ACSF2

gene
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Also known as FLJ20920ACSMW

Summary

ACSF2 (acyl-CoA synthetase family member 2, HGNC:26101) is a protein-coding gene on chromosome 17q21.33, encoding Medium-chain acyl-CoA ligase ACSF2, mitochondrial (Q96CM8). Acyl-CoA synthases catalyze the initial reaction in fatty acid metabolism, by forming a thioester with CoA.

Enables medium-chain fatty acid-CoA ligase activity. Predicted to be involved in fatty acid metabolic process. Located in mitochondrion.

Source: NCBI Gene 80221 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 166 total — 1 pathogenic
  • MANE Select transcript: NM_025149

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:26101
Approved symbolACSF2
Nameacyl-CoA synthetase family member 2
Location17q21.33
Locus typegene with protein product
StatusApproved
AliasesFLJ20920, ACSMW
Ensembl geneENSG00000167107
Ensembl biotypeprotein_coding
OMIM610465
Entrez80221

Gene structure

Transcript identifiers

Ensembl transcripts: 45 — 25 protein_coding, 10 retained_intron, 6 protein_coding_CDS_not_defined, 4 nonsense_mediated_decay

ENST00000300441, ENST00000427954, ENST00000502667, ENST00000503295, ENST00000503387, ENST00000503408, ENST00000504392, ENST00000504945, ENST00000506052, ENST00000506085, ENST00000506582, ENST00000507769, ENST00000507792, ENST00000508245, ENST00000508734, ENST00000509806, ENST00000510262, ENST00000510410, ENST00000511147, ENST00000511288, ENST00000512119, ENST00000512537, ENST00000513101, ENST00000513544, ENST00000570356, ENST00000893265, ENST00000893266, ENST00000893267, ENST00000893268, ENST00000893269, ENST00000893270, ENST00000893271, ENST00000893272, ENST00000893273, ENST00000893274, ENST00000916543, ENST00000942395, ENST00000942396, ENST00000942397, ENST00000942398, ENST00000942399, ENST00000942400, ENST00000942401, ENST00000942402, ENST00000942403

RefSeq mRNA: 6 — MANE Select: NM_025149 NM_001288968, NM_001288969, NM_001288970, NM_001288971, NM_001288972, NM_025149

CCDS: CCDS11567, CCDS74103, CCDS74104, CCDS74105

Canonical transcript exons

ENST00000300441 — 16 exons

ExonStartEnd
ENSE000011097475046124250461370
ENSE000020698415047450250474837
ENSE000034851655047389450474004
ENSE000034937705046242050462585
ENSE000035287305046315650463251
ENSE000035345965046067750460872
ENSE000035424825046218450462302
ENSE000035549345046163350461686
ENSE000035696575047242850472579
ENSE000036096175046421850464294
ENSE000036096535047102850471135
ENSE000036154325047366550473806
ENSE000036304375047419950474267
ENSE000036473415046381850463909
ENSE000036781585042621850426389
ENSE000036932285046339550463552

Expression profiles

Bgee: expression breadth ubiquitous, 244 present calls, max score 99.00.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.3133 / max 664.2887, expressed in 1775 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
16166210.02621594
1616616.24921703
1616640.03804

Top tissues by expression

277 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
right lobe of thyroid glandUBERON:000111999.00gold quality
right adrenal gland cortexUBERON:003582798.94gold quality
left lobe of thyroid glandUBERON:000112098.78gold quality
right adrenal glandUBERON:000123398.75gold quality
mucosa of transverse colonUBERON:000499198.50gold quality
left adrenal gland cortexUBERON:003582598.49gold quality
left adrenal glandUBERON:000123498.37gold quality
thyroid glandUBERON:000204698.13gold quality
adrenal cortexUBERON:000123597.79gold quality
adult mammalian kidneyUBERON:000008297.61gold quality
adrenal glandUBERON:000236997.44gold quality
skin of abdomenUBERON:000141697.28gold quality
right lobe of liverUBERON:000111496.96gold quality
cerebellar hemisphereUBERON:000224596.69gold quality
skin of legUBERON:000151196.66gold quality
right hemisphere of cerebellumUBERON:001489096.49gold quality
cerebellar cortexUBERON:000212996.46gold quality
rectumUBERON:000105296.06gold quality
body of pancreasUBERON:000115095.90gold quality
olfactory segment of nasal mucosaUBERON:000538695.80gold quality
transverse colonUBERON:000115795.75gold quality
adrenal tissueUBERON:001830395.72gold quality
right ovaryUBERON:000211895.59gold quality
left ovaryUBERON:000211995.54gold quality
right atrium auricular regionUBERON:000663195.52gold quality
hindlimb stylopod muscleUBERON:000425295.13gold quality
small intestine Peyer’s patchUBERON:000345495.05gold quality
nephron tubuleUBERON:000123194.96gold quality
right lungUBERON:000216794.90gold quality
cerebellumUBERON:000203794.70gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-CURD-119yes61.36
E-ANND-3yes5.71

