HGNC Approved Gene Symbol: ACSF3
SNOMEDCT: 702365002;
Cytogenetic location: 16q24.3 Genomic coordinates (GRCh38): 16:89,093,852-89,156,233 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 16q24.3 | Combined malonic and methylmalonic aciduria | 614265 | Autosomal recessive | 3 |
Fatty acids are incorporated into membranes and signaling molecules and have roles in energy storage and metabolism. These essential functions require activation of the fatty acid by acyl-coenzyme A (CoA) synthetases, such as ACSF3, which form an activating thioester linkage between the fatty acid and CoA (Watkins et al., 2007).
Using highly conserved acyl-CoA synthetase motifs 1 and 2 in a database search, followed by PCR of a liver cDNA library, Watkins et al. (2007) cloned human ACSF3. The deduced 576-amino acid protein contains all 5 motifs characteristic of acyl-CoA synthetases.
By Western blot analysis of mouse tissues, Witkowski et al. (2011) found highest Acsf3 expression in brown adipose tissue, followed by kidney, and liver. Lower expression was detected in brain, skeletal muscle, and heart.
By assaying human ACSF3 expressed in COS-1 cells, Watkins et al. (2007) showed that ACSF3 preferred a very long chain fatty acid, lignoceric acid (C24), over palmitate (C16) or octanoic acid (C8).
Sloan et al. (2011) compared human ACSF3 to Bradyrhizobium japonicum malonyl-CoA synthetase, a well-characterized enzyme, and found that the proteins were more identical (32%) and similar (50%) to each other than ACSF3 was to the next closest human ACS family member. Phylogenetic analyses rooted human ACSF3 with the malonyl-CoA synthetase (MCS) enzymes and not other ACSs. Sloan et al. (2011) found that ACSF3 activated malonate and methylmalonate, but not acetate, into the respective coenzyme thioesters. The specific activity of GST-tagged ACSF3 was higher with malonate as a substrate compared to methylmalonate, similar to its prokaryotic homologs. Because the first 59 amino acids of ACSF3 were predicted to be a mitochondrial leader sequence, Sloan et al. (2011) performed immunostaining with fibroblasts overexpressing ACSF3 and a C-terminal GFP-ACSF3 fusion protein to experimentally validate the subcellular localization. ACSF3 staining showed a distinct mitochondrial distribution and colocalized with a mitochondrial antibody. The comparative sequence analysis, enzymatic data, and subcellular localization suggested that ACSF3 is a mitochondrial methylmalonyl-CoA and MCS synthetase, an enzyme postulated to catalyze the first step of intramitochondrial fatty acid synthesis.
Independently, Witkowski et al. (2011) found that recombinant human ACSF3 converted malonate to malonyl-CoA in the presence of ATP, Mg(2+), and CoA. ACSF3 also used methylmalonate and, much more weakly, acetate. Mutation of a conserved arginine at position 354 abrogated malonyl-CoA synthetase activity. Knockdown of ACSF3 in HEK293T cells via small interfering RNA significantly reduced malonyl-CoA synthetase activity and reduced the amount of malonyl bound to acyl carrier protein (NDUFAB1; 603836).
Watkins et al. (2007) determined that the ACSF3 gene contains 11 exons.
By genomic sequence analysis, Watkins et al. (2007) mapped the ACSF3 gene to chromosome 16q24.3.
In 8 of 9 patients with combined malonic and methylmalonic aciduria (CMAMMA; 614265), Sloan et al. (2011) identified mutations in the ACSF3 gene in homozygosity or compound heterozygosity, including 9 missense mutations, 1 in-frame deletion, and 1 nonsense mutation. Four subjects were homozygous for their variants. Most of the variants resided in the C-terminal portion of ACSF3. Eight of the 9 missense mutations and the in-frame deletion were located in conserved ACS motifs predicted to be involved in AMP binding (motif I), conformational change and catalytic function (motif II), substrate binding (motifs III and IV), or catalysis (motif V). Protein analyses using fibroblasts from subjects 1 through 4 and 7 showed the presence of crossreactive ACSF3. Fibroblasts from subjects 1 through 4 produced 2.4- to 6-fold more MMA than control cells after chemical stimulation. Viral expression of ACSF3 but not GFP restored metabolism and provided validation of ACSF3 function in a cell culture biochemical assay.
