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.	6529
Gene name Gene Name - the full gene name approved by the HGNC.	Solute carrier family 6 member 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	SLC6A1
Synonyms (NCBI Gene) Gene synonyms aliases	GABATHG, GABATR, GAT1, MAE, hGAT-1
Chromosome Chromosome number	3
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	3p25.3
Summary Summary of gene provided in NCBI Entrez Gene.	The protein encoded by this gene is a gamma-aminobutyric acid (GABA) transporter that localizes to the plasma membrane. The encoded protein removes GABA from the synaptic cleft, restoring it to presynaptic terminals. [provided by RefSeq, Jan 2017]

Show/Hide all(36)

SNP ID	Visualize variation	Clinical significance	Consequence
rs745529755	C>A,T	Pathogenic	Stop gained, coding sequence variant, synonymous variant
rs749240316	G>A,C	Likely-pathogenic, pathogenic, uncertain-significance	Coding sequence variant, missense variant
rs752396911	G>A,C,T	Pathogenic	Coding sequence variant, missense variant
rs794726860	C>T	Pathogenic-likely-pathogenic, likely-pathogenic	Missense variant, coding sequence variant
rs876657400	G>A	Pathogenic	Missense variant, coding sequence variant
rs876657401	GG>-	Pathogenic	Frameshift variant, coding sequence variant
rs886042046	G>A,C	Pathogenic, likely-pathogenic	Missense variant, coding sequence variant
rs1064794981	G>A	Pathogenic, uncertain-significance	Missense variant, coding sequence variant
rs1064795098	C>T	Likely-pathogenic, not-provided	Stop gained, coding sequence variant
rs1064795099	C>A,G	Pathogenic, likely-pathogenic, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs1064796533	G>-	Pathogenic	Frameshift variant, coding sequence variant
rs1131691302	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs1199489242	G>-,GG	Pathogenic	Splice acceptor variant, coding sequence variant
rs1403165900	G>A,T	Uncertain-significance, pathogenic	Coding sequence variant, missense variant
rs1410013974	C>G,T	Likely-pathogenic	Coding sequence variant, synonymous variant, missense variant
rs1553688970	CTGGCCATCACGCTGGCCA>-	Pathogenic	Frameshift variant, coding sequence variant
rs1553689580	T>C	Pathogenic	Missense variant, coding sequence variant
rs1553689664	A>G	Pathogenic	Splice acceptor variant
rs1553689696	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs1553689859	C>T	Pathogenic	Missense variant, coding sequence variant
rs1553690421	C>GT	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1553690452	C>T	Pathogenic	Stop gained, coding sequence variant
rs1553690583	C>-	Pathogenic	Frameshift variant, coding sequence variant
rs1553690601	CTCT>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1553691674	G>A,T	Likely-pathogenic	Splice acceptor variant
rs1559626646	C>T	Likely-pathogenic	Stop gained, coding sequence variant
rs1559629701	C>A,G	Likely-pathogenic	Stop gained, coding sequence variant
rs1559633512	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs1559639240	T>C	Likely-pathogenic	Missense variant, coding sequence variant
rs1559640454	G>A	Pathogenic	Stop gained, coding sequence variant
rs1574906665	C>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1574907198	TCT>-	Likely-pathogenic	Inframe deletion, coding sequence variant
rs1574913614	C>-	Pathogenic, not-provided	Frameshift variant, coding sequence variant
rs1574917501	->T	Pathogenic	Frameshift variant, coding sequence variant
rs1574924801	G>C	Likely-pathogenic	Splice acceptor variant
rs1574929097	G>-	Pathogenic	Frameshift variant, coding sequence variant

