Free for academic non-profit institutions. Other users need a Commercial license

Aliases for SLC13A3 Gene

Aliases for SLC13A3 Gene

  • Solute Carrier Family 13 Member 3 2 3 3 5
  • Na(+)/Dicarboxylate Cotransporter 3 3 4
  • NaDC-3 3 4
  • HNaDC3 3 4
  • NADC3 3 4
  • SDCT2 3 4
  • Solute Carrier Family 13 (Sodium-Dependent Dicarboxylate Transporter), Member 3 2
  • Sodium-Dependent High Affinity Dicarboxylate Transporter 3 3
  • Sodium-Dependent High-Affinity Dicarboxylate Transporter 2 4

External Ids for SLC13A3 Gene

Previous GeneCards Identifiers for SLC13A3 Gene

  • GC20M044915
  • GC20M045824
  • GC20M045871
  • GC20M044619
  • GC20M045186
  • GC20M041927

Summaries for SLC13A3 Gene

Entrez Gene Summary for SLC13A3 Gene

  • 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]

GeneCards Summary for SLC13A3 Gene

SLC13A3 (Solute Carrier Family 13 Member 3) is a Protein Coding gene. Diseases associated with SLC13A3 include N-Acetylglutamate Synthase Deficiency. Among its related pathways are Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds. Gene Ontology (GO) annotations related to this gene include transporter activity and high-affinity sodium:dicarboxylate symporter activity. An important paralog of this gene is SLC13A5.

UniProtKB/Swiss-Prot for SLC13A3 Gene

  • High-affinity sodium-dicarboxylate cotransporter that accepts a range of substrates with 4-5 carbon atoms. The stoichiometry is probably 3 Na(+) for 1 divalent succinate.

Gene Wiki entry for SLC13A3 Gene

Additional gene information for SLC13A3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLC13A3 Gene

Genomics for SLC13A3 Gene

GeneHancer (GH) Regulatory Elements for SLC13A3 Gene

Promoters and enhancers for SLC13A3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH20J046687 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 658.9 -4.5 -4542 3.5 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 ZBTB7B YY1 SLC30A9 SLC13A3 ENSG00000271784 TP53RK LOC100419565 NCOA3 GC20M046686
GH20J046682 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 655.4 +0.5 515 2.3 ATF1 FOXA2 ARNT SIN3A TCF12 POLR2B E2F8 ATF7 SP3 SP5 SLC13A3 ENSG00000273893 SLC35C2 ZNF335 TP53RK NCOA5 CD40 PCIF1 SLC2A10 OCSTAMP
GH20J046650 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE dbSUPER 650.3 +33.1 33099 0.9 ELF3 FOXA2 ZFP64 ARID4B DMAP1 ZNF48 ZSCAN9 RAD21 ZNF614 THAP11 SLC13A3 ENSG00000273893 OCSTAMP
GH20J046642 Promoter/Enhancer 1 EPDnew dbSUPER 662.1 +41.9 41899 0.1 SP1 JUND RXRA HNF4A RAD21 ZKSCAN1 SLC13A3 SLC2A10 ENSG00000273893 OCSTAMP
GH20J046562 Enhancer 1.3 Ensembl ENCODE dbSUPER 19.7 +121.5 121455 2 HDGF PKNOX1 FOXA2 ARID4B SIN3A DMAP1 ZNF48 YY1 SLC30A9 ZNF143 SLC13A3 ZNF334 OCSTAMP ENSG00000273893
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SLC13A3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SLC13A3 gene promoter:

Genomic Locations for SLC13A3 Gene

Genomic Locations for SLC13A3 Gene
126,663 bases
Minus strand

Genomic View for SLC13A3 Gene

Genes around SLC13A3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLC13A3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLC13A3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC13A3 Gene

Proteins for SLC13A3 Gene

  • Protein details for SLC13A3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Solute carrier family 13 member 3
    Protein Accession:
    Secondary Accessions:
    • B4DIR8
    • E1P5U4
    • F6WI18
    • Q5JYC9
    • Q5JYD0
    • Q5JYD1
    • Q5TCQ2
    • Q8IVB1
    • Q8N8K4
    • Q96MM5
    • Q9BR25
    • Q9H1G1
    • Q9H3W4
    • Q9NQN5
    • Q9NS04

    Protein attributes for SLC13A3 Gene

    602 amino acids
    Molecular mass:
    66841 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAF73251.1; Type=Frameshift; Positions=188, 199; Evidence={ECO:0000305}; Sequence=CAC09447.2; Type=Miscellaneous discrepancy; Note=erroneous CDS prediction.; Evidence={ECO:0000305};

    Alternative splice isoforms for SLC13A3 Gene

neXtProt entry for SLC13A3 Gene

Post-translational modifications for SLC13A3 Gene

  • Glycosylation at isoforms=3, 5, 6596 and posLast=586586
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SLC13A3 Gene

Domains & Families for SLC13A3 Gene

Gene Families for SLC13A3 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins
  • Transporters

Protein Domains for SLC13A3 Gene


Graphical View of Domain Structure for InterPro Entry



  • Belongs to the SLC13A/DASS transporter (TC 2.A.47) family. NADC subfamily.
  • Belongs to the SLC13A/DASS transporter (TC 2.A.47) family. NADC subfamily.
genes like me logo Genes that share domains with SLC13A3: view

Function for SLC13A3 Gene

Molecular function for SLC13A3 Gene

UniProtKB/Swiss-Prot Function:
High-affinity sodium-dicarboxylate cotransporter that accepts a range of substrates with 4-5 carbon atoms. The stoichiometry is probably 3 Na(+) for 1 divalent succinate.

