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	10243
Gene name	Gephyrin
Gene symbol	GPHN
Synonyms (NCBI Gene)	GEPHGPHGPHRYNHKPX1MOCODC
Chromosome	14
Chromosome location	14q23.3-q24.1
Summary	This gene encodes a neuronal assembly protein that anchors inhibitory neurotransmitter receptors to the postsynaptic cytoskeleton via high affinity binding to a receptor subunit domain and tubulin dimers. In nonneuronal tissues, the encoded protein is als

Show/Hide all (2)

SNP ID	Visualize variation	Clinical significance	Consequence
rs121908539	A>T	Pathogenic, uncertain-significance	Missense variant, coding sequence variant, 5 prime UTR variant
rs150226537	C>G	Likely-benign, conflicting-interpretations-of-pathogenicity	5 prime UTR variant, coding sequence variant, missense variant

Show/Hide all (58)

miRTarBase ID	miRNA	Experiments	Reference
MIRT052292	hsa-let-7b-5p	CLASH	23622248
MIRT1029288	hsa-miR-1271	CLIP-seq
MIRT1029289	hsa-miR-138	CLIP-seq
MIRT1029290	hsa-miR-141	CLIP-seq
MIRT1029291	hsa-miR-182	CLIP-seq
MIRT1029292	hsa-miR-200a	CLIP-seq
MIRT1029293	hsa-miR-3133	CLIP-seq
MIRT1029294	hsa-miR-3607-3p	CLIP-seq
MIRT1029295	hsa-miR-3671	CLIP-seq
MIRT1029296	hsa-miR-3686	CLIP-seq
MIRT1029297	hsa-miR-3692	CLIP-seq
MIRT1029298	hsa-miR-4328	CLIP-seq
MIRT1029299	hsa-miR-4422	CLIP-seq
MIRT1029300	hsa-miR-4490	CLIP-seq
MIRT1029301	hsa-miR-4659a-3p	CLIP-seq
MIRT1029302	hsa-miR-4659b-3p	CLIP-seq
MIRT1029303	hsa-miR-4778-3p	CLIP-seq
MIRT1029304	hsa-miR-539	CLIP-seq
MIRT1029305	hsa-miR-548p	CLIP-seq
MIRT1029306	hsa-miR-584	CLIP-seq
MIRT1029307	hsa-miR-607	CLIP-seq
MIRT1029308	hsa-miR-622	CLIP-seq
MIRT1029309	hsa-miR-889	CLIP-seq
MIRT1029310	hsa-miR-96	CLIP-seq
MIRT1029311	hsa-miR-3065-3p	CLIP-seq
MIRT1029312	hsa-miR-4477b	CLIP-seq
MIRT1029301	hsa-miR-4659a-3p	CLIP-seq
MIRT1029302	hsa-miR-4659b-3p	CLIP-seq
MIRT1549346	hsa-miR-1184	CLIP-seq
MIRT1549347	hsa-miR-1205	CLIP-seq
MIRT1549348	hsa-miR-1909	CLIP-seq
MIRT1549349	hsa-miR-3158-5p	CLIP-seq
MIRT1549350	hsa-miR-3194-3p	CLIP-seq
MIRT1549351	hsa-miR-4292	CLIP-seq
MIRT1549352	hsa-miR-4308	CLIP-seq
MIRT1549346	hsa-miR-1184	CLIP-seq
MIRT1549347	hsa-miR-1205	CLIP-seq
MIRT2005401	hsa-miR-145	CLIP-seq
MIRT2005402	hsa-miR-198	CLIP-seq
MIRT2005403	hsa-miR-3143	CLIP-seq
MIRT1549349	hsa-miR-3158-5p	CLIP-seq
MIRT1029295	hsa-miR-3671	CLIP-seq
MIRT1029297	hsa-miR-3692	CLIP-seq
MIRT1029301	hsa-miR-4659a-3p	CLIP-seq
MIRT1029302	hsa-miR-4659b-3p	CLIP-seq
MIRT2005404	hsa-miR-511	CLIP-seq
MIRT2005405	hsa-miR-543	CLIP-seq
MIRT1029307	hsa-miR-607	CLIP-seq
MIRT1029308	hsa-miR-622	CLIP-seq
MIRT2005406	hsa-miR-935	CLIP-seq
MIRT1549346	hsa-miR-1184	CLIP-seq
MIRT1549347	hsa-miR-1205	CLIP-seq
MIRT1549349	hsa-miR-3158-5p	CLIP-seq
MIRT2238012	hsa-miR-330-3p	CLIP-seq
MIRT2238013	hsa-miR-4269	CLIP-seq
MIRT2238014	hsa-miR-4731-3p	CLIP-seq
MIRT2238015	hsa-miR-4801	CLIP-seq
MIRT2238016	hsa-miR-544	CLIP-seq

