GPHN

gene
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Also known as KIAA1385GEPHGPH

Summary

GPHN (gephyrin, HGNC:15465) is a protein-coding gene on chromosome 14q23.3, encoding Gephyrin (Q9NQX3). Microtubule-associated protein involved in membrane protein-cytoskeleton interactions.

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 also required for molybdenum cofactor biosynthesis. Mutations in this gene may be associated with the neurological condition hyperplexia and also lead to molybdenum cofactor deficiency. Numerous alternatively spliced transcript variants encoding different isoforms have been described; however, the full-length nature of all transcript variants is not currently known.

Source: NCBI Gene 10243 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): sulfite oxidase deficiency due to molybdenum cofactor deficiency type C (Strong, GenCC) — +2 more curated relationships
  • GWAS associations: 5
  • Clinical variants (ClinVar): 2,083 total — 94 pathogenic, 56 likely-pathogenic
  • Phenotypes (HPO): 52
  • Dosage sensitivity (ClinGen): haploinsufficiency little evidence, triplosensitivity no evidence
  • MANE Select transcript: NM_020806

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:15465
Approved symbolGPHN
Namegephyrin
Location14q23.3
Locus typegene with protein product
StatusApproved
AliasesKIAA1385, GEPH, GPH
Ensembl geneENSG00000171723
Ensembl biotypeprotein_coding
OMIM603930
Entrez10243

Gene structure

Transcript identifiers

Ensembl transcripts: 36 — 27 protein_coding, 4 nonsense_mediated_decay, 3 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000315266, ENST00000459628, ENST00000478722, ENST00000543237, ENST00000544752, ENST00000553936, ENST00000555456, ENST00000555503, ENST00000555527, ENST00000555668, ENST00000556020, ENST00000556240, ENST00000556501, ENST00000556633, ENST00000557654, ENST00000557678, ENST00000903921, ENST00000903922, ENST00000903923, ENST00000903924, ENST00000903925, ENST00000903926, ENST00000903927, ENST00000903928, ENST00000903929, ENST00000903930, ENST00000923413, ENST00000923414, ENST00000960380, ENST00000960381, ENST00000960382, ENST00000960383, ENST00000960384, ENST00000960385, ENST00000960386, ENST00000960387

RefSeq mRNA: 8 — MANE Select: NM_020806 NM_001024218, NM_001377514, NM_001377515, NM_001377516, NM_001377517, NM_001377518, NM_001377519, NM_020806

CCDS: CCDS32103, CCDS9777

Canonical transcript exons

ENST00000478722 — 23 exons

ExonStartEnd
ENSE000019556756718080467181803
ENSE000034622536711014067110259
ENSE000034760226682447466824566
ENSE000034895426705864967058786
ENSE000034926026692266666922938
ENSE000035007556714336267143449
ENSE000035122586677646466776521
ENSE000035180276711186167111919
ENSE000035295126717957867179674
ENSE000035568976692419466924292
ENSE000035756596711301867113171
ENSE000035856826710085667100911
ENSE000035869126715941567159488
ENSE000035947796702363367023675
ENSE000036032916668110766681185
ENSE000036156486696519166965325
ENSE000036398376716893367169036
ENSE000036570916691600366916069
ENSE000036664406716516267165226
ENSE000036734026687993966880033
ENSE000036777626712225667122377
ENSE000036906656708898367089075
ENSE000039009006650814766508591

Expression profiles

Bgee: expression breadth ubiquitous, 270 present calls, max score 95.81.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 35.8614 / max 602.8518, expressed in 1804 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter IDTPM avgSamples expressed
14019128.42451801
1401943.7870799
1401902.19911036
1401930.5913217
1401920.3678150
2072620.2507105
1401960.192653
1401950.048328

Top tissues by expression

286 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
cerebellar cortexUBERON:000212995.81gold quality
cerebellar hemisphereUBERON:000224595.80gold quality
right hemisphere of cerebellumUBERON:001489095.60gold quality
cortical plateUBERON:000534395.46gold quality
cerebellumUBERON:000203794.76gold quality
right lobe of liverUBERON:000111493.19gold quality
prefrontal cortexUBERON:000045193.15gold quality
right frontal lobeUBERON:000281092.47gold quality
anterior cingulate cortexUBERON:000983592.46gold quality
cingulate cortexUBERON:000302792.35gold quality
primary visual cortexUBERON:000243692.29gold quality
caudate nucleusUBERON:000187392.25gold quality
nucleus accumbensUBERON:000188292.22gold quality
dorsolateral prefrontal cortexUBERON:000983492.10gold quality
Brodmann (1909) area 9UBERON:001354091.81gold quality
neocortexUBERON:000195091.60gold quality
frontal cortexUBERON:000187091.36gold quality
frontal lobeUBERON:001652591.36gold quality
putamenUBERON:000187491.13gold quality
amygdalaUBERON:000187690.83gold quality
cerebral cortexUBERON:000095690.72gold quality
telencephalonUBERON:000189390.69gold quality
ganglionic eminenceUBERON:000402390.66gold quality
liverUBERON:000210790.34gold quality
colonic epitheliumUBERON:000039790.27gold quality
forebrainUBERON:000189089.74gold quality
brainUBERON:000095589.64gold quality
lower esophagus mucosaUBERON:003583489.35gold quality
Ammon’s hornUBERON:000195489.29gold quality
occipital lobeUBERON:000202189.28gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-CURD-119yes18.67
E-ANND-3yes12.23
E-MTAB-6678yes8.23

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

92 targeting GPHN, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-5692A100.0074.406850
HSA-MIR-8485100.0077.574731
HSA-MIR-569699.9872.364487
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-60799.9773.625593
HSA-MIR-590-3P99.9674.346478
HSA-LET-7C-3P99.9573.422862
HSA-MIR-96-5P99.9572.802140
HSA-MIR-651-3P99.9473.485177
HSA-MIR-141-3P99.9472.792421
HSA-MIR-200A-3P99.9472.682420
HSA-MIR-314399.9371.963104
HSA-MIR-539-5P99.9370.302855
HSA-MIR-450B-5P99.9271.483175
HSA-MIR-589-3P99.9169.622088
HSA-MIR-367199.9073.043897
HSA-MIR-368699.9070.532432
HSA-MIR-153-5P99.8973.866317
HSA-MIR-3065-3P99.8770.251407
HSA-MIR-579-3P99.8671.663628
HSA-MIR-383-3P99.8565.841359
HSA-MIR-664B-3P99.8471.653590
HSA-MIR-313399.8170.923506
HSA-MIR-44899.7972.372103
HSA-MIR-6817-3P99.7968.352126
HSA-MIR-4677-5P99.7070.091940
HSA-MIR-10394-5P99.6566.831852

Functional genomics

ClinGen dosage: haploinsufficiency 1 (little evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 30)

  • crystal structure of N terminal G domain (PMID:11554796)
  • Gephyrin may have a central organizer role in assembling and stabilizing inhibitory postsynaptic membranes in human brain and is similar in function to those observed in the rodent brain. (PMID:12535948)
  • the N10Y mutation and alternative splicing of GPHN transcripts do not affect interactions with glycine receptor but may affect other interactions with the cytoskeleton or gephyrin accessory proteins (PMID:12684523)
  • Review: A total of 32 different disease-causing mutations, including several common to more than one family, have been identified in molybdenum cofactor-deficient patients and their relatives (PMID:12754701)
  • Colocalization of immunoreactivities for gephyrin and glycine receptor subunits was detected in the dorsal and ventral horns of the spinal cord, the hypoglossal nucleus and the medial vestibular nucleus of the medulla. (PMID:14622920)
  • GPHN as an MLL-GPHN chimera is able to transform hematopoietic progenitors; a tubulin-binding domain of GPHN is necessary and sufficient for this activity and also confers oligomerization capacity on MLL protein, which may contribute to leukemogenesis (PMID:14751928)
  • Within clusters, we identified two subpopulations of GlyR with distinct degrees of stabilization between receptors and scaffolding proteins. (PMID:17293395)
  • Gephyrin plays a role in synaptic function by interacting with GRIP1 splice forms at GABAergic synapses in transfected cultured hippocampal neurons. (PMID:18315564)
  • Data are consistent with the postsynaptic gephyrin scaffold acting as a platform for protein phosphatase 1 (PP1), which regulates gephyrin cluster size by dephosphorylation of gephyrin- or cytoskeleton-associated proteins. (PMID:20206270)
  • Study propose that the collybistin-gephyrin complex has an intimate role in the clustering of GABA(A)Rs containing the alpha2 subunit. (PMID:20622020)
  • we did not obtain evidence for gephyrin gene mutations in patients with temporal lobe epilepsy (PMID:21071388)
  • Data demonstrate the direct interaction between DYNLL1 and peptides derived from ASFV p54 and gephyrin interacting sequences. (PMID:21094642)
  • Gephyrin expression is significantly lower in the temporal neocortex of temporal lobe epilepsy (TLE) patients and may be involved in the development of TLE. (PMID:21404332)
  • The authors have identified a protein kinase C (PKC) phosphorylation site within the cytoplasmic domain of the beta-subunit of the GlyR (residue S403) that causes a reduction of the binding affinity between the receptor and gephyrin. (PMID:21829170)
  • The gephyrin’s presence in a cytosolic 600 kDa protein complex suggests that its metabolic and/or other non-neuronal functions are exerted in the cytoplasm and are not confined to a particular subcellular compartment. (PMID:22270318)
  • Phosphorylation of gephyrin in hippocampal neurons by cyclin-dependent kinase CDK5 at Ser-270 is dependent on collybistin. (PMID:22778260)
  • A reduction in the number of gephyrin clusters in primary neurons reduces GABA signaling. (PMID:23077067)
  • Rare exonic deletions implicate the synaptic organizer Gephyrin (GPHN) in risk for autism, schizophrenia and seizures. (PMID:23393157)
  • Extracellular signal-regulated kinase and glycogen synthase kinase 3beta regulate gephyrin postsynaptic aggregation and GABAergic synaptic function in a calpain-dependent mechanism (PMID:23408424)
  • abnormal accumulations of gephyrin are highly correlated with the neuropathologic diagnosis of Alzheimer disease in 17 AD versus 14 control cases. Furthermore, gephyrin accumulations were specific for AD. (PMID:24128675)
  • The enhancement of Cb-induced gephyrin clustering by GTP-TC10 does not depend on the guanine nucleotide exchange activity of Cb but involves an interaction that resembles reported interactions of other small GTPases with their effectors (PMID:24297911)
  • Structural exonic microdeletions affecting the GPHN gene constitute a rare genetic risk factor for IGE and other neuropsychiatric disorders by an impairment of the GABAergic inhibitory synaptic transmission. (PMID:24561070)
  • The N-terminal region of GABRA3 and the GlyR beta subunit occupies the same binding site of gephyrin. (PMID:25531214)
  • Results show that PKC-dependent phosphorylation of GAP43 plays a critical role in regulating postsynaptic gephyrin aggregation in developing GABAergic synapses. (PMID:25755278)
  • A yin-yang haplotype pattern encompassing gephyrin consists of 284 divergent nucleotide states and both variants vary drastically from their mutual ancestral haplotype, suggesting rapid evolution. (PMID:25813846)
  • A missense mutation of gephyrin that was unable to synthesize MoCo and activate MoCo-dependent enzymes was identified. (PMID:26613940)
  • these data reveal that IQSEC3 acts together with gephyrin to regulate inhibitory synapse development. (PMID:27002143)
  • This study shown that the SNPs located in the rs723432 (Pallele=0.007; uncorrected) in the GPHN gene showed associated with Japanese individuals affected with schizophrenia. (PMID:28073605)
  • Using quantitative photoactivated localisation microscopy the authors found that alpha-1 and alpha-3 containing glycine receptors display the same alpha3:beta2 stoichiometry and gephyrin binding. (PMID:28883437)
  • Complex regulation of Gephyrin splicing is a determinant of inhibitory postsynaptic diversity. (PMID:35717442)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_reriogphnaENSDARG00000089076
danio_reriogphnbENSDARG00000100851
mus_musculusGphnENSMUSG00000047454
rattus_norvegicusGphnENSRNOG00000064630
drosophila_melanogastercinFBGN0000316
caenorhabditis_elegansWBGENE00003385

Protein

Protein identifiers

GephyrinQ9NQX3 (reviewed: Q9NQX3)

All UniProt accessions (9): Q9NQX3, F5H039, G3V355, G3V4D2, G3V4R0, G3V582, H0YIY4, H0YJ30, H0YJR5

UniProt curated annotations — full annotation on UniProt →

Function. Microtubule-associated protein involved in membrane protein-cytoskeleton interactions. It is thought to anchor the inhibitory glycine receptor (GLYR) to subsynaptic microtubules. Acts as a major instructive molecule at inhibitory synapses, where it also clusters GABA type A receptors. Also has a catalytic activity and catalyzes two steps in the biosynthesis of the molybdenum cofactor. In the first step, molybdopterin is adenylated. Subsequently, molybdate is inserted into adenylated molybdopterin and AMP is released.

Subunit / interactions. Homotrimer, homodimer and homooligomer. Interacts with GABARAP. Interacts with SRGAP2 (via SH3 domain). Interacts with GABRA3. Interacts with GLRB. GABRA3 and GLRB occupy overlapping binding sites. Interacts with ARHGAP32; IQSEC3, INSYN1 and INSYN2A.

Subcellular location. Postsynaptic cell membrane. Cell membrane. Cytoplasm. Cytosol. Cytoskeleton. Cell projection. Dendrite. Postsynaptic density.

Post-translational modifications. Palmitoylated. Palmitoylation is stimulated by GABA type A receptors activity. Palmitoylation by ZDHHC12 regulates clustering at synapses.

Disease relevance. Molybdenum cofactor deficiency C (MOCODC) [MIM:615501] A form of molybdenum cofactor deficiency, an autosomal recessive metabolic disorder leading to the pleiotropic loss of molybdoenzyme activities. It is clinically characterized by onset in infancy of poor feeding, intractable seizures, severe psychomotor retardation, and death in early childhood in most patients. The disease is caused by variants affecting the gene represented in this entry.

Activity regulation. Inhibited by copper and tungsten.

Pathway. Cofactor biosynthesis; molybdopterin biosynthesis.

Similarity. In the N-terminal section; belongs to the MoaB/Mog family. In the C-terminal section; belongs to the MoeA family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9NQX3-11yes
Q9NQX3-22

RefSeq proteins (8): NP_001019389, NP_001364443, NP_001364444, NP_001364445, NP_001364446, NP_001364447, NP_001364448, NP_065857* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001453MoaB/Mog_domDomain
IPR005110MoeA_linker/NDomain
IPR005111MoeA_C_domain_IVDomain
IPR008284MoCF_biosynth_CSConserved_site
IPR036135MoeA_linker/N_sfHomologous_superfamily
IPR036425MoaB/Mog-like_dom_sfHomologous_superfamily
IPR036688MoeA_C_domain_IV_sfHomologous_superfamily
IPR038987MoeA-likeFamily

Pfam: PF00994, PF03453, PF03454

Catalyzed reactions (Rhea), 2 shown:

  • molybdopterin + ATP + H(+) = adenylyl-molybdopterin + diphosphate (RHEA:31331)
  • adenylyl-molybdopterin + molybdate = Mo-molybdopterin + AMP + H(+) (RHEA:35047)

UniProt features (59 total): binding site 14, modified residue 10, helix 10, strand 7, region of interest 5, sequence variant 3, lipid moiety-binding region 2, mutagenesis site 2, compositionally biased region 2, chain 1, splice variant 1, sequence conflict 1, turn 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
1JLJX-RAY DIFFRACTION1.6

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9NQX3-F184.150.72

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (14): 524; 525; 525; 526; 526; 573; 573; 574; 575; 580; 626; 626

Post-translational modifications (12): 188, 194, 198, 200, 262, 265, 266, 268, 270, 305, 212, 284

Mutagenesis-validated functional residues (2):

PositionPhenotype
212decreased palmitoylation. decreased clustering at synaptic membranes. decreased function in gamma-aminobutyric acid rece
284decreased palmitoylation. decreased clustering at synaptic membranes. decreased function in gamma-aminobutyric acid rece

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-947581Molybdenum cofactor biosynthesis

MSigDB gene sets: 355 (showing top): GOBP_NEUROMUSCULAR_JUNCTION_DEVELOPMENT, GOBP_SYNAPSE_ASSEMBLY, GCANCTGNY_MYOD_Q6, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, GOBP_PROTEIN_LOCALIZATION_TO_CELL_PERIPHERY, ATGTTAA_MIR302C, GOBP_RESPONSE_TO_METAL_ION, NFKB_C, GOBP_CELL_JUNCTION_ORGANIZATION, GOBP_POSTSYNAPTIC_MEMBRANE_ORGANIZATION, TGIF_01, MORI_SMALL_PRE_BII_LYMPHOCYTE_DN, ACATATC_MIR190

