Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	11136
Gene name Gene Name - the full gene name approved by the HGNC.	Solute carrier family 7 member 9
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	SLC7A9
Synonyms (NCBI Gene) Gene synonyms aliases	BAT1, CSNU3
Chromosome Chromosome number	19
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	19q13.11
Summary Summary of gene provided in NCBI Entrez Gene.	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 t

Show/Hide all(27)

SNP ID	Visualize variation	Clinical significance	Consequence
rs12150890	A>C,G	Likely-benign, likely-pathogenic	Synonymous variant, missense variant, coding sequence variant, 5 prime UTR variant
rs79389353	C>A,T	Pathogenic-likely-pathogenic, likely-pathogenic	Intron variant, coding sequence variant, missense variant
rs79987078	G>A	Pathogenic	5 prime UTR variant, coding sequence variant, missense variant
rs121908479	C>T	Pathogenic	Intron variant, coding sequence variant, missense variant
rs121908480	C>T	Pathogenic	5 prime UTR variant, coding sequence variant, missense variant
rs121908482	C>T	Pathogenic	Intron variant, coding sequence variant, missense variant
rs121908483	C>T	Pathogenic, likely-pathogenic	Coding sequence variant, missense variant
rs121908484	G>A	Pathogenic, likely-pathogenic	Coding sequence variant, missense variant
rs121908485	A>G	Pathogenic	5 prime UTR variant, coding sequence variant, intron variant, missense variant
rs121908486	G>A	Pathogenic	Coding sequence variant, missense variant
rs121908487	T>C	Pathogenic	Intron variant, coding sequence variant, missense variant
rs140873167	G>A,C,T	Pathogenic	Missense variant, intron variant, coding sequence variant
rs745319034	->T	Pathogenic	Frameshift variant, coding sequence variant, intron variant
rs750849536	C>A,T	Likely-pathogenic	5 prime UTR variant, coding sequence variant, missense variant
rs755715459	->A	Pathogenic	Splice donor variant
rs758242098	G>A,T	Pathogenic	Synonymous variant, coding sequence variant, intron variant, missense variant
rs760264924	T>A,C	Pathogenic	Missense variant, coding sequence variant, stop gained
rs770340227	->CC	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1007096305	G>T	Likely-pathogenic	Stop gained, coding sequence variant
rs1060499787	C>G	Likely-pathogenic	Splice donor variant, 5 prime UTR variant
rs1085307095	T>C	Likely-pathogenic	Intron variant, splice acceptor variant
rs1213412404	T>C	Likely-pathogenic	Splice acceptor variant
rs1568530415	G>-	Pathogenic	Intron variant, coding sequence variant, stop gained
rs1568532461	C>-	Likely-pathogenic	Intron variant, coding sequence variant, frameshift variant, 5 prime UTR variant
rs1599648136	C>G	Likely-pathogenic	Intron variant
rs1599684627	AGA>-	Likely-pathogenic	Intron variant, coding sequence variant, inframe deletion
rs1599688589	A>G	Pathogenic	Intron variant, coding sequence variant, 5 prime UTR variant, missense variant

Show/Hide all(3)

miRTarBase ID	miRNA	Experiments	Reference
MIRT017909	hsa-miR-335-5p	Microarray	18185580
MIRT441125	hsa-miR-142-3p	HITS-CLIP	22473208
MIRT441125	hsa-miR-142-3p	HITS-CLIP	22473208

Show/Hide all(28)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003333	Process	Amino acid transmembrane transport	IBA
GO:0005515	Function	Protein binding	IPI	12167606, 25910212, 32494597
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	ISS
GO:0005886	Component	Plasma membrane	TAS	10471498
GO:0006865	Process	Amino acid transport	IEA
GO:0015171	Function	Amino acid transmembrane transporter activity	IEA
GO:0015175	Function	Neutral L-amino acid transmembrane transporter activity	IBA
GO:0015175	Function	Neutral L-amino acid transmembrane transporter activity	IMP	16609684
GO:0015184	Function	L-cystine transmembrane transporter activity	IBA
GO:0015184	Function	L-cystine transmembrane transporter activity	IMP	16609684
GO:0015297	Function	Antiporter activity	IDA	32494597
GO:0015804	Process	Neutral amino acid transport	IMP	16609684
GO:0015811	Process	L-cystine transport	IBA
GO:0015811	Process	L-cystine transport	IMP	16609684
GO:0016020	Component	Membrane	IEA
GO:0016324	Component	Apical plasma membrane	IDA	16609684
GO:0016324	Component	Apical plasma membrane	IEA
GO:0022857	Function	Transmembrane transporter activity	IEA
GO:0031526	Component	Brush border membrane	IDA	12167606
GO:0031526	Component	Brush border membrane	IEA
GO:0042605	Function	Peptide antigen binding	ISS
GO:0046982	Function	Protein heterodimerization activity	IDA	32494597
GO:0055085	Process	Transmembrane transport	IEA
GO:0065003	Process	Protein-containing complex assembly	TAS	10799513
GO:0180009	Function	Broad specificity neutral L-amino acid:basic L-amino acid antiporter activity	IDA	8663357
GO:1902475	Process	L-alpha-amino acid transmembrane transport	IEA
GO:1990822	Process	Basic amino acid transmembrane transport	IEA