Show/Hide all (68)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0003824	Function	Catalytic activity	IEA
GO:0005102	Function	Signaling receptor binding	IEA
GO:0005515	Function	Protein binding	IPI	21094642, 26613940, 27173435, 32296183, 33961781, 35271311
GO:0005524	Function	ATP binding	IEA
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IBA
GO:0005829	Component	Cytosol	IDA	22270318
GO:0005829	Component	Cytosol	IEA
GO:0005829	Component	Cytosol	ISS
GO:0005856	Component	Cytoskeleton	IEA
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS
GO:0006777	Process	Mo-molybdopterin cofactor biosynthetic process	IBA
GO:0006777	Process	Mo-molybdopterin cofactor biosynthetic process	IDA	26613940
GO:0006777	Process	Mo-molybdopterin cofactor biosynthetic process	IEA
GO:0006777	Process	Mo-molybdopterin cofactor biosynthetic process	IEA
GO:0006777	Process	Mo-molybdopterin cofactor biosynthetic process	IMP	9990024
GO:0007416	Process	Synapse assembly	IEA
GO:0007529	Process	Establishment of synaptic specificity at neuromuscular junction	IBA
GO:0008940	Function	Nitrate reductase activity	IMP	9990024
GO:0009898	Component	Cytoplasmic side of plasma membrane	IEA
GO:0010038	Process	Response to metal ion	IMP	9990024
GO:0014069	Component	Postsynaptic density	IEA
GO:0014069	Component	Postsynaptic density	ISS
GO:0016020	Component	Membrane	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0030425	Component	Dendrite	IBA
GO:0030425	Component	Dendrite	IDA	26613940
GO:0030425	Component	Dendrite	IEA
GO:0030674	Function	Protein-macromolecule adaptor activity	IMP	25025157
GO:0032324	Process	Molybdopterin cofactor biosynthetic process	IEA
GO:0042802	Function	Identical protein binding	IDA	25025157
GO:0042802	Function	Identical protein binding	IEA
GO:0042995	Component	Cell projection	IEA
GO:0043197	Component	Dendritic spine	IDA	25025157
GO:0043546	Function	Molybdopterin cofactor binding	IDA	9990024
GO:0045184	Process	Establishment of protein localization	IEA
GO:0045202	Component	Synapse	IEA
GO:0045211	Component	Postsynaptic membrane	IBA
GO:0045211	Component	Postsynaptic membrane	IDA	25025157
GO:0045211	Component	Postsynaptic membrane	IDA	26613940
GO:0045211	Component	Postsynaptic membrane	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0050808	Process	Synapse organization	IEA
GO:0051932	Process	Synaptic transmission, GABAergic	IDA	14993607, 23909897
GO:0051932	Process	Synaptic transmission, GABAergic	ISS
GO:0060077	Component	Inhibitory synapse	IEA
GO:0060090	Function	Molecular adaptor activity	IEA
GO:0061598	Function	Molybdopterin adenylyltransferase activity	IEA
GO:0061598	Function	Molybdopterin adenylyltransferase activity	ISS	23163752
GO:0061599	Function	Molybdopterin molybdotransferase activity	IBA
GO:0061599	Function	Molybdopterin molybdotransferase activity	IEA
GO:0061599	Function	Molybdopterin molybdotransferase activity	ISS	23163752
GO:0072579	Process	Glycine receptor clustering	IBA
GO:0072657	Process	Protein localization to membrane	IEA
GO:0097060	Component	Synaptic membrane	IDA	25025157
GO:0097060	Component	Synaptic membrane	ISS
GO:0097112	Process	Gamma-aminobutyric acid receptor clustering	IBA
GO:0097112	Process	Gamma-aminobutyric acid receptor clustering	IDA	26613940
GO:0097112	Process	Gamma-aminobutyric acid receptor clustering	IMP	25025157
GO:0098690	Component	Glycinergic synapse	IEA
GO:0098794	Component	Postsynapse	IEA
GO:0098982	Component	GABA-ergic synapse	IEA
GO:0099091	Component	Postsynaptic specialization, intracellular component	IEA
GO:0099572	Component	Postsynaptic specialization	IBA
GO:0099645	Process	Neurotransmitter receptor localization to postsynaptic specialization membrane	IEA

