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.	9152
Gene name Gene Name - the full gene name approved by the HGNC.	Solute carrier family 6 member 5
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	SLC6A5
Synonyms (NCBI Gene) Gene synonyms aliases	GLYT-2, GLYT2, HKPX3, NET1
Chromosome Chromosome number	11
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	11p15.1
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes a sodium- and chloride-dependent glycine neurotransmitter transporter. This integral membrane glycoprotein is responsible for the clearance of extracellular glycine during glycine-mediated neurotransmission. This protein is found in glyc

Show/Hide all(21)

SNP ID	Visualize variation	Clinical significance	Consequence
rs121908493	C>A	Pathogenic	Coding sequence variant, stop gained
rs121908494	A>G	Pathogenic	Coding sequence variant, missense variant
rs121908495	C>T	Pathogenic	Coding sequence variant, stop gained
rs121908496	C>G	Pathogenic	Coding sequence variant, intron variant, missense variant
rs121908497	A>G	Pathogenic	Coding sequence variant, missense variant
rs121908498	C>A,T	Pathogenic	Coding sequence variant, missense variant
rs281864923	C>-	Pathogenic	Intron variant, frameshift variant, 5 prime UTR variant, coding sequence variant, genic upstream transcript variant
rs281864924	G>TT	Pathogenic	Coding sequence variant, frameshift variant
rs281864925	T>C	Pathogenic	Coding sequence variant, missense variant
rs281864926	T>G	Pathogenic	Coding sequence variant, missense variant
rs376783257	C>G,T	Pathogenic	Missense variant, stop gained, genic upstream transcript variant, coding sequence variant, intron variant
rs752254977	C>A,T	Likely-pathogenic	Coding sequence variant, intron variant, 5 prime UTR variant, synonymous variant, stop gained, genic upstream transcript variant
rs767695215	C>-	Pathogenic	Coding sequence variant, frameshift variant
rs772652517	T>C	Pathogenic-likely-pathogenic	Coding sequence variant, missense variant
rs778603956	C>T	Pathogenic	Stop gained, coding sequence variant, intron variant
rs1085307782	T>C	Likely-pathogenic	Missense variant, coding sequence variant
rs1131691477	T>A	Likely-pathogenic	Missense variant, coding sequence variant
rs1555039090	C>T	Likely-pathogenic	Coding sequence variant, intron variant, stop gained
rs1565271429	G>A	Likely-pathogenic	Coding sequence variant, missense variant, intron variant, genic upstream transcript variant
rs1590154255	G>A	Likely-pathogenic	Genic upstream transcript variant, splice donor variant, intron variant
rs1590169700	T>C	Pathogenic	Coding sequence variant, missense variant

Show/Hide all(54)