GO Biological Process (14): Mo-molybdopterin cofactor biosynthetic process (GO:0006777), synapse assembly (GO:0007416), establishment of synaptic specificity at neuromuscular junction (GO:0007529), response to metal ion (GO:0010038), establishment of protein localization (GO:0045184), glycine receptor clustering (GO:0072579), gamma-aminobutyric acid receptor clustering (GO:0097112), neurotransmitter receptor localization to postsynaptic specialization membrane (GO:0099645), phosphate-containing compound metabolic process (GO:0006796), molybdopterin cofactor biosynthetic process (GO:0032324), synapse organization (GO:0050808), synaptic transmission, GABAergic (GO:0051932), protein localization to membrane (GO:0072657), organophosphate biosynthetic process (GO:0090407)

GO Molecular Function (14): signaling receptor binding (GO:0005102), ATP binding (GO:0005524), nitrate reductase activity (GO:0008940), protein-macromolecule adaptor activity (GO:0030674), identical protein binding (GO:0042802), molybdopterin cofactor binding (GO:0043546), metal ion binding (GO:0046872), molybdopterin adenylyltransferase activity (GO:0061598), molybdopterin molybdotransferase activity (GO:0061599), nucleotide binding (GO:0000166), catalytic activity (GO:0003824), protein binding (GO:0005515), transferase activity (GO:0016740), molecular adaptor activity (GO:0060090)

GO Cellular Component (19): cytoplasm (GO:0005737), cytosol (GO:0005829), cytoskeleton (GO:0005856), plasma membrane (GO:0005886), cytoplasmic side of plasma membrane (GO:0009898), postsynaptic density (GO:0014069), dendrite (GO:0030425), dendritic spine (GO:0043197), postsynaptic membrane (GO:0045211), inhibitory synapse (GO:0060077), synaptic membrane (GO:0097060), glycinergic synapse (GO:0098690), GABA-ergic synapse (GO:0098982), postsynaptic specialization, intracellular component (GO:0099091), postsynaptic specialization (GO:0099572), membrane (GO:0016020), cell projection (GO:0042995), synapse (GO:0045202), postsynapse (GO:0098794)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Metabolism of water-soluble vitamins and cofactors1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure5
synapse5
protein binding3
binding3
postsynapse3
synapse organization2
postsynaptic membrane organization2
neurotransmitter-gated ion channel clustering2
molecular_function2
intracellular membraneless organelle2
postsynaptic specialization2
molybdenum incorporation into molybdenum-molybdopterin complex1
Mo-molybdopterin cofactor metabolic process1
molybdopterin cofactor biosynthetic process1
GTP 3’,8’-cyclase activity1
cyclic pyranopterin monophosphate synthase activity1
nervous system development1
cell junction assembly1
neuromuscular junction development1
response to chemical1
establishment of localization1
protein-containing complex localization1
receptor localization to synapse1
regulation of postsynaptic membrane neurotransmitter receptor levels1
protein localization to postsynaptic specialization membrane1
metabolic process1
molybdopterin synthase activity1
cysteine desulfurase activity1
molybdopterin cofactor metabolic process1
molybdopterin adenylyltransferase activity1
molybdopterin-synthase sulfurtransferase activity1
molybdopterin-synthase adenylyltransferase activity1
organophosphate biosynthetic process1
cell junction organization1
chemical synaptic transmission1
intracellular protein localization1
localization within membrane1
biosynthetic process1
organophosphate metabolic process1
adenyl ribonucleotide binding1

Protein interactions and networks

STRING

2326 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
GPHNARHGEF9O43307997
GPHNNLGN2Q8NFZ4968
GPHNGARS1P41250963
GPHNGLRBP48167959
GPHNMOCS1Q9NZB8957
GPHNMOCS2O96007949
GPHNSLC32A1Q9H598940
GPHNGABARAPO95166932
GPHNGLRA1P23415900
GPHNDLG4P78352885
GPHNSUOXP51687878
GPHNPFN1P07737861
GPHNMTORP42345861
GPHNSLC6A5Q9Y345849
GPHNAOX1Q06278837

IntAct

67 interactions, top by confidence:

ABTypeScore
PRPF4PPIHpsi-mi:“MI:0914”(association)0.910
GPHNDYNLL1psi-mi:“MI:0407”(direct interaction)0.860
DYNLL1BLTP3Bpsi-mi:“MI:0914”(association)0.730
YWHAGBLTP3Bpsi-mi:“MI:0914”(association)0.640
AKT1RPS6KB1psi-mi:“MI:0914”(association)0.640
DYNLL2BLTP3Bpsi-mi:“MI:0914”(association)0.640
DVL1DVL2psi-mi:“MI:0914”(association)0.620
SYNGAP1IGF2BP3psi-mi:“MI:0914”(association)0.530
SYNGAP1SEC16Apsi-mi:“MI:0914”(association)0.530
ZAR1LBCL2L11psi-mi:“MI:0914”(association)0.530
CIMAP1DNMT2psi-mi:“MI:0914”(association)0.530
TSSK1BHSPA8psi-mi:“MI:0914”(association)0.530
LAGE3CTSApsi-mi:“MI:0914”(association)0.530
MAGEA4MAGEA8psi-mi:“MI:0914”(association)0.530
DYNLL1SHMT2psi-mi:“MI:0914”(association)0.510
DYNLL2SHMT2psi-mi:“MI:0914”(association)0.510
SRGAP2GPHNpsi-mi:“MI:0407”(direct interaction)0.440
Dynll1psi-mi:“MI:0915”(physical association)0.400
GPHNSPATS1psi-mi:“MI:0915”(physical association)0.370
GPHNGPHNpsi-mi:“MI:0915”(physical association)0.370
KHDRBS1GPHNpsi-mi:“MI:0915”(physical association)0.370
GPHNACADVLpsi-mi:“MI:0915”(physical association)0.370
CDCA5BDP1psi-mi:“MI:0914”(association)0.350
TCF4OGTpsi-mi:“MI:0914”(association)0.350

