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SLC7A9 solute carrier family 7 member 9 [ Homo sapiens (human) ]

Gene ID: 11136, updated on 3-Apr-2024

Summary

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Official Symbol
SLC7A9provided by HGNC
Official Full Name
solute carrier family 7 member 9provided by HGNC
Primary source
HGNC:HGNC:11067
See related
Ensembl:ENSG00000021488 MIM:604144; AllianceGenome:HGNC:11067
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
BAT1; CSNU3
Summary
This gene encodes a protein that belongs to a family of light subunits of amino acid transporters. This protein plays a role in the high-affinity and sodium-independent transport of cystine and neutral and dibasic amino acids, and appears to function in the reabsorption of cystine in the kidney tubule. Mutations in this gene cause non-type I cystinuria, a disease that leads to cystine stones in the urinary system due to impaired transport of cystine and dibasic amino acids. Alternate transcript variants, which encode the same protein, have been found for this gene. [provided by RefSeq, Jul 2011]
Expression
Biased expression in small intestine (RPKM 31.7), duodenum (RPKM 21.2) and 2 other tissues See more
Orthologs
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Genomic context

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Location:
19q13.11
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (32830511..32869767, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (35349240..35388495, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (33321417..33360673, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904690 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr19:33190064-33191263 Neighboring gene nudix hydrolase 19 Neighboring gene tudor domain containing 12 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14433 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14434 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:33270291-33271101 Neighboring gene Sharpr-MPRA regulatory region 1108 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33302663-33303164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33303165-33303664 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:33307591-33308186 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:33308187-33308780 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:33308781-33309375 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:33312663-33312898 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33319941-33320462 Neighboring gene GCM1 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:33358961-33359536 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33360978-33361500 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33361501-33362023 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33366062-33366947 Neighboring gene RN7SK pseudogene 22 Neighboring gene centrosomal protein 89 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33426525-33427026 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33427027-33427526 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14435 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10487 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14436 Neighboring gene ribosomal protein L31 pseudogene 60 Neighboring gene FA core complex associated protein 24

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. SLC7A9 as a Potential Biomarker for Lymph Node Metastasis of Esophageal Squamous Cell Carcinoma. Baba H, et al. Ann Surg Oncol, 2022 Apr. PMID 34773193
  2. A Novel Mutation in SLC7A9 Gene in Cystinuria. Fazaeli S, et al. Iran J Kidney Dis, 2017 Mar. PMID 28270646
  3. Cystinuria in a patient with a novel mutation in SLC7A9 gene. Koulivand L, et al. Iran J Kidney Dis, 2015 Jan. PMID 25599739
  4. A combined approach to the molecular analysis of cystinuria: from urinalysis to sequencing via genotyping. Lotan D, et al. Isr Med Assoc J, 2007 Jul. PMID 17710781
  5. LC-MS/MS determination of dibasic amino acids for the diagnosis of cystinuria. Application in a family affected by a novel splice-acceptor site mutation in the SLC7A9 gene. Al-Dirbashi OY, et al. J Inherit Metab Dis, 2007 Aug. PMID 17701443

See all (66) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. SLC7A9 as a Potential Biomarker for Lymph Node Metastasis of Esophageal Squamous Cell Carcinoma.
    Title: SLC7A9 as a Potential Biomarker for Lymph Node Metastasis of Esophageal Squamous Cell Carcinoma.
  4. 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.
  5. 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.
  6. 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.
  7. Study shows that various computational tools were able to distinguish cystinuria-causing mutations from benign polymorphisms. Only missense mutation V142A had a benign effect on the protein structure and function of SLC7A9. The intron variant c.604+66C>G in SLC7A9 gene probably affected the splicing process.
    Title: In silico analysis of SLC3A1 and SLC7A9 mutations in Iranian patients with Cystinuria.
  8. 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.
  9. 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.
  10. 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 (41)

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
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EBI GWAS Catalog

Description
A genome-wide association study of metabolic traits in human urine.
EBI GWAS Catalog
A whole-genome association study of major determinants for allopurinol-related Stevens-Johnson syndrome and toxic epidermal necrolysis in Japanese patients.
EBI GWAS Catalog
An atlas of genetic influences on human blood metabolites.
EBI GWAS Catalog
Genetic loci influencing kidney function and chronic kidney disease.
EBI GWAS Catalog
Genome-wide association study of metabolic traits reveals novel gene-metabolite-disease links.
EBI GWAS Catalog
Meta-analysis of genome-wide association studies identifies three new risk loci for atopic dermatitis.
EBI GWAS Catalog
New loci associated with kidney function and chronic kidney disease.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ94301

