SLC3A1 solute carrier family 3 member 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC3A1provided by HGNC
Official Full Name: solute carrier family 3 member 1provided by HGNC
Primary source: HGNC:HGNC:11025
See related: Ensembl:ENSG00000138079 MIM:104614; AllianceGenome:HGNC:11025
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: D2H; ATR1; NBAT; RBAT; CSNU1
Summary: This gene encodes a type II membrane glycoprotein which is one of the components of the renal amino acid transporter which transports neutral and basic amino acids in the renal tubule and intestinal tract. Mutations and deletions in this gene are associated with cystinuria. Alternatively spliced transcript variants have been described, but their biological validity has not been determined. [provided by RefSeq, Jul 2008]
Expression: Biased expression in kidney (RPKM 175.5), small intestine (RPKM 50.6) and 6 other tissues See more
Orthologs: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 2p21

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
110	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (44275480..44322437)
110	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (44280847..44326811)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (44502619..44548633)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Clinical profile of a Polish cohort of children and young adults with cystinuria.
Title: Clinical profile of a Polish cohort of children and young adults with cystinuria.
Structural basis for amino acid exchange by a human heteromeric amino acid transporter.
Title: Structural basis for amino acid exchange by a human heteromeric amino acid transporter.
A homozygous c.325G>A mutation in cationic amino cid transport proteins (SLC7A9) was identified in two patients, and six neutral and basic amino acid transporter protein (SLC3A1) mutations were found in five patients.
Title: Clinical, Biochemical, and Genetic Findings of Cystinuria in Chinese Children.
Study shows that various computational tools were able to distinguish cystinuria-causing mutations from benign polymorphisms. Four deleterious mutation (R362C, T216M, M467K/T) in the coding region of SLC3A1 were identified. The intron variant c.1136+2/3delT in SLC3A1 gene probably affected the splicing process.
Title: In silico analysis of SLC3A1 and SLC7A9 mutations in Iranian patients with Cystinuria.
Thirteen pediatric patients with cystine stones were evaluated in our clinic between 2012 and 2015. Gene mutations in SLC3A1 and SLC7A9 were investigated
Title: Clinical and genetic characterization of Chinese pediatric cystine stone patients.
Spectrum of SLC3A1 and SLC7A9 mutations in cystinuria patients presenting with prenatal hyperechoic colon has been described.
Title: Spectrum of mutations in cystinuria patients presenting with prenatal hyperechoic colon.
Analysis showing how different mutations in SLC3A1 and SLC7A9 affect severity of cystinuria.
Title: Associating mutations causing cystinuria with disease severity with the aim of providing precision medicine.
In a Saudi Arabian cohort of patients with cystinuria, two new variants in the SLC3A1 and SLC9A7 genes were discovered. All of the detected mutations were missense variants in three different exons, such as c.1711 T > A (p.Cys571Ser) (exon 10), c.1166C > T p.Thr389Met (exon 11) and c.1400 T > A p.Met467Lys (exon 8).
Title: Delineation of cystinuria in Saudi Arabia: A case series.
Here, the authors report that the expression level of the solute carrier family 3, member 1 (SLC3A1), the cysteine carrier, tightly correlated with clinical stages and patients' survival. Elevated SLC3A1 expression accelerated the cysteine uptake and the accumulation of reductive glutathione (GSH), leading to reduced reactive oxygen species (ROS).
Title: Cysteine transporter SLC3A1 promotes breast cancer tumorigenesis.
We found a novel mutation in the acceptor region in exon 1 (SLC3A1 gene) and detected a heterozygosity status for the described patients.
Title: A Novel Mutation in SLC3A1 Gene in Patients With Cystinuria.