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

10 targeting ACSF2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-96-5P99.9572.802140
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-444799.8567.812900
HSA-MIR-366099.6867.331149
HSA-MIR-452699.6867.071136
HSA-MIR-447299.5666.081478
HSA-MIR-4786-3P99.3668.351390
HSA-MIR-4763-5P98.7563.89854
HSA-MIR-445798.0967.121274
HSA-MIR-10397-5P97.3169.06710

Literature-anchored findings (GeneRIF, showing 1)

  • ACSF2 and lysine lactylation contribute to renal tubule injury in diabetes. (PMID:38676722)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_rerioacsf2ENSDARG00000061201
mus_musculusAcsf2ENSMUSG00000076435
rattus_norvegicusAcsf2ENSRNOG00000003330
drosophila_melanogasterAcsf2FBGN0031703

Paralogs (13): ACSM3 (ENSG00000005187), ACSM2B (ENSG00000066813), AACS (ENSG00000081760), ACSS3 (ENSG00000111058), ACSS2 (ENSG00000131069), ACSS1 (ENSG00000154930), AASDH (ENSG00000157426), ACSM1 (ENSG00000166743), ACSM6 (ENSG00000173124), ACSF3 (ENSG00000176715), ACSM5 (ENSG00000183549), ACSM2A (ENSG00000183747), ACSM4 (ENSG00000215009)

Protein

Protein identifiers

Medium-chain acyl-CoA ligase ACSF2, mitochondrialQ96CM8 (reviewed: Q96CM8)

All UniProt accessions (7): D6RF15, D6RF87, E7EN53, E9PF16, Q96CM8, H0Y8N1, H0Y8Y5

UniProt curated annotations — full annotation on UniProt →

Function. Acyl-CoA synthases catalyze the initial reaction in fatty acid metabolism, by forming a thioester with CoA. Has some preference toward medium-chain substrates. Plays a role in adipocyte differentiation.

Subcellular location. Mitochondrion.

Induction. By PPARG.

Similarity. Belongs to the ATP-dependent AMP-binding enzyme family.

Isoforms (4)

UniProt IDNamesCanonical?
Q96CM8-11yes
Q96CM8-22
Q96CM8-33
Q96CM8-44

RefSeq proteins (6): NP_001275897, NP_001275898, NP_001275899, NP_001275900, NP_001275901, NP_079425* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000873AMP-dep_synth/lig_domDomain
IPR020845AMP-binding_CSConserved_site
IPR025110AMP-bd_CDomain
IPR045851AMP-b_sfHomologous_superfamily

Pfam: PF00501, PF13193

Catalyzed reactions (Rhea), 2 shown:

  • octanoate + ATP + CoA = octanoyl-CoA + AMP + diphosphate (RHEA:33631)
  • a medium-chain fatty acid + ATP + CoA = a medium-chain fatty acyl-CoA + AMP + diphosphate (RHEA:48340)

UniProt features (23 total): modified residue 12, binding site 4, splice variant 3, sequence variant 2, transit peptide 1, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96CM8-F189.400.79

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (4): 263–271; 493; 508; 599

Post-translational modifications (12): 398, 478, 510, 544, 544, 570, 570, 599, 179, 182, 182, 340

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

IDPathway
R-HSA-77289Mitochondrial Fatty Acid Beta-Oxidation
R-HSA-1430728Metabolism
R-HSA-556833Metabolism of lipids
R-HSA-8978868Fatty acid metabolism