BioGRID (107): GPHN (Affinity Capture-MS), GPHN (Affinity Capture-MS), GPHN (Affinity Capture-MS), GPHN (Affinity Capture-MS), GPHN (Affinity Capture-MS), GPHN (Affinity Capture-MS), GPHN (Affinity Capture-MS), GPHN (Affinity Capture-MS), ARHGEF9 (Two-hybrid), GPHN (Affinity Capture-Western), VASP (Affinity Capture-Western), ENAH (Affinity Capture-Western), GPHN (Affinity Capture-MS), GPHN (Affinity Capture-MS), GPHN (Affinity Capture-MS)

ESM2 similar proteins: A0A1L8F5J9, A0JN27, F1LTR1, F1NBL0, O15294, P35438, P35439, P56558, P61201, P61202, P61203, P61599, P61600, P63138, P79101, P81436, Q03555, Q05586, Q13888, Q15303, Q27HV0, Q2PFM2, Q2TBV5, Q4L208, Q58ED9, Q5R1P0, Q5SP67, Q5ZJ75, Q61527, Q62956, Q6IQT4, Q6IR75, Q6P1K8, Q6P632, Q7ZXR3, Q8BUV3, Q8C6G8, Q8CGY8, Q8R4D1, Q91854

Diamond homologs: B8I7D0, O31703, P12281, P39205, P45210, P65407, P99139, P9WJQ4, P9WJQ5, Q03555, Q39054, Q44243, Q56066, Q56207, Q58080, Q58296, Q5HDT4, Q5HLX6, Q6G749, Q6GEG1, Q8BUV3, Q8CNE1, Q8NVA1, Q9NQX3, Q9PW38, O34457, P0AEZ9, P0AF00, P0AF03, P0AF04, P0AF05, P44645, P56421, P59014, P65406, P99137, Q56208, Q57631, Q5HDT2, Q5HLX4

SIGNOR signaling

7 interactions.

AEffectBMechanism
ERK1/2down-regulatesGPHNphosphorylation
GSK3Bdown-regulatesGPHNphosphorylation
GABARAP“up-regulates activity”GPHNbinding
GPHN“up-regulates activity”ARHGEF9binding
GPHN“up-regulates activity”NLGN2binding
GPHNup-regulatesSynaptic_plasticity
GPHN“up-regulates quantity by stabilization”GABA-Abinding

Disease & clinical

Clinical variants and AI predictions

ClinVar

2083 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic94
Likely pathogenic56
Uncertain significance1086
Likely benign625
Benign77

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1069066NM_020806.5(GPHN):c.1156_1159dup (p.Val387fs)Pathogenic
1071767NM_152443.3(RDH12):c.393T>A (p.Cys131Ter)Pathogenic
1074324NM_016026.4(RDH11):c.230del (p.Lys77fs)Pathogenic
1075236NC_000014.8:g.(?67243172)(67291294_?)delPathogenic
1301382NM_152443.3(RDH12):c.698T>A (p.Val233Asp)Pathogenic
1432165NM_016026.4(RDH11):c.237dup (p.Leu80fs)Pathogenic
1451652NM_152443.3(RDH12):c.52del (p.Met17_Val18insTer)Pathogenic
1452267NM_020806.5(GPHN):c.1907dup (p.Gly637fs)Pathogenic
1454036NM_152443.3(RDH12):c.43del (p.Leu15fs)Pathogenic
1454068NM_020806.5(GPHN):c.1234C>T (p.Arg412Ter)Pathogenic
1456691NC_000014.8:g.(?67490330)(67555812_?)delPathogenic
1456692NC_000014.8:g.(?67147805)(67291304_?)delPathogenic
1456696NC_000014.8:g.(?67346637)(67432062_?)delPathogenic
1457557NC_000014.8:g.(?67147805)(67243259_?)delPathogenic
1458284NC_000014.8:g.(?67243162)(67490412_?)delPathogenic
1458569NM_020806.5(GPHN):c.277C>T (p.Arg93Ter)Pathogenic
1459461NC_000014.8:g.(?67525346)(67567648_?)delPathogenic
1459465NC_000014.8:g.(?67382700)(67432062_?)delPathogenic
161115NM_016026.4(RDH11):c.199C>T (p.Arg67Ter)Pathogenic
161116NM_016026.4(RDH11):c.322C>T (p.Arg108Ter)Pathogenic
1711873GRCh37/hg19 14q23.3(chr14:66292119-67108035)x3Pathogenic
1929453NM_152443.3(RDH12):c.723del (p.Ser242fs)Pathogenic
1970808NM_152443.3(RDH12):c.546del (p.Ile183fs)Pathogenic
2014914NM_020806.5(GPHN):c.770_771del (p.His257fs)Pathogenic
2021431NM_020806.5(GPHN):c.802_803insG (p.Tyr268Ter)Pathogenic
2028217NM_020806.5(GPHN):c.630dup (p.Gln211fs)Pathogenic
2033928NM_020806.5(GPHN):c.747del (p.Ser250fs)Pathogenic
2036462NM_020806.5(GPHN):c.1560del (p.Thr520_Val521insTer)Pathogenic
2047NM_152443.3(RDH12):c.806_810del (p.Ala269fs)Pathogenic
2048NM_152443.3(RDH12):c.565C>T (p.Gln189Ter)Pathogenic

