Alternative titles; symbols
HGNC Approved Gene Symbol: SLC13A3
Cytogenetic location: 20q13.12 Genomic coordinates (GRCh38): 20:46,557,828-46,684,485 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 20q13.12 | Leukoencephalopathy, acute reversible, with increased urinary alpha-ketoglutarate | 618384 | Autosomal recessive | 3 |
The SLC13A3 gene encodes a plasma membrane Na+/dicarboxylate cotransporter that is mainly expressed in kidney, astrocytes, and the choroid plexus. It is expressed on both the basolateral membrane of proximal renal tubule cells and in the luminal membrane of renal collecting tubules. It is not expressed in neurons. The main substrates for the transporter are succinate, fumarate, malate, glutarate, alpha-ketoglutarate, and N-acetylaspartate (NAA) (summary by Dewulf et al., 2019).
Mammalian sodium-dicarboxylate cotransporters, which transport succinate and other Krebs cycle intermediates, fall into 2 categories based on their substrate affinity: low affinity (see SLC13A2, 604148) and high affinity (SLC13A3). Both the low- and high-affinity transporters play an important role in the handling of citrate by the kidneys.
Using rat NADC3 cDNA as a probe, Wang et al. (2000) cloned the human homolog, SLC13A3, from a human placenta cDNA library. The SLC13A3 cDNA encodes a deduced 602-amino acid protein with 12 transmembrane domains and a molecular mass of 66.9 kD. The protein also has 8 potential protein kinase C-dependent phosphorylation sites, 1 potential cAMP/cGMP-dependent protein kinase phosphorylation site, and 3 putative N-linked glycosylation sites. SLC13A3 also shares 45% sequence identity with the human low-affinity dicarboxylate transporters. The human and rat SLC13A3 proteins share 85% sequence identity, indicating that the protein is highly conserved across the species. Northern blot analysis detected expression of an approximately 3.6-kb transcript at highest levels in kidney, but also in placenta, brain, liver, and pancreas; no expression was detected in heart, lung, or skeletal muscle. SLC13A3 is expressed in the basolateral membrane of renal proximal tubular epithelial cells, sinusoidal membrane of hepatocytes, and brain synaptosomes (Pajor, 1999).
Using immunofluorescence analysis, Ma et al. (2016) showed that human NADC3 localized mainly to cellular membranes when expressed in human MRC5 fibroblasts.
By expressing SLC13A3 in Xenopus oocytes, Wang et al. (2000) found that SLC13A3 induces sodium-dependent inward currents in the presence of succinate and dimethylsuccinate. SLC13A3 accepts preferentially the divalent anionic form of citrate as a substrate. Functional analyses indicated that the catalytic domain of the transporter lies in the C-terminal half of the protein.
Ma et al. (2016) found that overexpression of NADC3 resulted in premature senescence in human diploid MRC5 and WI38 fibroblasts and primary renal tubular epithelial cells, with the cell cycle arrested at G1 phase. NADC3 overexpression increased cellular oxidative stress and damage and decreased respiratory complex activity and ATP level in MRC5 cells. These senescent phenotypes were alleviated by antioxidant treatment. Further analyses demonstrated that NADC3 overexpression increased production of intracellular NADH and reactive oxygen species by promoting transport of Krebs cycle intermediates into cells, thereby causing cellular senescence.
Schlessinger et al. (2014) constructed a homology structural model for human NADC3 and validated it by site-directed mutagenesis and docking of various substrates. The NADC3 model showed that the substrate- and cation-binding domains of NADC3 were composed of residues in the 2 opposing helical hairpin loops and unwound portions of adjacent helices. The 2 loops were inserted into the membrane from opposing sides, and each contained an SNT motif. The authors reported that the SNT motif is highly conserved among SLC13/DASS transporters and likely plays a role in determining substrate specificity.
Wang et al. (2000) determined that the SLC13A3 gene contains 13 exons and spans over 80 kb of genomic DNA.
By fluorescence in situ hybridization, Wang et al. (2000) mapped the SLC13A3 gene to chromosome 20q12-q13.1.
In 2 unrelated patients with acute reversible leukoencephalopathy with increased urinary alpha-ketoglutarate (ARLIAK; 618384), Dewulf et al. (2019) identified homozygous or compound heterozygous mutations in the SLC13A3 gene (606411.0001-606411.0003). There were 2 missense mutations and 1 splice site mutation. Transfection of the 2 missense mutations into HEK293 cells showed that both caused a significant reduction in transport of alpha-ketoglutarate, succinate, and NAA compared to wildtype. The mutations, which were found by exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the families.
