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Aliases for SLC19A3 Gene

Aliases for SLC19A3 Gene

  • Solute Carrier Family 19 Member 3 2 3 4 5
  • Solute Carrier Family 19 (Thiamine Transporter), Member 3 2 3
  • Thiamine Transporter 2 2 3
  • ThTr-2 3 4
  • Solute Carrier Family 19, Member 3 2
  • THMD2 3
  • THTR2 3
  • ThTr2 4
  • BBGD 3

External Ids for SLC19A3 Gene

Previous GeneCards Identifiers for SLC19A3 Gene

  • GC02M226571
  • GC02M227281
  • GC02M228513
  • GC02M228752
  • GC02M228375
  • GC02M228258
  • GC02M220392

Summaries for SLC19A3 Gene

Entrez Gene Summary for SLC19A3 Gene

  • This gene encodes a ubiquitously expressed transmembrane thiamine transporter that lacks folate transport activity. Mutations in this gene cause biotin-responsive basal ganglia disease (BBGD); a recessive disorder manifested in childhood that progresses to chronic encephalopathy, dystonia, quadriparesis, and death if untreated. Patients with BBGD have bilateral necrosis in the head of the caudate nucleus and in the putamen. Administration of high doses of biotin in the early progression of the disorder eliminates pathological symptoms while delayed treatment results in residual paraparesis, mild cognitive disability, or dystonia. Administration of thiamine is ineffective in the treatment of this disorder. Experiments have failed to show that this protein can transport biotin. Mutations in this gene also cause a Wernicke's-like encephalopathy.[provided by RefSeq, Jan 2010]

GeneCards Summary for SLC19A3 Gene

SLC19A3 (Solute Carrier Family 19 Member 3) is a Protein Coding gene. Diseases associated with SLC19A3 include Thiamine Metabolism Dysfunction Syndrome 2 and Infantile Spams-Psychomotor Retardation-Progressive Brain Atrophy-Basal Ganglia Disease Syndrome. Among its related pathways are Metabolism and Metabolism of water-soluble vitamins and cofactors. An important paralog of this gene is SLC19A2.

UniProtKB/Swiss-Prot for SLC19A3 Gene

  • Mediates high affinity thiamine uptake, probably via a proton anti-port mechanism. Has no folate transport activity.

Gene Wiki entry for SLC19A3 Gene

Additional gene information for SLC19A3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLC19A3 Gene

Genomics for SLC19A3 Gene

GeneHancer (GH) Regulatory Elements for SLC19A3 Gene

Promoters and enhancers for SLC19A3 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
GH02J227715 Promoter/Enhancer 2 EPDnew Ensembl ENCODE dbSUPER 671.3 +0.2 171 4.7 FOXA2 SIN3A ZNF48 RAD21 YY1 ZNF614 EGR1 NFKBIZ RXRA CEBPB SLC19A3 GC02M227705 GC02M227708
GH02J227705 Enhancer 1 ENCODE dbSUPER 13 +11.0 10997 2.3 FOXA2 MLX ZNF48 RAD21 RARA YY1 ZNF614 RXRA SP5 CEBPB SLC19A3 GC02M227708 GC02M227705 SCYGR5
GH02J227700 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 7.2 +15.2 15215 4 PKNOX1 FOXA2 ZFP64 NEUROD1 FEZF1 RAD21 RARA ETS1 RFX5 YY1 CCL20 SLC19A3 GC02M227708 SCYGR5
GH02J227674 Enhancer 0.5 FANTOM5 dbSUPER 16.2 +43.4 43422 0.3 SLC19A3 C2orf83 CCL20 SCYGR5 GC02M227708
GH02J227712 Enhancer 0.5 ENCODE dbSUPER 13.5 +4.1 4066 2.5 ZNF384 SLC19A3 GC02M227708 GC02M227705
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SLC19A3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SLC19A3 gene promoter:
  • C/EBPalpha
  • NF-kappaB2
  • NF-kappaB1
  • NF-kappaB
  • CUTL1
  • FOXD3
  • Hand1
  • E47
  • HNF-3beta
  • NF-AT

