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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	2741
Gene name	Glycine receptor alpha 1
Gene symbol	GLRA1
Synonyms (NCBI Gene)	HKPX1STHE
Chromosome	5
Chromosome location	5q33.1
Summary	The protein encoded by this gene is a subunit of a pentameric inhibitory glycine receptor, which mediates postsynaptic inhibition in the central nervous system. Defects in this gene are a cause of startle disease (STHE), also known as hereditary hyperekpl

Show/Hide all (8)

SNP ID	Visualize variation	Clinical significance	Consequence
rs121918410	T>C,G	Pathogenic	Coding sequence variant, missense variant
rs121918418	G>T	Pathogenic	Stop gained, coding sequence variant
rs281864913	G>A	Pathogenic, likely-pathogenic	Coding sequence variant, stop gained
rs281864919	C>T	Pathogenic	Missense variant, coding sequence variant
rs281864921	A>-	Pathogenic	Coding sequence variant, stop gained
rs1064795797	G>T	Likely-pathogenic	Missense variant, coding sequence variant
rs1064797316	C>T	Likely-pathogenic	5 prime UTR variant, coding sequence variant, stop gained
rs1181626947	C>T	Likely-pathogenic	Missense variant, coding sequence variant

Show/Hide all (6)

miRTarBase ID	miRNA	Experiments
MIRT2002633	hsa-miR-25	CLIP-seq
MIRT2002634	hsa-miR-32	CLIP-seq
MIRT2002635	hsa-miR-363	CLIP-seq
MIRT2002636	hsa-miR-367	CLIP-seq
MIRT2002637	hsa-miR-92a	CLIP-seq
MIRT2002638	hsa-miR-92b	CLIP-seq

Show/Hide all (1)

Transcription factor	Regulation	Reference
REST	Activation	12944912

Show/Hide all (79)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001964	Process	Startle response	IEA
GO:0001964	Process	Startle response	IMP	8298642
GO:0001964	Process	Startle response	IMP	8298642, 11973623
GO:0002087	Process	Regulation of respiratory gaseous exchange by nervous system process	IEA
GO:0004888	Function	Transmembrane signaling receptor activity	IEA
GO:0005216	Function	Monoatomic ion channel activity	IEA
GO:0005230	Function	Extracellular ligand-gated monoatomic ion channel activity	IEA
GO:0005231	Function	Excitatory extracellular ligand-gated monoatomic ion channel activity	IBA
GO:0005254	Function	Chloride channel activity	IBA
GO:0005254	Function	Chloride channel activity	IEA
GO:0005515	Function	Protein binding	IPI	11929858, 32296183, 35526563
GO:0005886	Component	Plasma membrane	IDA	2155780, 7506679, 16144831
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	IMP	11973623
GO:0005886	Component	Plasma membrane	TAS
GO:0006811	Process	Monoatomic ion transport	IDA	2155780
GO:0006811	Process	Monoatomic ion transport	IEA
GO:0006821	Process	Chloride transport	IDA	8137830
GO:0006821	Process	Chloride transport	IEA
GO:0006936	Process	Muscle contraction	IMP	11973623
GO:0007218	Process	Neuropeptide signaling pathway	IDA	2155780
GO:0007268	Process	Chemical synaptic transmission	IEA
GO:0007340	Process	Acrosome reaction	IEA
GO:0007601	Process	Visual perception	IEA
GO:0007628	Process	Adult walking behavior	IEA
GO:0008270	Function	Zinc ion binding	IMP	16144831
GO:0009897	Component	External side of plasma membrane	IEA
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	NAS	15952785
GO:0016594	Function	Glycine binding	IDA	2155780, 7920629, 8717357, 15748848
GO:0016594	Function	Glycine binding	IEA
GO:0016934	Function	Extracellularly glycine-gated chloride channel activity	IDA	2155780, 8137830, 16144831
GO:0016934	Function	Extracellularly glycine-gated chloride channel activity	IEA
GO:0016934	Function	Extracellularly glycine-gated chloride channel activity	IMP	7920629
GO:0019228	Process	Neuronal action potential	IEA
GO:0022824	Function	Transmitter-gated monoatomic ion channel activity	IEA
GO:0030425	Component	Dendrite	IEA
GO:0030977	Function	Taurine binding	IDA	15748848
GO:0034220	Process	Monoatomic ion transmembrane transport	IEA
GO:0034707	Component	Chloride channel complex	IEA
GO:0042391	Process	Regulation of membrane potential	IEA
GO:0042391	Process	Regulation of membrane potential	IMP	7920629
GO:0042802	Function	Identical protein binding	IPI	23994010
GO:0042995	Component	Cell projection	IEA
GO:0043005	Component	Neuron projection	IEA
GO:0043005	Component	Neuron projection	ISS
GO:0043025	Component	Neuronal cell body	IEA
GO:0043025	Component	Neuronal cell body	ISS
GO:0043204	Component	Perikaryon	IEA
GO:0043231	Component	Intracellular membrane-bounded organelle	IDA	7506679
GO:0043576	Process	Regulation of respiratory gaseous exchange	IEA
GO:0045202	Component	Synapse	IEA
GO:0045202	Component	Synapse	ISS
GO:0045211	Component	Postsynaptic membrane	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0050884	Process	Neuromuscular process controlling posture	IEA
GO:0050905	Process	Neuromuscular process	IEA
GO:0051970	Process	Negative regulation of transmission of nerve impulse	IMP	11973623
GO:0060012	Process	Synaptic transmission, glycinergic	IEA
GO:0060012	Process	Synaptic transmission, glycinergic	ISS
GO:0060013	Process	Righting reflex	IEA
GO:0060077	Component	Inhibitory synapse	IEA
GO:0060079	Process	Excitatory postsynaptic potential	IEA
GO:0060080	Process	Inhibitory postsynaptic potential	IEA
GO:0060080	Process	Inhibitory postsynaptic potential	ISS
GO:0071230	Process	Cellular response to amino acid stimulus	IDA	16144831
GO:0071294	Process	Cellular response to zinc ion	IDA	16144831
GO:0071361	Process	Cellular response to ethanol	IDA	25973519
GO:0097305	Process	Response to alcohol	IEA
GO:0097305	Process	Response to alcohol	ISS
GO:0098690	Component	Glycinergic synapse	IEA
GO:0099505	Process	Regulation of presynaptic membrane potential	IEA
GO:0099507	Function	Ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential	IDA	8137830
GO:0099507	Function	Ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential	IMP	8137830
GO:0099507	Function	Ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential	NAS	8137830
GO:1902476	Process	Chloride transmembrane transport	IBA
GO:1902476	Process	Chloride transmembrane transport	IDA	16144831
GO:1904315	Function	Transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential	IEA
GO:2000344	Process	Positive regulation of acrosome reaction	IMP	11751269

MIM	HGNC	e!Ensembl
138491	4326	ENSG00000145888

P23415

Protein name

Glycine receptor subunit alpha-1 (Glycine receptor 48 kDa subunit) (Glycine receptor strychnine-binding subunit)

Protein function

Subunit of heteromeric glycine-gated chloride channels (PubMed:14551753, PubMed:23994010, PubMed:25730860, PubMed:37821459). Plays an important role in the down-regulation of neuronal excitability (PubMed:8298642, PubMed:9009272). Contributes to

PDB

1MOT , 1VRY , 2M6B , 2M6I , 4X5T , 8DN2 , 8DN3 , 8DN4 , 8DN5

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF02931	Neur_chan_LBD	38 → 248	Neurotransmitter-gated ion-channel ligand binding domain	Family
PF02932	Neur_chan_memb	255 → 405	Neurotransmitter-gated ion-channel transmembrane region	Family

Sequence

MYSFNTLRLYLWETIVFFSLAASKEAEAARSAPKPMSPSDFLDKLMGRTSGYDARIRPNF
KGPPVNVSCNIFINSFGSIAETTMDYRVNIFLRQQWNDPRLAYNEYPDDSLDLDPSMLDS
IWKPDLFFANEKGAHFHEITTDNKLLRISRNGNVLYSIRITLTLACPMDLKNFPMDVQTC
IMQLESFGYTMNDLIFEWQEQGAVQVADGLTLPQFILKEEKDLRYCTKHYNTGKFTCIEA
RFHLERQMGYYLIQMYIPSLLIVILSWISFWINMDAAPARVGLGITTVLTMTTQSSGSRA
SLPKVSYVKAIDIWMAVCLLFVFSALLEYAAVNFVSRQHKELLRFRRKRRHHKSPMLNLF
QEDEAGEGRFNFSAYGMGPACLQAKDGISVKGANNSNTTNPPPAPSKSPEEMRKLFIQRA
KKIDKISRIGFPMAFLIFNMFYWIIYKIVRREDVHNQ

