SLC13A3 Gene

HGNC Family	Solute carriers (SLC)
Name	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 3
Description	Mammalian sodium-dicarboxylate cotransporters transport succinate and other Krebs cycle intermediates. They fall into 2 categories based on their substrate affinity: low affinity and high affinity. Both the low- and high-affinity transporters play an important role in the handling of citrate by the kidneys. The protein encoded by this gene represents the high-affinity form. Alternatively spliced transcript variants encoding different isoforms have been found for this gene, although the full-length nature of some of them have not been characterized yet. [provided by RefSeq, Jul 2008]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nSLC13A3 encodes the high‐affinity, sodium‐dependent dicarboxylate cotransporter 3 (NaDC3), which mediates the uptake of key dicarboxylates—including Krebs cycle intermediates such as succinate and α‐ketoglutarate as well as glutathione—from the extracellular space into the cytosol. Functional studies using heterologous expression systems (in Xenopus oocytes and mammalian cell lines) have demonstrated that NaDC3 exhibits strict substrate specificity and sodium‐dependence, and its proper basolateral localization in renal proximal tubule cells is ensured by a defined di‐hydrophobic motif in its N‐terminal domain. Moreover, overexpression experiments indicate that NaDC3 activity can influence intracellular energy balance by affecting the NAD⁺/NADH ratio, thereby modulating downstream metabolic pathways and cellular homeostasis."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "7"}]}, {"type": "t", "text": ""}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nIn addition to its fundamental transport role, genetic and functional studies have associated SLC13A3 with diverse pathophysiological conditions. Variants in SLC13A3 have been linked to susceptibilities in chronic kidney disease of unknown etiology and type 2 diabetes, while in liver cancer, β‐catenin activation drives upregulation of SLC13A3—resulting in altered glutathione handling, modulation of leucine transporter expression, and subsequent mTOR pathway inactivation leading to ferroptosis. Furthermore, pathogenic mutations in SLC13A3 have been implicated in neurodevelopmental disorders such as acute reversible leukoencephalopathy, underscoring its broader impact on human physiology."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "8", "end_ref": "11"}]}, {"type": "t", "text": ""}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Birgitta C Burckhardt, Julia Lorenz, Christoph Kobbe, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Substrate specificity of the human renal sodium dicarboxylate cotransporter, hNaDC-3, under voltage-clamp conditions."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Am J Physiol Renal Physiol (2005)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1152/ajprenal.00360.2004"}], "href": "https://doi.org/10.1152/ajprenal.00360.2004"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15561973"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15561973"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Xueyuan Bai, Xiangmei Chen, Zhe Feng, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Identification of basolateral membrane targeting signal of human sodium-dependent dicarboxylate transporter 3."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Cell Physiol (2006)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1002/jcp.20553"}], "href": "https://doi.org/10.1002/jcp.20553"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "16331647"}], "href": "https://pubmed.ncbi.nlm.nih.gov/16331647"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Weiping Liu, Quan Hong, Xue-Yuan Bai, et al. "}, {"type": "b", "children": [{"type": "t", "text": "High-affinity Na(+)-dependent dicarboxylate cotransporter promotes cellular senescence by inhibiting SIRT1."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mech Ageing Dev (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.mad.2010.08.006"}], "href": "https://doi.org/10.1016/j.mad.2010.08.006"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20813124"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20813124"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Marcel Kaufhold, Katharina Schulz, Davorka Breljak, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Differential interaction of dicarboxylates with human sodium-dicarboxylate cotransporter 3 and organic anion transporters 1 and 3."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Am J Physiol Renal Physiol (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1152/ajprenal.00169.2011"}], "href": "https://doi.org/10.1152/ajprenal.00169.2011"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21865262"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21865262"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Lena Schorbach, Wolfgang Krick, Gerhard Burckhardt, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Glutathione is a low-affinity substrate of the human sodium-dependent dicarboxylate transporter."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nephron Physiol (2013)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1159/000356419"}], "href": "https://doi.org/10.1159/000356419"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24247155"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24247155"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Elisabeth Schwob, Yohannes Hagos, Gerhard Burckhardt, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Transporters involved in renal excretion of N-carbamoylglutamate, an orphan drug to treat inborn n-acetylglutamate synthase deficiency."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Am J Physiol Renal Physiol (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1152/ajprenal.00482.2014"}], "href": "https://doi.org/10.1152/ajprenal.00482.2014"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "25354943"}], "href": "https://pubmed.ncbi.nlm.nih.gov/25354943"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Davorka Breljak, Marija Ljubojević, Yohannes Hagos, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Distribution of organic anion transporters NaDC3 and OAT1-3 along the human nephron."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Am J Physiol Renal Physiol (2016)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1152/ajprenal.00113.2016"}], "href": "https://doi.org/10.1152/ajprenal.00113.2016"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "27053689"}], "href": "https://pubmed.ncbi.nlm.nih.gov/27053689"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "J L Bento, N D Palmer, M Zhong, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Heterogeneity in gene loci associated with type 2 diabetes on human chromosome 20q13.1."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Genomics (2008)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.ygeno.2008.06.004"}], "href": "https://doi.org/10.1016/j.ygeno.2008.06.004"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "18602983"}], "href": "https://pubmed.ncbi.nlm.nih.gov/18602983"}]}, {"type": "r", "ref": 9, "children": [{"type": "t", "text": "Ravita Kumari, Shikha Tiwari, Mahendra Atlani, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Association of Single Nucleotide Polymorphisms in KCNA10 and SLC13A3 Genes with the Susceptibility to Chronic Kidney Disease of Unknown Etiology in Central Indian Patients."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Biochem Genet (2023)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1007/s10528-023-10335-7"}], "href": "https://doi.org/10.1007/s10528-023-10335-7"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "36696070"}], "href": "https://pubmed.ncbi.nlm.nih.gov/36696070"}]}, {"type": "r", "ref": 10, "children": [{"type": "t", "text": "Syeda Iqra Hussain, Nazif Muhammad, Salah Ud Din Shah, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Structural and functional implications of SLC13A3 and SLC9A6 mutations: an in silico approach to understanding intellectual disability."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "BMC Neurol (2023)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1186/s12883-023-03397-y"}], "href": "https://doi.org/10.1186/s12883-023-03397-y"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "37794328"}], "href": "https://pubmed.ncbi.nlm.nih.gov/37794328"}]}, {"type": "r", "ref": 11, "children": [{"type": "t", "text": "Wennan Zhao, Xue Wang, Lifeng Han, et al. "}, {"type": "b", "children": [{"type": "t", "text": "SLC13A3 is a major effector downstream of activated β-catenin in liver cancer pathogenesis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Commun (2024)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/s41467-024-51860-2"}], "href": "https://doi.org/10.1038/s41467-024-51860-2"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "39215042"}], "href": "https://pubmed.ncbi.nlm.nih.gov/39215042"}]}]}]}
Synonyms	SDCT2, NADC3
Proteins	S13A3_HUMAN
NCBI Gene ID	64849
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Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