Show/Hide all(115)

miRTarBase ID	miRNA	Experiments	Reference
MIRT490368	hsa-miR-4779	PAR-CLIP	20371350
MIRT490366	hsa-miR-211-3p	PAR-CLIP	20371350
MIRT490365	hsa-miR-151a-5p	PAR-CLIP	20371350
MIRT490364	hsa-miR-151b	PAR-CLIP	20371350
MIRT490363	hsa-miR-4285	PAR-CLIP	20371350
MIRT490362	hsa-miR-1538	PAR-CLIP	20371350
MIRT490361	hsa-miR-4745-3p	PAR-CLIP	20371350
MIRT490369	hsa-miR-548e-5p	PAR-CLIP	23592263
MIRT490370	hsa-miR-665	PAR-CLIP	23592263
MIRT490368	hsa-miR-4779	PAR-CLIP	23592263
MIRT490367	hsa-miR-7845-5p	PAR-CLIP	23592263
MIRT490366	hsa-miR-211-3p	PAR-CLIP	23592263
MIRT490365	hsa-miR-151a-5p	PAR-CLIP	23592263
MIRT490364	hsa-miR-151b	PAR-CLIP	23592263
MIRT490363	hsa-miR-4285	PAR-CLIP	23592263
MIRT490362	hsa-miR-1538	PAR-CLIP	23592263
MIRT490361	hsa-miR-4745-3p	PAR-CLIP	23592263
MIRT490368	hsa-miR-4779	PAR-CLIP	20371350
MIRT490366	hsa-miR-211-3p	PAR-CLIP	20371350
MIRT490365	hsa-miR-151a-5p	PAR-CLIP	20371350
MIRT490364	hsa-miR-151b	PAR-CLIP	20371350
MIRT490363	hsa-miR-4285	PAR-CLIP	20371350
MIRT490362	hsa-miR-1538	PAR-CLIP	20371350
MIRT490361	hsa-miR-4745-3p	PAR-CLIP	20371350
MIRT490369	hsa-miR-548e-5p	PAR-CLIP	23592263
MIRT490370	hsa-miR-665	PAR-CLIP	23592263
MIRT490368	hsa-miR-4779	PAR-CLIP	23592263
MIRT490367	hsa-miR-7845-5p	PAR-CLIP	23592263
MIRT490366	hsa-miR-211-3p	PAR-CLIP	23592263
MIRT490365	hsa-miR-151a-5p	PAR-CLIP	23592263
MIRT490364	hsa-miR-151b	PAR-CLIP	23592263
MIRT490363	hsa-miR-4285	PAR-CLIP	23592263
MIRT490362	hsa-miR-1538	PAR-CLIP	23592263
MIRT490361	hsa-miR-4745-3p	PAR-CLIP	23592263
MIRT1365862	hsa-miR-1229	CLIP-seq
MIRT1365863	hsa-miR-1255a	CLIP-seq
MIRT1365864	hsa-miR-1255b	CLIP-seq
MIRT1365865	hsa-miR-128	CLIP-seq
MIRT1365866	hsa-miR-151-5p	CLIP-seq
MIRT1365867	hsa-miR-1914	CLIP-seq
MIRT1365868	hsa-miR-2110	CLIP-seq
MIRT1365869	hsa-miR-23a	CLIP-seq
MIRT1365870	hsa-miR-23b	CLIP-seq
MIRT1365871	hsa-miR-23c	CLIP-seq
MIRT1365872	hsa-miR-27a	CLIP-seq
MIRT1365873	hsa-miR-27b	CLIP-seq
MIRT1365874	hsa-miR-3074-5p	CLIP-seq
MIRT1365875	hsa-miR-3150b-3p	CLIP-seq
MIRT1365876	hsa-miR-3167	CLIP-seq
MIRT1365877	hsa-miR-3185	CLIP-seq
MIRT1365878	hsa-miR-338-5p	CLIP-seq
MIRT1365879	hsa-miR-342-3p	CLIP-seq
