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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for GPHN |
 Gene summary |
| Gene information | Gene symbol | GPHN | Gene ID | 10243 |
| Gene name | gephyrin | |
| Synonyms | GEPH|GPH|GPHRYN|HKPX1|MOCODC | |
| Cytomap | 14q23.3-q24.1 | |
| Type of gene | protein-coding | |
| Description | gephyrin | |
| Modification date | 20200313 | |
| UniProtAcc | F5H039, | |
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| GPHN | GO:0032324 | molybdopterin cofactor biosynthetic process | 26613940 |
| GPHN | GO:0097112 | gamma-aminobutyric acid receptor clustering | 26613940 |
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Gene structures and expression levels for GPHN |
| Skipped exons in the ROSMAP, MSBB, and Mayo based on Ensembl gene isoform structure. * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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ENSG00000171723
| Differentially expressed gene analysis across multiple brain tissues between AD and control. |
| Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
| Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| CB | DOWN | ENST00000556240.1 | GPHN-212:protein_coding:GPHN | 1.786924e+02 | -1.168102e+00 | 2.350838e-16 | 1.817124e-13 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for GPHN |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_11254 | chr14 | 67122256:67122377:67143362:67143449:67165162:67165226 | 67143362:67143449 |
| exon_skip_115396 | chr14 | 66681107:66681185:66776464:66776521:66824474:66824566 | 66776464:66776521 |
| exon_skip_121160 | chr14 | 66508516:66508591:66551041:66551181:66681107:66681185 | 66551041:66551181 |
| exon_skip_150179 | chr14 | 66965191:66965325:66985682:66985738:67023633:67023675 | 66985682:66985738 |
| exon_skip_171308 | chr14 | 66776464:66776521:66824474:66824566:66879939:66880032 | 66824474:66824566 |
| exon_skip_172867 | chr14 | 67143367:67143449:67159415:67159488:67165162:67165226 | 67159415:67159488 |
| exon_skip_19664 | chr14 | 67110140:67110259:67111861:67111919:67113018:67113171 | 67111861:67111919 |
| exon_skip_207831 | chr14 | 66922666:66922938:66924194:66924292:66965191:66965325 | 66924194:66924292 |
| exon_skip_209374 | chr14 | 66824474:66824566:66842678:66842716:66879939:66880032 | 66842678:66842716 |
| exon_skip_209516 | chr14 | 66776464:66776521:66842678:66842716:66879939:66880032 | 66842678:66842716 |
| exon_skip_216800 | chr14 | 67165162:67165226:67168933:67169036:67179578:67179674 | 67168933:67169036 |
| exon_skip_222918 | chr14 | 66776464:66776521:66824474:66824566:66842678:66842716 | 66824474:66824566 |
| exon_skip_237972 | chr14 | 66965191:66965325:66985682:66985738:66996177:66996218 | 66985682:66985738 |
| exon_skip_251323 | chr14 | 67143362:67143449:67159415:67159488:67165162:67165226 | 67159415:67159488 |
| exon_skip_254987 | chr14 | 66965191:66965325:67023633:67023675:67058649:67058726 | 67023633:67023675 |
| exon_skip_263894 | chr14 | 66924194:66924292:66965191:66965325:67023633:67023675 | 66965191:66965325 |
| exon_skip_292490 | chr14 | 66879939:66880033:66916003:66916069:66922666:66922758 | 66916003:66916069 |
| exon_skip_34176 | chr14 | 66922721:66922938:66924194:66924292:66965191:66965325 | 66924194:66924292 |
| exon_skip_42177 | chr14 | 67023633:67023675:67058649:67058786:67088983:67089075 | 67058649:67058786 |
| exon_skip_46877 | chr14 | 67122256:67122377:67143362:67143449:67159415:67159488 | 67143362:67143449 |
| exon_skip_52931 | chr14 | 66824474:66824566:66879939:66880033:66916003:66916034 | 66879939:66880033 |
| exon_skip_68641 | chr14 | 67088983:67089075:67100856:67100911:67110140:67110259 | 67100856:67100911 |
| exon_skip_72995 | chr14 | 66922666:66922938:66965191:66965325:67023633:67023675 | 66965191:66965325 |
| exon_skip_78087 | chr14 | 66681107:66681185:66709357:66709458:66776464:66776521 | 66709357:66709458 |
