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

Summary

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: mouse all
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Genomic context

Location:: 19q13.11

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (32830511..32869767, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (35349240..35388495, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (33321417..33360673, complement)

Chromosome 19 - NC_000019.10 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: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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. 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.
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 (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	not available

EBI GWAS Catalog

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

MARC_15958-15959:1016225613:1 (e-PCR)
- UniSTS:267918

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

NG_008258.1 RefSeqGene

Range

5011..44267

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000019.10 Reference GRCh38.p14 Primary Assembly

Range

32830511..32869767 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

Q53FY4
XM_047438117.1 → XP_047294073.1 B(0,+)-type amino acid transporter 1 isoform X3

Alternate T2T-CHM13v2.0

Genomic

NC_060943.1 Alternate T2T-CHM13v2.0

Range

35349240..35388495 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

B2R9A6, P82251

UniProtKB/TrEMBL

Q53FY4
XM_054319678.1 → XP_054175653.1 B(0,+)-type amino acid transporter 1 isoform X2

UniProtKB/TrEMBL

Q53FY4
XM_054319679.1 → XP_054175654.1 B(0,+)-type amino acid transporter 1 isoform X3