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

Gene Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	6519
Gene name Gene Name - the full gene name approved by the HGNC.	Solute carrier family 3 member 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	SLC3A1
Synonyms (NCBI Gene) Gene synonyms aliases	ATR1, CSNU1, D2H, NBAT, RBAT
Chromosome Chromosome number	2
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	2p21
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes a type II membrane glycoprotein which is one of the components of the renal amino acid transporter which transports neutral and basic amino acids in the renal tubule and intestinal tract. Mutations and deletions in this gene are associat

Show/Hide all(26)

SNP ID	Visualize variation	Clinical significance	Consequence
rs114640930	C>G,T	Conflicting-interpretations-of-pathogenicity, benign	Intron variant
rs121912691	T>A,C	Conflicting-interpretations-of-pathogenicity, pathogenic	Coding sequence variant, missense variant
rs121912694	G>A,T	Pathogenic	Coding sequence variant, missense variant
rs121912697	G>A	Pathogenic	Coding sequence variant, missense variant
rs184648701	T>C,G	Likely-pathogenic	Missense variant, coding sequence variant
rs200483989	C>T	Pathogenic	Coding sequence variant, stop gained
rs201502095	C>A,G,T	Pathogenic	Coding sequence variant, synonymous variant, missense variant
rs368554884	C>G,T	Likely-pathogenic	Coding sequence variant, synonymous variant, missense variant
rs373176089	C>T	Pathogenic	Coding sequence variant, missense variant
rs375399468	C>G,T	Pathogenic	Coding sequence variant, missense variant
rs387907276	T>A,G	Pathogenic	Coding sequence variant, missense variant
rs567478582	G>A,C,T	Likely-pathogenic	Missense variant, coding sequence variant
rs758627758	T>A,C	Pathogenic	Splice donor variant
rs768467260	C>A,T	Pathogenic	Synonymous variant, coding sequence variant, stop gained
rs769712061	G>A,T	Pathogenic	Splice acceptor variant
rs778000327	G>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs779932118	C>-	Pathogenic	Frameshift variant, coding sequence variant
rs779941675	G>-	Pathogenic	Frameshift variant, coding sequence variant
rs797044609	->TG	Likely-pathogenic	Frameshift variant, coding sequence variant
rs886042834	G>A,T	Pathogenic	Splice donor variant
rs935314238	T>C	Likely-pathogenic	Missense variant, coding sequence variant
rs1553344107	->ATGCACGACATTGTCC	Pathogenic	Frameshift variant, coding sequence variant
rs1558450604	T>G	Likely-pathogenic	Splice donor variant
rs1558455633	G>T	Likely-pathogenic	Splice acceptor variant
rs1558455640	T>G	Likely-pathogenic	Stop gained, coding sequence variant
rs1572804699	A>G	Likely-pathogenic	Coding sequence variant, missense variant

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miRTarBase ID	miRNA	Experiments	Reference
MIRT443002	hsa-miR-548e-5p	PAR-CLIP	22100165
MIRT443001	hsa-miR-382-5p	PAR-CLIP	22100165
MIRT443002	hsa-miR-548e-5p	PAR-CLIP	22100165
MIRT443001	hsa-miR-382-5p	PAR-CLIP	22100165
MIRT2108036	hsa-miR-199a-5p	CLIP-seq
MIRT2108037	hsa-miR-199b-5p	CLIP-seq
MIRT2108038	hsa-miR-4711-3p	CLIP-seq
MIRT2459759	hsa-miR-1236	CLIP-seq
MIRT2459760	hsa-miR-18a	CLIP-seq
MIRT2459761	hsa-miR-18b	CLIP-seq
MIRT2108036	hsa-miR-199a-5p	CLIP-seq
MIRT2108037	hsa-miR-199b-5p	CLIP-seq
MIRT2459762	hsa-miR-203	CLIP-seq
MIRT2108038	hsa-miR-4711-3p	CLIP-seq
MIRT2459763	hsa-miR-4735-3p	CLIP-seq
MIRT2459764	hsa-miR-548m	CLIP-seq

Transcription factors

Show/Hide all(1)

Transcription factor	Regulation	Reference
PAX8	Activation	15673291

Show/Hide all(28)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	12167606, 32494597
GO:0005774	Component	Vacuolar membrane	IEA
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS	8054986
GO:0005975	Process	Carbohydrate metabolic process	IEA
GO:0006865	Process	Amino acid transport	IBA
GO:0006865	Process	Amino acid transport	IEA
GO:0006865	Process	Amino acid transport	TAS	10799513
GO:0010467	Process	Gene expression	IEA
GO:0015171	Function	Amino acid transmembrane transporter activity	TAS	10799513
GO:0015174	Function	Basic amino acid transmembrane transporter activity	TAS	8054986
GO:0015184	Function	L-cystine transmembrane transporter activity	TAS	8054986
GO:0015802	Process	Basic amino acid transport	TAS	8054986
GO:0015810	Process	Aspartate transmembrane transport	IEA
GO:0015811	Process	L-cystine transport	IEA
GO:0015811	Process	L-cystine transport	TAS	8054986
GO:0015813	Process	L-glutamate transmembrane transport	IEA
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	TAS	8054986
GO:0016324	Component	Apical plasma membrane	IEA
GO:0016324	Component	Apical plasma membrane	IEA
GO:0031526	Component	Brush border membrane	IDA	12167606
GO:0031526	Component	Brush border membrane	IEA
GO:0044877	Function	Protein-containing complex binding	IEA
GO:0046982	Function	Protein heterodimerization activity	IDA	32494597
GO:0046982	Function	Protein heterodimerization activity	IEA
GO:0070062	Component	Extracellular exosome	HDA	19056867
GO:1990822	Process	Basic amino acid transmembrane transport	IEA