| exon_skip_92227 | chr14 | 66985682:66985738:66996177:66996218:67023633:67023675 | 66996177:66996218 |
| exon_skip_96909 | chr14 | 66965224:66965325:66985682:66985738:67023633:67023675 | 66985682:66985738 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
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Open reading frame (ORF) annotation in the exon skipping event for GPHN |
| Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000315266 | 66776464 | 66776521 | Frame-shift |
| ENST00000315266 | 66916003 | 66916069 | Frame-shift |
| ENST00000315266 | 67023633 | 67023675 | Frame-shift |
| ENST00000315266 | 67100856 | 67100911 | Frame-shift |
| ENST00000315266 | 67111861 | 67111919 | Frame-shift |
| ENST00000315266 | 67143362 | 67143449 | Frame-shift |
| ENST00000315266 | 67159415 | 67159488 | Frame-shift |
| ENST00000315266 | 67168933 | 67169036 | Frame-shift |
| ENST00000315266 | 66824474 | 66824566 | In-frame |
| ENST00000315266 | 66965191 | 66965325 | In-frame |
| ENST00000315266 | 67058649 | 67058786 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000315266 | 66776464 | 66776521 | Frame-shift |
| ENST00000315266 | 66916003 | 66916069 | Frame-shift |
| ENST00000315266 | 67159415 | 67159488 | Frame-shift |
| ENST00000315266 | 67058649 | 67058786 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000315266 | 66776464 | 66776521 | Frame-shift |
| ENST00000315266 | 66879939 | 66880033 | Frame-shift |
| ENST00000315266 | 66916003 | 66916069 | Frame-shift |
| ENST00000315266 | 67023633 | 67023675 | Frame-shift |
| ENST00000315266 | 67100856 | 67100911 | Frame-shift |
| ENST00000315266 | 67111861 | 67111919 | Frame-shift |
| ENST00000315266 | 67143362 | 67143449 | Frame-shift |
| ENST00000315266 | 67159415 | 67159488 | Frame-shift |
| ENST00000315266 | 67168933 | 67169036 | Frame-shift |
| ENST00000315266 | 66824474 | 66824566 | In-frame |
| ENST00000315266 | 66965191 | 66965325 | In-frame |
| ENST00000315266 | 67058649 | 67058786 | In-frame |
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Infer the effects of exon skipping event on protein functional features for GPHN |
p-ENSG00000171723_img4.png |
| Loci of skipped exons in ROSMAP across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| ENST00000315266 | 4210 | 736 | 66824474 | 66824566 | 1324 | 1415 | 67 | 98 |
| ENST00000315266 | 4210 | 736 | 66965191 | 66965325 | 1852 | 1985 | 243 | 288 |
| ENST00000315266 | 4210 | 736 | 67058649 | 67058786 | 2030 | 2166 | 303 | 348 |
| Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| ENST00000315266 | 4210 | 736 | 67058649 | 67058786 | 2030 | 2166 | 303 | 348 |
| Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| ENST00000315266 | 4210 | 736 | 66824474 | 66824566 | 1324 | 1415 | 67 | 98 |
| ENST00000315266 | 4210 | 736 | 66965191 | 66965325 | 1852 | 1985 | 243 | 288 |
| ENST00000315266 | 4210 | 736 | 67058649 | 67058786 | 2030 | 2166 | 303 | 348 |
| Lost protein functional features of individual exon skipping events in ROSMAP. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| Q9NQX3 | 67 | 98 | 80 | 86 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1JLJ |
| Q9NQX3 | 67 | 98 | 89 | 91 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1JLJ |
| Q9NQX3 | 67 | 98 | 1 | 736 | Chain | ID=PRO_0000170964;Note=Gephyrin |
| Q9NQX3 | 67 | 98 | 63 | 75 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1JLJ |
| Q9NQX3 | 67 | 98 | 96 | 103 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1JLJ |
| Q9NQX3 | 67 | 98 | 14 | 166 | Region | Note=MPT Mo-transferase |
| Q9NQX3 | 243 | 288 | 243 | 243 | Alternative sequence | ID=VSP_021769;Note=In isoform 2. K->KKHPFYTSPAVVMAHGEQPIPGLINYSHHSTDER;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:11418245,ECO:0000303|PubMed:15489334;Dbxref=PMID:11418245,PMID:15489334 |
| Q9NQX3 | 243 | 288 | 1 | 736 | Chain | ID=PRO_0000170964;Note=Gephyrin |