Phenotypes From GWAS Catalog for SLC13A3 Gene

Gene Ontology (GO) - Molecular Function for SLC13A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005215 transporter activity IBA --
GO:0015137 citrate transmembrane transporter activity IBA --
GO:0015141 succinate transmembrane transporter activity IBA --
GO:0015293 symporter activity IEA --
GO:0015362 high-affinity sodium:dicarboxylate symporter activity TAS --
genes like me logo Genes that share ontologies with SLC13A3: view
genes like me logo Genes that share phenotypes with SLC13A3: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SLC13A3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for SLC13A3 Gene

Localization for SLC13A3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC13A3 Gene

Cell membrane; Multi-pass membrane protein.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SLC13A3 gene
Compartment Confidence
plasma membrane 5
extracellular 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SLC13A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IBA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA,IBA --
GO:0070062 extracellular exosome HDA 19056867
genes like me logo Genes that share ontologies with SLC13A3: view

Pathways & Interactions for SLC13A3 Gene

genes like me logo Genes that share pathways with SLC13A3: view

Interacting Proteins for SLC13A3 Gene

Gene Ontology (GO) - Biological Process for SLC13A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006811 ion transport IEA --
GO:0006814 sodium ion transport IEA --
GO:0006835 dicarboxylic acid transport IEA --
GO:0015746 citrate transport IBA --
GO:0055085 transmembrane transport IEA --
genes like me logo Genes that share ontologies with SLC13A3: view

No data available for SIGNOR curated interactions for SLC13A3 Gene

Drugs & Compounds for SLC13A3 Gene

(3) Drugs for SLC13A3 Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Succinic acid Approved Nutra Full agonist, Agonist, Target 0

(4) Additional Compounds for SLC13A3 Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • Na(+)
  • Na+
  • SODIUM ion
genes like me logo Genes that share compounds with SLC13A3: view

Transcripts for SLC13A3 Gene

Unigene Clusters for SLC13A3 Gene

Solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SLC13A3

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SLC13A3 Gene

ExUns: 1 ^ 2 ^ 3a · 3b · 3c ^ 4a · 4b · 4c ^ 5a · 5b ^ 6 ^ 7a · 7b · 7c ^ 8a · 8b · 8c · 8d ^ 9a · 9b · 9c ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^
SP1: - - - - - - -
SP2: - - - - - - -
SP3: - - - - - - -
SP4: - -
SP5: - - - - - - -
SP9: - - - - - - -
SP10: - - - - - - - -
SP11: -
SP12: - -
SP13: - - - - - - - -

ExUns: 14 ^ 15 ^ 16a · 16b ^ 17a · 17b · 17c ^ 18 ^ 19a · 19b · 19c ^ 20a · 20b · 20c · 20d · 20e · 20f
SP1: - - - - - -
SP6: - - - - -
SP7: - - - -
SP8: - - -
SP13: - - - - -
SP15: -
SP16: - -

Relevant External Links for SLC13A3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SLC13A3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SLC13A3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SLC13A3 Gene

This gene is overexpressed in Kidney - Cortex (x30.9).

Protein differential expression in normal tissues from HIPED for SLC13A3 Gene

This gene is overexpressed in Kidney (33.6), Urine (19.2), and Platelet (7.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SLC13A3 Gene

Protein tissue co-expression partners for SLC13A3 Gene

NURSA nuclear receptor signaling pathways regulating expression of SLC13A3 Gene:


SOURCE GeneReport for Unigene cluster for SLC13A3 Gene:


mRNA Expression by UniProt/SwissProt for SLC13A3 Gene:

Tissue specificity: Expression is highest in kidney. Detected in placenta, brain, liver and pancreas.

