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 ... See more...

Aliases for SLC6A20 Gene

Aliases for SLC6A20 Gene

  • Solute Carrier Family 6 Member 20 2 3 4 5
  • SIT1 2 3 4
  • XT3 2 3 4
  • Solute Carrier Family 6 (Proline IMINO Transporter), Member 20 2 3
  • Sodium- And Chloride-Dependent Transporter XTRP3 3 4
  • Sodium-Dependent Imino Acid Transporter 1 2 3
  • Sodium/Imino-Acid Transporter 1 3 4
  • Transporter RB21A Homolog 3 4
  • IMINO 2 3
  • Xtrp3 2 3
  • Solute Carrier Family 6 (Neurotransmitter Transporter), Member 20 3
  • Neurotransmitter Transporter RB21A 3
  • X Transporter Protein 3 3
  • Orphan Transporter XT3 3
  • SLC6A20 5
  • XTRP3 4

External Ids for SLC6A20 Gene

Previous GeneCards Identifiers for SLC6A20 Gene

  • GC03M045758
  • GC03M045771
  • GC03M045796

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 NRF2 pathway. 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 Summary 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

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SLC6A20 Gene

Genomics for SLC6A20 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SLC6A20 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 SLC6A20 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SLC6A20

Top Transcription factor binding sites by QIAGEN in the SLC6A20 gene promoter:
  • ATF-2
  • E2F
  • E2F-1
  • FOXO3
  • FOXO3a
  • FOXO3b
  • FOXO4
  • Hlf
  • PPAR-gamma1
  • PPAR-gamma2

Genomic Locations for SLC6A20 Gene

Genomic Locations for SLC6A20 Gene
chr3:45,755,449-45,796,553
(GRCh38/hg38)
Size:
41,105 bases
Orientation:
Minus strand
chr3:45,796,941-45,838,035
(GRCh37/hg19)
Size:
41,095 bases
Orientation:
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:
    Q9NP91-S6A20_HUMAN
    Recommended name:
    Sodium- and chloride-dependent transporter XTRP3
    Protein Accession:
    Q9NP91
    Secondary Accessions:
    • A1A4F2
    • O75590
    • Q8TF10
    • Q9NPQ2
    • Q9NQ77

    Protein attributes for SLC6A20 Gene

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

    Alternative splice isoforms for SLC6A20 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SLC6A20 Gene

Post-translational modifications for SLC6A20 Gene

  • Glycosylation at Asn131 and Asn357
  • 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

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

Protein Domains for SLC6A20 Gene

InterPro:
Blocks:
  • Orphan neurotransmitter transporter signature
ProtoNet:

Suggested Antigen Peptide Sequences for SLC6A20 Gene

GenScript: Design optimal peptide antigens:
  • Transporter (B7ZLW4_HUMAN)
  • Transporter (C9JIN6_HUMAN)
  • Transporter rB21A homolog (S6A20_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9NP91

UniProtKB/Swiss-Prot:

S6A20_HUMAN :
  • Belongs to the sodium:neurotransmitter symporter (SNF) (TC 2.A.22) family. SLC6A20 subfamily.
Family:
  • 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 IDA,TAS --
GO:0015193 L-proline transmembrane transporter activity IBA 21873635
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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SLC6A20

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

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 SLC6A20 gene
Compartment Confidence
plasma membrane 5
extracellular 2
cytoskeleton 1
mitochondrion 1
peroxisome 1
nucleus 1
endoplasmic reticulum 1
endosome 1
cytosol 1
lysosome 1
golgi apparatus 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 --
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:0003333 amino acid transmembrane transport IEA --
GO:0006810 transport IBA 21873635
GO:0006836 neurotransmitter transport IEA --
GO:0006865 amino acid transport TAS --
GO:0015816 glycine 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 Nutra 6556

(1) Additional Compounds for SLC6A20 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 SLC6A20: view

Transcripts for SLC6A20 Gene

mRNA/cDNA for SLC6A20 Gene

2 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SLC6A20

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: - - -
SP2:
SP3:

Relevant External Links for SLC6A20 Gene

GeneLoc Exon Structure for
SLC6A20

Expression for SLC6A20 Gene

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



Protein tissue co-expression partners for SLC6A20 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SLC6A20

SOURCE GeneReport for Unigene cluster for SLC6A20 Gene:

Hs.413095

mRNA Expression by UniProt/SwissProt for SLC6A20 Gene:

Q9NP91-S6A20_HUMAN
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(2.5)
  • Skin(2.4)
  • Nervous system(2.3)
  • Blood(2.2)
  • Liver(2.1)

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

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

Primer Products

Orthologs for SLC6A20 Gene

This gene was present in the common ancestor of animals.

Orthologs for SLC6A20 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SLC6A20 30 31
  • 98.43 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SLC6A20 30 31
  • 89.54 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SLC6A20 30 31
  • 89.13 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Slc6a20a 30 17 31
  • 87.84 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Slc6a20 30
  • 87.67 (n)
Oppossum
(Monodelphis domestica)
Mammalia SLC6A20 31
  • 87 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SLC6A20 31
  • 80 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SLC6A20 30 31
  • 78.66 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SLC6A20 31
  • 80 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia LOC100497079 30
  • 67.35 (n)
Zebrafish
(Danio rerio)
Actinopterygii SLC6A20 31
  • 33 (a)
OneToMany
Fruit Fly
(Drosophila melanogaster)
Insecta ine 31
  • 22 (a)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea snf-10 31
  • 16 (a)
OneToOne
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 30 (a)
OneToMany
-- 31
  • 22 (a)
OneToMany
Species where no ortholog for SLC6A20 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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

ENSEMBL:
Gene Tree for SLC6A20 (if available)
TreeFam:
Gene Tree for SLC6A20 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SLC6A20: view image

Paralogs for SLC6A20 Gene

(21) SIMAP similar genes for SLC6A20 Gene using alignment to 3 proteins:

  • S6A20_HUMAN
  • B7ZLW4_HUMAN
  • C9JIN6_HUMAN
genes like me logo Genes that share paralogs with SLC6A20: view

Variants for SLC6A20 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SLC6A20 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
899511 Uncertain Significance: Hyperglycinuria 45,755,636(-) T/A THREE_PRIME_UTR_VARIANT
899512 Uncertain Significance: Hyperglycinuria 45,755,658(-) G/C THREE_PRIME_UTR_VARIANT
899573 Uncertain Significance: Hyperglycinuria 45,756,780(-) A/G THREE_PRIME_UTR_VARIANT
899574 Uncertain Significance: Hyperglycinuria 45,756,953(-) C/T THREE_PRIME_UTR_VARIANT
899575 Uncertain Significance: Hyperglycinuria 45,756,991(-) C/T THREE_PRIME_UTR_VARIANT

Additional dbSNP identifiers (rs#s) for SLC6A20 Gene

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)
SLC6A20
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SLC6A20

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLC6A20 Gene

Disorders for SLC6A20 Gene

MalaCards: The human disease database

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

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

UniProtKB/Swiss-Prot

S6A20_HUMAN
  • 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 23
  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
  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
  4. A genome-wide association study of metabolic traits in human urine. (PMID: 21572414) Suhre K … Nauck M (Nature genetics 2011) 3 41
  5. Sodium translocation by the iminoglycinuria associated imino transporter (SLC6A20). (PMID: 19657969) Bröer A … Bröer S (Molecular membrane biology 2009) 3 23

Products for SLC6A20 Gene

Sources for SLC6A20 Gene