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

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: mouse all
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Genomic context

Location:: 3p21.31

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (45755449..45796536, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (45771093..45812175, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (45796941..45838028, complement)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

SIT1 transporter as a potential novel target in treatment of COVID-19.
Title: SIT1 transporter as a potential novel target in treatment of COVID-19.
Integrative approach identifies SLC6A20 and CXCR6 as putative causal genes for the COVID-19 GWAS signal in the 3p21.31 locus.
Title: Integrative approach identifies SLC6A20 and CXCR6 as putative causal genes for the COVID-19 GWAS signal in the 3p21.31 locus.
Genome and epigenome editing identify CCR9 and SLC6A20 as target genes at the 3p21.31 locus associated with severe COVID-19.
Title: Genome and epigenome editing identify CCR9 and SLC6A20 as target genes at the 3p21.31 locus associated with severe COVID-19.
Associations of SLC6A20 genetic polymorphisms with Hirschsprung's disease in a Southern Chinese population.
Title: Associations of SLC6A20 genetic polymorphisms with Hirschsprung's disease in a Southern Chinese population.
Characterization and substrate specificity of the Na+ coupled IMINO transport system in apical brush border membranes of epithelial cells. Identically found in kidney proximal tubule.
Title: Kinetics of the intestinal brush border proline (Imino) carrier.
SIT1 is not expressed in small intestine of human newborns.
Title: Intestinal IMINO transporter SIT1 is not expressed in human newborns.
Imputed meta-analysis revealed that 13 SLC6A20 SNPs were significantly associated with Hirschsprung disease. In further subgroup analysis, SLC6A20 polymorphisms appeared to have increased associations with Long-Segment Hirschsprung disease.
Title: Association Analysis of SLC6A20 Polymorphisms With Hirschsprung Disease.
SIT1, B(0)AT1 and ACE2 were co-localized in the brush-border membrane of small intestine enterocytes.
Title: Human intestine luminal ACE2 and amino acid transporter expression increased by ACE-inhibitors.
genetic association studies in two populations, European/Rotterdam and Chinese Han/Shanghai: Data suggest that an SNP in SLC6A20 (rs13062383) is associated with predisposition of type 2 diabetes. [META-ANALYSIS]
Title: A genetic variant in SLC6A20 is associated with Type 2 diabetes in white-European and Chinese populations.
Using homology modeling we identified two highly conserved Na(+)-binding sites and a putative Cl(-)-binding site of SLC6A20.
Title: Sodium translocation by the iminoglycinuria associated imino transporter (SLC6A20).

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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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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	IBA Inferred from Biological aspect of Ancestor more info
involved_in glycine import across plasma membrane	IDA Inferred from Direct Assay more info	PubMed
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

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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

NG_023204.1 RefSeqGene

Range

5008..46095

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001385683.1 → NP_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:2 → 588

SLC6sbd_SIT1; Na(+)- and Cl(-)-dependent imino acid transporter SIT1; solute-binding domain
NM_001406066.1 → NP_001392995.1 sodium- and chloride-dependent transporter XTRP3 isoform 4

Status: REVIEWED

Source sequence(s)

AC098476

UniProtKB/TrEMBL

B7ZLW4
NM_001406067.1 → NP_001392996.1 sodium- and chloride-dependent transporter XTRP3 isoform 5

Status: REVIEWED

Source sequence(s)

AC098476
NM_001406069.1 → NP_001392998.1 sodium- and chloride-dependent transporter XTRP3 isoform 6

Status: REVIEWED

Source sequence(s)

AC098476
NM_020208.4 → NP_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:2 → 577

SLC6sbd_SIT1; Na(+)- and Cl(-)-dependent imino acid transporter SIT1; solute-binding domain
NM_022405.4 → NP_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:2 → 540

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

RNA

NR_176011.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC098476
NR_176012.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC098476

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

45755449..45796536 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011533847.3 → XP_011532149.1 sodium- and chloride-dependent transporter XTRP3 isoform X1

Conserved Domains (1) summary

cl00456
Location:1 → 478

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain