ACSM2B
protein-codingacyl-CoA synthetase medium chain family member 2B, the group of Acyl-CoA synthetase family
Gene summary
Enables benzoate-CoA ligase activity. Predicted to be involved in acyl-CoA metabolic process and fatty acid biosynthetic process. Located in mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]
- ACSM2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~40.2 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 ACSM2B variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001105069.2. 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 | 2 | 2 | ||||
| missense | 57 | 3 | 1 | 61 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 58 | 3 | 3 | 64 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001098539.1 | 13 | MANE Select | |
| Ensembl | ENSP00000327453.6 | 13 | MANE Select | |
| RefSeq | NP_001397831.1 | 12 | Standard | |
| RefSeq | NP_872423.3 | 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
- Conjugation of benzoate with glycine
- Conjugation of phenylacetate with glutamine
Biological Process
- fatty acid biosynthetic process
- acyl-CoA metabolic process
- xenobiotic metabolic process
Molecular Function
- molecular_function
- acyl-CoA ligase activity
- fatty-acyl-CoA synthase activity
- ATP binding
- fatty acid ligase activity
Cellular Component
- mitochondrion
- mitochondrial matrix
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000329697
- Coding exons
- 13
- Length
- 40202
- Individuals with no LoFs
- 125427
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 319
- Defined
- 125748
- p
- 0.00128
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -1.98 | 417 | 318 | 1.31 | 0.0000168 | 3728 |
| Missense (PolyPhen) | 152 | 107.68 | 1.4116 | 1337 | ||
| Synonymous | -2.61 | 152 | 116 | 1.31 | 0.00000599 | 1114 |
| Loss of Function | -0.430 | 37 | 34.3 | 1.08 | 0.00000197 | 338 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0077 | 0.0077 | notable |
| Latino/Admixed American | 0.0015 | 0.0014 | notable |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.0011 | 0.0011 | notable |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.00085 | 0.00084 | rare |
| South Asian | 0.00076 | 0.00075 | rare |
| Other | 0.00066 | 0.00065 | rare |
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). {ECO:0000269|PubMed:12616642}.;
Recessive Scores
- pRec
- 0.0729
Intolerance Scores
- LoFtool
- 0.939
- RVIS EVS
- 0.56
- RVIS percentile EVS
- 81.71
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |