SLC7A9 (solute carrier family 7 member 9)

Gene

• Entrez ID: 11136
• Gene name: Solute carrier family 7 member 9
• Gene symbol: SLC7A9
• Synonyms (NCBI Gene): BAT1, CSNU3
• Chromosome: 19
• Chromosome location: 19q13.11
• 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 t

SNPs

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

miRNA

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

Gene ontology (GO)

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

Other IDs

• MIM: 604144
• HGNC: 11067
• e!Ensembl: 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

Pathways

KEGG:

Protein digestion and absorption

Reactome:

Basigin interactions
Amino acid transport across the plasma membrane
Defective SLC3A1 causes cystinuria (CSNU)
Defective SLC7A9 causes cystinuria (CSNU)

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Cystine urolithiasis	Pathogenic; Likely pathogenic	rs760264924, rs1599684627, rs1568530415, rs1599688589, rs1599648136, rs755715459	RCV000991121 RCV000991113 RCV000991106 RCV000991120 RCV000991107 RCV000991119	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Cystinuria	Pathogenic; Likely pathogenic	rs753692696, rs753121162, rs769448665, rs2145788754, rs988712826, rs779653925, rs372306844, rs1968829014, rs760452532, rs2145846311, rs753324280, rs121908479, rs121908480, rs121908482, rs121908483, rs2513608437, rs121908484, rs121908485, rs146815072, rs1085307095, rs2513609886, rs766981518, rs745319034, rs2513609715, rs748402420, rs1060499787, rs750849536, rs1007096305, rs1599688589, rs1599648136, rs755715459, rs1294838201, rs774124697, rs1967855547	RCV001536032 RCV001536102 RCV001535874 RCV001784990 RCV001783776 RCV001783777 RCV005023319 RCV004762237 RCV002251115 RCV002251243 RCV005027935 RCV000006136 RCV000006137 RCV000006139 RCV000006140 RCV000006142 RCV000006143 RCV000006144 RCV005028045 RCV000490455 RCV003140582 RCV003131530 RCV000286788 RCV003335843 RCV003455848 RCV000454228 RCV005027841 RCV002499211 RCV004761854 RCV004761852 RCV005408617 RCV001199108 RCV002281176 RCV001281279	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
SLC7A9-related disorder	Likely pathogenic; Pathogenic	rs1394513127, rs121908480, rs121908484, rs745319034, rs2513557082, rs2513617524	RCV003394026 RCV004752686 RCV003398451 RCV003417906 RCV003402182 RCV003397731	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Acute myeloid leukemia	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ALZHEIMER DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bethlem myopathy 1A	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHRONIC KIDNEY DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CYSTINURIA TYPE B	—	GWAS catalog, Orphanet GWAS catalog, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CYSTINURIA, TYPE B	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EOSINOPHILIC ESOPHAGITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Uncertain significance; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GASTROESOPHAGEAL REFLUX DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GOUT	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
KIDNEY DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
KIDNEY DISEASES	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
POLYCYSTIC KIDNEY DISEASE 1	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Polycystic kidney disease, adult type	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Uncertain significance; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Ataxia	Ataxia	Pubtator	20052367	Associate	★☆☆☆☆ Found in Text Mining only
Autoimmune Diseases	Autoimmune Diseases	BEFREE	1352699		★☆☆☆☆ Found in Text Mining only
Chagas Cardiomyopathy	Chagas Cardiomyopathy	BEFREE	16619187		★☆☆☆☆ Found in Text Mining only
Chronic Kidney Diseases	Kidney Disease	BEFREE	20383146, 21691125, 28302371, 28501300		★☆☆☆☆ Found in Text Mining only
Chronic Kidney Diseases	Kidney Disease	GWASDB_DG	20383146, 22479191		★☆☆☆☆ Found in Text Mining only
Chronic Kidney Diseases	Kidney Disease	GWASCAT_DG	29545352		★☆☆☆☆ Found in Text Mining only
Chronic Lymphocytic Leukemia	Lymphocytic Leukemia	BEFREE	31292126		★☆☆☆☆ Found in Text Mining only
Congenital neurologic anomalies	Drachtman Weinblatt Sitarz syndrome	HPO_DG			★☆☆☆☆ Found in Text Mining only
Coronary Aneurysm	Coronary aneurysm	Pubtator	35740890	Associate	★☆☆☆☆ Found in Text Mining only
Coronary Restenosis	Coronary restenosis	Pubtator	35740890	Associate	★☆☆☆☆ Found in Text Mining only