SpliceAI

7831 predictions. Top by Δscore:

VariantEffectΔscore
14:66513650:G:GTdonor_gain1.0000
14:66681095:A:AGacceptor_gain1.0000
14:66681096:T:Gacceptor_gain1.0000
14:66681101:A:AGacceptor_gain1.0000
14:66681102:T:Gacceptor_gain1.0000
14:66681102:TTTAG:Tacceptor_loss1.0000
14:66681104:TAGTG:Tacceptor_gain1.0000
14:66681105:A:AGacceptor_gain1.0000
14:66681105:AGT:Aacceptor_gain1.0000
14:66681105:AGTGA:Aacceptor_gain1.0000
14:66681106:G:GCacceptor_gain1.0000
14:66681106:GT:Gacceptor_gain1.0000
14:66681106:GTG:Gacceptor_gain1.0000
14:66681106:GTGA:Gacceptor_gain1.0000
14:66681106:GTGAG:Gacceptor_gain1.0000
14:66681181:TCTTT:Tdonor_gain1.0000
14:66681183:TTT:Tdonor_gain1.0000
14:66681183:TTTG:Tdonor_loss1.0000
14:66681184:TT:Tdonor_gain1.0000
14:66681184:TTGT:Tdonor_loss1.0000
14:66681185:TGT:Tdonor_loss1.0000
14:66681186:G:GGdonor_gain1.0000
14:66681186:G:Tdonor_loss1.0000
14:66681187:TG:Tdonor_loss1.0000
14:66681188:GAGTA:Gdonor_loss1.0000
14:66681189:A:AAdonor_loss1.0000
14:66681190:G:Cdonor_loss1.0000
14:66681190:G:GGdonor_gain1.0000
14:66824469:TTCA:Tacceptor_loss1.0000
14:66824471:CAG:Cacceptor_loss1.0000

AlphaMissense

5022 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
14:66508579:G:AG18R1.000
14:66508579:G:CG18R1.000
14:66508580:G:AG18E1.000
14:66508586:T:CL20P1.000
14:66681139:G:CD33H1.000
14:66681158:T:CL39P1.000
14:66824481:T:CL70P1.000
14:66824489:T:AW73R1.000
14:66824489:T:CW73R1.000
14:66824517:T:AI82K1.000
14:66824529:G:AG86E1.000
14:66824532:G:AG87E1.000
14:66824537:G:AG89R1.000
14:66824537:G:CG89R1.000
14:66824538:G:AG89E1.000
14:66824540:T:CF90L1.000
14:66824542:T:AF90L1.000
14:66824542:T:GF90L1.000
14:66880027:T:CL128P1.000
14:66880033:G:CR130T1.000
14:66880033:G:TR130M1.000
14:66916010:T:CC133R1.000
14:66916012:T:GC133W1.000
14:66916013:G:AG134R1.000
14:66916013:G:CG134R1.000
14:66916014:G:AG134E1.000
14:66916032:T:CL140P1.000
14:66916035:T:AI141K1.000
14:66916042:C:AN143K1.000
14:66916042:C:GN143K1.000

dbSNP variants (sampled 300 via entrez): RS1000001299 (14:67283740 G>A), RS1000004027 (14:67372494 A>G), RS1000006035 (14:67455502 T>C), RS1000009227 (14:66911925 C>T), RS1000009300 (14:66920292 C>T), RS1000009876 (14:67719329 T>C), RS1000013774 (14:66742821 G>A), RS1000016137 (14:67453565 C>T), RS1000018226 (14:67127724 A>T), RS1000022562 (14:67314113 T>C), RS1000026875 (14:66912493 G>A), RS1000031806 (14:67135092 G>A,C), RS1000031994 (14:66702961 G>A), RS1000039190 (14:66764488 A>G), RS1000040280 (14:67455241 G>A)

Disease associations

OMIM: gene MIM:603930 | disease phenotypes: MIM:615501, MIM:612712, MIM:204000, MIM:149400, MIM:616108, MIM:268000, MIM:618010, MIM:181500, MIM:120970, MIM:252150

GenCC curated gene-disease

DiseaseClassificationInheritance
sulfite oxidase deficiency due to molybdenum cofactor deficiency type CStrongAutosomal recessive
complex neurodevelopmental disorderModerateAutosomal dominant
hereditary hyperekplexiaSupportiveAutosomal dominant

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
sulfite oxidase deficiency due to molybdenum cofactor deficiency type CModerateAR

Mondo (20): sulfite oxidase deficiency due to molybdenum cofactor deficiency type C (MONDO:0014212), Leber congenital amaurosis 13 (MONDO:0012990), Leber congenital amaurosis (MONDO:0018998), hyperekplexia 1 (MONDO:0007868), retinitis pigmentosa-juvenile cataract-short stature-intellectual disability syndrome (MONDO:0014495), atypical Rett syndrome (MONDO:0017746), retinitis pigmentosa (MONDO:0019200), inherited retinal dystrophy (MONDO:0019118), glycosylphosphatidylinositol biosynthesis defect 17 (MONDO:0060724), optic atrophy (MONDO:0003608), prostate cancer (MONDO:0008315), schizophrenia (MONDO:0005090), cone-rod dystrophy (MONDO:0015993), neurodevelopmental disorder (MONDO:0700092), sulfite oxidase deficiency due to molybdenum cofactor deficiency type A (MONDO:0009643)