Genomic Locations for SLC19A3 Gene

Genomic Locations for SLC19A3 Gene
34,269 bases
Minus strand
32,820 bases
Minus strand

Genomic View for SLC19A3 Gene

Genes around SLC19A3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLC19A3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLC19A3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC19A3 Gene

Proteins for SLC19A3 Gene

  • Protein details for SLC19A3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Thiamine transporter 2
    Protein Accession:

    Protein attributes for SLC19A3 Gene

    496 amino acids
    Molecular mass:
    55665 Da
    Quaternary structure:
    No Data Available

neXtProt entry for SLC19A3 Gene

Post-translational modifications for SLC19A3 Gene

  • Glycosylation at isoforms=166 and posLast=4545
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SLC19A3 Gene

Domains & Families for SLC19A3 Gene

Gene Families for SLC19A3 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Potential drug targets
  • Predicted membrane proteins
  • Transporters

Protein Domains for SLC19A3 Gene

Suggested Antigen Peptide Sequences for SLC19A3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the reduced folate carrier (RFC) transporter (TC 2.A.48) family.
  • Belongs to the reduced folate carrier (RFC) transporter (TC 2.A.48) family.
genes like me logo Genes that share domains with SLC19A3: view

Function for SLC19A3 Gene

Molecular function for SLC19A3 Gene

UniProtKB/Swiss-Prot Function:
Mediates high affinity thiamine uptake, probably via a proton anti-port mechanism. Has no folate transport activity.

Phenotypes From GWAS Catalog for SLC19A3 Gene

Gene Ontology (GO) - Molecular Function for SLC19A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0015234 thiamine transmembrane transporter activity IEA,TAS --
GO:0022857 transmembrane transporter activity IBA --
GO:0090482 vitamin transmembrane transporter activity IEA --
genes like me logo Genes that share ontologies with SLC19A3: view
genes like me logo Genes that share phenotypes with SLC19A3: view

Human Phenotype Ontology for SLC19A3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SLC19A3 Gene

MGI Knock Outs for SLC19A3:

Animal Model Products

  • Taconic Biosciences Mouse Models for SLC19A3

CRISPR Products

miRNA for SLC19A3 Gene

miRTarBase miRNAs that target SLC19A3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SLC19A3

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SLC19A3 Gene

Localization for SLC19A3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC19A3 Gene

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 SLC19A3 gene
Compartment Confidence
plasma membrane 5
mitochondrion 2
nucleus 2
cytosol 2
extracellular 1
endoplasmic reticulum 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SLC19A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA,NAS 11136550
genes like me logo Genes that share ontologies with SLC19A3: view

Pathways & Interactions for SLC19A3 Gene

genes like me logo Genes that share pathways with SLC19A3: view

Pathways by source for SLC19A3 Gene

Interacting Proteins for SLC19A3 Gene

STRING Interaction Network Preview (showing 2 interactants - click image to see details)
Selected Interacting proteins: Q9BZV2-S19A3_HUMAN ENSP00000258403 for SLC19A3 Gene via IID STRING MINT

Gene Ontology (GO) - Biological Process for SLC19A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0015888 thiamine transport IEA --
GO:0035461 vitamin transmembrane transport IEA --
GO:0042723 thiamine-containing compound metabolic process TAS --
GO:0051180 vitamin transport IEA --
GO:0055085 transmembrane transport IBA --
genes like me logo Genes that share ontologies with SLC19A3: view

No data available for SIGNOR curated interactions for SLC19A3 Gene

Drugs & Compounds for SLC19A3 Gene

(3) Drugs for SLC19A3 Gene - From: DrugBank, DGIdb, IUPHAR, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
L-Cysteine Approved Nutra Target 0
[<sup>3</sup>H]thiamine Pharma 0
genes like me logo Genes that share compounds with SLC19A3: view

Transcripts for SLC19A3 Gene

mRNA/cDNA for SLC19A3 Gene

Unigene Clusters for SLC19A3 Gene

Solute carrier family 19, member 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SLC19A3

Alternative Splicing Database (ASD) splice patterns (SP) for SLC19A3 Gene

No ASD Table

Relevant External Links for SLC19A3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SLC19A3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SLC19A3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SLC19A3 Gene

This gene is overexpressed in Adipose - Visceral (Omentum) (x13.6), Adipose - Subcutaneous (x13.5), and Breast - Mammary Tissue (x7.7).