MIRT1365880	hsa-miR-34a	CLIP-seq
MIRT1365881	hsa-miR-34c-5p	CLIP-seq
MIRT1365882	hsa-miR-365	CLIP-seq
MIRT1365883	hsa-miR-3677-5p	CLIP-seq
MIRT1365884	hsa-miR-369-3p	CLIP-seq
MIRT1365885	hsa-miR-374c	CLIP-seq
MIRT1365886	hsa-miR-377	CLIP-seq
MIRT1365887	hsa-miR-4264	CLIP-seq
MIRT1365888	hsa-miR-4271	CLIP-seq
MIRT1365889	hsa-miR-4277	CLIP-seq
MIRT1365890	hsa-miR-4278	CLIP-seq
MIRT1365891	hsa-miR-4328	CLIP-seq
MIRT1365892	hsa-miR-4446-5p	CLIP-seq
MIRT1365893	hsa-miR-4450	CLIP-seq
MIRT1365894	hsa-miR-4460	CLIP-seq
MIRT1365895	hsa-miR-449a	CLIP-seq
MIRT1365896	hsa-miR-449b	CLIP-seq
MIRT1365897	hsa-miR-4666-3p	CLIP-seq
MIRT1365898	hsa-miR-4689	CLIP-seq
MIRT1365899	hsa-miR-4698	CLIP-seq
MIRT1365900	hsa-miR-4709-3p	CLIP-seq
MIRT1365901	hsa-miR-4725-3p	CLIP-seq
MIRT1365902	hsa-miR-4727-3p	CLIP-seq
MIRT1365903	hsa-miR-4784	CLIP-seq
MIRT1365904	hsa-miR-4797-3p	CLIP-seq
MIRT1365905	hsa-miR-513a-5p	CLIP-seq
MIRT1365906	hsa-miR-578	CLIP-seq
MIRT1365907	hsa-miR-580	CLIP-seq
MIRT1365908	hsa-miR-655	CLIP-seq
MIRT1365909	hsa-miR-876-5p	CLIP-seq
MIRT1365910	hsa-miR-935	CLIP-seq
MIRT1365911	hsa-miR-938	CLIP-seq
MIRT1553824	hsa-miR-1180	CLIP-seq
MIRT1553825	hsa-miR-1298	CLIP-seq
MIRT1553826	hsa-miR-1908	CLIP-seq
MIRT1553827	hsa-miR-3960	CLIP-seq
MIRT1553828	hsa-miR-4467	CLIP-seq
MIRT1553829	hsa-miR-4706	CLIP-seq
MIRT1553830	hsa-miR-4749-5p	CLIP-seq
MIRT1553831	hsa-miR-663	CLIP-seq
MIRT1365878	hsa-miR-338-5p	CLIP-seq
MIRT2108643	hsa-miR-4316	CLIP-seq
MIRT2332254	hsa-miR-132	CLIP-seq
MIRT2332255	hsa-miR-212	CLIP-seq
MIRT2332256	hsa-miR-4773	CLIP-seq
MIRT2332257	hsa-miR-873	CLIP-seq
MIRT1553824	hsa-miR-1180	CLIP-seq
MIRT1553825	hsa-miR-1298	CLIP-seq
MIRT1553826	hsa-miR-1908	CLIP-seq
MIRT1553827	hsa-miR-3960	CLIP-seq
MIRT1553828	hsa-miR-4467	CLIP-seq
MIRT1553829	hsa-miR-4706	CLIP-seq
MIRT1553830	hsa-miR-4749-5p	CLIP-seq
MIRT1553831	hsa-miR-663	CLIP-seq
MIRT1365865	hsa-miR-128	CLIP-seq
MIRT1365872	hsa-miR-27a	CLIP-seq
MIRT1365873	hsa-miR-27b	CLIP-seq
MIRT2440551	hsa-miR-4477a	CLIP-seq
MIRT2440552	hsa-miR-4477b	CLIP-seq
MIRT2440553	hsa-miR-4699-3p	CLIP-seq
MIRT2459836	hsa-miR-1976	CLIP-seq
MIRT2459837	hsa-miR-518a-5p	CLIP-seq
MIRT2459838	hsa-miR-527	CLIP-seq