MSigDB gene sets: 123 (showing top): GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_LONG_CHAIN_FATTY_ACID_METABOLIC_PROCESS, GOBP_MONOCARBOXYLIC_ACID_METABOLIC_PROCESS, SHEPARD_BMYB_MORPHOLINO_DN, GOBP_NUCLEOBASE_CONTAINING_SMALL_MOLECULE_METABOLIC_PROCESS, MCBRYAN_PUBERTAL_BREAST_4_5WK_DN, GOBP_AMIDE_METABOLIC_PROCESS, MCBRYAN_PUBERTAL_BREAST_3_4WK_UP, DELYS_THYROID_CANCER_DN, HNF4_01, MCBRYAN_PUBERTAL_BREAST_5_6WK_UP, GOZGIT_ESR1_TARGETS_UP, GOBP_LIPID_METABOLIC_PROCESS, GOBP_ORGANIC_ACID_METABOLIC_PROCESS, AACTTT_UNKNOWN

GO Biological Process (4): fatty acid metabolic process (GO:0006631), acyl-CoA metabolic process (GO:0006637), long-chain fatty acid metabolic process (GO:0001676), lipid metabolic process (GO:0006629)

GO Molecular Function (7): long-chain fatty acid-CoA ligase activity (GO:0004467), ATP binding (GO:0005524), medium-chain fatty acid-CoA ligase activity (GO:0031956), nucleotide binding (GO:0000166), catalytic activity (GO:0003824), protein binding (GO:0005515), ligase activity (GO:0016874)

GO Cellular Component (2): mitochondrion (GO:0005739), mitochondrial matrix (GO:0005759)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Fatty acid metabolism1
Metabolism1
Metabolism of lipids1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
fatty acid-CoA ligase activity2
lipid metabolic process1
monocarboxylic acid metabolic process1
nucleoside phosphate metabolic process1
sulfur compound metabolic process1
purine-containing compound metabolic process1
fatty acid metabolic process1
primary metabolic process1
long-chain fatty acid metabolic process1
adenyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
nucleoside phosphate binding1
heterocyclic compound binding1
molecular_function1
binding1
catalytic activity1
cytoplasm1
intracellular membrane-bounded organelle1
mitochondrion1
intracellular organelle lumen1

Protein interactions and networks

STRING

2611 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ACSF2LIPEQ05469791
ACSF2ATP5MC3P48201710
ACSF2IREB2P48200639
ACSF2EMC2Q15006621
ACSF2RPL8P25120580
ACSF2SLC2A4P14672568
ACSF2AIFM2Q9BRQ8542
ACSF2AASDHQ4L235521
ACSF2HADHAP40939521
ACSF2CSO75390502
ACSF2GPX4P36969462
ACSF2PPARGP37231459
ACSF2ECHS1P30084443
ACSF2SQLEQ14534428
ACSF2ZBTB8BQ8NAP8417

IntAct

132 interactions, top by confidence:

ABTypeScore
ARL6IP1ACSF2psi-mi:“MI:0915”(physical association)0.830
CMTM5ACSF2psi-mi:“MI:0915”(physical association)0.740
ACSF2CMTM5psi-mi:“MI:0915”(physical association)0.740
HSPD1NUDT19psi-mi:“MI:0914”(association)0.710
ACSF2AGTRAPpsi-mi:“MI:0915”(physical association)0.670
AGTRAPACSF2psi-mi:“MI:0915”(physical association)0.670
COQ9ACSF2psi-mi:“MI:0915”(physical association)0.670
ACSF2CMTM5psi-mi:“MI:0915”(physical association)0.560
DGAT2L6ACSF2psi-mi:“MI:0915”(physical association)0.560
CLEC10AACSF2psi-mi:“MI:0915”(physical association)0.560
APOC1ACSF2psi-mi:“MI:0915”(physical association)0.560
MICOS13ACSF2psi-mi:“MI:0915”(physical association)0.560
APOA5ACSF2psi-mi:“MI:0915”(physical association)0.560
GPR152ACSF2psi-mi:“MI:0915”(physical association)0.560
RHBDD2ACSF2psi-mi:“MI:0915”(physical association)0.560
RDH10ACSF2psi-mi:“MI:0915”(physical association)0.560
ACSF2SENP2psi-mi:“MI:0915”(physical association)0.560
ARL13BACSF2psi-mi:“MI:0915”(physical association)0.560
SYNGR3ACSF2psi-mi:“MI:0915”(physical association)0.560
ACSF2SIGLEC12psi-mi:“MI:0915”(physical association)0.560

