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Aliases for SLC6A20 Gene

Aliases for SLC6A20 Gene

  • Solute Carrier Family 6 Member 20 2 3 4 5
  • Solute Carrier Family 6 (Proline IMINO Transporter), Member 20 2 3
  • Sodium/Imino-Acid Transporter 1 3 4
  • Transporter RB21A Homolog 3 4
  • Xtrp3 3 4
  • SIT1 3 4
  • XT3 3 4
  • Solute Carrier Family 6 (Neurotransmitter Transporter), Member 20 3
  • Sodium- And Chloride-Dependent Transporter XTRP3 3
  • Neurotransmitter Transporter RB21A 3
  • X Transporter Protein 3 3
  • Orphan Transporter XT3 3

External Ids for SLC6A20 Gene

Previous GeneCards Identifiers for SLC6A20 Gene

  • GC03M045758
  • GC03M045771

Summaries for SLC6A20 Gene

Entrez Gene Summary for SLC6A20 Gene

  • Transport of small hydrophilic substances across cell membranes is mediated by substrate-specific transporter proteins which have been classified into several families of related genes. The protein encoded by this gene is a member of the subgroup of transporter with unidentified substrates within the Na+ and Cl- coupled transporter family. This gene is expressed in kidney, and its alternative splicing generates 2 transcript variants. [provided by RefSeq, Jul 2008]

GeneCards Summary for SLC6A20 Gene

SLC6A20 (Solute Carrier Family 6 Member 20) is a Protein Coding gene. Diseases associated with SLC6A20 include Iminoglycinuria and Hyperglycinuria. Among its related pathways are Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds and Amino acid transport across the plasma membrane. Gene Ontology (GO) annotations related to this gene include amino acid transmembrane transporter activity and neurotransmitter:sodium symporter activity. An important paralog of this gene is SLC6A18.

UniProtKB/Swiss-Prot for SLC6A20 Gene

  • Mediates the calcium-dependent uptake of imino acids such as L-proline, N-methyl-L-proline and pipecolate as well as N-methylated amino acids. Involved in the transport of glycine.

Gene Wiki entry for SLC6A20 Gene

Additional gene information for SLC6A20 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLC6A20 Gene

Genomics for SLC6A20 Gene

GeneHancer (GH) Regulatory Elements for SLC6A20 Gene

Promoters and enhancers for SLC6A20 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
GH03I045794 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE dbSUPER 550.8 +0.5 542 2.6 LEF1 SUZ12 BACH1 ZMYM3 BMI1 ZNF143 EZH2 SMARCA5 RNF2 HLF SLC6A20 GC03M045749
GH03I045860 Enhancer 1 ENCODE dbSUPER 11.6 -64.8 -64848 1.6 FOXA2 SMAD1 BMI1 BATF IRF4 ATF7 ETV6 BCLAF1 IKZF2 RUNX3 SDHDP4 SLC6A20 CCR9 LZTFL1 LIMD1 LARS2 GC03P045849 GC03M045883
GH03I045771 Enhancer 0.8 ENCODE dbSUPER 12.2 +21.8 21847 6.5 HLF USF2 ZNF140 CBFA2T3 CEBPG ATF2 NFIC CREB1 ATF7 RUNX3 SACM1L RN7SL145P SLC6A20 LZTFL1 SDHDP4 CCR9 LIMD1 CDCP1 GC03M045749
GH03I045165 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 5 +628.3 628317 5.3 HDGF PKNOX1 SIN3A FEZF1 POLR2B ZNF766 FOS REST SMARCB1 ZNF592 CDCP1 TMEM158 ENSG00000202268 LARS2-AS1 SLC6A20 LIMD1 RPS24P8 LOC101928636
GH03I045816 Enhancer 1 Ensembl ENCODE 5.8 -21.4 -21365 3.8 PKNOX1 FEZF1 RAD21 ZEB1 ZNF366 RCOR1 FOS ZNF362 SMARCC1 USF2 LZTFL1 SDHDP4 CCR9 SLC6A20 CXCR6 PIR58059
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SLC6A20 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SLC6A20 gene promoter:

Genomic Locations for SLC6A20 Gene

Genomic Locations for SLC6A20 Gene
41,113 bases
Minus strand

Genomic View for SLC6A20 Gene

Genes around SLC6A20 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLC6A20 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLC6A20 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC6A20 Gene

Proteins for SLC6A20 Gene

  • Protein details for SLC6A20 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Sodium- and chloride-dependent transporter XTRP3
    Protein Accession:
    Secondary Accessions:
    • A1A4F2
    • O75590
    • Q8TF10
    • Q9NPQ2
    • Q9NQ77

    Protein attributes for SLC6A20 Gene

    592 amino acids
    Molecular mass:
    65914 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAL75944.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for SLC6A20 Gene


neXtProt entry for SLC6A20 Gene

Post-translational modifications for SLC6A20 Gene

  • Glycosylation at posLast=131131 and posLast=357357
  • Modification sites at PhosphoSitePlus