MIM	HGNC	e!Ensembl
603930	15465	ENSG00000171723

Q9NQX3

Protein name

Gephyrin [Includes: Molybdopterin adenylyltransferase (MPT adenylyltransferase) (EC 2.7.7.75) (Domain G); Molybdopterin molybdenumtransferase (MPT Mo-transferase) (EC 2.10.1.1) (Domain E)]

Protein function

Microtubule-associated protein involved in membrane protein-cytoskeleton interactions. It is thought to anchor the inhibitory glycine receptor (GLYR) to subsynaptic microtubules (By similarity). Acts as a major instructive molecule at inhibitory

PDB

1JLJ

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00994	MoCF_biosynth	18 → 164	Probable molybdopterin binding domain	Domain
PF03453	MoeA_N	324 → 489	MoeA N-terminal region (domain I and II)	Family
PF00994	MoCF_biosynth	502 → 645	Probable molybdopterin binding domain	Domain
PF03454	MoeA_C	658 → 733	MoeA C-terminal region (domain IV)	Domain

Sequence

MATEGMILTNHDHQIRVGVLTVSDSCFRNLAEDRSGINLKDLVQDPSLLGGTISAYKIVP
DEIEEIKETLIDWCDEKELNLILTTGGTGFAPRDVTPEATKEVIEREAPGMALAMLMGSL
NVTPLGMLSRPVCGIRGKTLIINLPGSKKGSQECFQFILPALPHAIDLLRDAIVKVKEVH
DELEDLPSPPPPLSPPPTTSPHKQTEDKGVQCEEEEEEKKDSGVASTEDSSSSHITAAAI
AAKIPDSIISRGVQVLPRDTASLSTTPSESPRAQATSRLSTASCPTPKVQSRCSSKENIL
RASHSAVDITKVARRHRMSPFPLTSMDKAFITVLEMTPVLGTEIINYRDGMGRVLAQDVY
AKDNLPPFPASVKDGYAVRAADGPGDRFIIGESQAGEQPTQTVMPGQVMRVTTGAPIPCG
ADAVVQVEDTELIRESDDGTEELEVRILVQARPGQDIRPIGHDIKRGECVLAKGTHMGPS
EIGLLATVGVTEVEVNKFPVVAVMSTGNELLNPEDDLLPGKIRDSNRSTLLATIQEHGYP
TINLGIVGDNPDDLLNALNEGISRADVIITSGGVSMGEKDYLKQVLDIDLHAQIHFGRVF
MKPGLPTTFATLDIDGVRKIIFALPGNPVSAVVTCNLFVVPALRKMQGILDPRPTIIKAR
LSCDVKLDPRPEYHRCILTWHHQEPLPWAQSTGNQMSSRLMSMRSANGLLMLPPKTEQYV
ELHKGEVVDVMVIGRL

Sequence length

736

Interactions

View interactions

	KEGG		Reactome
	Folate biosynthesis Metabolic pathways Biosynthesis of cofactors GABAergic synapse		Molybdenum cofactor biosynthesis