Cystinuria	Cystinuria	CLINVAR_DG	10471498, 11157794, 12234283, 12234930, 12371955, 12820697, 15635077, 15670723, 16138908, 17539912, 19782624, 21255007, 22480232, 25109415, 25296721, 25964309, 26123750, 28717662, 28812535		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Cystinuria	Cystinuria	CLINGEN_DG	10471498, 11157794, 12234930, 12915471, 16609684, 18332091, 23532419, 25296721, 25613900		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Cystinuria	Cystinuria	UNIPROT_DG	10471498, 11157794, 12234283, 12371955, 12820697, 15635077, 16138908, 16609684, 18752446, 19782624		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Cystinuria	Cystinuria	BEFREE	11260385, 11318953, 11377971, 11396607, 11509015, 11770798, 12234283, 12239244, 12371955, 12474640, 12779097, 12820697, 12841020, 14531788, 15021200, 15050971, 15635077, 16138908, 16225397, 16374432, 16609684, 16629225, 17701443, 18359399, 18752446, 19782624, 21255007, 22480232, 23532419, 24045899, 25109415, 25599739, 26123750, 26537754, 26540609, 26837681, 28270646, 28646536, 28812535, 30069816, 30342472		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Cystinuria	Cystinuria	Pubtator	12234283, 12841020, 16374432, 17710781, 20052367, 25296721, 25964309, 28049243, 28166740, 33169184, 33349102, 34669168, 36421847, 38114997, 40428323	Associate	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Cystinuria	Cystinuria	LHGDN	14531788, 15818799, 15818803, 16138908, 16609684, 17701443, 18778962		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Cystinuria	Cystinuria	CTD_human_DG			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Cystinuria	Cystinuria	HPO_DG			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Cystinuria	Cystinuria	GENOMICS_ENGLAND_DG			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Cystinuria Type A	Cystinuria	Pubtator	12234283, 16374432, 20052367, 28166740	Associate	★☆☆☆☆ Found in Text Mining only
Cystinuria type B	Cystinuria	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cystinuria, Type B	Cystinuria	BEFREE	14561219, 16374432, 28166740		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cystinuria, Type B	Cystinuria	ORPHANET_DG	21255007		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Diabetes	Diabetes	BEFREE	12653967		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes Mellitus	BEFREE	12653967		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Insulin-Dependent	Diabetes Mellitus	BEFREE	12653967, 15028669		★☆☆☆☆ Found in Text Mining only
Heart Diseases	Heart Diseases	BEFREE	29768622		★☆☆☆☆ Found in Text Mining only
Hematological Disease	Hematological Disease	BEFREE	31292126		★☆☆☆☆ Found in Text Mining only
Hemorrhage	Hemorrhage	Pubtator	24566624	Associate	★☆☆☆☆ Found in Text Mining only
Hypersensitivity Immediate	Hypersensitivity	Pubtator	12841020, 35577790	Associate	★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	20052367	Associate	★☆☆☆☆ Found in Text Mining only
Kidney Calculi	Kidney stone	BEFREE	17710781, 20728256		★☆☆☆☆ Found in Text Mining only
Kidney Diseases	Kidney Disease	CTD_human_DG	21572414		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Kidney Diseases	Kidney Disease	BEFREE	28302371		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Kidney Diseases	Kidney disease	Pubtator	28302371	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Kidney Failure, Chronic	Kidney Failure	GWASCAT_DG	20383146, 29545352		★☆☆☆☆ Found in Text Mining only
Leprosy	Leprosy	BEFREE	22071774, 24578538		★☆☆☆☆ Found in Text Mining only
Lupus Erythematosus, Systemic	Lupus Erythematosus	BEFREE	16971954		★☆☆☆☆ Found in Text Mining only
Lysinuric Protein Intolerance	Lysinuric Protein Intolerance	BEFREE	11377971		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	31292126		★☆☆☆☆ Found in Text Mining only
Myasthenia Gravis	Myasthenia Gravis	BEFREE	1352699		★☆☆☆☆ Found in Text Mining only
Myocardial Infarction	Myocardial Infarction	BEFREE	12426569, 15843211, 17517687		★☆☆☆☆ Found in Text Mining only
Myocardial Infarction	Myocardial infarction	Pubtator	32132739	Associate	★☆☆☆☆ Found in Text Mining only
Nephritis	Nephritis	BEFREE	16971954		★☆☆☆☆ Found in Text Mining only
Nephritis, Interstitial	Nephritis	GENOMICS_ENGLAND_DG			★☆☆☆☆ Found in Text Mining only
Nephritis, Tubulointerstitial	Nephritis	GENOMICS_ENGLAND_DG			★☆☆☆☆ Found in Text Mining only
Nephrolithiasis	Nephrolithiasis	BEFREE	17710781, 20728256		★☆☆☆☆ Found in Text Mining only
Nephrolithiasis	Nephrolithiasis	Pubtator	25296721, 40428323	Associate	★☆☆☆☆ Found in Text Mining only
Nephrolithiasis	Nephrolithiasis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Periodontal Diseases	Periodontal Diseases	BEFREE	30176756		★☆☆☆☆ Found in Text Mining only
Periodontitis	Periodontitis	BEFREE	24566624		★☆☆☆☆ Found in Text Mining only
Periodontitis	Periodontitis	Pubtator	24566624	Associate	★☆☆☆☆ Found in Text Mining only
Psoriasis	Psoriasis	BEFREE	28256194		★☆☆☆☆ Found in Text Mining only
Renal Insufficiency	Renal Insufficiency	HPO_DG			★☆☆☆☆ Found in Text Mining only
Rheumatoid Arthritis	Rheumatoid arthritis	BEFREE	11170743, 16971954, 18381799		★☆☆☆☆ Found in Text Mining only
Sensory neuropathy	Sensory neuropathy	BEFREE	18240960		★☆☆☆☆ Found in Text Mining only