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SLC6A20 Gene(Protein Coding)

Solute Carrier Family 6 Member 20

GCID:
GC03M045796
GIFtS:
59
Genes Participants
UDN Logo

Aliases for SLC6A20 Gene

Aliases for SLC6A20 Gene

  • Solute Carrier Family 6 Member 20 2 3 4
  • Solute Carrier Family 6 (Proline IMINO Transporter), Member 20 2 3 5
  • 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
  • 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, Digenic and Hyperglycinuria. Among its related pathways are Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds. 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

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

Genomics for SLC6A20 Gene

Products:

  1. Regulatory Element

Regulatory Elements for SLC6A20 Gene

Enhancers for SLC6A20 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around SLC6A20 on UCSC Golden Path with GeneCards custom track

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

Genomic Location for SLC6A20 Gene

Chromosome:
3
Start:
45,755,449 bp from pter
End:
45,796,561 bp from pter
Size:
41,113 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 Structure • Gene Density

RefSeq DNA sequence for SLC6A20 Gene

Proteins for SLC6A20 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • 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

Proteomics data for SLC6A20 Gene at MOPED

Protein Expression for SLC6A20 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for SLC6A20 Gene

  • Glycosylation at Asn 131 and Asn 357
  • Modification sites at PhosphoSitePlus

Other Protein References for SLC6A20 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SLC6A20 Gene

Domains & Families for SLC6A20 Gene

Gene Families for SLC6A20 Gene

HGNC:
IUPHAR :

Protein Domains for SLC6A20 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for SLC6A20 Gene

GenScript: Design optimal peptide antigens:

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

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

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.

Gene Ontology (GO) - Molecular Function for SLC6A20 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
GO:0015171 amino acid transmembrane transporter activity IDA,TAS --
GO:0015375 glycine:sodium symporter activity IBA --
genes like me logo Genes that share ontologies with SLC6A20: view

Phenotypes for SLC6A20 Gene

GenomeRNAi human phenotypes for SLC6A20:
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

miRNA for SLC6A20 Gene

miRTarBase miRNAs that target SLC6A20

Inhibitory RNA Products

Flow Cytometry 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

COMPARTMENTS
Jensen Localization Image for SLC6A20 Gene 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 --
genes like me logo Genes that share ontologies with SLC6A20: view

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 TAS --
GO:0015824 proline transport IMP 19033659
GO:0036233 glycine import IBA --
GO:0055085 transmembrane transport IEA --
GO:0060012 synaptic transmission, glycinergic IBA --
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

Products:

  1. Drug

(1) Drugs for SLC6A20 Gene - From: HMDB

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

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
sodium
  • Sodium
  • Sodium ion
 7440-23-5
genes like me logo Genes that share compounds with SLC6A20: view

Transcripts for SLC6A20 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for SLC6A20 Gene

(5) REFSEQ mRNAs :
(8) Additional mRNA sequences :
(53) Selected AceView cDNA sequences:
(7) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SLC6A20 Gene

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

CRISPR Products

Inhibitory RNA Products

Flow Cytometry 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: - - -
SP2:
SP3:

Relevant External Links for SLC6A20 Gene

GeneLoc Exon Structure for
SLC6A20
ECgene alternative splicing isoforms for
SLC6A20

Expression for SLC6A20 Gene

Products:

  1. Primer

mRNA expression in normal human tissues for SLC6A20 Gene

mRNA expression in normal human tissues for SLC6A20 Gene
mRNA expression by BioGPS for SLC6A20 GenemRNA expression by GTEx 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



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.
genes like me logo Genes that share expression patterns with SLC6A20: view