Orphanet (14): Sulfite oxidase deficiency due to molybdenum cofactor deficiency type C (Orphanet:308400), Encephalopathy due to sulfite oxidase deficiency (Orphanet:833), Leber congenital amaurosis (Orphanet:65), Hereditary hyperekplexia (Orphanet:3197), Retinitis pigmentosa-juvenile cataract-short stature-intellectual disability syndrome (Orphanet:436245), Atypical Rett syndrome (Orphanet:3095), Retinitis pigmentosa (Orphanet:791), OBSOLETE: Inherited retinal disorder (Orphanet:71862), Familial prostate cancer (Orphanet:1331), Cone rod dystrophy (Orphanet:1872), Sulfite oxidase deficiency due to molybdenum cofactor deficiency type A (Orphanet:308386), Hyperekplexia (Orphanet:306773), Hereditary breast and/or ovarian cancer syndrome (Orphanet:145), NON RARE IN EUROPE: Schizophrenia (Orphanet:3140)

HPO phenotypes

52 total (30 of 52 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000007Autosomal recessive inheritance
HP:0000023Inguinal hernia
HP:0000817Reduced eye contact
HP:0001249Intellectual disability
HP:0001250Seizure
HP:0001251Ataxia
HP:0001257Spasticity
HP:0001276Hypertonia
HP:0001288Gait disturbance
HP:0001290Generalized hypotonia
HP:0001321Cerebellar hypoplasia
HP:0001336Myoclonus
HP:0001347Hyperreflexia
HP:0001373Joint dislocation
HP:0001387Joint stiffness
HP:0001537Umbilical hernia
HP:0002020Gastroesophageal reflux
HP:0002036Hiatus hernia
HP:0002063Rigidity
HP:0002069Bilateral tonic-clonic seizure
HP:0002104Apnea
HP:0002123Generalized myoclonic seizure
HP:0002126Polymicrogyria
HP:0002197Generalized-onset seizure
HP:0002267Exaggerated startle response
HP:0002359Frequent falls
HP:0002360Sleep disturbance
HP:0002375Hypokinesia
HP:0002380Fasciculations

GWAS associations

5 associations (top):

StudyTraitp-value
GCST001802_2Depression (quantitative trait)3.000000e-06
GCST003055_4Tandem gait2.000000e-07
GCST008161_62Waist circumference adjusted for body mass index6.000000e-06
GCST009087_1Pneumococcal meningitis9.000000e-06
GCST90000025_538Appendicular lean mass2.000000e-12

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0007789BMI-adjusted waist circumference
EFO:0004980appendicular lean mass

MeSH disease descriptors (13)

DescriptorNameTree numbers
D000071700Cone-Rod DystrophiesC11.270.152; C11.768.585.658.250; C16.320.290.152
D003704DementiaC10.228.140.380; F03.615.400
D061325Hereditary Breast and Ovarian Cancer SyndromeC04.588.180.483; C04.588.322.455.431; C04.700.517; C12.050.351.500.056.630.705.431; C12.050.351.937.418.685.431; C12.100.250.056.630.705.431; C12.900.418.685.431; C16.320.700.517; C17.800.090.500.483; C19.344.410.431; C19.391.630.705.431
D000071017HyperekplexiaC10.228.590
D057130Leber Congenital AmaurosisC11.270.516; C11.768.364
D065886Neurodevelopmental DisordersF03.625
D009896Optic AtrophyC10.292.700.225; C11.640.451
D011471Prostatic NeoplasmsC04.588.945.440.770; C12.100.500.260.750; C12.100.500.565.625; C12.200.294.260.750; C12.200.294.565.625; C12.200.758.409.750; C12.900.619.750
D058499Retinal DystrophiesC11.768.585.658
D012174Retinitis PigmentosaC11.270.684; C11.768.585.658.500; C16.320.290.684
C567197Leber Congenital Amaurosis 13 (supp.)
C565372Molybdenum Cofactor Deficiency, Complementation Group A (supp.)
C565374Molybdenum Cofactor Deficiency, Complementation Group C (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

49 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyrenedecreases expression, increases methylation5
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression4
Cisplatindecreases expression, increases expression3
Valproic Acidaffects expression, increases expression3
Aflatoxin B1affects expression, decreases methylation, increases methylation3
sodium arseniteincreases abundance, decreases expression, affects cotreatment2
Cyclosporinedecreases expression, increases expression2
aristolochic acid Idecreases expression1
FR900359affects phosphorylation1
bisphenol Faffects cotreatment, increases methylation1
chloroacetaldehydedecreases expression1
methyleugenoldecreases expression1
triphenyl phosphateaffects expression1
pirinixic acidaffects binding, increases activity, increases expression1
senecioninedecreases expression1
senkirkinedecreases expression1
sodium arsenatedecreases expression1
heliotrinedecreases expression1
arseniteaffects binding, decreases reaction, increases reaction1
manganese chloridedecreases expression, increases abundance, affects cotreatment1
benzo(e)pyreneincreases methylation1
potassium chromate(VI)affects cotreatment, decreases expression1
nickel sulfatedecreases expression1
coumarinaffects phosphorylation1
beta-methylcholineaffects expression1
epigallocatechin gallateaffects cotreatment, decreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
bisphenol Saffects cotreatment, decreases methylation1
LDN 193189affects cotreatment, increases expression1
Bortezomibdecreases expression1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_SQ39HAP1 GPHN (-)Cancer cell lineMale

Clinical trials (associated diseases)

274 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT00717080PHASE4COMPLETEDThe Role of Capsular Tension Ring (CTR) in Anterior Capsular Contraction
NCT00999609PHASE3ACTIVE_NOT_RECRUITINGSafety and Efficacy Study in Subjects With Leber Congenital Amaurosis
NCT06891443PHASE3RECRUITINGStudy to Evaluate Sepofarsen in Subjects With Leber Congenital Amaurosis (LCA) Type 10 (HYPERION)
NCT00000114PHASE3COMPLETEDRandomized Trial of Vitamin A and Vitamin E Supplementation for Retinitis Pigmentosa
NCT00000116PHASE3COMPLETEDRandomized Trial of DHA for Retinitis Pigmentosa Patients Receiving Vitamin A
NCT00346333PHASE3COMPLETEDClinical Trial of Lutein for Patients With Retinitis Pigmentosa Receiving Vitamin A
NCT01786395PHASE3TERMINATEDPhase III Efficacy and Safety Clinical Study of UF-021 for Treatment of Retinitis Pigmentosa
NCT04224207PHASE3COMPLETEDManagement of Retinitis Pigmentosa by Mesenchymal Stem Cells by Wharton’s Jelly Derived Mesenchymal Stem Cells
NCT04636853PHASE3COMPLETEDCB-PRP in Retinitis Pigmentosa and Dry Age-related Macular Degeneration
NCT05537220PHASE3ACTIVE_NOT_RECRUITINGOral N-acetylcysteine for Retinitis Pigmentosa
NCT05800301PHASE3COMPLETEDManagement of Retinitis Pigmentosa Via Combination of Wharton’s Jelly-derived Mesenchymal Stem Cells and Magnovision
NCT05926583PHASE3ACTIVE_NOT_RECRUITINGA Study of AAV5-hRKp.RPGR for the Treatment of Japanese Participants With X-linked Retinitis Pigmentosa
NCT06388200PHASE3ACTIVE_NOT_RECRUITINGA Phase 3 Study Of OCU400 Gene Therapy for the Treatment Of Retinitis Pigmentosa
NCT07082855PHASE3NOT_YET_RECRUITINGA Multicenter, Randomized, Double-Blind, Controlled Clinical Study of Minocycline for the Treatment of Retinitis Pigmentosa
NCT07290530PHASE3NOT_YET_RECRUITING24-Month Trial of NPI-001 for the Preservation of Photoreceptors in Retinitis Pigmentosa Associated With Usher Syndrome
NCT00100230PHASE2COMPLETEDDHA and X-Linked Retinitis Pigmentosa
NCT00447980PHASE2COMPLETEDA Study of Encapsulated Cell Technology (ECT) Implant for Participants With Early Stage Retinitis Pigmentosa
NCT00447993PHASE2COMPLETEDA Study of Encapsulated Cell Technology (ECT) Implant for Patients With Late Stage Retinitis Pigmentosa
NCT01233609PHASE2COMPLETEDTrial of Oral Valproic Acid for Retinitis Pigmentosa
NCT01399515PHASE2COMPLETEDEfficacy and Safety of Oral Valproic Acid for Retinitis Pigmentosa
NCT01530659PHASE2COMPLETEDRetinal Imaging in CNTF -Releasing Encapsulated Cell Implant Treated Patients for Early-stage Retinitis Pigmentosa
NCT01560715PHASE2COMPLETEDAutologous Bone Marrow-Derived Stem Cells Transplantation For Retinitis Pigmentosa
NCT02609165PHASE2COMPLETEDNerve Growth Factor Eye Drops Treatment in Patients With Retinitis Pigmentosa and Cystoid Macular Edema
NCT02661711PHASE2COMPLETEDAflibercept for Macular Oedema With Underlying Retinitis Pigmentosa (AMOUR) Study
NCT02804360PHASE2UNKNOWNIntravitreal Dexamethasone Implant in Retinitis Pigmentosa-related Macular Edema- a Retrospective Study
NCT02837640PHASE2UNKNOWNStudying a Potential Protective Effect of L-Dopa on Retinitis Pigmentosa
NCT03073733PHASE2COMPLETEDSafety and Efficacy of Intravitreal Injection of Human Retinal Progenitor Cells in Adults With Retinitis Pigmentosa
NCT04068207PHASE2COMPLETEDMinocycline Treatment in Retinitis Pigmentosa
NCT04356716PHASE2COMPLETEDSildenafil for Treatment of Choroidal Ischemia
NCT04604899PHASE2COMPLETEDSafety of Repeat Intravitreal Injection of Human Retinal Progenitor Cells (jCell) in Adult Subjects With Retinitis Pigmentosa
NCT04763369PHASE2UNKNOWNInvestigation of Therapeutic Efficacy and Safety of UMSCs for the Management of Retinitis Pigmentosa (RP)
NCT04864496PHASE2UNKNOWNEffects of Treatment With N- Acetylcysteine on Visual Outcomes in Patients With Retinitis Pigmentosa
NCT04945772PHASE2COMPLETEDEfficacy and Safety of MCO-010 Optogenetic Therapy in Adults With Retinitis Pigmentosa [RESTORE]
NCT05085964PHASE2TERMINATEDAn Open-Label Extension Study to Evaluate Safety & Tolerability of QR-421a in Subjects With Retinitis Pigmentosa
NCT05392179PHASE2COMPLETEDA Study in Subjects With Retinitis Pigmentosa
NCT06627179PHASE2RECRUITINGStudy to Evaluate Ultevursen in Subjects With Retinitis Pigmentosa (RP) Due to Mutations in Exon 13 of the USH2A Gene
NCT06628947PHASE2RECRUITINGA Phase II Study of Intravitreal KIO-301 in Patients With Late-stage Retinitis Pigmentosa
NCT06912633PHASE2RECRUITINGSafety of a Single, Intravitreal Injection of 6.0M jCell (Famzeretcel) in Retinitis Pigmentosa (RP)
NCT03763227PHASE2COMPLETEDIntravitreal Ranibizumab (Lucentis®) in the Treatment of Non-leaking Macular Cysts in Retinal Dystrophy
NCT00516477PHASE1COMPLETEDSafety Study in Subjects With Leber Congenital Amaurosis