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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	6536
Gene name	Solute carrier family 6 member 9
Gene symbol	SLC6A9
Synonyms (NCBI Gene)	GCENSGGLYT1
Chromosome	1
Chromosome location	1p34.1
Summary	The amino acid glycine acts as an inhibitory neurotransmitter in the central nervous system. The protein encoded by this gene is one of two transporters that stop glycine signaling by removing it from the synaptic cleft. [provided by RefSeq, Jun 2016]

Show/Hide all (6)

SNP ID	Visualize variation	Clinical significance	Consequence
rs201267211	C>G,T	Likely-pathogenic	Intron variant, missense variant, coding sequence variant, non coding transcript variant
rs201437896	G>A	Pathogenic	Non coding transcript variant, coding sequence variant, stop gained
rs1057519313	T>C	Pathogenic	Missense variant, coding sequence variant, non coding transcript variant
rs1057519314	G>A	Pathogenic	Stop gained, coding sequence variant, non coding transcript variant
rs1057519315	TTGAC>-	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant
rs1553160504	AA>-	Likely-pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant

125

Show/Hide all (125)

miRTarBase ID	miRNA	Experiments	Reference
MIRT017329	hsa-miR-335-5p	Microarray	18185580
MIRT024167	hsa-miR-221-3p	Sequencing	20371350
MIRT025716	hsa-miR-7-5p	Sequencing	20371350
MIRT027081	hsa-miR-103a-3p	Sequencing	20371350
MIRT029053	hsa-miR-26b-5p	Microarray	19088304
MIRT561571	hsa-miR-4463	PAR-CLIP	20371350
MIRT561572	hsa-miR-4436b-3p	PAR-CLIP	20371350
MIRT561570	hsa-miR-4632-5p	PAR-CLIP	20371350
MIRT561569	hsa-miR-6735-5p	PAR-CLIP	20371350
MIRT561568	hsa-miR-6879-5p	PAR-CLIP	20371350
MIRT561567	hsa-miR-7843-5p	PAR-CLIP	20371350
MIRT561566	hsa-miR-3616-3p	PAR-CLIP	20371350
MIRT025716	hsa-miR-7-5p	PAR-CLIP	20371350
MIRT561565	hsa-miR-4747-5p	PAR-CLIP	20371350
MIRT561564	hsa-miR-5196-5p	PAR-CLIP	20371350
MIRT561563	hsa-miR-450a-1-3p	PAR-CLIP	20371350
MIRT561562	hsa-miR-3122	PAR-CLIP	20371350
MIRT561561	hsa-miR-3913-5p	PAR-CLIP	20371350
MIRT561560	hsa-miR-887-5p	PAR-CLIP	20371350
MIRT561559	hsa-miR-6513-5p	PAR-CLIP	20371350
MIRT561571	hsa-miR-4463	PAR-CLIP	20371350
MIRT561572	hsa-miR-4436b-3p	PAR-CLIP	20371350
MIRT561570	hsa-miR-4632-5p	PAR-CLIP	20371350
MIRT561569	hsa-miR-6735-5p	PAR-CLIP	20371350
MIRT561568	hsa-miR-6879-5p	PAR-CLIP	20371350
MIRT561567	hsa-miR-7843-5p	PAR-CLIP	20371350
MIRT561566	hsa-miR-3616-3p	PAR-CLIP	20371350
MIRT025716	hsa-miR-7-5p	PAR-CLIP	20371350
MIRT561565	hsa-miR-4747-5p	PAR-CLIP	20371350
MIRT561564	hsa-miR-5196-5p	PAR-CLIP	20371350
MIRT561563	hsa-miR-450a-1-3p	PAR-CLIP	20371350
MIRT561562	hsa-miR-3122	PAR-CLIP	20371350
MIRT561561	hsa-miR-3913-5p	PAR-CLIP	20371350
MIRT561560	hsa-miR-887-5p	PAR-CLIP	20371350
MIRT561559	hsa-miR-6513-5p	PAR-CLIP	20371350
MIRT1366669	hsa-miR-1273	CLIP-seq
MIRT1366670	hsa-miR-140-3p	CLIP-seq
MIRT1366671	hsa-miR-151-5p	CLIP-seq
MIRT1366672	hsa-miR-151b	CLIP-seq
MIRT1366673	hsa-miR-3123	CLIP-seq
MIRT1366674	hsa-miR-3689d	CLIP-seq
MIRT1366675	hsa-miR-3919	CLIP-seq
MIRT1366676	hsa-miR-4488	CLIP-seq
MIRT1366677	hsa-miR-4494	CLIP-seq
MIRT1366678	hsa-miR-4499	CLIP-seq
MIRT1366679	hsa-miR-4505	CLIP-seq
MIRT1366680	hsa-miR-4649-5p	CLIP-seq
MIRT1366681	hsa-miR-4666-3p	CLIP-seq
MIRT1366682	hsa-miR-4697-5p	CLIP-seq
MIRT1366683	hsa-miR-4724-5p	CLIP-seq
MIRT1366684	hsa-miR-4731-5p	CLIP-seq
MIRT1366685	hsa-miR-485-5p	CLIP-seq
MIRT1366686	hsa-miR-520d-5p	CLIP-seq
MIRT1366687	hsa-miR-524-5p	CLIP-seq
MIRT1366688	hsa-miR-637	CLIP-seq
MIRT1366689	hsa-miR-1203	CLIP-seq
MIRT1366690	hsa-miR-1207-5p	CLIP-seq
MIRT1366691	hsa-miR-1254	CLIP-seq
MIRT1366692	hsa-miR-1268	CLIP-seq
MIRT1366693	hsa-miR-1268b	CLIP-seq
MIRT1366669	hsa-miR-1273	CLIP-seq
MIRT1366694	hsa-miR-1294	CLIP-seq
MIRT1366695	hsa-miR-137	CLIP-seq
MIRT1366670	hsa-miR-140-3p	CLIP-seq
MIRT1366696	hsa-miR-141	CLIP-seq
MIRT1366671	hsa-miR-151-5p	CLIP-seq
MIRT1366672	hsa-miR-151b	CLIP-seq
MIRT1366697	hsa-miR-1909	CLIP-seq
MIRT1366698	hsa-miR-1915	CLIP-seq
MIRT1366699	hsa-miR-200a	CLIP-seq
MIRT1366700	hsa-miR-221	CLIP-seq
MIRT1366701	hsa-miR-222	CLIP-seq
MIRT1366702	hsa-miR-2355-5p	CLIP-seq
MIRT1366703	hsa-miR-2467-3p	CLIP-seq
MIRT1366704	hsa-miR-30a	CLIP-seq
MIRT1366705	hsa-miR-30b	CLIP-seq
MIRT1366706	hsa-miR-30c	CLIP-seq
MIRT1366707	hsa-miR-30d	CLIP-seq
MIRT1366708	hsa-miR-30e	CLIP-seq
MIRT1366709	hsa-miR-3116	CLIP-seq
MIRT1366673	hsa-miR-3123	CLIP-seq
MIRT1366710	hsa-miR-3127-3p	CLIP-seq
MIRT1366711	hsa-miR-3144-5p	CLIP-seq
MIRT1366712	hsa-miR-3159	CLIP-seq
MIRT1366713	hsa-miR-3191	CLIP-seq
MIRT1366674	hsa-miR-3689d	CLIP-seq
MIRT1366675	hsa-miR-3919	CLIP-seq
MIRT1366676	hsa-miR-4488	CLIP-seq
MIRT1366714	hsa-miR-4495	CLIP-seq
MIRT1366679	hsa-miR-4505	CLIP-seq
MIRT1366715	hsa-miR-4514	CLIP-seq
MIRT1366716	hsa-miR-455-5p	CLIP-seq
MIRT1366717	hsa-miR-4642	CLIP-seq
MIRT1366680	hsa-miR-4649-5p	CLIP-seq
MIRT1366718	hsa-miR-4652-5p	CLIP-seq
MIRT1366681	hsa-miR-4666-3p	CLIP-seq
MIRT1366719	hsa-miR-4667-5p	CLIP-seq
MIRT1366720	hsa-miR-4690-3p	CLIP-seq
MIRT1366721	hsa-miR-4692	CLIP-seq
MIRT1366682	hsa-miR-4697-5p	CLIP-seq
MIRT1366722	hsa-miR-4700-5p	CLIP-seq
MIRT1366684	hsa-miR-4731-5p	CLIP-seq
MIRT1366723	hsa-miR-4736	CLIP-seq
MIRT1366724	hsa-miR-4763-3p	CLIP-seq
MIRT1366725	hsa-miR-4797-5p	CLIP-seq
MIRT1366685	hsa-miR-485-5p	CLIP-seq
MIRT1366726	hsa-miR-486-3p	CLIP-seq
MIRT1366727	hsa-miR-548v	CLIP-seq
MIRT1366728	hsa-miR-550a	CLIP-seq
MIRT1366688	hsa-miR-637	CLIP-seq
MIRT1366729	hsa-miR-661	CLIP-seq
MIRT1366730	hsa-miR-877	CLIP-seq
MIRT1366690	hsa-miR-1207-5p	CLIP-seq
MIRT1366697	hsa-miR-1909	CLIP-seq
MIRT1366715	hsa-miR-4514	CLIP-seq
MIRT1366721	hsa-miR-4692	CLIP-seq
MIRT1366723	hsa-miR-4736	CLIP-seq
MIRT1366724	hsa-miR-4763-3p	CLIP-seq
MIRT1366726	hsa-miR-486-3p	CLIP-seq
MIRT1366711	hsa-miR-3144-5p	CLIP-seq
MIRT1366713	hsa-miR-3191	CLIP-seq
MIRT1366718	hsa-miR-4652-5p	CLIP-seq
MIRT2332405	hsa-miR-7	CLIP-seq
MIRT1366679	hsa-miR-4505	CLIP-seq
MIRT1366684	hsa-miR-4731-5p	CLIP-seq