Canavan disease (271900) is caused by mutations in the gene encoding aspartoacylase (ASPA; 608034) and is characterized by excessive brain storage of N-acetyl-aspartate (NAA) and by astroglial and intramyelinic vacuolation. Wang et al. (2021) found that homozygous knockout of Slc13a3 in mice with Canavan disease normalized their brain NAA, increased their body weight, improved rotarod performance, and prevented cerebellar and thalamic vacuolation. Heterozygous Slc13a3 deletion in Canavan disease mice also suppressed brain NAA elevation, enhanced accelerating rotarod performance, and partly prevented cerebellar, but not thalamic, vacuolation.
In a 25-year-old man (patient 1), born of consanguineous parents, with acute reversible leukoencephalopathy with increased urinary alpha-ketoglutarate (ARLIAK; 618384), Dewulf et al. (2019) identified a homozygous c.761C-A transversion in the SLC13A3 gene, resulting in an ala254-to-asp (A254D) substitution. The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. HEK293 cells transfected with the mutation showed normal expression of unglycosylated and glycosylated SLC13A3 similar to cells transfected with wildtype SLC13A3, as well as probable membrane localization. However, functional expression studies showed that the mutant A254D variant almost abolished the transport activity of the protein. Molecular modeling suggested that the ala254 residue is located in transmembrane 5b, which is part of the substrate-binding site.
In a girl (patient 2) with acute reversible leukoencephalopathy with increased urinary alpha-ketoglutarate (ARLIAK; 618384), Dewulf et al. (2019) identified compound heterozygous mutations in the SLC13A3 gene: a c.1642G-A transition, resulting in a gly548-to-ser (G548S) substitution, and an A-to-G transition in intron 7 (c.1016+3A-G; 606411.0003) that was demonstrated to cause aberrant splicing in patient tissue. The mutations, which were found by exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. HEK293 cells transfected with the G548S variant showed normal expression of unglycosylated and glycosylated SLC13A3 similar to cells transfected with wildtype SLC13A3, as well as probable membrane localization. However, functional expression studies showed that the mutant G548S variant had significantly reduced transport activity due to a decrease in V(max). Molecular modeling suggested that the gly548 residue is located in transmembrane 11, within the alpha-helix bundle of the transport domain.
For discussion of the A-to-G transition in intron 7 (c.1016+3A-G) of the SLC13A3 gene, that was found in compound heterozygous state in a patient with acute reversible leukoencephalopathy with increased urinary alpha-ketoglutarate (ARLIAK; 618384) by Dewulf et al. (2019), see 606411.0002.
Dewulf, J. P., Wiame, E., Dorboz, I., Elmaleh-Berges, M., Imbard, A., Dumitriu, D., Rak, M., Bourillon, A., Helaers, R., Malla, A., Renaldo, F., Boespflug-Tanguy, O., Vincent, M.-F., Benoist, J.-F., Wevers, R. A., Schlessinger, A., Van Schaftingen, E., Nassogne, M.-C., Schiff, M. SLC13A3 variants cause acute reversible leukoencephalopathy and alpha-ketoglutarate accumulation. Ann. Neurol. 85: 385-395, 2019. [PubMed: 30635937] [Full Text: https://doi.org/10.1002/ana.25412]
Ma, Y., Bai, X.-Y., Du, X., Fu, B., Chen, X. NaDC3 induces premature cellular senescence by promoting transport of Krebs cycle intermediates, increasing NADH, and exacerbating oxidative damage. J. Gerontol. A Biol. Sci. Med. Sci. 71: 1-12, 2016. [PubMed: 25384549] [Full Text: https://doi.org/10.1093/gerona/glu198]
Pajor, A. M. Sodium-coupled transporters for Krebs cycle intermediates. Annu. Rev. Physiol. 61: 663-682, 1999. [PubMed: 10099705] [Full Text: https://doi.org/10.1146/annurev.physiol.61.1.663]
Schlessinger, A., Sun, N. N., Colas, C., Pajor, A. M. Determinants of substrate and cation transport in the human Na(+)/dicarboxylate cotransporter NaDC3. J. Biol. Chem. 289: 16998-17008, 2014. [PubMed: 24808185] [Full Text: https://doi.org/10.1074/jbc.M114.554790]
Wang, H., Fei, Y.-J., Kekuda, R., Yang-Feng, T. L., Devoe, L. D., Leibach, F. H., Prasad, P. D., Ganapathy, V. Structure, function, and genomic organization of human Na(+)-dependent high-affinity dicarboxylate transporter. Am. J. Physiol. Cell Physiol. 278: C1019-C1030, 2000. [PubMed: 10794676] [Full Text: https://doi.org/10.1152/ajpcell.2000.278.5.C1019]
Wang, Y., Hull, V., Sternbach, S., Popovich, B., Burns, T., McDonough, J., Guo, F., Pleasure, D. Ablating the transporter sodium-dependent dicarboxylate transporter 3 prevents leukodystrophy in Canavan disease mice. Ann. Neurol. 90: 845-850, 2021. [PubMed: 34498299] [Full Text: https://doi.org/10.1002/ana.26211]