In 2 probands with CMAMMA detected through the Quebec, Canada, newborn urine screening program, Alfares et al. (2011) identified homozygous mutations in the ACSF3 gene. Patient 2 and her affected younger brother were found to have an E359K mutation (614245.0003) by exome sequencing. The parents were heterozygous for the mutation. Sequencing of the ACSF3 gene in patient 1 revealed an R471W mutation (614245.0004).
Levtova et al. (2019) performed ACFS3 sequencing in 19 of 25 patients with CMAMMA. The most common mutations were E359K (614245.0003) and R558W (614245.0001), representing 38.2% and 20.6% of alleles in genotyped families, respectively. All mutations were missense except for a splice site mutation (c.1239+2T-G; 614245.0010) in 2 patients, representing 2/50 alleles, and 3 frameshift mutations. All genotyped patients carried at least 1 missense allele.
In 4 individuals with combined malonic and methylmalonic aciduria (CMAMMA; 614265), Sloan et al. (2011) identified a C-to-T transition at nucleotide 1672 in exon 11 of the ACSF3 gene, resulting in an arg-to-trp substitution at codon 558 (R558W). One of the patients was homozygous; she presented at 22 months of age with seizure, encephalopathy, and recurrent ketoacidosis. The other individuals, who were compound heterozygous, presented in adulthood at ages ranging from 43 to 55 years with neurologic manifestations. The R558W mutation occurs in motif V of the ACSF3 protein, a conserved region involved in catalysis.
In a 51-year-old man with combined malonic and methylmalonic aciduria (CMAMMA; 614265), Sloan et al. (2011) identified a C-to-T transition at nucleotide 1567 in exon 10 of the ACSF3 gene, resulting in an arg-to-ter substitution at codon 523 (R523X). The patient presented with complex partial seizures and memory problems that had onset at age 43. He carried the R558W mutation (614245.0001) on the other allele. The R523X mutation occurs in motif II of the ACSF3 protein, a conserved region involved in conformational change and catalytic function.
In a woman with combined malonic and methylmalonic aciduria (CMAMMA; 614265), Sloan et al. (2011) identified compound heterozygosity for a G-to-A transition at nucleotide 1075 in exon 6 of the ACSF3 gene, resulting in a glu-to-lys substitution at codon 359 (E359K). The patient presented at age 55 with psychiatric symptoms and T2 hyperintensities on brain MRI and died at the age of 60. The other allele of the patient carried the R558W mutation (614245.0001). The E359K mutation occurs in motif III, involved in substrate binding, of the ACSF3 gene.
In a 4-year-old French Canadian girl (patient 2) with CMAMMA detected through the Quebec newborn urine screening program, Alfares et al. (2011) identified a homozygous c.1075G-A transition in the ACSF3 gene, resulting in a glu359-to-lys (E359K) substitution. The mutation, which was identified by whole-exome sequencing, was said to occur in exon 5. The patient was born at term and was clinically asymptomatic; she had normal cardiac examinations and age-appropriate development. She had a similarly affected 2-year-old brother who was also homozygous for the mutation. The parents were heterozygous for the mutation.
In a 66-year-old female with combined malonic and methylmalonic aciduria (CMAMMA; 614265), Sloan et al. (2011) found homozygosity for a c.1411C-T transition in exon 9 of the ACSF3 gene, resulting in an arg-to-trp substitution at codon 471 (R471W). The mutation occurs in motif II, involved in conformational change and catalytic function. The patient presented with incontinence and mild memory problems.
In a 14-year-old Ashkenazi Jewish boy with CMAMMA detected through the Quebec newborn urine screening program, Alfares et al. (2011) identified a homozygous c.1411C-T transition in the ACSF3 gene, resulting in an arg471-to-trp (R471W) substitution. The mutation was identified by Sanger sequencing and was said to occur in exon 8. The patient was clinically asymptomatic with age-appropriate development.
In a 5-year-old female with combined malonic and methylmalonic aciduria (CMAMMA; 614265), Sloan et al. (2011) identified a G-to-A transition at nucleotide 1412 in exon 9 of the ACSF3 gene, resulting in arg-to-gln substitution at codon 471 (R471Q). This mutation was found in compound heterozygosity with a thr358-to-ile mutation (614245.0006). The patient presented at the age of 4 years with hypoglycemia, acidosis, poor weight gain, and diarrhea episodes. The R471Q mutation occurs in motif II of the ACSF3 protein, involved in conformational change and catalytic function.