Show/Hide all(49)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003333	Process	Amino acid transmembrane transport	IEA
GO:0005283	Function	Amino acid:sodium symporter activity	IEA
GO:0005332	Function	Gamma-aminobutyric acid:sodium:chloride symporter activity	IBA
GO:0005332	Function	Gamma-aminobutyric acid:sodium:chloride symporter activity	IDA	10973981
GO:0005332	Function	Gamma-aminobutyric acid:sodium:chloride symporter activity	IEA
GO:0005332	Function	Gamma-aminobutyric acid:sodium:chloride symporter activity	IMP	30132828
GO:0005332	Function	Gamma-aminobutyric acid:sodium:chloride symporter activity	TAS
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IDA	10973981
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS
GO:0006836	Process	Neurotransmitter transport	IEA
GO:0006865	Process	Amino acid transport	IBA
GO:0007268	Process	Chemical synaptic transmission	TAS	8530094
GO:0007613	Process	Memory	IEA
GO:0007613	Process	Memory	ISS
GO:0008306	Process	Associative learning	IEA
GO:0008306	Process	Associative learning	ISS
GO:0009986	Component	Cell surface	IBA
GO:0015185	Function	Gamma-aminobutyric acid transmembrane transporter activity	IEA
GO:0015185	Function	Gamma-aminobutyric acid transmembrane transporter activity	ISS
GO:0015293	Function	Symporter activity	IEA
GO:0015378	Function	Sodium:chloride symporter activity	IDA	10973981
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	TAS	2387399, 8530094
GO:0022857	Function	Transmembrane transporter activity	IEA
GO:0030424	Component	Axon	IBA
GO:0030424	Component	Axon	IEA
GO:0030424	Component	Axon	ISS
GO:0035725	Process	Sodium ion transmembrane transport	IBA
GO:0042995	Component	Cell projection	IEA
GO:0043025	Component	Neuronal cell body	IEA
GO:0043025	Component	Neuronal cell body	ISS
GO:0045202	Component	Synapse	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0050808	Process	Synapse organization	IEA
GO:0050808	Process	Synapse organization	ISS
GO:0051936	Process	Gamma-aminobutyric acid reuptake	TAS
GO:0051939	Process	Gamma-aminobutyric acid import	IDA	10973981
GO:0051939	Process	Gamma-aminobutyric acid import	IEA
GO:0051939	Process	Gamma-aminobutyric acid import	ISS
GO:0098658	Process	Inorganic anion import across plasma membrane	IDA	10973981
GO:0098719	Process	Sodium ion import across plasma membrane	IDA	10973981
GO:0098793	Component	Presynapse	IEA
GO:0098810	Process	Neurotransmitter reuptake	IEA
GO:0098982	Component	GABA-ergic synapse	IEA
GO:0150104	Process	Transport across blood-brain barrier	NAS	30280653
GO:1902476	Process	Chloride transmembrane transport	IDA	10973981

