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SLC6A20 solute carrier family 6 member 20 [ Homo sapiens (human) ]

Gene ID: 54716, updated on 24-Nov-2020

Summary

Official Symbol
SLC6A20provided by HGNC
Official Full Name
solute carrier family 6 member 20provided by HGNC
Primary source
HGNC:HGNC:30927
See related
Ensembl:ENSG00000163817 MIM:605616
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
XT3; SIT1; IMINO; Xtrp3
Summary
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 belongs to the sodium:neurotransmitter symporter (SNF) family and functions as a proline transporter expressed in kidney and small intestine. Mutations in this gene are associated with Hyperglycinuria and Iminoglycinuria. [provided by RefSeq, Jul 2020]
Expression
Biased expression in duodenum (RPKM 11.0), small intestine (RPKM 8.2) and 4 other tissues See more
Orthologs

Genomic context

See SLC6A20 in Genome Data Viewer
Location:
3p21.31
Exon count:
12
Annotation release Status Assembly Chr Location
109.20201120 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (45755449..45796553, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (45796941..45838039, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene tRNA-Arg (anticodon ACG) 2-1 Neighboring gene SAC1 like phosphatidylinositide phosphatase Neighboring gene RNA, 7SL, cytoplasmic 145, pseudogene Neighboring gene uncharacterized LOC107986082 Neighboring gene uncharacterized LOC107986083 Neighboring gene leucine zipper transcription factor like 1 Neighboring gene succinate dehydrogenase complex subunit D pseudogene 4

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
A genome-wide association study identifies potential susceptibility Loci for hirschsprung disease.
GeneReviews: Not available
A genome-wide association study of metabolic traits in human urine.
GeneReviews: Not available
An atlas of genetic influences on human blood metabolites.
GeneReviews: Not available
Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients.
GeneReviews: Not available
Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris.
GeneReviews: Not available
Hyperglycinuria
MedGen: C0543541 OMIM: 138500 GeneReviews: Not available
Compare labs
Iminoglycinuria
MedGen: C0268654 OMIM: 242600 GeneReviews: Not available
Compare labs

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Vif vif HIV-1 Vif downregulates the expression of solute carrier family 6, member 20 (SLC6A20) in Vif-expression T cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC161475

Gene Ontology Provided by GOA

Function Evidence Code Pubs
L-isoleucine transmembrane transporter activity ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
L-proline transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
L-proline transmembrane transporter activity IDA
Inferred from Direct Assay
more info
PubMed 
L-proline transmembrane transporter activity IGI
Inferred from Genetic Interaction
more info
PubMed 
amino acid transmembrane transporter activity IDA
Inferred from Direct Assay
more info
PubMed 
amino acid transmembrane transporter activity ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
amino acid transmembrane transporter activity TAS
Traceable Author Statement
more info
 
amino-acid betaine transmembrane transporter activity ISS
Inferred from Sequence or Structural Similarity
more info
 
neutral amino acid transmembrane transporter activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
neutral amino acid transmembrane transporter activity ISS
Inferred from Sequence or Structural Similarity
more info
 
proline:sodium symporter activity ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
L-isoleucine import across plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
L-proline import across plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
L-proline import across plasma membrane IGI
Inferred from Genetic Interaction
more info
PubMed 
amino acid import across plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
amino acid transport IDA
Inferred from Direct Assay
more info
PubMed 
amino acid transport TAS
Traceable Author Statement
more info
 
amino-acid betaine transport ISS
Inferred from Sequence or Structural Similarity
more info
 
glycine transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
proline import across plasma membrane IMP
Inferred from Mutant Phenotype
more info
PubMed 
proline transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
sodium ion transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transport across blood-brain barrier NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
apical plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
apical plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
integral component of plasma membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
sodium- and chloride-dependent transporter XTRP3
Names
X transporter protein 3
neurotransmitter transporter RB21A
orphan transporter XT3
sodium-dependent imino acid transporter 1
sodium/imino-acid transporter 1
solute carrier family 6 (neurotransmitter transporter), member 20
solute carrier family 6 (proline IMINO transporter), member 20
transporter rB21A homolog

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_023204.1 RefSeqGene

    Range
    5008..46095
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001385683.1NP_001372612.1  sodium- and chloride-dependent transporter XTRP3 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC098476
  2. NM_020208.4NP_064593.1  sodium- and chloride-dependent transporter XTRP3 isoform 1

    See identical proteins and their annotated locations for NP_064593.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform 1.
    Source sequence(s)
    AC098476, AJ276207, DR006419, EL949345
    Consensus CDS
    CCDS43077.1
    UniProtKB/Swiss-Prot
    Q9NP91
    Related
    ENSP00000346298.4, ENST00000358525.9
    Conserved Domains (1) summary
    cd11518
    Location:2577
    SLC6sbd_SIT1; Na(+)- and Cl(-)-dependent imino acid transporter SIT1; solute-binding domain
  3. NM_022405.4NP_071800.1  sodium- and chloride-dependent transporter XTRP3 isoform 2

    See identical proteins and their annotated locations for NP_071800.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1, resulting in a shorter protein (isoform 2) compared to isoform 1.
    Source sequence(s)
    AC098476, AJ276208, DR006419, EL949345
    Consensus CDS
    CCDS2730.1
    UniProtKB/Swiss-Prot
    Q9NP91
    Related
    ENSP00000296133.5, ENST00000353278.8
    Conserved Domains (1) summary
    cl00456
    Location:2540
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20201120

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    45755449..45796553 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011533847.2XP_011532149.1  sodium- and chloride-dependent transporter XTRP3 isoform X1

    Conserved Domains (1) summary
    cl00456
    Location:1478
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  2. XM_011533848.2XP_011532150.1  sodium- and chloride-dependent transporter XTRP3 isoform X2

    Related
    ENSP00000395506.1, ENST00000413781.1
    Conserved Domains (1) summary
    cl00456
    Location:2312
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
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