Sequence length

457

Interactions

View interactions

	KEGG		Reactome
	Neuroactive ligand-receptor interaction		Neurotransmitter receptors and postsynaptic signal transmission

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
GLRA1-related disorder	Likely pathogenic	rs281864914	RCV004730861	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Hereditary hyperekplexia	Pathogenic; Likely pathogenic	rs765708068, rs751659671, rs758811460, rs2113359152, rs757488419, rs1753918029, rs750107200, rs1165958512, rs2480063069, rs2479981350, rs1581623910, rs182383995, rs2479991693, rs2479991264, rs199547699 View all (24 more)	RCV001383034 RCV002034594 RCV001987384 RCV001900431 RCV001949676 View all (35 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Hyperekplexia 1	Pathogenic; Likely pathogenic	rs2113349880, rs751659671, rs199547699, rs2480063154, rs2479903658, rs121918408, rs121918409, rs121918410, rs121918411, rs121918412, rs121918413, rs281864915, rs121918415, rs121918417, rs121918418 View all (17 more)	RCV001783385 RCV001782203 RCV000490459 RCV003145868 RCV003226089 View all (29 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (15)

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.
CENTRAL NERVOUS SYSTEM CANCER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DYSTONIA DISORDERS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DYSTONIC DISORDERS	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLIOBLASTOMA MULTIFORME	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLIOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEREDITARY HYPEREXPLEXIA	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hyperekplexia	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPEREXPLEXIA HEREDITARY	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCOLIOSIS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Seizure	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (52)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
5q-syndrome	5q-syndrome	BEFREE	12036901, 18508791		★★★★★ ★☆☆☆☆ Found in Text Mining only
Adult-Onset Dystonias	Dystonia	CTD_human_DG	17114051		★★★★★ ★☆☆☆☆ Found in Text Mining only
Adult-Onset Idiopathic Focal Dystonias	Dystonia	CTD_human_DG	17114051		★★★★★ ★☆☆☆☆ Found in Text Mining only
Adult-Onset Idiopathic Torsion Dystonias	Dystonia	CTD_human_DG	17114051		★★★★★ ★☆☆☆☆ Found in Text Mining only
Autosomal Dominant Familial Dystonia	Dystonia	CTD_human_DG	17114051		★★★★★ ★☆☆☆☆ Found in Text Mining only
Autosomal Recessive Familial Dystonia	Dystonia	CTD_human_DG	17114051		★★★★★ ★☆☆☆☆ Found in Text Mining only
Childhood Onset Dystonias	Dystonia	CTD_human_DG	17114051		★★★★★ ★☆☆☆☆ Found in Text Mining only
Chromosome 5q Deletion Syndrome	Chromosome 5q deletion syndrome	Pubtator	18508791	Inhibit	★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital exomphalos	Congenital Exomphalos	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Dyssomnias	Dyssomnia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Dystonia Disorders	Dystonia	CTD_human_DG	17114051		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Dystonia, Primary	Dystonia	CTD_human_DG	17114051		★★★★★ ★☆☆☆☆ Found in Text Mining only
Dystonia, Secondary	Dystonia	CTD_human_DG	17114051		★★★★★ ★☆☆☆☆ Found in Text Mining only
Dystonias, Sporadic	Dystonia	CTD_human_DG	17114051		★★★★★ ★☆☆☆☆ Found in Text Mining only
Epilepsy	Epilepsy	BEFREE	28554717		★★★★★ ★☆☆☆☆ Found in Text Mining only
Esophagitis	Esophagitis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Familial Dystonia	Dystonia	CTD_human_DG	17114051		★★★★★ ★☆☆☆☆ Found in Text Mining only
Focal Dystonia	Focal dystonia	CTD_human_DG	17114051		★★★★★ ★☆☆☆☆ Found in Text Mining only