Protein differential expression in normal tissues from HIPED for SLC19A3 Gene

This gene is overexpressed in Liver (24.5), Blymphocyte (17.6), Spleen (6.8), and Gallbladder (6.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SLC19A3 Gene

NURSA nuclear receptor signaling pathways regulating expression of SLC19A3 Gene:


SOURCE GeneReport for Unigene cluster for SLC19A3 Gene:


mRNA Expression by UniProt/SwissProt for SLC19A3 Gene:

Tissue specificity: Widely expressed but most abundant in placenta, kidney and liver.

Evidence on tissue expression from TISSUES for SLC19A3 Gene

  • Nervous system(4.3)
  • Liver(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SLC19A3 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cerebellum
  • cerebrospinal fluid
  • cranial nerve
  • eye
  • eyelid
  • face
  • head
  • meninges
  • mouth
  • neck
  • pharynx
  • chest wall
  • esophagus
  • lung
  • abdominal wall
  • liver
  • stomach
  • foot
  • lower limb
  • blood
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal cord
  • white blood cell
genes like me logo Genes that share expression patterns with SLC19A3: view

No data available for Protein tissue co-expression partners for SLC19A3 Gene

Orthologs for SLC19A3 Gene

This gene was present in the common ancestor of animals.

Orthologs for SLC19A3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SLC19A3 34 33
  • 99.26 (n)
(Canis familiaris)
Mammalia LOC486151 33
  • 85.25 (n)
SLC19A3 34
  • 82 (a)
(Bos Taurus)
Mammalia SLC19A3 34 33
  • 83.26 (n)
(Mus musculus)
Mammalia Slc19a3 16 34 33
  • 75.36 (n)
(Ornithorhynchus anatinus)
Mammalia SLC19A3 34
  • 74 (a)
(Rattus norvegicus)
Mammalia Slc19a3 33
  • 73.83 (n)
(Monodelphis domestica)
Mammalia -- 34
  • 65 (a)
-- 34
  • 63 (a)
(Gallus gallus)
Aves SLC19A3 33
  • 64.55 (n)
-- 34
  • 62 (a)
-- 34
  • 61 (a)
(Anolis carolinensis)
Reptilia SLC19A3 34
  • 61 (a)
African clawed frog
(Xenopus laevis)
Amphibia MGC52872 33
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.8267 33
(Danio rerio)
Actinopterygii LOC557854 33
  • 55.23 (n)
slc19a3b 34
  • 45 (a)
slc19a3a 34
  • 43 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG6574 34 35 33
  • 49.31 (n)
CG17036 34 35
  • 37 (a)
CG14694 34 35
  • 32 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012955 33
  • 47.32 (n)
(Caenorhabditis elegans)
Secernentea folt-1 34
  • 35 (a)
folt-3 34
  • 33 (a)
folt-2 34
  • 33 (a)
F37B4.7 35
  • 32 (a)
C06H2.4 35
  • 31 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 46 (a)
Species where no ortholog for SLC19A3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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 SLC19A3 Gene

Gene Tree for SLC19A3 (if available)
Gene Tree for SLC19A3 (if available)
Evolutionary constrained regions (ECRs) for SLC19A3: view image

Paralogs for SLC19A3 Gene

Paralogs for SLC19A3 Gene

(2) SIMAP similar genes for SLC19A3 Gene using alignment to 7 proteins:

