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	9152
Gene name	Solute carrier family 6 member 5
Gene symbol	SLC6A5
Synonyms (NCBI Gene)	GLYT-2GLYT2HKPX3NET1
Chromosome	11
Chromosome location	11p15.1
Summary	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

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)

779

Show/Hide Causal Diseases (3)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Exaggerated startle response	Pathogenic	rs1590169700, rs767695215	RCV000852297 RCV000852298
Hyperekplexia 3	Pathogenic; Likely pathogenic	rs142573911, rs2133788446, rs2133775660, rs1203538648, rs2133774690, rs2133798401, rs1468013577, rs2133809394, rs186704689, rs755040627, rs931802079, rs2133808393, rs745539706, rs2494105581, rs1251099671 View all (25 more)	RCV001784989 RCV001378436 RCV003221344 RCV001898465 RCV001964103 RCV001875217 RCV001950916 RCV001941869 RCV001958731 RCV001863615 RCV001962839 RCV001957023 RCV003071720 RCV002760611 RCV002806522 RCV002846594 RCV002846749 RCV000006117 RCV000006118 RCV000006120 RCV000006121 RCV000006122 RCV002957235 RCV002982705 RCV003007800 RCV002976089 RCV003646670 RCV003646690 RCV003646729 RCV003852929 RCV003990105 RCV003990723 RCV000024247 RCV001857938 RCV000031924 RCV000031925 RCV000650379 RCV000702191 RCV003768301 RCV000779055 RCV000814781 RCV000807685
SLC6A5-related disorder	Likely pathogenic; Pathogenic	rs1590174665, rs772652517	RCV003416840 RCV004754517

Show/Hide Unknown Diseases (6)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Acute myeloid leukemia	Benign	rs2276430	RCV005915741
Hyperekplexia	Benign; Likely benign; Conflicting classifications of pathogenicity; Uncertain significance	rs7952227, rs555196341, rs58405430, rs755131121, rs61736602, rs7109418, rs61736605, rs61736604, rs2241941, rs1443548, rs34505618, rs1443551, rs3740870, rs1805091, rs2276433 View all (49 more)	RCV000310980 RCV000356399 RCV000261613 RCV000312706 RCV000300040 RCV000404538 RCV000305417 RCV000360174 RCV000265297 RCV000365666 RCV000332516 RCV000338104 RCV000358141 RCV000393595 RCV000371455 RCV000342278 RCV000401148 RCV000308486 RCV000344607 RCV000301135 RCV000274638 RCV000376976 RCV000291892 RCV000392439 RCV000354866 RCV000320363 RCV000386966 RCV000343092 RCV000303323 RCV000333953 RCV000374997 RCV000347972 RCV000368517 RCV000316725 RCV000380671 RCV000352386 RCV000271019 RCV000381210 RCV000296115 RCV000292425 RCV000399414 RCV000279669 RCV000309298 RCV000370006 RCV000287316 RCV000267462 RCV000322512 RCV000382839 RCV000288143 RCV000349052 RCV000390888 RCV000326120 RCV000393572 RCV000364083 RCV000274703 RCV000329763 RCV000280512 RCV000407323 RCV000407325 RCV000313953 RCV000274017 RCV000355906 RCV000393772 RCV000309980
Lung cancer	Benign	rs2276430	RCV005915743
Malignant lymphoma, large B-cell, diffuse	Benign	rs3819252, rs72932998	RCV005916736 RCV005892958
Malignant tumor of esophagus	Benign	rs2276430	RCV005915742
Uterine carcinosarcoma	Benign	rs72932998	RCV005892959

Show/Hide Text Mining Associations (12)

Disease Name	Relationship Type	References
Associations from Text MiningDisease 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)