MIM	HGNC	e!Ensembl
604144	11067	ENSG00000021488

Protein

UniProt ID

P82251

Protein name

b(0,+)-type amino acid transporter 1 (b(0,+)AT1) (Glycoprotein-associated amino acid transporter b0,+AT1) (Solute carrier family 7 member 9)

Protein function

Associates with SLC3A1 to form a functional transporter complex that mediates the electrogenic exchange between cationic amino acids and neutral amino acids, with a stoichiometry of 1:1 (PubMed:16825196, PubMed:32494597, PubMed:32817565, PubMed:

PDB

6LI9 , 6LID , 6YUP , 6YV1

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF13520	AA_permease_2	30 → 449	Amino acid permease	Family

Tissue specificity

TISSUE SPECIFICITY: Expressed in the brush border membrane in the kidney (at protein level). Kidney, small intestine, liver and placenta. {ECO:0000269|PubMed:10471498, ECO:0000269|PubMed:12167606}.

Sequence

MGDTGLRKRREDEKSIQSQEPKTTSLQKELGLISGISIIVGTIIGSGIFVSPKSVLSNTE
AVGPCLIIWAACGVLATLGALCFAELGTMITKSGGEYPYLMEAYGPIPAYLFSWASLIVI
KPTSFAIICLSFSEYVCAPFYVGCKPPQIVVKCLAAAAILFISTVNSLSVRLGSYVQNIF
TAAKLVIVAIIIISGLVLLAQGNTKNFDNSFEGAQLSVGAISLAFYNGLWAYDGWNQLNY
ITEELRNPYRNLPLAIIIGIPLVTACYILMNVSYFTVMTATELLQSQAVAVTFGDRVLYP
ASWIVPLFVAFSTIGAANGTCFTAGRLIYVAGREGHMLKVLSYISVRRLTPAPAIIFYGI
IATIYIIPGDINSLVNYFSFAAWLFYGLTILGLIVMRFTRKELERPIKVPVVIPVLMTLI
SVFLVLAPIISKPTWEYLYCVLFILSGLLFYFLFVHYKFGWAQKISKPITMHLQMLMEVV
PPEEDPE

Sequence length

487

Interactions

View interactions

	KEGG		Reactome
	Protein digestion and absorption		Basigin interactions Amino acid transport across the plasma membrane Defective SLC3A1 causes cystinuria (CSNU) Defective SLC7A9 causes cystinuria (CSNU)

Show/Hide Causal Diseases (1)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Cystinuria	cystinuria	rs121908482, rs755715459, rs121908483, rs121908484, rs121908485, rs1085307095, rs745319034, rs1060499787, rs750849536, rs1007096305, rs121908479, rs1599688589, rs121908480, rs1599648136	N/A

Show/Hide Unknown Diseases (3)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Eosinophilia	Eosinophilic esophagitis	N/A	N/A	GWAS
Gout	Gout	N/A	N/A	GWAS
Kidney Disease	Chronic kidney disease	N/A	N/A	GWAS

Show/Hide Text Mining Associations (19)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Acute Coronary Syndrome	Associate	32132739
AIDS Associated Nephropathy	Associate	24896147
Ataxia	Associate	20052367
Coronary Aneurysm	Associate	35740890
Coronary Restenosis	Associate	35740890
Cystinuria	Associate	12234283, 12841020, 16374432, 17710781, 20052367, 25296721, 25964309, 28049243, 28166740, 33169184, 33349102, 34669168, 36421847, 38114997, 40428323
Cystinuria Type A	Associate	12234283, 16374432, 20052367, 28166740
Genetic Diseases Inborn	Associate	34669168
Hemorrhage	Associate	24566624
Hypersensitivity Immediate	Associate	12841020, 35577790
Intellectual Disability	Associate	20052367
Intestinal Failure	Associate	37375564
Kidney Calculi	Associate	25296721
Kidney Diseases	Associate	28302371
Myocardial Infarction	Associate	32132739
Nephrocalcinosis	Associate	25296721
Nephrolithiasis	Associate	25296721, 40428323
Periodontitis	Associate	24566624
Renal Insufficiency Chronic	Associate	20383145, 20383146, 28302371, 31924810

SLC7A9 (solute carrier family 7 member 9)