MIM	HGNC	e!Ensembl
137165	11042	ENSG00000157103

Protein

UniProt ID

P30531

Protein name

Sodium- and chloride-dependent GABA transporter 1 (GAT-1) (Solute carrier family 6 member 1)

Protein function

Mediates transport of gamma-aminobutyric acid (GABA) together with sodium and chloride and is responsible for the reuptake of GABA from the synapse (PubMed:30132828). The translocation of GABA, however, may also occur in the reverse direction le

PDB

7SK2 , 7Y7V , 7Y7W , 7Y7Y , 7Y7Z

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00209	SNF	44 → 559	Sodium:neurotransmitter symporter family	Family

Sequence

MATNGSKVADGQISTEVSEAPVANDKPKTLVVKVQKKAADLPDRDTWKGRFDFLMSCVGY
AIGLGNVWRFPYLCGKNGGGAFLIPYFLTLIFAGVPLFLLECSLGQYTSIGGLGVWKLAP
MFKGVGLAAAVLSFWLNIYYIVIISWAIYYLYNSFTTTLPWKQCDNPWNTDRCFSNYSMV
NTTNMTSAVVEFWERNMHQMTDGLDKPGQIRWPLAITLAIAWILVYFCIWKGVGWTGKVV
YFSATYPYIMLIILFFRGVTLPGAKEGILFYITPNFRKLSDSEVWLDAATQIFFSYGLGL
GSLIALGSYNSFHNNVYRDSIIVCCINSCTSMFAGFVIFSIVGFMAHVTKRSIADVAASG
PGLAFLAYPEAVTQLPISPLWAILFFSMLLMLGIDSQFCTVEGFITALVDEYPRLLRNRR
ELFIAAVCIISYLIGLSNITQGGIYVFKLFDYYSASGMSLLFLVFFECVSISWFYGVNRF
YDNIQEMVGSRPCIWWKLCWSFFTPIIVAGVFIFSAVQMTPLTMGNYVFPKWGQGVGWLM
ALSSMVLIPGYMAYMFLTLKGSLKQRIQVMVQPSEDIVRPENGPEQPQAGSSTSKEAYI

Sequence length

599

Interactions

View interactions

	KEGG		Reactome
	Synaptic vesicle cycle GABAergic synapse		Na+/Cl- dependent neurotransmitter transporters Reuptake of GABA

Show/Hide Causal Diseases (4)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Epilepsy	Autosomal dominant epilepsy	rs794726859	N/A
Developmental Delay	global developmental delay	rs886042046	N/A
Mental retardation	intellectual disability	rs1574907198	N/A
seizure	Seizure	rs1064794981	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.
Glioblastoma	Glioblastoma	N/A	N/A	GWAS
Myoclonic-Astatic Epilepsy	myoclonic-astatic epilepsy	N/A	N/A	GenCC
Ovarian cancer	Epithelial ovarian cancer	N/A	N/A	GWAS

Show/Hide Text Mining Associations (39)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Alcohol Related Disorders	Associate	35761184
Alcoholism	Associate	26727527
Alzheimer Disease	Associate	37264161
Anxiety	Associate	18607529
Anxiety Disorders	Associate	18607529
Aortic Valve Stenosis	Associate	32375772
Ataxia	Associate	29315614
Attention Deficit Disorder with Hyperactivity	Associate	23527680, 32375772
Auditory Perceptual Disorders	Associate	23527680
Autistic Disorder	Associate	33527113, 34028503, 35761184
Brain Diseases	Associate	26716362, 32660967, 40624551
Cholangiocarcinoma	Associate	30452401
Colonic Neoplasms	Associate	37023088
Colorectal Neoplasms	Associate	35251372
Developmental Disabilities	Associate	31932766, 32660967, 34028503, 35761184
Disruptive Impulse Control and Conduct Disorders	Associate	23527680
Epilepsies Myoclonic	Associate	27600546
Epilepsies Partial	Associate	29315614
Epilepsy	Associate	27600546, 29315614, 32660967, 35761184, 39344240, 39923323
Epilepsy Absence	Associate	34028503
Epilepsy Generalized	Associate	29315614, 31401500
Epilepsy Temporal Lobe	Associate	39344240
Epileptic Syndromes	Associate	34028503, 39923323
Generalized Epilepsy With Febrile Seizures Plus Type 1	Associate	31401500
Glioma	Associate	36405708
Intellectual Disability	Associate	29315614, 32660967, 34028503
Language Development Disorders	Associate	29315614, 32375772
Language Disorders	Associate	29315614
Lymphoma Non Hodgkin	Associate	36405708
Mental Disorders	Associate	16470700, 34633442
Mental Retardation X Linked Syndromic Christianson Type	Associate	34653234
Motor Skills Disorders	Associate	32375772
Myopia	Associate	32375772
Neurologic Manifestations	Associate	40624551
Obesity	Associate	16470700
Panic Disorder	Associate	18607529
Schizophrenia	Associate	31932766
Seizures	Associate	27600546, 29315614, 31401500, 32660967, 39923323
Substance Related Disorders	Associate	26727527

SLC6A1 (solute carrier family 6 member 1)