This gene encodes a protein belonging to the solute carrier family 13 group of proteins. This family member is a sodium-dependent citrate cotransporter that may regulate metabolic processes. Mutations in this gene cause early infantile epileptic encephalopathy 25. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2014] See more...

Aliases for SLC13A5 Gene

Aliases for SLC13A5 Gene

  • Solute Carrier Family 13 Member 5 2 3 4 5
  • Solute Carrier Family 13 (Sodium-Dependent Citrate Transporter), Member 5 2 3
  • Na(+)/Citrate Cotransporter 3 4
  • NACT 3 4
  • Sodium-Dependent Dicarboxylate Transporter 3
  • Na+-Coupled Citrate Transporter Protein 3
  • Sodium-Dependent Citrate Transporter 4
  • Sodium-Coupled Citrate Transporter 4
  • EIEE25 3
  • MIndy 3
  • INDY 3
  • NaCT 4

External Ids for SLC13A5 Gene

Previous GeneCards Identifiers for SLC13A5 Gene

  • GC17M006532
  • GC17M006788
  • GC17M006529
  • GC17M006588
  • GC17M006483

Summaries for SLC13A5 Gene

Entrez Gene Summary for SLC13A5 Gene

  • This gene encodes a protein belonging to the solute carrier family 13 group of proteins. This family member is a sodium-dependent citrate cotransporter that may regulate metabolic processes. Mutations in this gene cause early infantile epileptic encephalopathy 25. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2014]

GeneCards Summary for SLC13A5 Gene

SLC13A5 (Solute Carrier Family 13 Member 5) is a Protein Coding gene. Diseases associated with SLC13A5 include Epileptic Encephalopathy, Early Infantile, 25, With Amelogenesis Imperfecta and Kohlschutter-Tonz Syndrome. 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 citrate transmembrane transporter activity. An important paralog of this gene is SLC13A2.

UniProtKB/Swiss-Prot Summary for SLC13A5 Gene

  • High-affinity sodium/citrate cotransporter that mediates citrate entry into cells. The transport process is electrogenic; it is the trivalent form of citrate rather than the divalent form that is recognized as a substrate. May facilitate the utilization of circulating citrate for the generation of metabolic energy and for the synthesis of fatty acids and cholesterol.

Additional gene information for SLC13A5 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SLC13A5 Gene

Genomics for SLC13A5 Gene

GeneHancer (GH) Regulatory Elements for SLC13A5 Gene

Promoters and enhancers for SLC13A5 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SLC13A5 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SLC13A5 gene promoter:
  • AhR
  • AP-2alpha
  • AP-2alphaA
  • AP-2beta
  • AREB6
  • Arnt
  • E2F
  • E2F-1
  • GATA-1
  • GATA-3

Genomic Locations for SLC13A5 Gene

Genomic Locations for SLC13A5 Gene
chr17:6,684,713-6,713,567
(GRCh38/hg38)
Size:
28,855 bases
Orientation:
Minus strand
chr17:6,588,032-6,616,886
(GRCh37/hg19)
Size:
28,855 bases
Orientation:
Minus strand

Genomic View for SLC13A5 Gene

Genes around SLC13A5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLC13A5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLC13A5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC13A5 Gene

Proteins for SLC13A5 Gene

  • Protein details for SLC13A5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q86YT5-S13A5_HUMAN
    Recommended name:
    Solute carrier family 13 member 5
    Protein Accession:
    Q86YT5
    Secondary Accessions:
    • B3KXR0
    • B7Z4P2
    • B7ZLB4
    • F8W7N2
    • Q6ZMG1

    Protein attributes for SLC13A5 Gene

    Size:
    568 amino acids
    Molecular mass:
    63062 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for SLC13A5 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SLC13A5 Gene

Post-translational modifications for SLC13A5 Gene

  • Glycosylation at Asn562
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SLC13A5 Gene

Domains & Families for SLC13A5 Gene

Gene Families for SLC13A5 Gene

Protein Domains for SLC13A5 Gene

Suggested Antigen Peptide Sequences for SLC13A5 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ45898 fis, clone OCBBF3025475, highly similar to Homo sapiens solute carrier family 13 (sodium-dependent citrate transporter), member 5, mRNA (B3KXR0_HUMAN)
  • Sodium-dependent citrate transporter (S13A5_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q86YT5

UniProtKB/Swiss-Prot:

S13A5_HUMAN :
  • Belongs to the SLC13A/DASS transporter (TC 2.A.47) family. NADC subfamily.
Family:
  • Belongs to the SLC13A/DASS transporter (TC 2.A.47) family. NADC subfamily.
genes like me logo Genes that share domains with SLC13A5: view

Function for SLC13A5 Gene

Molecular function for SLC13A5 Gene

UniProtKB/Swiss-Prot Function:
High-affinity sodium/citrate cotransporter that mediates citrate entry into cells. The transport process is electrogenic; it is the trivalent form of citrate rather than the divalent form that is recognized as a substrate. May facilitate the utilization of circulating citrate for the generation of metabolic energy and for the synthesis of fatty acids and cholesterol.