| Q9NQX3 | 243 | 288 | 262 | 262 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q8BUV3 |
| Q9NQX3 | 243 | 288 | 265 | 265 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q8BUV3 |
| Q9NQX3 | 243 | 288 | 266 | 266 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:16964243;Dbxref=PMID:16964243 |
| Q9NQX3 | 243 | 288 | 268 | 268 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q8BUV3 |
| Q9NQX3 | 243 | 288 | 270 | 270 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q8BUV3 |
| Q9NQX3 | 243 | 288 | 140 | 316 | Region | Note=Interaction with GABARAP;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q9NQX3 | 243 | 288 | 261 | 261 | Sequence conflict | Note=A->V;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9NQX3 | 303 | 348 | 1 | 736 | Chain | ID=PRO_0000170964;Note=Gephyrin |
| Q9NQX3 | 303 | 348 | 305 | 305 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24275569;Dbxref=PMID:24275569 |
| Q9NQX3 | 303 | 348 | 140 | 316 | Region | Note=Interaction with GABARAP;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q9NQX3 | 303 | 348 | 326 | 736 | Region | Note=MPT adenylyltransferase |
| Lost protein functional features of individual exon skipping events in MSBB. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| Q9NQX3 | 303 | 348 | 1 | 736 | Chain | ID=PRO_0000170964;Note=Gephyrin |
| Q9NQX3 | 303 | 348 | 305 | 305 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24275569;Dbxref=PMID:24275569 |
| Q9NQX3 | 303 | 348 | 140 | 316 | Region | Note=Interaction with GABARAP;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q9NQX3 | 303 | 348 | 326 | 736 | Region | Note=MPT adenylyltransferase |
| Lost protein functional features of individual exon skipping events in Mayo. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| Q9NQX3 | 67 | 98 | 80 | 86 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1JLJ |
| Q9NQX3 | 67 | 98 | 89 | 91 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1JLJ |
| Q9NQX3 | 67 | 98 | 1 | 736 | Chain | ID=PRO_0000170964;Note=Gephyrin |
| Q9NQX3 | 67 | 98 | 63 | 75 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1JLJ |
| Q9NQX3 | 67 | 98 | 96 | 103 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1JLJ |
| Q9NQX3 | 67 | 98 | 14 | 166 | Region | Note=MPT Mo-transferase |
| Q9NQX3 | 243 | 288 | 243 | 243 | Alternative sequence | ID=VSP_021769;Note=In isoform 2. K->KKHPFYTSPAVVMAHGEQPIPGLINYSHHSTDER;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:11418245,ECO:0000303|PubMed:15489334;Dbxref=PMID:11418245,PMID:15489334 |
| Q9NQX3 | 243 | 288 | 1 | 736 | Chain | ID=PRO_0000170964;Note=Gephyrin |
| Q9NQX3 | 243 | 288 | 262 | 262 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q8BUV3 |
| Q9NQX3 | 243 | 288 | 265 | 265 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q8BUV3 |
| Q9NQX3 | 243 | 288 | 266 | 266 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:16964243;Dbxref=PMID:16964243 |
| Q9NQX3 | 243 | 288 | 268 | 268 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q8BUV3 |
| Q9NQX3 | 243 | 288 | 270 | 270 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q8BUV3 |
| Q9NQX3 | 243 | 288 | 140 | 316 | Region | Note=Interaction with GABARAP;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q9NQX3 | 243 | 288 | 261 | 261 | Sequence conflict | Note=A->V;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9NQX3 | 303 | 348 | 1 | 736 | Chain | ID=PRO_0000170964;Note=Gephyrin |
| Q9NQX3 | 303 | 348 | 305 | 305 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24275569;Dbxref=PMID:24275569 |
| Q9NQX3 | 303 | 348 | 140 | 316 | Region | Note=Interaction with GABARAP;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q9NQX3 | 303 | 348 | 326 | 736 | Region | Note=MPT adenylyltransferase |
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3'-UTR located exon skipping events that lost miRNA binding sites in GPHN |
