | 13 | Standard | |
| Ensembl | ENSP00000301956.3 | 13 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Butanoate metabolism - Homo sapiens (human)
- Valproic Acid Pathway, Pharmacokinetics
- Phenylacetate Metabolism
- Valproic Acid Metabolism Pathway
- Mitochondrial Beta-Oxidation of Medium Chain Saturated Fatty Acids
Biological Process
- fatty acid biosynthetic process
- acyl-CoA metabolic process
- xenobiotic metabolic process
- energy derivation by oxidation of organic compounds
- benzoate metabolic process
Molecular Function
- acyl-CoA ligase activity
- fatty-acyl-CoA synthase activity
- ATP binding
- GTP binding
- fatty acid ligase activity
Cellular Component
- mitochondrial matrix
- extracellular exosome
- blood microparticle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000307493
- Coding exons
- 13
- Length
- 75654
- Individuals with no LoFs
- 125497
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 251
- Defined
- 125748
- p
- 0.000999
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.204 | 320 | 330 | 0.968 | 0.0000182 | 3740 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00062 | 0.00062 | rare |
| Latino/Admixed American | 0.0024 | 0.0024 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00092 | 0.00092 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.0011 | 0.0011 | notable |
| South Asian | 0.00036 | 0.00036 | rare |
| Other | 0.0015 | 0.0015 | notable |
dbNSFP Gene Annotations
Source:
- 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}.;
Recessive Scores
- pRec
- 0.111
Intolerance Scores
- LoFtool
- 0.973
- RVIS EVS
- 0.12
- RVIS percentile EVS
- 62.17
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.541
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |