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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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GPHN
gephyrin
Chromosome 14 Β· 14q23.3-q24.1
NCBI Gene: 10243Ensembl: ENSG00000171723.17HGNC: HGNC:15465UniProt: Q9NQX3
122PubMed Papers
21Diseases
0Drugs
48Pathogenic Variants
FUNCTIONAL ROLE
Highly Constrained
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
identical protein bindingsynaptic membranemolybdopterin cofactor bindingprotein bindingsulfite oxidase deficiency due to molybdenum cofactor deficiency type Cencephalopathy due to sulfite oxidase deficiencyhereditary hyperekplexiadevelopmental and epileptic encephalopathy
✦AI Summary

GPHN (gephyrin) is a multifunctional protein with critical roles in synaptic organization and molybdenum cofactor biosynthesis. Structurally, the GPHN gene spans approximately 800 kb on chromosome 14 with 27 exons, generating 11 distinct transcript isoforms through alternative splicing, with 10 specific to neuronal tissue 1. The protein functions as a peripheral membrane organizer that clusters and localizes inhibitory glycine receptors (GlyR) and GABA(A) receptors to the postsynaptic membrane through interactions mediated by its C-terminal MoeA homology domain 12. Beyond synaptic roles, gephyrin catalyzes two sequential steps in molybdenum cofactor biosynthesis: adenylation of molybdopterin followed by molybdate insertion 3. Mutations in GPHN cause molybdenum cofactor deficiency type C, an autosomal-recessive disorder resulting in combined loss of all molybdoenzyme activities (aldehyde oxidase, xanthine oxidoreductase, sulfite oxidase, and mARC) 3. Clinically, GPHN dysfunction produces progressive neurological damage in early childhood, with phenotypes resembling hyperekplexia (startle disease), though gephyrin mutations are less frequent than glycine receptor alterations in this condition 2. Additionally, the GPHN locus at 14q23.3 contains the FRA14B common fragile site, where focal deletions occur in approximately 5% of cancer cells and germline copy number variants associate with neurodevelopmental disorders including autism spectrum disorder 45.

Sources cited
1
GPHN gene structure (27 exons, ~800 kb on chromosome 14q), dual functions in GlyR localization and molybdenum cofactor biosynthesis, disease associations with molybdenum cofactor deficiency
PMID: 11418245
2
GPHN generates 11 transcript isoforms (10 neuronal-specific) through alternative splicing, GlyR clustering mechanism via C-terminal MoeA homology domain, missense mutation analysis in hyperekplexia
PMID: 12684523
3
GPHN mutations cause molybdenum cofactor deficiency type C, role in biosynthesis of all molybdoenzymes, inheritance pattern and clinical outcomes
PMID: 21031595
4
GPHN location within FRA14B common fragile site at 14q23.3, focal deletions disrupting GPHN in ~5% of cancer cells, germline CNVs associated with neurodevelopmental disorders
PMID: 30411419
5
GPHN identified as candidate gene for autism spectrum disorder susceptibility through CNV and SNV analysis
PMID: 32081867
Disease Associationsβ“˜21
sulfite oxidase deficiency due to molybdenum cofactor deficiency type COpen Targets
0.78Strong
encephalopathy due to sulfite oxidase deficiencyOpen Targets
0.55Moderate
hereditary hyperekplexiaOpen Targets
0.48Moderate
developmental and epileptic encephalopathyOpen Targets
0.37Weak
genetic developmental and epileptic encephalopathyOpen Targets
0.37Weak
post term pregnancyOpen Targets
0.29Weak
colorectal carcinomaOpen Targets
0.27Weak
cervical carcinomaOpen Targets
0.27Weak
infectious meningitisOpen Targets
0.27Weak
exostosisOpen Targets
0.25Weak
placenta praeviaOpen Targets
0.25Weak
HydrocephalusOpen Targets
0.23Weak
neoplasmOpen Targets
0.20Weak
genetic disorderOpen Targets
0.19Weak
melanomaOpen Targets
0.19Weak
clear cell renal carcinomaOpen Targets
0.19Weak
lung adenocarcinomaOpen Targets
0.19Weak
urinary bladder carcinomaOpen Targets
0.19Weak
squamous cell lung carcinomaOpen Targets
0.19Weak
acute myeloid leukemiaOpen Targets
0.19Weak
Molybdenum cofactor deficiency CUniProt
Pathogenic Variants48
NM_020806.5(GPHN):c.828+1G>ALikely pathogenic
Sulfite oxidase deficiency due to molybdenum cofactor deficiency type C
β˜…β˜…β˜†β˜†2025
NM_020806.5(GPHN):c.577_578del (p.Leu193fs)Pathogenic
not provided|Sulfite oxidase deficiency due to molybdenum cofactor deficiency type C