Phenotypes From GWAS Catalog for SLC13A5 Gene

Gene Ontology (GO) - Molecular Function for SLC13A5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0015137 citrate transmembrane transporter activity TAS --
GO:0015141 succinate transmembrane transporter activity IBA 21873635
GO:0015142 tricarboxylic acid transmembrane transporter activity IEA --
GO:0015293 symporter activity IEA --
GO:0017153 sodium:dicarboxylate symporter activity IBA 21873635
genes like me logo Genes that share ontologies with SLC13A5: view
genes like me logo Genes that share phenotypes with SLC13A5: view

Human Phenotype Ontology for SLC13A5 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SLC13A5 Gene

MGI Knock Outs for SLC13A5:

Animal Model Products

CRISPR Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targets and HOMER Transcription for SLC13A5 Gene

Localization for SLC13A5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC13A5 Gene

Membrane; Multi-pass membrane protein. Cell membrane.

Subcellular locations from

COMPARTMENTS
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 SLC13A5 gene
Compartment Confidence
plasma membrane 5
extracellular 1
mitochondrion 1
nucleus 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SLC13A5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IBA,IEA 21873635
genes like me logo Genes that share ontologies with SLC13A5: view

Pathways & Interactions for SLC13A5 Gene

genes like me logo Genes that share pathways with SLC13A5: view

Gene Ontology (GO) - Biological Process for SLC13A5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006811 ion transport IEA --
GO:0006814 sodium ion transport IEA --
GO:0006842 tricarboxylic acid transport IEA --
GO:0015744 succinate transport IEA --
GO:0015746 citrate transport IDA 26384929
genes like me logo Genes that share ontologies with SLC13A5: view

No data available for SIGNOR curated interactions for SLC13A5 Gene

Drugs & Compounds for SLC13A5 Gene

(1) Drugs for SLC13A5 Gene - From: DrugBank

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Sodium citrate Approved, Investigational Pharma Transporter, substrate 1437

(1) Additional Compounds for SLC13A5 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
sodium
  • Na(+)
  • Na+
  • SODIUM ion
7440-23-5
genes like me logo Genes that share compounds with SLC13A5: view

Transcripts for SLC13A5 Gene

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SLC13A5 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b · 4c ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14
SP1: - - - - -
SP2: - - - -
SP3: - -
SP4: - - - - -
SP5: -
SP6:
SP7: - - -
SP8:

Relevant External Links for SLC13A5 Gene

GeneLoc Exon Structure for
SLC13A5
ECgene alternative splicing isoforms for
SLC13A5

Expression for SLC13A5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SLC13A5 Gene

mRNA differential expression in normal tissues according to GTEx for SLC13A5 Gene

This gene is overexpressed in Liver (x47.4).

Protein differential expression in normal tissues from HIPED for SLC13A5 Gene

This gene is overexpressed in Liver (31.2), Fetal Liver (24.6), Frontal cortex (7.0), and Retina (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SLC13A5 Gene



Protein tissue co-expression partners for SLC13A5 Gene

NURSA nuclear receptor signaling pathways regulating expression of SLC13A5 Gene:

SLC13A5

SOURCE GeneReport for Unigene cluster for SLC13A5 Gene:

Hs.399496

mRNA Expression by UniProt/SwissProt for SLC13A5 Gene:

Q86YT5-S13A5_HUMAN
Tissue specificity: Expressed most predominantly in the liver, with moderate expression detectable in the brain and testis.

Evidence on tissue expression from TISSUES for SLC13A5 Gene

  • Liver(4.7)
  • Nervous system(4.6)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SLC13A5 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • eye
  • face
  • forehead
  • head
  • lip
  • mouth
  • nose
  • pharynx
  • skull
Thorax:
  • chest wall
  • diaphragm
  • esophagus
  • lung
  • rib
  • rib cage
Abdomen:
  • abdominal wall
  • intestine
  • large intestine
  • stomach
Pelvis:
  • pelvis
  • rectum
Limb:
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • upper limb
General:
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with SLC13A5: view