In a patient with combined malonic and methylmalonic aciduria (CMAMMA; 614265), Sloan et al. (2011) identified a C-to-T transition in exon 6 at nucleotide 1073 of the ACSF3 gene, resulting in a thr358-to-ile substitution at codon 358 (T358I). This mutation was found in compound heterozygosity with an R471Q mutation (614245.0005). The T358I mutation occurs in motif III of the ACSF3 protein, involved in substrate binding.
In a 16-month-old male with combined malonic and methylmalonic aciduria (CMAMMA; 614265), Sloan et al. (2011) identified a homozygous C-to-T transition at nucleotide 728 in exon 4 of the ACSF3 gene, resulting in a pro-to-leu substitution at codon 243 (P243L). Both parents were heterozygotes. The patient presented at 6 months of age with failure to thrive and elevated transaminases. This mutation occurs in motif IV of the ACSF3 protein, involved in substrate binding.
In a 17-month-old male with combined malonic and methylmalonic aciduria (CMAMMA; 614265), Sloan et al. (2011) identified a T-to-G transversion at nucleotide 593 in exon 3 of the ACSF3 gene, resulting in a met-to-arg substitution at codon 198 (M198R). This mutation was found in homozygosity; the parents were second cousins. The patient presented with psychomotor delay without regression at 5 months, microcephaly, dystonia, axial hypotonia, and speech delay. The mutation occurs in motif I, involved in AMP binding.
In a 46-year-old female with combined malonic and methylmalonic aciduria (CMAMMA; 614265), Sloan et al. (2011) identified 2 mutations in cis in the ACSF3 gene: an A-to-C transversion at nucleotide 1385 resulting in a lys-to-thr substitution at codon 462 (K462T), and an in-frame deletion from nucleotide 1394 to 1411 encompassing the glutamine at position 465 to the glycine at position 470 (del1394_1411, gln465_gly470del). This complex mutation was found in compound heterozygosity with the R558W mutation (614245.0001). The patient presented at age 43 with ocular migraines, memory problems, and T2 hyperintensities on brain MRI.
In 2 unrelated patients, a 5-year-old girl and a 16-year-old boy (patients 5 and 19, respectively), with combined malonic and methylmalonic aciduria (CMAMMA; 614265), Levtova et al. (2019) identified compound heterozygous mutations in the ACSF3 gene. Both patients had a c.1239+2T-G splice site mutation; the girl also had an R558W mutation (614245.0001) and the boy had an E359K mutation (614245.0003).
Alfares, A., Nunez, L. D., Al-Thihli, K., Mitchell, J., Melancon, S., Anastasio, N., Ha, K. C., Majewski, J., Rosenblatt, D. S., Braverman, N. Combined malonic and methylmalonic aciduria: exome sequencing reveals mutations in the ACSF3 gene in patients with a non-classic phenotype. J. Med. Genet. 48: 602-605, 2011. [PubMed: 21785126] [Full Text: https://doi.org/10.1136/jmedgenet-2011-100230]
Levtova, A., Waters, P. J., Buhas, D., Levesque, S., Auray-Blais, C., Clarke, J. T. R., Laframboise, R., Maranda, B., Mitchell, G. A., Brunel-Guitton, C., Braverman, N. E. Combined malonic and methylmalonic aciduria due to ACSF3 mutations: Benign clinical course in an unselected cohort. J. Inherit. Metab. Dis. 42: 107-116, 2019. [PubMed: 30740739] [Full Text: https://doi.org/10.1002/jimd.12032]
Sloan, J. L., Johnston, J. J., Manoli, I., Chandler, R. J., Krause, C., Carrillo-Carrasco, N., Chandrasekaran, S. D., Sysol, J. R., O'Brien, K., Hauser, N. S., Sapp, J. C., Dorward, H. M., and 13 others. Exome sequencing identifies ACSF3 as a cause of combined malonic and methylmalonic aciduria. Nature Genet. 43: 883-886, 2011. [PubMed: 21841779] [Full Text: https://doi.org/10.1038/ng.908]
Watkins, P. A., Maiguel, D., Jia, Z., Pevsner, J. Evidence for 26 distinct acyl-coenzyme A synthetase genes in the human genome. J. Lipid Res. 48: 2736-2750, 2007. [PubMed: 17762044] [Full Text: https://doi.org/10.1194/jlr.M700378-JLR200]
Witkowski, A., Thweatt, J., Smith, S. Mammalian ACSF3 protein is a malonyl-CoA synthetase that supplies the chain extender units for mitochondrial fatty acid synthesis. J. Biol. Chem. 286: 33729-33736, 2011. [PubMed: 21846720] [Full Text: https://doi.org/10.1074/jbc.M111.291591]