SLC6A19 (solute carrier family 6 member 19)

Gene

• Entrez ID: 340024
• Gene name: Solute carrier family 6 member 19
• Gene symbol: SLC6A19
• Synonyms (NCBI Gene): B0AT1, HND
• Chromosome: 5
• Chromosome location: 5p15.33
• Summary: This gene encodes a system B(0) transmembrane protein that actively transports most neutral amino acids across the apical membrane of epithelial cells. Mutations in this gene may result in Hartnup disorder, an inherited disease with symptoms such as pella

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs35329108	G>A,T	Pathogenic	Intron variant
rs121434346	G>A	Pathogenic-likely-pathogenic, pathogenic	Coding sequence variant, missense variant
rs121434347	C>T	Pathogenic	Stop gained, coding sequence variant
rs142979576	T>C,G	Pathogenic	Splice donor variant
rs369804798	C>A,T	Likely-pathogenic, uncertain-significance	Missense variant, coding sequence variant, stop gained
rs762942358	GT>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs778611489	TG>-	Pathogenic	Coding sequence variant, frameshift variant
rs1554033750	C>G	Likely-pathogenic	Coding sequence variant, stop gained

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT019476	hsa-miR-148b-3p	Microarray	17612493
MIRT1366187	hsa-miR-1207-3p	CLIP-seq
MIRT1366188	hsa-miR-1208	CLIP-seq
MIRT1366189	hsa-miR-1276	CLIP-seq
MIRT1366190	hsa-miR-140-3p	CLIP-seq
MIRT1366191	hsa-miR-193a-3p	CLIP-seq
MIRT1366192	hsa-miR-193b	CLIP-seq
MIRT1366193	hsa-miR-214	CLIP-seq
MIRT1366194	hsa-miR-219-5p	CLIP-seq
MIRT1366195	hsa-miR-2278	CLIP-seq
MIRT1366196	hsa-miR-3138	CLIP-seq
MIRT1366197	hsa-miR-3183	CLIP-seq
MIRT1366198	hsa-miR-329	CLIP-seq
MIRT1366199	hsa-miR-3619-5p	CLIP-seq
MIRT1366200	hsa-miR-362-3p	CLIP-seq
MIRT1366201	hsa-miR-3664-5p	CLIP-seq
MIRT1366202	hsa-miR-3679-3p	CLIP-seq
MIRT1366203	hsa-miR-3689a-3p	CLIP-seq
MIRT1366204	hsa-miR-3689c	CLIP-seq
MIRT1366205	hsa-miR-3918	CLIP-seq
MIRT1366206	hsa-miR-3926	CLIP-seq
MIRT1366207	hsa-miR-4291	CLIP-seq
MIRT1366208	hsa-miR-4491	CLIP-seq
MIRT1366209	hsa-miR-4639-3p	CLIP-seq
MIRT1366210	hsa-miR-4645-3p	CLIP-seq
MIRT1366211	hsa-miR-4657	CLIP-seq
MIRT1366212	hsa-miR-4685-5p	CLIP-seq
MIRT1366213	hsa-miR-4723-3p	CLIP-seq
MIRT1366214	hsa-miR-4728-5p	CLIP-seq
MIRT1366215	hsa-miR-4733-3p	CLIP-seq
MIRT1366216	hsa-miR-4755-3p	CLIP-seq
MIRT1366217	hsa-miR-4782-3p	CLIP-seq
MIRT1366218	hsa-miR-4800-5p	CLIP-seq
MIRT1366219	hsa-miR-487a	CLIP-seq
MIRT1366220	hsa-miR-488	CLIP-seq
MIRT1366221	hsa-miR-517b	CLIP-seq
MIRT1366222	hsa-miR-542-3p	CLIP-seq
MIRT1366223	hsa-miR-572	CLIP-seq
MIRT1366224	hsa-miR-596	CLIP-seq
MIRT1366225	hsa-miR-635	CLIP-seq
MIRT1366226	hsa-miR-660	CLIP-seq
MIRT1366227	hsa-miR-668	CLIP-seq
MIRT1366228	hsa-miR-761	CLIP-seq
MIRT1366229	hsa-miR-892b	CLIP-seq
MIRT1366230	hsa-miR-922	CLIP-seq
MIRT2108717	hsa-miR-1228	CLIP-seq
