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

Gene ID: 54716, updated on 17-Jun-2024

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; AllianceGenome:HGNC:30927
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]
Annotation information
Note: This gene has been reviewed for its involvement in coronavirus biology, and is locus in the vicinity of disease-associated variant(s).
Expression
Biased expression in duodenum (RPKM 11.0), small intestine (RPKM 8.2) and 4 other tissues See more
Orthologs
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Genomic context

See SLC6A20 in Genome Data Viewer
Location:
3p21.31
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (45755449..45796536, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (45771093..45812175, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (45796941..45838028, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19784 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14286 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19785 Neighboring gene tRNA-Arg (anticodon ACG) 2-1 Neighboring gene SAC1 like phosphatidylinositide phosphatase Neighboring gene ReSE screen-validated silencer GRCh37_chr3:45769094-45769290 Neighboring gene RNA, 7SL, cytoplasmic 145, pseudogene Neighboring gene uncharacterized LOC107986082 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:45859284-45860483 Neighboring gene leucine zipper transcription factor like 1 Neighboring gene uncharacterized LOC124909374 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:45921781-45921937 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

EBI GWAS Catalog

Description
A genome-wide association study identifies potential susceptibility Loci for hirschsprung disease.
EBI GWAS Catalog
A genome-wide association study of metabolic traits in human urine.
EBI GWAS Catalog
An atlas of genetic influences on human blood metabolites.
EBI GWAS Catalog
Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients.
EBI GWAS Catalog
Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris.
EBI GWAS Catalog

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

Clone Names

  • MGC161475

Gene Ontology Provided by GOA

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

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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
    Consensus CDS
    CCDS93258.1
    UniProtKB/TrEMBL
    A0A8V8TQV4
    Related
    ENSP00000515266.1, ENST00000703343.1
    Conserved Domains (1) summary
    cd11518
    Location:2588
    SLC6sbd_SIT1; Na(+)- and Cl(-)-dependent imino acid transporter SIT1; solute-binding domain
  2. NM_001406066.1NP_001392995.1  sodium- and chloride-dependent transporter XTRP3 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC098476
    UniProtKB/TrEMBL
    B7ZLW4
  3. NM_001406067.1NP_001392996.1  sodium- and chloride-dependent transporter XTRP3 isoform 5

    Status: REVIEWED

    Source sequence(s)
    AC098476
  4. NM_001406069.1NP_001392998.1  sodium- and chloride-dependent transporter XTRP3 isoform 6

    Status: REVIEWED

    Source sequence(s)
    AC098476
  5. 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
    A1A4F2, O75590, Q8TF10, Q9NP91, Q9NPQ2, Q9NQ77
    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
  6. 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

RNA

  1. NR_176011.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC098476
  2. NR_176012.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC098476

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    45755449..45796536 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011533847.3XP_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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    45771093..45812175 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054346951.1XP_054202926.1  sodium- and chloride-dependent transporter XTRP3 isoform X1