684

Show/Hide Causal Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Hepatocellular carcinoma	Likely pathogenic	rs2082439915	RCV005913536
Seizure	Likely pathogenic	rs2066910297	RCV001078183
Sulfite oxidase deficiency due to molybdenum cofactor deficiency type C	Pathogenic; Likely pathogenic	rs2153668269, rs2153561495, rs533003321, rs2153685300, rs2153668310, rs2140003018, rs2153717733, rs2061323841, rs2543059971, rs2549619766, rs2543060389, rs2549068048, rs1214630241, rs2549615369, rs2543402851 View all (22 more)	RCV001380809 RCV003771985 RCV001823444 RCV002024387 RCV001941687 RCV002050084 RCV001994508 RCV001949542 RCV003062639 RCV002861720 RCV002825508 RCV002861595 RCV002862648 RCV002867008 RCV002899166 RCV002885319 RCV002957360 RCV002937103 RCV003007806 RCV003015783 RCV003019403 RCV003025285 RCV003506036 RCV003506252 RCV003506554 RCV003505588 RCV003505631 RCV003505574 RCV003505739 RCV003616586 RCV003616660 RCV003616823 RCV000808752 RCV001057847 RCV003883166 RCV000074361 RCV004799488
Thyroid cancer, nonmedullary, 1	Likely pathogenic	rs2140003018	RCV005922829

Show/Hide Unknown Diseases (19)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Acute myeloid leukemia	Benign; Likely benign	rs56264248, rs3752992, rs10147356	RCV005909636 RCV005919146 RCV005922995
Cervical cancer	Likely benign; Benign	rs3752992, rs9323485, rs10147356	RCV005919148 RCV005916739 RCV005922996
Cholangiocarcinoma	Benign	rs10147356	RCV005923000
Dementia	Likely benign	rs200060659	RCV005626274
Familial cancer of breast	Benign	rs56264248	RCV005909635
Gastric cancer	Benign	rs9323485, rs10147356	RCV005916741 RCV005922997
GPHN-related disorder	Likely benign; Benign; Uncertain significance	rs565205810, rs757111014, rs747289580, rs376650247, rs745860575, rs2542613189, rs150226537, rs150799851, rs41285470, rs142608987	RCV003938862 RCV003951324 RCV003963598 RCV003926470 RCV003403999 RCV003404650 RCV003925653 RCV003962522 RCV003915563 RCV003918034
Hereditary breast ovarian cancer syndrome	Uncertain significance	rs2153686282	RCV001374503
Hyperekplexia	Uncertain significance	rs121908539	RCV000006337
Hyperekplexia 1	Uncertain significance; Benign; Likely benign; Conflicting classifications of pathogenicity	rs2059386675, rs121908539, rs41285470, rs41285476, rs117256383, rs777009433	RCV001329795 RCV000031964 RCV002491021 RCV002497132 RCV002507188 RCV002499259
Lung cancer	Likely benign; Benign	rs3752992, rs116568307	RCV005919149 RCV005922120
Malignant lymphoma, large B-cell, diffuse	Benign	rs56264248	RCV005909637
Malignant tumor of esophagus	Likely benign; Benign	rs3752992, rs9323485	RCV005919147 RCV005916738
Ovarian serous cystadenocarcinoma	Benign	rs9323485, rs10147356	RCV005916742 RCV005922998
Sarcoma	Benign	rs9323485, rs116568307	RCV005916740 RCV005922119
Schizophrenia	Uncertain significance	rs2549671985	RCV002463514
Sulfite oxidase deficiency due to molybdenum cofactor deficiency type A	Benign; Likely benign	rs150226537, rs41285470	RCV000610229 RCV000615079
Thymoma	Benign	rs56264248, rs9323485, rs10147356	RCV005909638 RCV005916743 RCV005922999
Uterine corpus endometrial carcinoma	Likely benign; Benign	rs3752992, rs9323485, rs116568307	RCV005919150 RCV005916744 RCV005922121

Show/Hide Text Mining Associations (16)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Anxiety	Associate	18615734
Autism Spectrum Disorder	Associate	23275889, 32081867
Autistic Disorder	Associate	37817707, 38048114
Brain Diseases	Associate	26613940, 37817707
Breech Presentation	Associate	37817707
Epilepsies Myoclonic	Associate	26613940
Epilepsy	Associate	18615734
Hemangioblastoma	Associate	26768750
Heredodegenerative Disorders Nervous System	Associate	35717442
Melanocytic nevus syndrome congenital	Associate	37817707
Mental Disorders	Associate	35717442
Mental Retardation X Linked	Associate	21807943
Molybdenum cofactor deficiency	Associate	11095995, 31477743, 37817707
Nerve Degeneration	Associate	26613940
Temple Baraitser Syndrome	Associate	37817707
Zimmerman Laband syndrome	Associate	37817707

GPHN (gephyrin)