miRTarBase ID	miRNA	Experiments	Reference
MIRT699250	hsa-miR-4662a-3p	HITS-CLIP	21572407
MIRT686856	hsa-miR-5011-5p	HITS-CLIP	21572407
MIRT686855	hsa-miR-1272	HITS-CLIP	21572407
MIRT686854	hsa-miR-1322	HITS-CLIP	21572407
MIRT686853	hsa-miR-7112-3p	HITS-CLIP	21572407
MIRT686852	hsa-miR-4711-5p	HITS-CLIP	21572407
MIRT686850	hsa-miR-190a-3p	HITS-CLIP	21572407
MIRT686847	hsa-miR-1277-5p	HITS-CLIP	21572407
MIRT699250	hsa-miR-4662a-3p	HITS-CLIP	23313552
MIRT686856	hsa-miR-5011-5p	HITS-CLIP	23313552
MIRT686855	hsa-miR-1272	HITS-CLIP	23313552
MIRT686854	hsa-miR-1322	HITS-CLIP	23313552
MIRT686853	hsa-miR-7112-3p	HITS-CLIP	23313552
MIRT686852	hsa-miR-4711-5p	HITS-CLIP	23313552
MIRT686850	hsa-miR-190a-3p	HITS-CLIP	23313552
MIRT686847	hsa-miR-1277-5p	HITS-CLIP	23313552
MIRT686857	hsa-miR-4803	HITS-CLIP	23313552
MIRT686856	hsa-miR-5011-5p	HITS-CLIP	23313552
MIRT686855	hsa-miR-1272	HITS-CLIP	23313552
MIRT686854	hsa-miR-1322	HITS-CLIP	23313552
MIRT686853	hsa-miR-7112-3p	HITS-CLIP	23313552
MIRT686852	hsa-miR-4711-5p	HITS-CLIP	23313552
MIRT686851	hsa-miR-194-5p	HITS-CLIP	23313552
MIRT686850	hsa-miR-190a-3p	HITS-CLIP	23313552
MIRT686849	hsa-miR-579-3p	HITS-CLIP	23313552
MIRT686848	hsa-miR-664b-3p	HITS-CLIP	23313552
MIRT686847	hsa-miR-1277-5p	HITS-CLIP	23313552
MIRT699250	hsa-miR-4662a-3p	HITS-CLIP	21572407
MIRT686856	hsa-miR-5011-5p	HITS-CLIP	21572407
MIRT686855	hsa-miR-1272	HITS-CLIP	21572407
MIRT686854	hsa-miR-1322	HITS-CLIP	21572407
MIRT686853	hsa-miR-7112-3p	HITS-CLIP	21572407
MIRT686852	hsa-miR-4711-5p	HITS-CLIP	21572407
MIRT686850	hsa-miR-190a-3p	HITS-CLIP	21572407
MIRT686847	hsa-miR-1277-5p	HITS-CLIP	21572407
MIRT699250	hsa-miR-4662a-3p	HITS-CLIP	23313552
MIRT686856	hsa-miR-5011-5p	HITS-CLIP	23313552
MIRT686855	hsa-miR-1272	HITS-CLIP	23313552
MIRT686854	hsa-miR-1322	HITS-CLIP	23313552
MIRT686853	hsa-miR-7112-3p	HITS-CLIP	23313552
MIRT686852	hsa-miR-4711-5p	HITS-CLIP	23313552
MIRT686850	hsa-miR-190a-3p	HITS-CLIP	23313552
MIRT686847	hsa-miR-1277-5p	HITS-CLIP	23313552
MIRT686857	hsa-miR-4803	HITS-CLIP	23313552
MIRT686856	hsa-miR-5011-5p	HITS-CLIP	23313552
MIRT686855	hsa-miR-1272	HITS-CLIP	23313552
MIRT686854	hsa-miR-1322	HITS-CLIP	23313552
MIRT686853	hsa-miR-7112-3p	HITS-CLIP	23313552
MIRT686852	hsa-miR-4711-5p	HITS-CLIP	23313552
MIRT686851	hsa-miR-194-5p	HITS-CLIP	23313552
MIRT686850	hsa-miR-190a-3p	HITS-CLIP	23313552
MIRT686849	hsa-miR-579-3p	HITS-CLIP	23313552
MIRT686848	hsa-miR-664b-3p	HITS-CLIP	23313552
MIRT686847	hsa-miR-1277-5p	HITS-CLIP	23313552

Show/Hide all(24)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005768	Component	Endosome	ISS
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IDA	16751771
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	IMP	31370103
GO:0005886	Component	Plasma membrane	TAS
GO:0006836	Process	Neurotransmitter transport	IEA
GO:0007268	Process	Chemical synaptic transmission	TAS	9845349
GO:0015293	Function	Symporter activity	IEA
GO:0015375	Function	Glycine:sodium symporter activity	IBA
GO:0015375	Function	Glycine:sodium symporter activity	IDA	9845349, 10381548, 16751771
GO:0015375	Function	Glycine:sodium symporter activity	IMP	10606742, 31370103
GO:0015375	Function	Glycine:sodium symporter activity	TAS	9845349
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	TAS	9845349
GO:0022857	Function	Transmembrane transporter activity	IEA
GO:0031045	Component	Dense core granule	ISS
GO:0035725	Process	Sodium ion transmembrane transport	IBA
GO:0045202	Component	Synapse	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0060012	Process	Synaptic transmission, glycinergic	IBA
GO:0060012	Process	Synaptic transmission, glycinergic	IMP	16751771
GO:1903804	Process	Glycine import across plasma membrane	IBA
GO:1903804	Process	Glycine import across plasma membrane	IDA	16751771