β˜…β˜…β˜†β˜†2023β†’ Residue 193
NM_020806.5(GPHN):c.744C>G (p.Tyr248Ter)Pathogenic
Sulfite oxidase deficiency due to molybdenum cofactor deficiency type C
β˜…β˜†β˜†β˜†2026β†’ Residue 248
NM_020806.5(GPHN):c.1666C>T (p.Arg556Ter)Pathogenic
Sulfite oxidase deficiency due to molybdenum cofactor deficiency type C
β˜…β˜†β˜†β˜†2026β†’ Residue 556
NM_020806.5(GPHN):c.747_748dup (p.Ser250fs)Pathogenic
Sulfite oxidase deficiency due to molybdenum cofactor deficiency type C
β˜…β˜†β˜†β˜†2025β†’ Residue 250
NM_020806.5(GPHN):c.2079+2T>CLikely pathogenic
Sulfite oxidase deficiency due to molybdenum cofactor deficiency type C|Hepatocellular carcinoma
β˜…β˜†β˜†β˜†2025
NM_020806.5(GPHN):c.828+1G>TLikely pathogenic
Sulfite oxidase deficiency due to molybdenum cofactor deficiency type C
β˜…β˜†β˜†β˜†2025
NM_020806.5(GPHN):c.1560del (p.Thr520_Val521insTer)Pathogenic
Sulfite oxidase deficiency due to molybdenum cofactor deficiency type C
β˜…β˜†β˜†β˜†2024β†’ Residue 520
NM_020806.5(GPHN):c.1463A>G (p.Gln488Arg)Pathogenic
Sulfite oxidase deficiency due to molybdenum cofactor deficiency type C
β˜…β˜†β˜†β˜†2024β†’ Residue 488
NM_020806.5(GPHN):c.802_803insG (p.Tyr268Ter)Pathogenic
Sulfite oxidase deficiency due to molybdenum cofactor deficiency type C
β˜…β˜†β˜†β˜†2024β†’ Residue 268
NM_020806.5(GPHN):c.1156C>T (p.Arg386Ter)Pathogenic
Sulfite oxidase deficiency due to molybdenum cofactor deficiency type C
β˜…β˜†β˜†β˜†2024β†’ Residue 386
NM_020806.5(GPHN):c.770_771del (p.His257fs)Pathogenic
Sulfite oxidase deficiency due to molybdenum cofactor deficiency type C
β˜…β˜†β˜†β˜†2024β†’ Residue 257
NM_020806.5(GPHN):c.1472+1G>ALikely pathogenic
Sulfite oxidase deficiency due to molybdenum cofactor deficiency type C
β˜…β˜†β˜†β˜†2024
NM_020806.5(GPHN):c.158dup (p.Ser54fs)Pathogenic
Sulfite oxidase deficiency due to molybdenum cofactor deficiency type C
β˜…β˜†β˜†β˜†2024β†’ Residue 54
NM_020806.5(GPHN):c.788del (p.Pro263fs)Pathogenic
Sulfite oxidase deficiency due to molybdenum cofactor deficiency type C
β˜…β˜†β˜†β˜†2024β†’ Residue 263
NM_020806.5(GPHN):c.277C>T (p.Arg93Ter)Pathogenic
Sulfite oxidase deficiency due to molybdenum cofactor deficiency type C
β˜…β˜†β˜†β˜†2024β†’ Residue 93
NM_020806.5(GPHN):c.1834A>T (p.Lys612Ter)Pathogenic
Sulfite oxidase deficiency due to molybdenum cofactor deficiency type C
β˜…β˜†β˜†β˜†2024β†’ Residue 612
NM_020806.5(GPHN):c.400G>A (p.Gly134Arg)Pathogenic
Sulfite oxidase deficiency due to molybdenum cofactor deficiency type C
β˜…β˜†β˜†β˜†2024β†’ Residue 134
NM_020806.5(GPHN):c.294+1G>TLikely pathogenic
Sulfite oxidase deficiency due to molybdenum cofactor deficiency type C
β˜…β˜†β˜†β˜†2024
NM_020806.5(GPHN):c.1275dup (p.Ser426fs)Pathogenic
Sulfite oxidase deficiency due to molybdenum cofactor deficiency type C
β˜…β˜†β˜†β˜†2023β†’ Residue 426
View on ClinVar β†—
Related Genes
VASPProtein interaction100%NLGN2Protein interaction100%NLGN1Protein interaction100%NLGN4XProtein interaction100%GLRA1Protein interaction100%GLRBProtein interaction100%
Tissue Expression6 tissues
Liver
100%
Brain
51%
Heart
49%
Ovary
25%
Lung
24%
Bone Marrow
17%
Gene Interaction Network
Click a node to explore
GPHNVASPNLGN2NLGN1NLGN4XGLRA1GLRB
PROTEIN STRUCTURE
Preparing viewer…
PDB1JLJ Β· 1.60 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.24Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.09 [0.04–0.24]
RankingsWhere GPHN stands among ~20K protein-coding genes
  • #3,852of 20,598
    Most Researched122 Β· top quartile
  • #1,368of 5,498
    Most Pathogenic Variants48 Β· top quartile
  • #701of 17,882
    Most Constrained (LOEUF)0.24 Β· top 5%
Genes detectedGPHN
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
The human gephyrin (GPHN) gene: structure, chromosome localization and expression in non-neuronal cells.
PMID: 11418245
Gene Β· 2001
1.00
2
Anti-BCL2 therapy eliminates giant congenital melanocytic nevus by senolytic and immune induction.
PMID: 40374605
Signal Transduct Target Ther Β· 2025
0.90
3
Isoform heterogeneity of the human gephyrin gene (GPHN), binding domains to the glycine receptor, and mutation analysis in hyperekplexia.
PMID: 12684523
J Biol Chem Β· 2003
0.80
4
Topical therapy for regression and melanoma prevention of congenital giant nevi.
PMID: 35561684
Cell Β· 2022
0.70
5
Melanoma on congenital melanocytic nevi.
PMID: 38518732
Pathol Res Pract Β· 2024
0.60