MIRT1366198	hsa-miR-329	CLIP-seq
MIRT2108718	hsa-miR-342-3p	CLIP-seq
MIRT1366200	hsa-miR-362-3p	CLIP-seq
MIRT2108719	hsa-miR-377	CLIP-seq
MIRT2108720	hsa-miR-3941	CLIP-seq
MIRT2108721	hsa-miR-4726-3p	CLIP-seq
MIRT1366215	hsa-miR-4733-3p	CLIP-seq
MIRT2108722	hsa-miR-4789-3p	CLIP-seq
MIRT2108723	hsa-miR-4789-5p	CLIP-seq
MIRT2108724	hsa-miR-603	CLIP-seq
MIRT2332344	hsa-miR-1293	CLIP-seq
MIRT2332345	hsa-miR-1915	CLIP-seq
MIRT2332346	hsa-miR-3132	CLIP-seq
MIRT1366198	hsa-miR-329	CLIP-seq
MIRT2332347	hsa-miR-3591-3p	CLIP-seq
MIRT1366200	hsa-miR-362-3p	CLIP-seq
MIRT2108719	hsa-miR-377	CLIP-seq
MIRT2108720	hsa-miR-3941	CLIP-seq
MIRT2332348	hsa-miR-4447	CLIP-seq
MIRT2332349	hsa-miR-4472	CLIP-seq
MIRT2332350	hsa-miR-4483	CLIP-seq
MIRT2332351	hsa-miR-451b	CLIP-seq
MIRT2332352	hsa-miR-4651	CLIP-seq
MIRT1366212	hsa-miR-4685-5p	CLIP-seq
MIRT2108721	hsa-miR-4726-3p	CLIP-seq
MIRT2108722	hsa-miR-4789-3p	CLIP-seq
MIRT2332353	hsa-miR-499-3p	CLIP-seq
MIRT2332354	hsa-miR-499a-3p	CLIP-seq
MIRT2108724	hsa-miR-603	CLIP-seq
MIRT2332355	hsa-miR-608	CLIP-seq
MIRT2394805	hsa-miR-4666-5p	CLIP-seq
MIRT2459842	hsa-miR-105	CLIP-seq
MIRT1366198	hsa-miR-329	CLIP-seq
MIRT2459843	hsa-miR-3622b-5p	CLIP-seq
MIRT1366200	hsa-miR-362-3p	CLIP-seq
MIRT2108720	hsa-miR-3941	CLIP-seq
MIRT2459844	hsa-miR-4719	CLIP-seq
MIRT2459845	hsa-miR-4720-5p	CLIP-seq
MIRT2459846	hsa-miR-4799-3p	CLIP-seq
MIRT2108724	hsa-miR-603	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003333	Process	Amino acid transmembrane transport	IEA
GO:0005515	Function	Protein binding	IPI	19185582, 32132184, 34189428
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS
GO:0006865	Process	Amino acid transport	IEA
GO:0006865	Process	Amino acid transport	TAS
GO:0007584	Process	Response to nutrient	IEA
GO:0015171	Function	Amino acid transmembrane transporter activity	TAS
GO:0015175	Function	Neutral L-amino acid transmembrane transporter activity	IBA
GO:0015175	Function	Neutral L-amino acid transmembrane transporter activity	IDA	18424768
GO:0015175	Function	Neutral L-amino acid transmembrane transporter activity	IEA
GO:0015293	Function	Symporter activity	IEA
GO:0015804	Process	Neutral amino acid transport	IBA
GO:0015804	Process	Neutral amino acid transport	IEA
GO:0016020	Component	Membrane	IEA
GO:0016324	Component	Apical plasma membrane	IBA
GO:0016324	Component	Apical plasma membrane	IDA	18424768
GO:0016324	Component	Apical plasma membrane	IEA
GO:0019058	Process	Viral life cycle	NAS	33737693
GO:0022857	Function	Transmembrane transporter activity	IEA
GO:0031526	Component	Brush border membrane	IBA
GO:0031526	Component	Brush border membrane	IDA	25534429
GO:0031526	Component	Brush border membrane	IEA
GO:0035725	Process	Sodium ion transmembrane transport	IBA
GO:0070062	Component	Extracellular exosome	HDA	19056867