Orthologs for SLC13A5 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SLC13A5 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SLC13A5 33 32
  • 99.18 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SLC13A5 33 32
  • 87.31 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SLC13A5 33 32
  • 85.92 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Slc13a5 32
  • 81.46 (n)
mouse
(Mus musculus)
Mammalia Slc13a5 17 33 32
  • 80.11 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SLC13A5 33
  • 69 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SLC13A5 33
  • 58 (a)
OneToOne
chicken
(Gallus gallus)
Aves SLC13A5 33 32
  • 65.04 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SLC13A5 33
  • 67 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia slc13a5 32
  • 65.13 (n)
zebrafish
(Danio rerio)
Actinopterygii slc13a5a 33 32
  • 65.25 (n)
OneToMany
slc13a5b 33
  • 56 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Indy 33
  • 34 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea nac-3 33
  • 39 (a)
ManyToMany
nac-1 33
  • 38 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PHO91 35
sea squirt
(Ciona savignyi)
Ascidiacea -- 33
  • 37 (a)
ManyToMany
Cin.7160 32
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.7160 32
Species where no ortholog for SLC13A5 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 (Oryza sativa)
  • 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 SLC13A5 Gene

ENSEMBL:
Gene Tree for SLC13A5 (if available)
TreeFam:
Gene Tree for SLC13A5 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SLC13A5: view image

Paralogs for SLC13A5 Gene

Paralogs for SLC13A5 Gene

(5) SIMAP similar genes for SLC13A5 Gene using alignment to 9 proteins:

  • S13A5_HUMAN
  • B3KXR0_HUMAN
  • F8W7N2_HUMAN
  • I3L2Y7_HUMAN
  • I3L424_HUMAN
  • I3L4S9_HUMAN
  • I3L4V4_HUMAN
  • I3L4X6_HUMAN
  • K7END6_HUMAN
genes like me logo Genes that share paralogs with SLC13A5: view

Variants for SLC13A5 Gene

Sequence variations from dbSNP and Humsavar for SLC13A5 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs1042746956 likely-benign, Seizures 6,701,072(-) G/A coding_sequence_variant, synonymous_variant
rs1057519449 pathogenic, Epileptic encephalopathy, early infantile, 25 6,687,629(-) A/G 3_prime_UTR_variant, coding_sequence_variant, intron_variant, missense_variant
rs1206208725 uncertain-significance, Epileptic encephalopathy, early infantile, 25 6,693,079(-) G/A/C coding_sequence_variant, missense_variant, synonymous_variant
rs138520827 likely-benign, Seizures 6,701,102(-) G/A/C coding_sequence_variant, synonymous_variant
rs138537951 likely-benign, not specified, Epileptic encephalopathy, early infantile, 25 6,707,115(-) G/A coding_sequence_variant, intron_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for SLC13A5 Gene

Variant ID Type Subtype PubMed ID
nsv574278 CNV gain 21841781

Variation tolerance for SLC13A5 Gene

Residual Variation Intolerance Score: 6.98% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.15; 23.33% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SLC13A5 Gene

Human Gene Mutation Database (HGMD)
SLC13A5
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SLC13A5

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLC13A5 Gene

Disorders for SLC13A5 Gene

MalaCards: The human disease database

(20) MalaCards diseases for SLC13A5 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

S13A5_HUMAN
  • Epileptic encephalopathy, early infantile, 25, with amelogenesis imperfecta (EIEE25) [MIM:615905]: An autosomal recessive disease characterized by subclinical seizures appearing in the first days of life, evolving to severe epileptic disease. Affected individuals have profound or severe delayed development with lack of speech, and most patients do not acquire the ability to sit. Additional variable features include axial hypotonia, peripheral hypertonia, and abnormal involuntary movements such as dystonia and choreoathetosis. Dental abnormalities, including delayed eruption, hypodontia, tooth hypoplasia, yellow discoloration, thin enamel, and enamel chipping are observed in most patients. {ECO:0000269 PubMed:24995870, ECO:0000269 PubMed:26384929}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SLC13A5

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SLC13A5: view

No data available for Genatlas for SLC13A5 Gene

Publications for SLC13A5 Gene

  1. Human Na+ -coupled citrate transporter: primary structure, genomic organization, and transport function. (PMID: 12445824) Inoue K … Ganapathy V (Biochemical and biophysical research communications 2002) 2 3 4 23 56
  2. Recessive mutations in SLC13A5 result in a loss of citrate transport and cause neonatal epilepsy, developmental delay and teeth hypoplasia. (PMID: 26384929) Hardies K … autosomal recessive working group of the EuroEPINOMICS RES Consortium (Brain : a journal of neurology 2015) 3 4 56
  3. Mutations in SLC13A5 cause autosomal-recessive epileptic encephalopathy with seizure onset in the first days of life. (PMID: 24995870) Thevenon J … Rivière JB (American journal of human genetics 2014) 3 4 56
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 43 56
  5. Identification of transport pathways for citric acid cycle intermediates in the human colon carcinoma cell line, Caco-2. (PMID: 18194662) Weerachayaphorn J … Pajor AM (Biochimica et biophysica acta 2008) 3 23 56

Products for SLC13A5 Gene

  • Biorbyt antibodies for SLC13A5

Sources for SLC13A5 Gene