Submit: New GeneRIF Correction See all GeneRIFs (44)

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Cystinuria MedGen: C0010691 OMIM: 220100 GeneReviews: Not available	Compare labs

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

RH69205 (e-PCR)
- UniSTS:66590

RH94171 (e-PCR)
- UniSTS:84535

GDB:681418 (e-PCR)
- UniSTS:158621

GDB:681433 (e-PCR)
- UniSTS:158622

GDB:681454 (e-PCR)
- UniSTS:158623

D2S2947 (e-PCR)
- UniSTS:474529

GDB:681472 (e-PCR)
- UniSTS:158625

D2S2945 (e-PCR)
- UniSTS:474530

GDB:681483 (e-PCR)
- UniSTS:158626

D2S2946 (e-PCR)
- UniSTS:474531

D2S2562 (e-PCR)
- UniSTS:3758

RH19832 (e-PCR)
- UniSTS:57017

GDB:335819 (e-PCR)
- UniSTS:156608

G62856 (e-PCR)
- UniSTS:139981

RH12757 (e-PCR)
- UniSTS:15330

Homology

Homologs of the SLC3A1 gene: The SLC3A1 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, fruit fly, mosquito, M.oryzae, N.crassa, and frog.
Orthologs from Annotation Pipeline: 496 organisms have orthologs with human gene SLC3A1
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables L-cystine transmembrane transporter activity	TAS Traceable Author Statement more info	PubMed
enables amino acid transmembrane transporter activity	TAS Traceable Author Statement more info	PubMed
enables basic amino acid transmembrane transporter activity	TAS Traceable Author Statement more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein heterodimerization activity	IDA Inferred from Direct Assay more info	PubMed
enables protein-containing complex binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in L-cystine transport	IEA Inferred from Electronic Annotation more info
involved_in L-glutamate transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in amino acid transport	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in aspartate transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in basic amino acid transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in basic amino acid transport	TAS Traceable Author Statement more info	PubMed
involved_in carbohydrate metabolic process	IEA Inferred from Electronic Annotation more info
involved_in gene expression	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in apical plasma membrane	IEA Inferred from Electronic Annotation more info
located_in brush border membrane	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
located_in membrane	TAS Traceable Author Statement more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info
located_in vacuolar membrane	IEA Inferred from Electronic Annotation more info

General protein information

Go to the top of the page Help

Preferred Names: neutral and basic amino acid transport protein rBAT

Names: B(0,+)-type amino acid transport protein; amino acid transporter 1; solute carrier family 3 (amino acid transporter heavy chain), member 1; solute carrier family 3 (cystine, dibasic and neutral amino acid transporters), member 1; solute carrier family 3 (cystine, dibasic and neutral amino acid transporters, activator of cystine, dibasic and neutral amino acid transport), member 1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_008233.1 RefSeqGene

Range

5023..51037

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_000341.4 → NP_000332.2 neutral and basic amino acid transport protein rBAT

See identical proteins and their annotated locations for NP_000332.2

Status: REVIEWED

Source sequence(s)

AC013717, AK223146, BC093626

Consensus CDS

CCDS1819.1

UniProtKB/Swiss-Prot

Q07837, Q52M94

UniProtKB/TrEMBL

A0A0S2Z4E1

Related

ENSP00000260649.6, ENST00000260649.11

Conserved Domains (1) summary

cd11359
Location:116 → 569

AmyAc_SLC3A1; Alpha amylase catalytic domain found in Solute Carrier family 3 member 1 proteins

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

44275480..44322437

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011533047.4 → XP_011531349.1 neutral and basic amino acid transport protein rBAT isoform X1

UniProtKB/TrEMBL

B8ZZK1

Related

ENSP00000387308.1, ENST00000409387.5

Conserved Domains (3) summary

cd11359
Location:116 → 539

AmyAc_SLC3A1; Alpha amylase catalytic domain found in Solute Carrier family 3 member 1 proteins

pfam00128
Location:140 → 488

Alpha-amylase; Alpha amylase, catalytic domain

pfam13900
Location:543 → 564

GVQW; Putative domain of unknown function