MIM	HGNC	e!Ensembl
604159	11051	ENSG00000165970

Protein

UniProt ID

Q9Y345

Protein name

Sodium- and chloride-dependent glycine transporter 2 (GlyT-2) (GlyT2) (Solute carrier family 6 member 5)

Protein function

Sodium- and chloride-dependent glycine transporter (PubMed:10381548, PubMed:10606742, PubMed:16751771, PubMed:31370103, PubMed:9845349). Terminates the action of glycine by its high affinity sodium-dependent reuptake into presynaptic terminals (

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00209	SNF	191 → 740	Sodium:neurotransmitter symporter family	Family

Tissue specificity

TISSUE SPECIFICITY: Expressed in medulla, and to a lesser extent in spinal cord and cerebellum. {ECO:0000269|PubMed:9845349}.

Sequence

MDCSAPKEMNKLPANSPEAAAAQGHPDGPCAPRTSPEQELPAAAAPPPPRVPRSASTGAQ
TFQSADARACEAERPGVGSCKLSSPRAQAASAALRDLREAQGAQASPPPGSSGPGNALHC
KIPFLRGPEGDANVSVGKGTLERNNTPVVGWVNMSQSTVVLATDGITSVLPGSVATVATQ
EDEQGDENKARGNWSSKLDFILSMVGYAVGLGNVWRFPYLAFQNGGGAFLIPYLMMLALA
GLPIFFLEVSLGQFASQGPVSVWKAIPALQGCGIAMLIISVLIAIYYNVIICYTLFYLFA
SFVSVLPWGSCNNPWNTPECKDKTKLLLDSCVISDHPKIQIKNSTFCMTAYPNVTMVNFT
SQANKTFVSGSEEYFKYFVLKISAGIEYPGEIRWPLALCLFLAWVIVYASLAKGIKTSGK
VVYFTATFPYVVLVILLIRGVTLPGAGAGIWYFITPKWEKLTDATVWKDAATQIFFSLSA
AWGGLITLSSYNKFHNNCYRDTLIVTCTNSATSIFAGFVIFSVIGFMANERKVNIENVAD
QGPGIAFVVYPEALTRLPLSPFWAIIFFLMLLTLGLDTMFATIETIVTSISDEFPKYLRT
HKPVFTLGCCICFFIMGFPMITQGGIYMFQLVDTYAASYALVIIAIFELVGISYVYGLQR
FCEDIEMMIGFQPNIFWKVCWAFVTPTILTFILCFSFYQWEPMTYGSYRYPNWSMVLGWL
MLACSVIWIPIMFVIKMHLAPGRFIERLKLVCSPQPDWGPFLAQHRGERYKNMIDPLGTS
SLGLKLPVKDLELGTQC

Sequence length

797

Interactions

View interactions

	KEGG		Reactome
	Synaptic vesicle cycle		Na+/Cl- dependent neurotransmitter transporters Defective SLC6A5 causes hyperekplexia 3 (HKPX3)

Show/Hide Causal Diseases (1)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Hyperekplexia	hyperekplexia 3	rs281864926, rs281864925, rs281864923, rs752254977, rs772652517, rs376783257, rs121908493, rs767695215, rs281864924, rs770660705, rs121908495, rs778603956, rs121908496, rs1590154255, rs121908497	N/A

Show/Hide Unknown Diseases (2)

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.
Hereditary Hyperekplexia	hereditary hyperekplexia	N/A	N/A	GenCC
Psoriasis	Psoriasis	N/A	N/A	GWAS

Show/Hide Text Mining Associations (12)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Adenocarcinoma	Associate	27738327
Apnea	Associate	31604777
Carcinoma Squamous Cell	Associate	27738327
Hyperekplexia	Associate	20631190, 31604777
Hyperexplexia hereditary	Associate	33120686
Metabolic Diseases	Associate	27907186
Muscle Hypertonia	Associate	31604777
Nerve Degeneration	Associate	29767851
Neurologic Manifestations	Associate	33120686
Obesity	Associate	27907186
Pain	Associate	29767851
Schizophrenia	Associate	18638388

SLC6A5 (solute carrier family 6 member 5)