BioGRID (110): ACSF2 (Two-hybrid), ACSF2 (Two-hybrid), CMTM5 (Two-hybrid), ACSF2 (Affinity Capture-MS), ACSF2 (Two-hybrid), ACSF2 (Two-hybrid), ACSF2 (Two-hybrid), ACSF2 (Affinity Capture-MS), ACSF2 (Affinity Capture-MS), ACSF2 (Affinity Capture-MS), ACSF2 (Affinity Capture-MS), ACSF2 (Affinity Capture-MS), ACSF2 (Affinity Capture-MS), ACSF2 (Affinity Capture-MS), ACSF2 (Affinity Capture-MS)

ESM2 similar proteins: A2AV36, A2VD33, A4QP75, A7DZP8, A7MBI3, A8E657, F1QF89, O14531, O35098, O46504, O77784, P32232, P35520, P35571, P37142, P49080, Q17QJ1, Q29RU9, Q3KRD0, Q3TQB2, Q499N5, Q4R510, Q503J2, Q58H57, Q5EA45, Q5R9G9, Q62951, Q63342, Q64FG0, Q64FW2, Q6DCP1, Q6JQN1, Q6NUM9, Q6V1X1, Q7TSQ8, Q80YA7, Q8NCN5, Q8VHE9, Q90635, Q91YP0

Diamond homologs: A0A0C1BUW8, A0A0C1E3B7, A0A0S1RUN4, A0A0S2E7V8, A0A0S2E7W3, A0A0S2E7W7, A0A0S2E7X0, A0A0S2E7Z1, A0A179HJB8, A0A336U965, A0A6F9DYX9, A7XRY0, B2HGV4, B3FWS8, B7STY1, C5D6U5, F8P1W3, I3PB36, I6NXV7, M4IRL4, M4IS88, M4IS92, O31826, P12276, P27743, P39518, P44446, P49327, P9WES4, Q0CBN5, Q0CRX1, Q0CT94, Q0CU19, Q0CWD0, Q0D034, Q0DV32, Q0K844, Q1MWN4, Q5B7T4, Q5FVE4

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 101 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

GO biological processes:

GO termPartnersFoldFDR
mitochondrial large ribosomal subunit assembly552.2×2e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

166 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance136
Likely benign5
Benign3

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
2692406Single allelePathogenic

SpliceAI

4428 predictions. Top by Δscore:

VariantEffectΔscore
17:50460675:A:AGacceptor_gain1.0000
17:50460676:G:GGacceptor_gain1.0000
17:50460867:G:GTdonor_gain1.0000
17:50460869:GGAG:Gdonor_gain1.0000
17:50460870:G:GTdonor_gain1.0000
17:50461628:A:AGacceptor_gain1.0000
17:50461629:CCA:Cacceptor_loss1.0000
17:50461630:CAG:Cacceptor_loss1.0000
17:50461632:G:GTacceptor_loss1.0000
17:50461632:GGT:Gacceptor_gain1.0000
17:50461683:GAAG:Gdonor_gain1.0000
17:50461684:A:Tdonor_gain1.0000
17:50461684:AAG:Adonor_loss1.0000
17:50461685:AG:Adonor_loss1.0000
17:50461686:GGTAC:Gdonor_loss1.0000
17:50461687:G:GAdonor_loss1.0000
17:50461688:T:Adonor_loss1.0000
17:50462179:CACAG:Cacceptor_loss1.0000
17:50462181:CAGG:Cacceptor_loss1.0000
17:50462182:A:ATacceptor_loss1.0000
17:50462182:AGGT:Aacceptor_gain1.0000
17:50462182:AGGTG:Aacceptor_gain1.0000
17:50462183:G:GCacceptor_loss1.0000
17:50462183:GGT:Gacceptor_gain1.0000
17:50462183:GGTG:Gacceptor_gain1.0000
17:50462183:GGTGG:Gacceptor_gain1.0000
17:50462299:AGAG:Adonor_loss1.0000
17:50462300:GAG:Gdonor_gain1.0000
17:50462301:AGGT:Adonor_loss1.0000
17:50462302:GG:Gdonor_loss1.0000