Protein tissue co-expression partners for SLC6A20 Gene

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
cow
(Bos Taurus)
 Mammalia SLC6A20 35
  • 89.13 (n)
  • 90.37 (a)
SLC6A20 36
  • 90 (a)
 OneToOne
dog
(Canis familiaris)
 Mammalia SLC6A20 35
  • 89.54 (n)
  • 90.53 (a)
SLC6A20 36
  • 90 (a)
 OneToOne
mouse
(Mus musculus)
 Mammalia Slc6a20a 35
  • 87.84 (n)
  • 92.06 (a)
Slc6a20a 16
Slc6a20a 36
  • 92 (a)
 OneToOne
chimpanzee
(Pan troglodytes)
 Mammalia SLC6A20 35
  • 98.43 (n)
  • 98.03 (a)
SLC6A20 36
  • 99 (a)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Slc6a20 35
  • 87.67 (n)
  • 90.88 (a)
oppossum
(Monodelphis domestica)
 Mammalia SLC6A20 36
  • 87 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia SLC6A20 36
  • 80 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves SLC6A20 35
  • 78.66 (n)
  • 83.28 (a)
SLC6A20 36
  • 80 (a)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia SLC6A20 36
  • 80 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia LOC100497079 35
  • 67.35 (n)
  • 74.74 (a)
zebrafish
(Danio rerio)
 Actinopterygii SLC6A20 36
  • 33 (a)
 OneToMany
fruit fly
(Drosophila melanogaster)
 Insecta ine 36
  • 22 (a)
 OneToOne
worm
(Caenorhabditis elegans)
 Secernentea snf-10 36
  • 16 (a)
 OneToOne
sea squirt
(Ciona savignyi)
 Ascidiacea -- 36
  • 22 (a)
 OneToMany
-- 36
  • 30 (a)
 OneToMany
Species with no ortholog for SLC6A20:
  • 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

ENSEMBL:
Gene Tree for SLC6A20 (if available)
TreeFam:
Gene Tree for SLC6A20 (if available)

Paralogs for SLC6A20 Gene

Paralogs for SLC6A20 Gene

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

Pseudogenes.org Pseudogenes 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 Sequence Context AA Info Type
rs2271615 - 45,796,394(+) AGTTG(C/G)CCCAC reference, missense
rs17279437 - 45,772,602(+) ACGCC(A/G)TGAAA intron-variant, reference, missense
rs720625 -- 45,768,602(+) TAACA(A/G)GCATG intron-variant
rs720626 -- 45,768,646(+) TTGTC(C/T)CACCC intron-variant
rs758386 -- 45,775,926(-) GAGTG(C/T)GAGAA reference, synonymous-codon

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

Variant ID Type Subtype PubMed ID
nsv876734 CNV Gain 21882294
nsv876735 CNV Loss 21882294
nsv834678 CNV Gain 17160897
esv2670527 CNV Deletion 23128226
esv267840 CNV Insertion 20981092
esv2725225 CNV Deletion 23290073
esv2192183 CNV Deletion 18987734
esv2725226 CNV Deletion 23290073
esv1614687 CNV Deletion 17803354

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)

Relevant External Links for SLC6A20 Gene

Human Gene Mutation Database (HGMD)
SLC6A20

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

Disorders for SLC6A20 Gene

MalaCards: The human disease database

(4) MalaCards diseases for SLC6A20 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
iminoglycinuria, digenic
  • iminoglycinuria
hyperglycinuria
  • glycinuria with or without oxalate nephrolithiasis
slc6a20-related hyperglycinuria
hartnup disorder
  • hartnup disease
- 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.

Relevant External Links for SLC6A20

Genetic Association Database (GAD)
SLC6A20
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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. 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 J.P. (Genomics 2001) 2 3 4 67
  2. Sodium translocation by the iminoglycinuria associated imino transporter (SLC6A20). (PMID: 19657969) BrAPer A. … BrAPer S. (Mol. Membr. Biol. 2009) 3 23
  3. Identification of mammalian proline transporter SIT1 (SLC6A20) with characteristics of classical system imino. (PMID: 15632147) Takanaga H. … Hediger M.A. (J. Biol. Chem. 2005) 3 23
  4. Cloning, gene structure, and genomic localization of an orphan transporter from mouse kidney with six alternatively-spliced isoforms. (PMID: 9932288) Nash S.R. … Caron M.G. (Recept. Channels 1998) 2 3
  5. Human intestine luminal ACE2 and amino acid transporter expression increased by ACE-inhibitors. (PMID: 25534429) Vuille-dit-Bille R.N. … Verrey F. (Amino Acids 2015) 3

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