  • S19A3_HUMAN
  • B8ZZ39_HUMAN
  • C9J4J5_HUMAN
  • E7EM61_HUMAN
  • F5H2M8_HUMAN Pseudogenes for SLC19A3 Gene

genes like me logo Genes that share paralogs with SLC19A3: view

Variants for SLC19A3 Gene

Sequence variations from dbSNP and Humsavar for SLC19A3 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs1037322341 uncertain-significance, Thiamine Metabolism Dysfunction Syndrome 227,687,097(-) C/T 3_prime_UTR_variant
rs1055957 likely-benign, Thiamine Metabolism Dysfunction Syndrome 227,685,293(-) A/G 3_prime_UTR_variant
rs111409314 benign, Thiamine Metabolism Dysfunction Syndrome 227,685,401(-) A/G 3_prime_UTR_variant
rs111467219 benign, Thiamine Metabolism Dysfunction Syndrome 227,686,397(-) T/C 3_prime_UTR_variant
rs112957132 uncertain-significance, Thiamine Metabolism Dysfunction Syndrome 227,687,049(-) T/G 3_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for SLC19A3 Gene

Variant ID Type Subtype PubMed ID
dgv7321n54 CNV gain 21841781
dgv7322n54 CNV gain 21841781
esv2721563 CNV deletion 23290073
nsv1000263 CNV gain 25217958
nsv1009159 CNV loss 25217958
nsv10221 CNV loss 18304495
nsv520733 CNV gain 19592680
nsv834561 CNV gain 17160897

Variation tolerance for SLC19A3 Gene

Residual Variation Intolerance Score: 81.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.60; 56.34% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SLC19A3 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLC19A3 Gene

Disorders for SLC19A3 Gene

MalaCards: The human disease database

(10) MalaCards diseases for SLC19A3 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
thiamine metabolism dysfunction syndrome 2
  • thmd2
infantile spams-psychomotor retardation-progressive brain atrophy-basal ganglia disease syndrome
leigh syndrome with leukodystrophy
  • infantile subacute necrotizing encephalopathy with leukodystrophy
basal ganglia disease
  • basal ganglia diseases
biotin-thiamine-responsive basal ganglia disease
  • thiamine metabolism dysfunction syndrome 2
- elite association - COSMIC cancer census association via MalaCards


  • Thiamine metabolism dysfunction syndrome 2, biotin- or thiamine-responsive type (THMD2) [MIM:607483]: An autosomal recessive metabolic disorder characterized by episodic encephalopathy, often triggered by febrile illness, presenting as confusion, seizures, external ophthalmoplegia, dysphagia, and sometimes coma and death. If untreated, encephalopathies can result in permanent dystonia. Brain imaging may show characteristic bilateral lesions of the basal ganglia. {ECO:0000269 PubMed:15871139}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SLC19A3

genes like me logo Genes that share disorders with SLC19A3: view

No data available for Genatlas for SLC19A3 Gene

Publications for SLC19A3 Gene

  1. Identification and characterization of the human and mouse SLC19A3 gene: a novel member of the reduced folate family of micronutrient transporter genes. (PMID: 11136550) Eudy JD … Finnell RH (Molecular genetics and metabolism 2000) 2 3 4 22 58
  2. Biotin-responsive basal ganglia disease maps to 2q36.3 and is due to mutations in SLC19A3. (PMID: 15871139) Zeng WQ … Gusella JF (American journal of human genetics 2005) 2 3 4 58
  3. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PMID: 15815621) Hillier LW … Wilson RK (Nature 2005) 3 4 58
  4. Differentiation-dependent up-regulation of intestinal thiamin uptake: cellular and molecular mechanisms. (PMID: 16055442) Nabokina SM … Said HM (The Journal of biological chemistry 2005) 3 22 58
  5. Biotin deficiency reduces expression of SLC19A3, a potential biotin transporter, in leukocytes from human blood. (PMID: 15623830) Vlasova TI … Mock DM (The Journal of nutrition 2005) 3 22 58

Products for SLC19A3 Gene

Sources for SLC19A3 Gene

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