Other Protein References for SLC6A20 Gene

No data available for DME Specific Peptides for SLC6A20 Gene

Domains & Families for SLC6A20 Gene

Gene Families for SLC6A20 Gene

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

Suggested Antigen Peptide Sequences for SLC6A20 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the sodium:neurotransmitter symporter (SNF) (TC 2.A.22) family. SLC6A20 subfamily.
  • Belongs to the sodium:neurotransmitter symporter (SNF) (TC 2.A.22) family. SLC6A20 subfamily.
genes like me logo Genes that share domains with SLC6A20: view

Function for SLC6A20 Gene

Molecular function for SLC6A20 Gene

UniProtKB/Swiss-Prot Function:
Mediates the calcium-dependent uptake of imino acids such as L-proline, N-methyl-L-proline and pipecolate as well as N-methylated amino acids. Involved in the transport of glycine.

Phenotypes From GWAS Catalog for SLC6A20 Gene

Gene Ontology (GO) - Molecular Function for SLC6A20 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005328 neurotransmitter:sodium symporter activity IEA --
GO:0005515 protein binding IPI 25416956
GO:0015171 amino acid transmembrane transporter activity IEA,TAS --
GO:0015193 L-proline transmembrane transporter activity IEA --
GO:0015293 symporter activity IEA --
genes like me logo Genes that share ontologies with SLC6A20: view
genes like me logo Genes that share phenotypes with SLC6A20: view

Human Phenotype Ontology for SLC6A20 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for SLC6A20 Gene

Localization for SLC6A20 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC6A20 Gene

Apical cell membrane; Multi-pass membrane protein. Note=Located in the apical brush border membrane of kidney proximal tubule cells. {ECO:0000250}.

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 SLC6A20 gene
Compartment Confidence
plasma membrane 5
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for SLC6A20 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IEA,IBA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0016324 apical plasma membrane ISS --
genes like me logo Genes that share ontologies with SLC6A20: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SLC6A20 Gene

Pathways & Interactions for SLC6A20 Gene

genes like me logo Genes that share pathways with SLC6A20: view

Gene Ontology (GO) - Biological Process for SLC6A20 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006836 neurotransmitter transport IEA --
GO:0006865 amino acid transport TAS --
GO:0015816 glycine transport IMP 19033659
GO:0015824 proline transport IMP 19033659
genes like me logo Genes that share ontologies with SLC6A20: view

No data available for SIGNOR curated interactions for SLC6A20 Gene

Drugs & Compounds for SLC6A20 Gene

(1) Drugs for SLC6A20 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Approved Nutra 0

(1) Additional Compounds for SLC6A20 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • Sodium
  • Sodium ion
genes like me logo Genes that share compounds with SLC6A20: view

Transcripts for SLC6A20 Gene

Unigene Clusters for SLC6A20 Gene

Solute carrier family 6 (proline IMINO transporter), member 20:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SLC6A20 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b
SP1: - - -

Relevant External Links for SLC6A20 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SLC6A20 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SLC6A20 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SLC6A20 Gene

This gene is overexpressed in Small Intestine - Terminal Ileum (x11.9), Nerve - Tibial (x9.0), and Pancreas (x4.8).

Protein differential expression in normal tissues from HIPED for SLC6A20 Gene

This gene is overexpressed in Plasma (60.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SLC6A20 Gene

Protein tissue co-expression partners for SLC6A20 Gene

NURSA nuclear receptor signaling pathways regulating expression of SLC6A20 Gene:


SOURCE GeneReport for Unigene cluster for SLC6A20 Gene:


mRNA Expression by UniProt/SwissProt for SLC6A20 Gene:

Tissue specificity: Kidney and small intestine. Expressed in the S3 segment of the proximal tubule.

Evidence on tissue expression from TISSUES for SLC6A20 Gene

  • Intestine(2.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SLC6A20 Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • nervous
  • urinary
Head and neck:
  • brain
  • eye
  • head
  • kidney
  • ureter
genes like me logo Genes that share expression patterns with SLC6A20: view

Orthologs for SLC6A20 Gene

This gene was present in the common ancestor of animals.