Other IDs

• MIM: 608893
• HGNC: 27960
• e!Ensembl: ENSG00000174358

Protein

• UniProt ID: Q695T7
• Protein name: Sodium-dependent neutral amino acid transporter B(0)AT1 (Solute carrier family 6 member 19) (System B(0) neutral amino acid transporter AT1)
• Protein function: Transporter that mediates resorption of neutral amino acids across the apical membrane of renal and intestinal epithelial cells (PubMed:15286787, PubMed:15286788, PubMed:18424768, PubMed:18484095, PubMed:19185582, PubMed:26240152). This uptake i
• PDB: 6M17, 6M18, 6M1D, 7DWX, 7V61, 8I92, 8I93, 8WBY, 8WBZ
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00209	SNF	32 → 608	Sodium:neurotransmitter symporter family	Family

• Tissue specificity: TISSUE SPECIFICITY: Robust expression in kidney and small intestine, with minimal expression in pancreas (PubMed:15286787, PubMed:18424768). Also expressed in stomach, liver, duodenum, ileocecum, colon and prostate. Not detected in testis, whole brain, ce
• Sequence:

  MVRLVLPNPGLDARIPSLAELETIEQEEASSRPKWDNKAQYMLTCLGFCVGLGNVWRFPY
  LCQSHGGGAFMIPFLILLVLEGIPLLYLEFAIGQRLRRGSLGVWSSIHPALKGLGLASML
  TSFMVGLYYNTIISWIMWYLFNSFQEPLPWSDCPLNENQTGYVDECARSSPVDYFWYRET
  LNISTSISDSGSIQWWMLLCLACAWSVLYMCTIRGIETTGKAVYITSTLPYVVLTIFLIR
  GLTLKGATNGIVFLFTPNVTELAQPDTWLDAGAQVFFSFSLAFGGLISFSSYNSVHNNCE
  KDSVIVSIINGFTSVYVAIVVYSVIGFRATQRYDDCFSTNILTLINGFDLPEGNVTQENF
  VDMQQRCNASDPAAYAQLVFQTCDINAFLSEAVEGTGLAFIVFTEAITKMPLSPLWSVLF
  FIMLFCLGLSSMFGNMEGVVVPLQDLRVIPPKWPKEVLTGLICLGTFLIGFIFTLNSGQY
  WLSLLDSYAGSIPLLIIAFCEMFSVVYVYGVDRFNKDIEFMIGHKPNIFWQVTWRVVSPL
  LMLIIFLFFFVVEVSQELTYSIWDPGYEEFPKSQKISYPNWVYVVVVIVAGVPSLTIPGY
  AIYKLIRNHCQKPGDHQGLVSTLSTASMNGDLKY

• Sequence length: 634

Pathways

KEGG:

Protein digestion and absorption
Mineral absorption

Reactome:

Amino acid transport across the plasma membrane
Na+/Cl- dependent neurotransmitter transporters
Defective SLC6A19 causes Hartnup disorder (HND)
Defective SLC6A19 causes Hartnup disorder (HND)