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables L-cystine transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables L-cystine transmembrane transporter activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables antiporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables broad specificity neutral L-amino acid:basic L-amino acid antiporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables neutral L-amino acid transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables neutral L-amino acid transmembrane transporter activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables peptide antigen binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein heterodimerization activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in L-alpha-amino acid transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
involved_in L-cystine transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in L-cystine transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in amino acid transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in basic amino acid transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
involved_in neutral amino acid transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein-containing complex assembly TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in apical plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in brush border membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
B(0,+)-type amino acid transporter 1
Names
b(0,+)AT
cystinuria type 3
glycoprotein-associated amino acid transporter b0,+AT1
solute carrier family 7 (amino acid transporter light chain, bo,+ system), member 9
solute carrier family 7 (cationic amino acid transporter, y+ system), member 9
solute carrier family 7 (glycoprotein-associated amino acid transporter light chain, bo,+ system), member 9

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_008258.1 RefSeqGene

    Range
    5011..44267
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001126335.2 → NP_001119807.1  B(0,+)-type amino acid transporter 1

    See identical proteins and their annotated locations for NP_001119807.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1, 2, and 3 encode the same protein.
    Source sequence(s)
    AK313708, BP276659, CK300669
    Consensus CDS
    CCDS12425.1
    UniProtKB/Swiss-Prot
    B2R9A6, P82251
    UniProtKB/TrEMBL
    Q53FY4
    Related
    ENSP00000468439.1, ENST00000587772.1
    Conserved Domains (1) summary
    TIGR00911
    Location:26 → 484
    2A0308; L-type amino acid transporter

  2. NM_001243036.2 → NP_001229965.1  B(0,+)-type amino acid transporter 1

    See identical proteins and their annotated locations for NP_001229965.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 1. Variants 1, 2, and 3 encode the same protein.
    Source sequence(s)
    AF141289, AK313708, BC017962, BP276659
    Consensus CDS
    CCDS12425.1
    UniProtKB/Swiss-Prot
    B2R9A6, P82251
    UniProtKB/TrEMBL
    Q53FY4
    Related
    ENSP00000464822.1, ENST00000590341.5
    Conserved Domains (1) summary
    TIGR00911
    Location:26 → 484
    2A0308; L-type amino acid transporter

  3. NM_014270.5 → NP_055085.1  B(0,+)-type amino acid transporter 1

    See identical proteins and their annotated locations for NP_055085.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2, and 3 encode the same protein.
    Source sequence(s)
    AK026446, BC017962, BP276659
    Consensus CDS
    CCDS12425.1
    UniProtKB/Swiss-Prot
    B2R9A6, P82251
    UniProtKB/TrEMBL
    Q53FY4
    Related
    ENSP00000023064.3, ENST00000023064.9
    Conserved Domains (1) summary
    TIGR00911
    Location:26 → 484
    2A0308; L-type amino acid transporter

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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    32830511..32869767 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011526402.4 → XP_011524704.1  B(0,+)-type amino acid transporter 1 isoform X1

    See identical proteins and their annotated locations for XP_011524704.1

    UniProtKB/Swiss-Prot
    B2R9A6, P82251
    UniProtKB/TrEMBL
    Q53FY4
    Conserved Domains (1) summary
    TIGR00911
    Location:26 → 484
    2A0308; L-type amino acid transporter

  2. XM_017026230.1 → XP_016881719.1  B(0,+)-type amino acid transporter 1 isoform X2

    UniProtKB/TrEMBL
    Q53FY4

  3. XM_047438117.1 → XP_047294073.1  B(0,+)-type amino acid transporter 1 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    35349240..35388495 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054319677.1 → XP_054175652.1  B(0,+)-type amino acid transporter 1 isoform X1

    UniProtKB/Swiss-Prot
    B2R9A6, P82251

  2. XM_054319678.1 → XP_054175653.1  B(0,+)-type amino acid transporter 1 isoform X2

  3. XM_054319679.1 → XP_054175654.1  B(0,+)-type amino acid transporter 1 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P82251.1 GenPept UniProtKB/Swiss-Prot:P82251

Gene LinkOut

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