Orthologs for SLC6A20 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SLC6A20 33 34
  • 98.43 (n)
(Canis familiaris)
Mammalia SLC6A20 33 34
  • 89.54 (n)
(Bos Taurus)
Mammalia SLC6A20 33 34
  • 89.13 (n)
(Mus musculus)
Mammalia Slc6a20a 33 16 34
  • 87.84 (n)
(Rattus norvegicus)
Mammalia Slc6a20 33
  • 87.67 (n)
(Monodelphis domestica)
Mammalia SLC6A20 34
  • 87 (a)
(Ornithorhynchus anatinus)
Mammalia SLC6A20 34
  • 80 (a)
(Gallus gallus)
Aves SLC6A20 33 34
  • 78.66 (n)
(Anolis carolinensis)
Reptilia SLC6A20 34
  • 80 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100497079 33
  • 67.35 (n)
(Danio rerio)
Actinopterygii SLC6A20 34
  • 33 (a)
fruit fly
(Drosophila melanogaster)
Insecta ine 34
  • 22 (a)
(Caenorhabditis elegans)
Secernentea snf-10 34
  • 16 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 30 (a)
-- 34
  • 22 (a)
Species where no ortholog for SLC6A20 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)
  • 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 SLC6A20 Gene

Gene Tree for SLC6A20 (if available)
Gene Tree for SLC6A20 (if available)

Paralogs for SLC6A20 Gene

Paralogs for SLC6A20 Gene

genes like me logo Genes that share paralogs with SLC6A20: view

Variants for SLC6A20 Gene

Sequence variations from dbSNP and Humsavar for SLC6A20 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1006705338 uncertain-significance, Hyperglycinuria 45,758,061(-) C/T 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1013173157 uncertain-significance, Hyperglycinuria 45,796,518(-) G/C 5_prime_UTR_variant, genic_upstream_transcript_variant
rs1016732744 uncertain-significance, Hyperglycinuria 45,758,334(-) G/A 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1032895519 uncertain-significance, Hyperglycinuria 45,757,376(-) G/A/C/T 3_prime_UTR_variant, genic_downstream_transcript_variant
rs115438130 likely-benign, Hyperglycinuria 45,756,331(-) A/G 3_prime_UTR_variant, genic_downstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for SLC6A20 Gene

Variant ID Type Subtype PubMed ID
dgv293e215 CNV deletion 23714750
esv1614687 CNV deletion 17803354
esv2192183 CNV deletion 18987734
esv2670527 CNV deletion 23128226
esv2725225 CNV deletion 23290073
esv2725226 CNV deletion 23290073
esv3033190 CNV deletion 24192839
esv3365430 CNV insertion 20981092
nsv1127955 CNV deletion 24896259
nsv834678 CNV gain 17160897

Variation tolerance for SLC6A20 Gene

Residual Variation Intolerance Score: 33.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.76; 73.48% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SLC6A20 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 SLC6A20 Gene

Disorders for SLC6A20 Gene

MalaCards: The human disease database

(3) MalaCards diseases for SLC6A20 Gene - From: HGMD, OMIM, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
  • iminoglycinuria, digenic
  • glycinuria with or without oxalate urolithiasis
hartnup disorder
  • hnd
- elite association - COSMIC cancer census association via MalaCards


  • Hyperglycinuria (HG) [MIM:138500]: A condition characterized by excess of glycine in the urine. In some cases it is associated with renal colic and renal oxalate stones. {ECO:0000269 PubMed:19033659}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Iminoglycinuria (IG) [MIM:242600]: A disorder of renal tubular reabsorption of glycine and imino acids (proline and hydroxyproline), marked by excessive levels of all three substances in the urine. {ECO:0000269 PubMed:19033659}. Note=The disease is caused by mutations affecting the gene represented in this entry. Haploinsufficiency of SLC6A20 combined with deficiency of the neutral amino acid transporter SLC6A19 or partially inactivating mutations in SLC36A2, is responsible for iminoglycinuria. Additional polymorphisms and mutations in SLC6A18 can contribute to the IG phenotype in some families.

Additional Disease Information for SLC6A20

genes like me logo Genes that share disorders with SLC6A20: view

No data available for Genatlas for SLC6A20 Gene

Publications for SLC6A20 Gene

  1. Identification of mammalian proline transporter SIT1 (SLC6A20) with characteristics of classical system imino. (PMID: 15632147) Takanaga H … Hediger MA (The Journal of biological chemistry 2005) 3 4 22 58
  2. The LZTFL1 gene is a part of a transcriptional map covering 250 kb within the common eliminated region 1 (C3CER1) in 3p21.3. (PMID: 11352561) Kiss H … Dumanski JP (Genomics 2001) 2 3 4 58
  3. Cloning, gene structure and genomic localization of an orphan transporter from mouse kidney with six alternatively-spliced isoforms. (PMID: 9932288) Nash SR … Caron MG (Receptors & channels 1998) 2 3 4 58
  4. A genome-wide association study of metabolic traits in human urine. (PMID: 21572414) Suhre K … Nauck M (Nature genetics 2011) 3 44 58
  5. Sodium translocation by the iminoglycinuria associated imino transporter (SLC6A20). (PMID: 19657969) Bröer A … Bröer S (Molecular membrane biology 2009) 3 22 58

Products for SLC6A20 Gene

Sources for SLC6A20 Gene

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