Evidence on tissue expression from TISSUES for SLC13A3 Gene

  • Nervous system(4.9)
  • Kidney(4.8)
genes like me logo Genes that share expression patterns with SLC13A3: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SLC13A3 Gene

Orthologs for SLC13A3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SLC13A3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SLC13A3 34 33
  • 99.45 (n)
(Canis familiaris)
Mammalia SLC13A3 34 33
  • 89.85 (n)
(Bos Taurus)
Mammalia SLC13A3 34 33
  • 88.76 (n)
(Rattus norvegicus)
Mammalia Slc13a3 33
  • 86.83 (n)
(Mus musculus)
Mammalia Slc13a3 16 34 33
  • 85.98 (n)
(Monodelphis domestica)
Mammalia SLC13A3 34
  • 85 (a)
(Ornithorhynchus anatinus)
Mammalia SLC13A3 34
  • 80 (a)
(Gallus gallus)
Aves SLC13A3 34 33
  • 74.97 (n)
(Anolis carolinensis)
Reptilia SLC13A3 34
  • 74 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia slc13a3 33
  • 66.28 (n)
(Danio rerio)
Actinopterygii slc13a3 34 33
  • 66.08 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG7309 34
  • 21 (a)
(Caenorhabditis elegans)
Secernentea nac-2 33
  • 45.89 (n)
nac-3 34
  • 37 (a)
F31F6.6 35
  • 37 (a)
nac-1 34
  • 36 (a)
B0285.6 35
  • 34 (a)
R107.1 35
  • 33 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PHO87 36
(Oryza sativa)
Liliopsida Os.15092 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 40 (a)
Species where no ortholog for SLC13A3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SLC13A3 Gene

Gene Tree for SLC13A3 (if available)
Gene Tree for SLC13A3 (if available)
Evolutionary constrained regions (ECRs) for SLC13A3: view image

Paralogs for SLC13A3 Gene

Paralogs for SLC13A3 Gene

(5) SIMAP similar genes for SLC13A3 Gene using alignment to 6 proteins:

  • S13A3_HUMAN
  • B4E181_HUMAN
  • C9J4A3_HUMAN
  • C9J7L4_HUMAN
  • F6WI18_HUMAN
  • H7C0C8_HUMAN
genes like me logo Genes that share paralogs with SLC13A3: view

Variants for SLC13A3 Gene

Sequence variations from dbSNP and Humsavar for SLC13A3 Gene

SNP ID Clin Chr 20 pos Variation AA Info Type
rs188700676 uncertain-significance, Malignant tumor of prostate 46,560,194(-) C/T coding_sequence_variant, missense_variant
rs201443231 uncertain-significance, not provided 46,613,545(-) T/A 5_prime_UTR_variant, coding_sequence_variant, missense_variant
rs1000022600 -- 46,597,054(-) AAAAAAAA/AAAAAAA/AAAAAAAAA intron_variant
rs1000033359 -- 46,666,265(-) G/A genic_upstream_transcript_variant, intron_variant
rs1000047408 -- 46,576,006(-) G/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SLC13A3 Gene

Variant ID Type Subtype PubMed ID
dgv2258n106 CNV deletion 24896259
dgv783e214 CNV gain 21293372
esv2722460 CNV deletion 23290073
esv2722462 CNV deletion 23290073
esv2722463 CNV deletion 23290073
esv2722464 CNV deletion 23290073
esv2758797 CNV gain 17122850
esv32661 CNV gain 17666407
esv34663 CNV gain 17911159
esv3645955 CNV loss 21293372
esv6676 CNV gain 19470904
nsv1061899 CNV loss 25217958
nsv179106 CNV deletion 16902084
nsv179609 CNV deletion 16902084
nsv475262 CNV novel sequence insertion 20440878
nsv509771 CNV insertion 20534489
nsv828733 CNV gain 20364138
nsv833994 CNV gain 17160897
nsv9812 CNV gain 18304495

Variation tolerance for SLC13A3 Gene

Residual Variation Intolerance Score: 33.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.14; 38.90% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SLC13A3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLC13A3 Gene

Disorders for SLC13A3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SLC13A3 Gene - From: GeneCards

Disorder Aliases PubMed IDs
n-acetylglutamate synthase deficiency
  • nagsd
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SLC13A3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SLC13A3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SLC13A3 Gene

Publications for SLC13A3 Gene

  1. Structure, function, and genomic organization of human Na(+)-dependent high-affinity dicarboxylate transporter. (PMID: 10794676) Wang H … Ganapathy V (American journal of physiology. Cell physiology 2000) 2 3 4 22 58
  2. Heterogeneity in gene loci associated with type 2 diabetes on human chromosome 20q13.1. (PMID: 18602983) Bento JL … Mychaleckyj JC (Genomics 2008) 3 22 44 58
  3. Substrate specificity of the human renal sodium dicarboxylate cotransporter, hNaDC-3, under voltage-clamp conditions. (PMID: 15561973) Burckhardt BC … Burckhardt G (American journal of physiology. Renal physiology 2005) 3 22 25 58
  4. Mycophenolic acid (MPA) and its glucuronide metabolites interact with transport systems responsible for excretion of organic anions in the basolateral membrane of the human kidney. (PMID: 17526543) Wolff NA … Armstrong VW (Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association 2007) 22 25 58
  5. Membrane topology structure of human high-affinity, sodium-dependent dicarboxylate transporter. (PMID: 17426067) Bai XY … Fu B (FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2007) 4 22 58

Products for SLC13A3 Gene

Sources for SLC13A3 Gene

Loading form....