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
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Genomic context

Location:: 2p21

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (44275480..44322437)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (44280847..44327754)
RS_2024_09	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

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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?

Novel compound heterozygous pathogenic variants in the SLC3A1 gene in a Chinese family with cystinuria.
Title: Novel compound heterozygous pathogenic variants in the SLC3A1 gene in a Chinese family with cystinuria.
Interpretation of SLC3A1 and SLC7A9 variants in cystinuria patients: The significance of the PM3 criterion and protein stability.
Title: Interpretation of SLC3A1 and SLC7A9 variants in cystinuria patients: The significance of the PM3 criterion and protein stability.
Population genetics analysis of SLC3A1 and SLC7A9 revealed the etiology of cystine stone may be more than what our current genetic knowledge can explain.
Title: Population genetics analysis of SLC3A1 and SLC7A9 revealed the etiology of cystine stone may be more than what our current genetic knowledge can explain.
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.

Submit: New GeneRIF Correction See all GeneRIFs (47)

Phenotypes

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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

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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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

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
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

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Preferred Names: amino acid transporter heavy chain SLC3A1

Names: B(0,+)-type amino acid transport protein; amino acid transporter 1; b(0,+)-type amino acid transporter-related heavy chain; neutral and basic amino acid transport protein rBAT; 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)

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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_008233.1 RefSeqGene

Range

5023..51037

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_000341.4 → NP_000332.2 amino acid transporter heavy chain SLC3A1

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

A8K0S1, O00658, Q07837, Q15295, Q4J6B4, Q4J6B5, Q4J6B6, Q4J6B7, Q4J6B8, Q4J6B9, Q52M92, Q52M94

UniProtKB/TrEMBL

A0A0S2Z4E1, B2R7X8

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: 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_000002.12 Reference GRCh38.p14 Primary Assembly

Range

44275480..44322437

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011533047.4 → XP_011531349.1 amino acid transporter heavy chain SLC3A1 isoform X1

UniProtKB/TrEMBL

A0A087X0R9, 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