Show/Hide all (50)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001504	Process	Neurotransmitter uptake	IEA
GO:0005283	Function	Amino acid:sodium symporter activity	IBA
GO:0005283	Function	Amino acid:sodium symporter activity	IEA
GO:0005768	Component	Endosome	IEA
GO:0005768	Component	Endosome	ISS
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	ISS
GO:0005886	Component	Plasma membrane	TAS	8183239
GO:0006836	Process	Neurotransmitter transport	IEA
GO:0006865	Process	Amino acid transport	IEA
GO:0009925	Component	Basal plasma membrane	IDA	11159884
GO:0014069	Component	Postsynaptic density	IEA
GO:0015187	Function	Glycine transmembrane transporter activity	IEA
GO:0015187	Function	Glycine transmembrane transporter activity	ISS
GO:0015187	Function	Glycine transmembrane transporter activity	TAS	11159884
GO:0015293	Function	Symporter activity	IEA
GO:0015375	Function	Glycine:sodium symporter activity	IDA	8183239
GO:0015375	Function	Glycine:sodium symporter activity	IEA
GO:0015375	Function	Glycine:sodium symporter activity	TAS	8183239
GO:0015816	Process	Glycine transport	IEA
GO:0015816	Process	Glycine transport	IEA
GO:0015816	Process	Glycine transport	ISS
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	TAS	8183239
GO:0016323	Component	Basolateral plasma membrane	IDA	11159884
GO:0016324	Component	Apical plasma membrane	IDA	11159884
GO:0016328	Component	Lateral plasma membrane	IDA	11159884
GO:0022857	Function	Transmembrane transporter activity	IEA
GO:0030672	Component	Synaptic vesicle membrane	IEA
GO:0031045	Component	Dense core granule	IEA
GO:0031045	Component	Dense core granule	ISS
GO:0032279	Component	Asymmetric synapse	IEA
GO:0035725	Process	Sodium ion transmembrane transport	IBA
GO:0042734	Component	Presynaptic membrane	IEA
GO:0045211	Component	Postsynaptic membrane	IEA
GO:0046985	Process	Positive regulation of hemoglobin biosynthetic process	IEA
GO:0046985	Process	Positive regulation of hemoglobin biosynthetic process	ISS
GO:0060092	Process	Regulation of synaptic transmission, glycinergic	IEA
GO:0060092	Process	Regulation of synaptic transmission, glycinergic	ISS
GO:0061537	Process	Glycine secretion, neurotransmission	IEA
GO:0070455	Process	Positive regulation of heme biosynthetic process	IEA
GO:0070455	Process	Positive regulation of heme biosynthetic process	ISS
GO:0098686	Component	Hippocampal mossy fiber to CA3 synapse	IEA
GO:0098688	Component	Parallel fiber to Purkinje cell synapse	IEA
GO:0150104	Process	Transport across blood-brain barrier	NAS	26590417, 30280653
GO:1903804	Process	Glycine import across plasma membrane	IBA
GO:1903804	Process	Glycine import across plasma membrane	IEA
GO:1903804	Process	Glycine import across plasma membrane	ISS
GO:1903804	Process	Glycine import across plasma membrane	TAS	11159884

MIM	HGNC	e!Ensembl
601019	11056	ENSG00000196517

P48067

Protein name

Sodium- and chloride-dependent glycine transporter 1 (GlyT-1) (GlyT1) (Solute carrier family 6 member 9)

Protein function

Sodium- and chloride-dependent glycine transporter (PubMed:8183239). Essential for regulating glycine concentrations at inhibitory glycinergic synapses. ; [Isoform GlyT-1B]: So

PDB

6ZBV , 6ZPL , 8WFI , 8WFJ , 8WFK , 8WFL , 9J8B , 9J8C , 9J8D

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00209	SNF	100 → 635	Sodium:neurotransmitter symporter family	Family