| 3'-UTR exon skipping evnets lost miRNA binding. |
| Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
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SNVs in the skipped exons for GPHN |
| - Differential PSIs between mutated versus non-mutated samples. |
| - Depth of Coverage in the skipped exon of the mutated samples. |
| - Sashimi plot in the skipped exon of the mutated samples. |
| - Non-synonymous mutations located in the skipped exons. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| - Non-synonymous mutations located in the skipped exons in CCLE. |
| Sample | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
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AD stage-associated exon skippint events for GPHN |
| Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
| AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
| ADstage | MSBB | IFG | exon_skip_150179 | -4.041502e-01 | 3.292407e-02 | chr14 | + | 66965191 | 66965325 | 66985682 | 66985738 | 67023633 | 67023675 |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for GPHN |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
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Correlation with RNA binding proteins (RBPs) for GPHN |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | PCBP2 | exon_skip_207831 | -4.247431e-01 | 4.014797e-08 |
| CB | SRSF9 | exon_skip_207831 | -4.180015e-01 | 6.889375e-08 |
| CB | NUP42 | exon_skip_150179 | 4.924069e-01 | 1.013613e-10 |
| CB | SRSF9 | exon_skip_150179 | 4.498637e-01 | 5.417604e-09 |
| CB | FUBP1 | exon_skip_172867 | -4.665026e-01 | 5.730707e-10 |
| CB | NUP42 | exon_skip_172867 | 4.499468e-01 | 2.678391e-09 |
| CB | PTBP1 | exon_skip_172867 | -4.906854e-01 | 5.169886e-11 |
| DLPFC | KHDRBS2 | exon_skip_150179 | 5.049983e-01 | 2.517135e-17 |
| FL | ELAVL4 | exon_skip_207831 | -4.176769e-01 | 5.426218e-09 |
| HCC | RBM6 | exon_skip_207831 | 5.313508e-01 | 8.771475e-21 |
| HCC | RBM47 | exon_skip_207831 | 4.625593e-01 | 1.653370e-15 |
| HCC | PCBP4 | exon_skip_207831 | 4.825346e-01 | 6.411264e-17 |
| HCC | MSI1 | exon_skip_150179 | -5.040446e-01 | 1.125972e-18 |
| HCC | RBM5 | exon_skip_150179 | -4.238828e-01 | 4.118652e-13 |
| IFG | EWSR1 | exon_skip_209374 | -4.050468e-01 | 3.250121e-02 |
| IFG | ELAVL4 | exon_skip_207831 | -6.953550e-01 | 4.003813e-05 |
| IFG | RBM47 | exon_skip_207831 | 5.050755e-01 | 6.118804e-03 |
| IFG | NOVA1 | exon_skip_207831 | -4.806748e-01 | 9.621318e-03 |
| IFG | IGF2BP2 | exon_skip_150179 | -5.150352e-01 | 5.038447e-03 |
| IFG | KHDRBS3 | exon_skip_150179 | 5.656603e-01 | 1.706279e-03 |
| PCC | ELAVL4 | exon_skip_207831 | -5.535616e-01 | 3.270558e-17 |
| PCC | PCBP4 | exon_skip_207831 | 4.018230e-01 | 4.842067e-09 |
| PCC | MSI1 | exon_skip_96909 | -4.661726e-01 | 3.074412e-12 |
| PG | ELAVL4 | exon_skip_207831 | -5.647006e-01 | 5.205991e-14 |
| PG | NOVA1 | exon_skip_207831 | -4.255514e-01 | 5.678116e-08 |
| PG | KHDRBS3 | exon_skip_150179 | 4.806215e-01 | 4.828178e-10 |
| TC | ELAVL4 | exon_skip_34176 | -8.416909e-01 | 1.902034e-41 |
| TC | HNRNPD | exon_skip_34176 | -5.325936e-01 | 2.299588e-12 |
| TC | NOVA1 | exon_skip_34176 | -6.439990e-01 | 6.127766e-19 |
| TC | KHDRBS2 | exon_skip_150179 | 7.058808e-01 | 1.105331e-24 |
| TC | KHDRBS3 | exon_skip_150179 | 6.986190e-01 | 5.205475e-24 |
| TC | HNRNPA0 | exon_skip_150179 | 6.718430e-01 | 1.078887e-21 |
| TC | NUP42 | exon_skip_150179 | 5.694689e-01 | 1.057277e-14 |
| TC | SRSF9 | exon_skip_150179 | 4.182355e-01 | 6.123915e-08 |
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RelatedDrugs for GPHN |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| Q9NQX3 | approved|vet_approved | DB03766 | Propanoic acid | small molecule | Q9NQX3 |
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RelatedDiseases for GPHN |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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