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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	6519
Gene name	Solute carrier family 3 member 1
Gene symbol	SLC3A1
Synonyms (NCBI Gene)	ATR1CSNU1D2HNBATRBAT
Chromosome	2
Chromosome location	2p21
Summary	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

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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

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)

364

Show/Hide Causal Diseases (8)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Autism spectrum disorder	Pathogenic	rs200483989	RCV003313951
Cystine urolithiasis	Pathogenic; Likely pathogenic	rs375399468, rs1572804699, rs768467260, rs368554884, rs779941675, rs373176089, rs368796166, rs1361526419, rs769712061, rs758627758	RCV000991112 RCV000991117 RCV000991110 RCV000991123 RCV000991111 RCV000991109 RCV000991124 RCV000991105 RCV000991118 RCV000991122
Cystinuria	Pathogenic; Likely pathogenic	rs755432720, rs768222969, rs765828196, rs777575410, rs201376169, rs772810111, rs2104364101, rs2104342335, rs139251285, rs1206425661, rs369603431, rs567478582, rs2104385536, rs542026439, rs2104385579 View all (45 more)	RCV001374412 RCV001374419 RCV001390784 RCV001384053 RCV001761809 RCV003506537 RCV001783769 RCV001999110 RCV001961514 RCV001977751 RCV002013904 RCV001956176 RCV001972524 RCV001947095 RCV002251021 RCV002612511 RCV002664233 RCV002755885 RCV000192842 RCV002912849 RCV002923352 RCV003134071 RCV003152900 RCV003156159 RCV003156162 RCV003156163 RCV003156164 RCV003228714 RCV001037564 RCV003330373 RCV003333288 RCV000332132 RCV003506534 RCV003506538 RCV003506541 RCV003506543 RCV000402894 RCV003504873 RCV003616826 RCV003992078 RCV000019743 RCV000019744 RCV000019745 RCV000019746 RCV004557283 RCV000416445 RCV000497086 RCV000030727 RCV001234999 RCV001257095 RCV001067849 RCV000688389 RCV000798029 RCV000796237 RCV004761853 RCV001313669 RCV001238859 RCV003141911 RCV001064226 RCV001216584 RCV001213233 RCV001225547 RCV001257094
Kidney disorder	Likely pathogenic; Pathogenic	rs121912691	RCV005624699
Nephrocalcinosis	Likely pathogenic; Pathogenic	rs778000327	RCV000662323
Nephrolithiasis	Likely pathogenic; Pathogenic	rs778000327	RCV000662323
See cases	Likely pathogenic; Pathogenic	rs758627758, rs121912691	RCV002253101 RCV002251914
SLC3A1-related disorder	Pathogenic; Likely pathogenic	rs1671994225, rs200483989, rs1672093562, rs121912691, rs775827496, rs368796166, rs369641941	RCV003421029 RCV004754396 RCV003946874 RCV004754266 RCV003415724 RCV004754420 RCV004754669 RCV003963130

Show/Hide Unknown Diseases (5)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Acute myeloid leukemia	Benign; Likely benign	rs72802978, rs114640930	RCV005923214 RCV005896188
Cholangiocarcinoma	Benign	rs72802978	RCV005923215
Lung cancer	Uncertain significance	rs267599386	RCV005925495
Malignant tumor of esophagus	Benign	rs78474108	RCV005916719
Uterine corpus endometrial carcinoma	Benign	rs78474108	RCV005916720

Show/Hide Text Mining Associations (13)

Disease Name	Relationship Type	References
Associations from Text MiningDisease 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)