AlphaMissense

4030 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:50471052:A:CS414R0.996
17:50471054:T:AS414R0.996
17:50471054:T:GS414R0.996
17:50461305:T:AW130R0.994
17:50461305:T:CW130R0.994
17:50463442:C:GC312W0.991
17:50463835:G:AG355D0.991
17:50460862:T:CL105P0.990
17:50463446:G:CG314R0.990
17:50472495:G:CR464P0.990
17:50473733:G:CR515P0.990
17:50471047:A:TE412V0.989
17:50472428:G:CA442P0.989
17:50463834:G:CG355R0.988
17:50471038:G:AG409E0.988
17:50461345:C:AA143D0.987
17:50462577:T:CF262L0.987
17:50462579:C:AF262L0.987
17:50462579:C:GF262L0.987
17:50461326:T:AW137R0.986
17:50461326:T:CW137R0.986
17:50463447:G:AG314D0.986
17:50471038:G:TG409V0.984
17:50472497:G:TG465W0.984
17:50463212:C:AN283K0.983
17:50463212:C:GN283K0.983
17:50471113:G:AG434D0.983
17:50461264:T:CL116P0.982
17:50463512:T:CF336L0.982
17:50463514:C:AF336L0.982

dbSNP variants (sampled 300 via entrez): RS1000126054 (17:50439121 A>C), RS1000216443 (17:50438820 G>A), RS1000336505 (17:50473151 C>A,T), RS1000378435 (17:50426385 C>G,T), RS1000531912 (17:50449079 C>T), RS1000552224 (17:50437101 C>A,T), RS1000609863 (17:50432559 C>T), RS1000702588 (17:50467835 G>A), RS1000715109 (17:50424978 T>G), RS1000716033 (17:50461824 T>C), RS1000757546 (17:50455144 G>A), RS1000776012 (17:50469192 C>T), RS1000857951 (17:50450307 C>G), RS1000880439 (17:50426365 G>A,C), RS1000954982 (17:50471533 T>A,G)

Disease associations

OMIM: gene MIM:610465 | disease phenotypes: MIM:166200

GenCC curated gene-disease

Mondo (1): osteogenesis imperfecta type 1 (MONDO:0008146)

Orphanet (2): Osteogenesis imperfecta type 1 (Orphanet:216796), Osteogenesis imperfecta (Orphanet:666)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

StudyTraitp-value
GCST006979_503Heel bone mineral density1.000000e-09

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0009270heel bone mineral density

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

68 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects cotreatment, increases methylation, decreases expression, increases expression, affects expression5
Valproic Acidaffects cotreatment, increases expression, affects expression, decreases methylation5
sodium arsenitedecreases expression, affects cotreatment, increases abundance3
Benzo(a)pyreneaffects methylation, decreases expression, decreases methylation, increases methylation3
Acetaminophendecreases expression, increases expression2
Arsenicaffects cotreatment, decreases expression, increases abundance2
Dexamethasoneincreases expression, affects cotreatment2
Nickeldecreases expression2
Silicon Dioxidedecreases expression2
Cyclosporinedecreases expression2
Particulate Matterdecreases expression, increases abundance, affects cotreatment, increases expression2
aristolochic acid Iincreases expression1
afuresertibincreases expression1
bisphenol Fincreases expression1
triphenyl phosphateaffects expression1
deoxynivalenoldecreases expression1
glycidyl methacrylatedecreases expression1
lead acetatedecreases expression1
2-methyl-4-isothiazolin-3-onedecreases expression1
trichostatin Aincreases expression1
tris(2-butoxyethyl) phosphateaffects expression1
mono-(2-ethylhexyl)phthalateincreases expression1
sulforaphanedecreases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
perfluorooctanoic acidincreases expression1
manganese chlorideaffects cotreatment, decreases expression, increases abundance1
cupric chloridedecreases expression1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression1
isobutyl alcoholincreases abundance, increases expression, affects cotreatment1
perfluorooctane sulfonic aciddecreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): osteogenesis imperfecta type 1