Tissue specificity

TISSUE SPECIFICITY: [Isoform GlyT-1A]: Expressed in the brain, kidney, pancreas, lung, placenta and liver. {ECO:0000269|PubMed:8183239}.; TISSUE SPECIFICITY: [Isoform GlyT-1B]: Expressed in the brain, kidney, pancreas, lung, placenta and liver. {ECO:00002

Sequence

MSGGDTRAAIARPRMAAAHGPVAPSSPEQVTLLPVQRSFFLPPFSGATPSTSLAESVLKV
WHGAYNSGLLPQLMAQHSLAMAQNGAVPSEATKRDQNLKRGNWGNQIEFVLTSVGYAVGL
GNVWRFPYLCYRNGGGAFMFPYFIMLIFCGIPLFFMELSFGQFASQGCLGVWRISPMFKG
VGYGMMVVSTYIGIYYNVVICIAFYYFFSSMTHVLPWAYCNNPWNTHDCAGVLDASNLTN
GSRPAALPSNLSHLLNHSLQRTSPSEEYWRLYVLKLSDDIGNFGEVRLPLLGCLGVSWLV
VFLCLIRGVKSSGKVVYFTATFPYVVLTILFVRGVTLEGAFDGIMYYLTPQWDKILEAKV
WGDAASQIFYSLGCAWGGLITMASYNKFHNNCYRDSVIISITNCATSVYAGFVIFSILGF
MANHLGVDVSRVADHGPGLAFVAYPEALTLLPISPLWSLLFFFMLILLGLGTQFCLLETL
VTAIVDEVGNEWILQKKTYVTLGVAVAGFLLGIPLTSQAGIYWLLLMDNYAASFSLVVIS
CIMCVAIMYIYGHRNYFQDIQMMLGFPPPLFFQICWRFVSPAIIFFILVFTVIQYQPITY
NHYQYPGWAVAIGFLMALSSVLCIPLYAMFRLCRTDGDTLLQRLKNATKPSRDWGPALLE
HRTGRYAPTIAPSPEDGFEVQPLHPDKAQIPIVGSNGSSRLQDSRI

Sequence length

706

Interactions

View interactions

	KEGG		Reactome
	Synaptic vesicle cycle		Na+/Cl- dependent neurotransmitter transporters

261

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Atypical glycine encephalopathy	Likely pathogenic; Pathogenic	rs2154305890, rs2154306852, rs746910535, rs2086575319, rs1057519313, rs1057519314, rs1057519315, rs201437896	RCV001638193 RCV002005098 RCV003317692 RCV003331707 RCV000415674 RCV000415706 RCV000415630 RCV000688466

Show/Hide Unknown Diseases (15)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Acute myeloid leukemia	Benign	rs80095976	RCV005917268
Cervical cancer	Benign	rs61733181	RCV005898445
Clear cell carcinoma of kidney	Benign	rs61733181	RCV005898446
Colon adenocarcinoma	Benign	rs61733181	RCV005898442
Familial cancer of breast	Likely benign	rs137855830	RCV005921387
Familial pancreatic carcinoma	Benign	rs61733181	RCV005898447
Lung cancer	Benign	rs80095976	RCV005917271
Malignant tumor of esophagus	Benign; Likely benign; Uncertain significance	rs80095976, rs137855830, rs537261471, rs61733181	RCV005917269 RCV005921388 RCV005930397 RCV005898443
Nonpapillary renal cell carcinoma	Likely benign; Benign	rs768886219, rs61733181	RCV005939208 RCV005898444
Ovarian serous cystadenocarcinoma	Benign	rs80095976, rs61733181	RCV005917270 RCV005898449
Prostate cancer	Uncertain significance	rs193921002	RCV000149393
Sarcoma	Benign	rs61733181	RCV005898448
SCOLIOSIS, ISOLATED, SUSCEPTIBILITY TO, 6	Likely benign	rs192630770	RCV006257246
SLC6A9-related disorder	Likely benign; Benign; Uncertain significance	rs200011312, rs2248829, rs376444778, rs149979593, rs560460657, rs779879426, rs149578481, rs144161106, rs145104753, rs201127652, rs139332952, rs202054416	RCV003953716 RCV003980606 RCV003903552 RCV003911319 RCV003408633 RCV003410571 RCV003894165 RCV003911911 RCV003981261 RCV003968983 RCV003936016 RCV003923143
Uterine corpus endometrial carcinoma	Benign	rs80095976	RCV005917272

Show/Hide Text Mining Associations (6)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Essential Hypertension	Associate	19556729
Malaria	Associate	32801995
Malaria Cerebral	Associate	32801995
Schizophrenia	Associate	18638388
Urinary Bladder Overactive	Associate	19556729
Warts	Associate	31569353

SLC6A9 (solute carrier family 6 member 9)