SLC13A3 has 5,218 functional associations with biological entities spanning 9 categories (molecular profile, organism, chemical, disease, phenotype or trait, functional term, phrase or reference, structural feature, cell line, cell type or tissue, gene, protein or microRNA, sequence feature) extracted from 126 datasets.

Click the + buttons to view associations for SLC13A3 from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

SLC13A3 Gene

Functional Associations

Please acknowledge the Harmonizome in your publications by citing the following reference(s):

	Dataset	Summary
	Achilles Cell Line Gene Essentiality Profiles	cell lines with fitness changed by SLC13A3 gene knockdown relative to other cell lines from the Achilles Cell Line Gene Essentiality Profiles dataset.
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of SLC13A3 gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	tissues with high or low expression of SLC13A3 gene relative to other tissues from the Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	tissue samples with high or low expression of SLC13A3 gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of SLC13A3 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	tissue samples with high or low expression of SLC13A3 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of SLC13A3 gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
	BioGPS Cell Line Gene Expression Profiles	cell lines with high or low expression of SLC13A3 gene relative to other cell lines from the BioGPS Cell Line Gene Expression Profiles dataset.
	BioGPS Human Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of SLC13A3 gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset.
	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of SLC13A3 gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset.
	Carcinogenome Chemical Perturbation Carcinogenicity Signatures	small molecule perturbations changing expression of SLC13A3 gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of SLC13A3 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	CCLE Cell Line Gene Expression Profiles	cell lines with high or low expression of SLC13A3 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with SLC13A3 gene from the CellMarker Gene-Cell Type Associations dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of SLC13A3 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of SLC13A3 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of SLC13A3 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	ClinVar Gene-Phenotype Associations 2025	phenotypes associated with SLC13A3 gene from the curated ClinVar Gene-Phenotype Associations 2025 dataset.
	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	gene perturbations changing expression of SLC13A3 gene from the CM4AI KOLF21J CRISPRi Gene Perturbation Atlas dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of SLC13A3 gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing SLC13A3 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing SLC13A3 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with SLC13A3 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with SLC13A3 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of SLC13A3 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with SLC13A3 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Chemical Interactions	chemicals interacting with SLC13A3 gene/protein from the curated CTD Gene-Chemical Interactions dataset.
	CTD Gene-Disease Associations	diseases associated with SLC13A3 gene/protein from the curated CTD Gene-Disease Associations dataset.
	dbGAP Gene-Trait Associations	traits associated with SLC13A3 gene in GWAS and other genetic association datasets from the dbGAP Gene-Trait Associations dataset.
	DepMap CRISPR Gene Dependency	cell lines with fitness changed by SLC13A3 gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
	DGIdb Drug Targets 2026	interacting drugs for SLC13A3 protein from the DGIdb Drug Targets 2026 dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	diseases associated with SLC13A3 gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores 2025 dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with SLC13A3 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with SLC13A3 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Disease Associations	diseases associated with SLC13A3 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with SLC13A3 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Phenoptype Associations dataset.
	DrugBank Drug Targets	interacting drugs for SLC13A3 protein from the curated DrugBank Drug Targets dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at SLC13A3 gene from the ENCODE Histone Modification Site Profiles dataset.
	ENCODE Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of SLC13A3 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of SLC13A3 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.