MIM	HGNC	e!Ensembl
104614	11025	ENSG00000138079

Protein

UniProt ID

Q07837

Protein name

Amino acid transporter heavy chain SLC3A1 (D2h) (Neutral and basic amino acid transport protein) (NBAT) (Solute carrier family 3 member 1) (b(0,+)-type amino acid transporter-related heavy chain) (rBAT)

Protein function

Acts as a chaperone that facilitates biogenesis and trafficking of functional transporter heteromers to the plasma membrane (By similarity) (PubMed:10588648, PubMed:11318953, PubMed:16609684, PubMed:16825196, PubMed:32494597, PubMed:32817565, Pu

PDB

6LI9 , 6LID , 6YUP , 6YUZ

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00128	Alpha-amylase	140 → 492	Alpha amylase, catalytic domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Expressed in the brush border membrane in the kidney (at protein level). Predominantly expressed in the kidney, small intestine and pancreas. Weakly expressed in liver. {ECO:0000269|PubMed:12167606, ECO:0000269|PubMed:7686906, ECO:0000

Sequence

MAEDKSKRDSIEMSMKGCQTNNGFVHNEDILEQTPDPGSSTDNLKHSTRGILGSQEPDFK
GVQPYAGMPKEVLFQFSGQARYRIPREILFWLTVASVLVLIAATIAIIALSPKCLDWWQE
GPMYQIYPRSFKDSNKDGNGDLKGIQDKLDYITALNIKTVWITSFYKSSLKDFRYGVEDF
REVDPIFGTMEDFENLVAAIHDKGLKLIIDFIPNHTSDKHIWFQLSRTRTGKYTDYYIWH
DCTHENGKTIPPNNWLSVYGNSSWHFDEVRNQCYFHQFMKEQPDLNFRNPDVQEEIKEIL
RFWLTKGVDGFSLDAVKFLLEAKHLRDEIQVNKTQIPDTVTQYSELYHDFTTTQVGMHDI
VRSFRQTMDQYSTEPGRYRFMGTEAYAESIDRTVMYYGLPFIQEADFPFNNYLSMLDTVS
GNSVYEVITSWMENMPEGKWPNWMIGGPDSSRLTSRLGNQYVNVMNMLLFTLPGTPITYY
GEEIGMGNIVAANLNESYDINTLRSKSPMQWDNSSNAGFSEASNTWLPTNSDYHTVNVDV
QKTQPRSALKLYQDLSLLHANELLLNRGWFCHLRNDSHYVVYTRELDGIDRIFIVVLNFG
ESTLLNLHNMISGLPAKMRIRLSTNSADKGSKVDTSGIFLDKGEGLIFEHNTKNLLHRQT
AFRDRCFVSNRACYSSVLNILYTSC

Sequence length

685

Interactions

View interactions

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

Show/Hide Causal Diseases (2)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Cystinuria	cystinuria	rs777149216, rs200483989, rs768467260, rs368796166, rs201502095, rs1361526419, rs775827496, rs758627758, rs1553344107, rs767801148, rs121912691, rs779932118, rs121912693, rs778000327, rs121912694 View all (6 more)	N/A
autism spectrum disorder	Autism spectrum disorder	rs200483989	N/A

Show/Hide Text Mining Associations (13)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Carcinoma Renal Cell	Associate	31140607, 37304236
Cystinosis	Associate	36421847
Cystinuria	Associate	10620184, 10805464, 11524703, 12234283, 12841020, 16374432, 25964309, 28049243, 28166740, 33169184, 35577790, 36421847, 37525149, 38114997, 40428323, 7539209, 7568194, 9186880, 9648063 View all (4 more)
Cystinuria type 1	Associate	16385448
Cystinuria Type A	Associate	10620184, 10805464, 11524703, 12234283, 16374432, 28166740, 35577790, 38114997
Distal myopathy Nonaka type	Associate	38114997
Hypersensitivity Immediate	Associate	35577790, 7568194
Hypotonia Cystinuria Syndrome	Associate	24610330, 34612606
Mucolipidoses	Associate	12841020
Myasthenic Syndromes Congenital	Associate	24610330
Nephrocalcinosis	Associate	28893421
Nephrolithiasis	Associate	40428323
Xanthinuria Type I	Associate	37525149

SLC3A1 (solute carrier family 3 member 1)