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)

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (3)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Exaggerated startle response	Pathogenic	rs1590169700, rs767695215	RCV000852297 RCV000852298	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
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 View all (37 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
SLC6A5-related disorder	Likely pathogenic; Pathogenic	rs1590174665, rs772652517	RCV003416840 RCV004754517	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (16)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Acute myeloid leukemia	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
APNEA	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BRAIN DISEASES	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEREDITARY HYPEREKPLEXIA	—	GWAS catalog, Orphanet GWAS catalog, Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEREDITARY HYPEREXPLEXIA	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hyperekplexia	Benign; Likely benign; Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPEREXPLEXIA HEREDITARY	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OBESITY	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PSORIASIS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 1 DIABETES MELLITUS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (42)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Apnea	Apnea	Pubtator	31604777	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Brain Neoplasms	Brain Neoplasms	BEFREE	21979892		★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	21857017		★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma	Carcinoma	BEFREE	12115476		★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Squamous Cell	Squamous cell carcinoma	Pubtator	27738327	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cervical Intraepithelial Neoplasia	Cervical Intraepithelial Neoplasia	BEFREE	12115476		★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital exomphalos	Congenital Exomphalos	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Dentinogenesis Imperfecta	Dentinogenesis Imperfecta	BEFREE	19029076		★★★★★ ★☆☆☆☆ Found in Text Mining only
Dyssomnias	Dyssomnia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Encephalopathies	Epileptic encephalopathy	CTD_human_DG	25480793		★★★★★ ★☆☆☆☆ Found in Text Mining only
Esophagitis	Esophagitis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Gastric Adenocarcinoma	Gastric Cancer	BEFREE	16552434		★★★★★ ★☆☆☆☆ Found in Text Mining only
Gastroesophageal reflux disease	Gastroesophageal Reflux Disease	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	BEFREE	24030948		★★★★★ ★☆☆☆☆ Found in Text Mining only
Hereditary hyperekplexia	Hereditary Hyperekplexia	Orphanet			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hereditary Hyperexplexia	Hyperekplexia	CTD_human_DG	25480793		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hiatal Hernia	Hiatal Hernia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hyperekplexia	Hyperekplexia	Pubtator	20631190, 31604777	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPEREKPLEXIA 1	Hyperekplexia	GENOMICS_ENGLAND_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
HYPEREKPLEXIA 3	Hyperekplexia	UNIPROT_DG	16751771, 31370103		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
HYPEREKPLEXIA 3	Hyperekplexia	GENOMICS_ENGLAND_DG	16751771, 22753417		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
HYPEREKPLEXIA 3	Hyperekplexia	CLINVAR_DG	22700964		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Hyperexplexia hereditary	Hyperexplexia hereditary	Pubtator	33120686	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual Disability	Mental retardation	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	18214716, 22378020, 23636606, 27216880, 30301500, 30867719, 31544556		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	21857017		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	UNIPROT_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	26080853		★★★★★ ★☆☆☆☆ Found in Text Mining only
Metabolic Diseases	Metabolic syndrome	Pubtator	27907186	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Movement Disorders	Movement Disorders	BEFREE	27262149		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	16552434, 21979892, 30301500, 31544556, 31657628		★★★★★ ★☆☆☆☆ Found in Text Mining only
nervous system disorder	Nervous System Disorder	BEFREE	29446202, 31370103		★★★★★ ★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	26459749		★★★★★ ★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	Pubtator	27907186	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Osteoarthritis, Knee	Knee osteoarthritis	BEFREE	30881475		★★★★★ ★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	BEFREE	18638388, 22272310		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Schizophrenia	LHGDN	18638388		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Schizophrenia	PSYGENET_DG	18638388, 22272310		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Schizophrenia	Pubtator	18638388	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sleep Disorders	Sleep Disorders	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of skin	Skin carcinoma	BEFREE	24196235, 26080853		★★★★★ ★☆☆☆☆ Found in Text Mining only
Stiff-Person Syndrome	Stiff-Person Syndrome	BEFREE	27262149		★★★★★ ★☆☆☆☆ Found in Text Mining only

SLC6A5 (solute carrier family 6 member 5)