Gastroesophageal reflux disease	Gastroesophageal Reflux Disease	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	GENOMICS_ENGLAND_DG	1352015, 27843043		★★★★★ ★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	BEFREE	24030948		★★★★★ ★☆☆☆☆ Found in Text Mining only
Head and Neck Neoplasms	Head and neck neoplasm	Pubtator	8651283	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hereditary Hyperekplexia	Hereditary Hyperekplexia	BEFREE	14673895, 15771552, 28985719, 31392847, 7925268, 8651283		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Hereditary hyperekplexia	Hereditary Hyperekplexia	Orphanet			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Hereditary Hyperexplexia	Hyperekplexia	BEFREE	14673895, 15771552, 28985719, 31392847, 7925268, 8298642, 8651283		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hereditary Hyperexplexia	Hyperekplexia	CTD_human_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hiatal Hernia	Hiatal Hernia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hyperekplexia	Hyperekplexia	Pubtator	11395484, 15066993, 20631190, 21835920, 24108130, 24969041, 25036534, 25356525, 27028707, 28985719, 29602144, 30866851, 31757808, 32332682, 32844405, 33842008, 8651283, 8733061, 9920650 View all (4 more)	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hyperekplexia	Hyperekplexia	Pubtator	1334371	Stimulate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPEREKPLEXIA 1	Hyperekplexia	CLINVAR_DG	10514101, 11389164, 12169101, 15771552, 16236274, 19732286, 20631190, 24108130, 25036534, 28122427, 28138086, 7518444, 7611730, 7881416, 8298642, 8733061 View all (1 more)		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
HYPEREKPLEXIA 1	Hyperekplexia	UNIPROT_DG	10514101, 24108130, 25730860, 7611730, 7881416, 7925268, 7981700, 8298642, 8571969, 8733061, 9009272, 9067762, 9920650		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
HYPEREKPLEXIA 1	Hyperekplexia	GENOMICS_ENGLAND_DG	1352015		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
HYPEREKPLEXIA 2	Hyperekplexia	BEFREE	10514101		★★★★★ ★☆☆☆☆ Found in Text Mining only
Hyperexplexia hereditary	Hyperexplexia hereditary	Pubtator	21835920, 23238346, 27028707, 30866851, 7775436, 9009272, 9920650	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Idiopathic familial dystonia	Dystonia	CTD_human_DG	17114051		★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Mild Mental Retardation	Mental retardation	BEFREE	22264702		★★★★★ ★☆☆☆☆ Found in Text Mining only
Mild Mental Retardation	Mental retardation	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Myelodysplastic Syndrome with Isolated del(5q)	Myelodysplastic syndrome	BEFREE	12036901, 18508791		★★★★★ ★☆☆☆☆ Found in Text Mining only
Myoclonic Epilepsy	Myoclonic Epilepsy	BEFREE	30078784		★★★★★ ★☆☆☆☆ Found in Text Mining only
nervous system disorder	Nervous System Disorder	BEFREE	11973623, 12359314, 16751771, 7925268, 9920650		★★★★★ ★☆☆☆☆ Found in Text Mining only
Nocturnal epilepsy	Nocturnal Epilepsy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	12944912		★★★★★ ★☆☆☆☆ Found in Text Mining only
Paraparesis Spastic	Paraparesis	Pubtator	8733061	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Pseudodystonia	Pycnodysostosis	CTD_human_DG	17114051		★★★★★ ★☆☆☆☆ Found in Text Mining only
Seizures	Seizures	Pubtator	27028707	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Sleep Disorders	Sleep Disorders	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Small cell carcinoma of lung	Lung carcinoma	BEFREE	12944912		★★★★★ ★☆☆☆☆ Found in Text Mining only
Stiff-Person Syndrome	Stiff-Person Syndrome	BEFREE	23090334		★★★★★ ★☆☆☆☆ Found in Text Mining only
Tremor	Tremor	Pubtator	27028707	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Tremor	Tremor	Pubtator	27028707	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Writer`s Cramp	Writer`s Cramp	CTD_human_DG	17114051		★★★★★ ★☆☆☆☆ Found in Text Mining only

GLRA1 (glycine receptor alpha 1)