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
Hyperglycinuria	Likely pathogenic; Pathogenic	rs554777392, rs121434346, rs121434347, rs2477939209, rs147837686	RCV002476847 RCV000763127 RCV002482814 RCV003337756 RCV001536072	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Iminoglycinuria	Likely pathogenic; Pathogenic	rs554777392, rs121434346, rs121434347, rs147837686	RCV002476847 RCV000763127 RCV002482814 RCV001536072	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neutral 1 amino acid transport defect	Likely pathogenic; Pathogenic	rs554777392, rs757679627, rs745524993, rs778611489, rs121434346, rs121434347, rs200842846, rs1236852017, rs146608591, rs759094266, rs2477951256, rs142979576, rs1746389144, rs147837686	RCV002476847 RCV005397229 RCV002283376 RCV000002095 RCV000002096 RCV000002097 RCV005034829 RCV005034830 RCV003128306 RCV003129594 RCV003226087 RCV000002094 RCV001171523 RCV001174897	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
SLC6A19-related disorder	Likely pathogenic; Pathogenic	rs121434346, rs142979576, rs147837686	RCV003415626 RCV003905313 RCV003413970	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Clear cell carcinoma of kidney	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLYCINURIA WITH OR WITHOUT OXALATE UROLITHIASIS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
High myopia	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Iminoglycinuria, digenic	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
KIDNEY CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SEVERE MYOPIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
UTERINE FIBROID	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Amino Acid Metabolism, Inborn Errors	Disorder of amino acid metabolism	BEFREE	30046012		★☆☆☆☆ Found in Text Mining only
Anxiety	Anxiety Disorder	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Encephalitis	Encephalitis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Episodic Ataxia	Episodic Ataxia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Gingivitis	Gingivitis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Glossitis	Glossitis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hallucinations	Hallucinations	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hartnup Disease	Hartnup Disease	BEFREE	15286787, 15286788, 15681018, 15772300, 17555458, 18484095, 19335424, 19472175, 20399395, 21636576, 25082825, 30589598		★☆☆☆☆ Found in Text Mining only
Hartnup Disease	Hartnup Disease	ORPHANET_DG	15286787, 15286788		★☆☆☆☆ Found in Text Mining only
Hartnup Disease	Hartnup Disease	UNIPROT_DG	15286787, 15286788, 18424768, 18484095, 19185582		★☆☆☆☆ Found in Text Mining only
Hartnup disease	Hartnup Disease	Orphanet			★☆☆☆☆ Found in Text Mining only
Hartnup Disease	Hartnup Disease	CLINVAR_DG	15286788, 17555458, 18484095, 19185582		★☆☆☆☆ Found in Text Mining only
Hartnup Disease	Hartnup Disease	GENOMICS_ENGLAND_DG	15592994, 19335424		★☆☆☆☆ Found in Text Mining only
Hartnup Disease	Hartnup Disease	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
HYPERGLYCINURIA (disorder)	Hyperglycinuria	BEFREE	19033659		★☆☆☆☆ Found in Text Mining only
HYPERGLYCINURIA (disorder)	Hyperglycinuria	GENOMICS_ENGLAND_DG	19335424		★☆☆☆☆ Found in Text Mining only
HYPERGLYCINURIA (disorder)	Hyperglycinuria	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
HYPERGLYCINURIA (disorder)	Hyperglycinuria	HPO_DG			★☆☆☆☆ Found in Text Mining only
HYPERGLYCINURIA (disorder)	Hyperglycinuria	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Hypertension Pulmonary	Pulmonary hypertension	Pubtator	26352407	Associate	★☆☆☆☆ Found in Text Mining only
Hypertensive disease	Hypertension	BEFREE	18671945		★☆☆☆☆ Found in Text Mining only
Hypertensive disease	Hypertension	LHGDN	18671945		★☆☆☆☆ Found in Text Mining only
Iminoglycinuria	Iminoglycinuria	BEFREE	19033659		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Iminoglycinuria	Iminoglycinuria	ORPHANET_DG	19033659		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Iminoglycinuria	Iminoglycinuria	Pubtator	19033659	Associate	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Iminoglycinuria	Iminoglycinuria	Orphanet			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Iminoglycinuria	Iminoglycinuria	GENOMICS_ENGLAND_DG	19335424		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Iminoglycinuria	Iminoglycinuria	CLINVAR_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Iminoglycinuria	Iminoglycinuria	CTD_human_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Inflammatory Bowel Diseases	Inflammatory Bowel Disease	BEFREE	28827067		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	29522993		★☆☆☆☆ Found in Text Mining only
Liver neoplasms	Liver neoplasms	BEFREE	29522993		★☆☆☆☆ Found in Text Mining only
Malabsorption Syndrome	Malabsorption Syndrome	BEFREE	31470570		★☆☆☆☆ Found in Text Mining only
Malabsorption Syndrome	Malabsorption Syndrome	HPO_DG			★☆☆☆☆ Found in Text Mining only
Malnutrition	Malnutrition	BEFREE	31635319		★☆☆☆☆ Found in Text Mining only
Migraine Disorders	Migraine	HPO_DG			★☆☆☆☆ Found in Text Mining only
Mood swings	Mood swings	HPO_DG			★☆☆☆☆ Found in Text Mining only
NEPHROLITHIASIS, CALCIUM OXALATE	Nephronophthisis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Phenylketonurias	Phenylketonuria	BEFREE	30046012		★☆☆☆☆ Found in Text Mining only
Prolinuria	Prolinuria	HPO_DG			★☆☆☆☆ Found in Text Mining only
Psychotic Disorders	Psychosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	40102553	Associate	★☆☆☆☆ Found in Text Mining only
Strabismus	Strabismus	HPO_DG			★☆☆☆☆ Found in Text Mining only