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| Open reading frame (ORF) annotation in the exon skipping event |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
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Gene summary for HNF4A |
 Gene summary |
| Gene information | Gene symbol | HNF4A | Gene ID | 3172 |
| Gene name | hepatocyte nuclear factor 4 alpha | |
| Synonyms | FRTS4|HNF4|HNF4a7|HNF4a8|HNF4a9|HNF4alpha|MODY|MODY1|NR2A1|NR2A21|TCF|TCF14 | |
| Cytomap | 20q13.12 | |
| Type of gene | protein-coding | |
| Description | hepatocyte nuclear factor 4-alphaHNF4alpha10/11/12TCF-14hepatic nuclear factor 4 alphanuclear receptor subfamily 2 group A member 1transcription factor 14transcription factor HNF-4 | |
| Modification date | 20180528 | |
| UniProtAcc | P41235 | |
| Context | PubMed: HNF4A [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| HNF4A | GO:0006357 | regulation of transcription by RNA polymerase II | 10330009|12911579 |
| HNF4A | GO:0007596 | blood coagulation | 12911579 |
| HNF4A | GO:0019216 | regulation of lipid metabolic process | 10551874 |
| HNF4A | GO:0045893 | positive regulation of transcription, DNA-templated | 16488887 |
| HNF4A | GO:0045944 | positive regulation of transcription by RNA polymerase II | 7615825 |
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Exon skipping events across known transcript of Ensembl for HNF4A from UCSC genome browser |
| Skipped exons in TCGA and GTEx 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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Gene isoform structures and expression levels for HNF4A |
| Expression levels of gene isoforms across TCGA. |
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| Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for HNF4A |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_352133 | 20 | 42984444:42984493:43019097:43019319:43034697:43034872 | 43019097:43019319 | ENSG00000101076.12 | ENST00000609262.1 |
| exon_skip_352143 | 20 | 43029940:43030127:43031193:43031284:43034697:43034872 | 43031193:43031284 | ENSG00000101076.12 | ENST00000372920.1 |
| exon_skip_352144 | 20 | 43034697:43034872:43036020:43036115:43042333:43042440 | 43036020:43036115 | ENSG00000101076.12 | ENST00000316673.4,ENST00000443598.2,ENST00000415691.2,ENST00000372920.1,ENST00000457232.1,ENST00000609795.1,ENST00000316099.4 |
| exon_skip_352145 | 20 | 43043146:43043302:43047064:43047152:43048360:43048516 | 43047064:43047152 | ENSG00000101076.12 | ENST00000316673.4,ENST00000443598.2,ENST00000415691.2,ENST00000372920.1,ENST00000457232.1,ENST00000609795.1,ENST00000316099.4 |
| exon_skip_352146 | 20 | 43047064:43047152:43048360:43048516:43052657:43052894 | 43048360:43048516 | ENSG00000101076.12 | ENST00000316673.4,ENST00000443598.2,ENST00000415691.2,ENST00000372920.1,ENST00000457232.1,ENST00000609795.1,ENST00000316099.4 |
| exon_skip_352148 | 20 | 43048360:43048516:43052657:43052894:43056974:43057097 | 43052657:43052894 | ENSG00000101076.12 | ENST00000316673.4,ENST00000415691.2,ENST00000372920.1,ENST00000457232.1,ENST00000316099.4 |
| exon_skip_352151 | 20 | 43052657:43052894:43056974:43057097:43058162:43058311 | 43056974:43057097 | ENSG00000101076.12 | ENST00000415691.2,ENST00000457232.1 |
| exon_skip_352153 | 20 | 43052657:43052894:43056974:43057127:43058162:43058311 | 43056974:43057127 | ENSG00000101076.12 | ENST00000316673.4,ENST00000372920.1,ENST00000316099.4 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for HNF4A |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_352143 | 20 | 43029940:43030127:43031193:43031284:43034697:43034872 | 43031193:43031284 | ENSG00000101076.12 | ENST00000372920.1 |
| exon_skip_352144 | 20 | 43034697:43034872:43036020:43036115:43042333:43042440 | 43036020:43036115 | ENSG00000101076.12 | ENST00000316673.4,ENST00000609795.1,ENST00000457232.1,ENST00000372920.1,ENST00000443598.2,ENST00000316099.4,ENST00000415691.2 |
| exon_skip_352145 | 20 | 43043146:43043302:43047064:43047152:43048360:43048516 | 43047064:43047152 | ENSG00000101076.12 | ENST00000316673.4,ENST00000609795.1,ENST00000457232.1,ENST00000372920.1,ENST00000443598.2,ENST00000316099.4,ENST00000415691.2 |
| exon_skip_352146 | 20 | 43047064:43047152:43048360:43048516:43052657:43052894 | 43048360:43048516 | ENSG00000101076.12 | ENST00000316673.4,ENST00000609795.1,ENST00000457232.1,ENST00000372920.1,ENST00000443598.2,ENST00000316099.4,ENST00000415691.2 |
| exon_skip_352148 | 20 | 43048360:43048516:43052657:43052894:43056974:43057097 | 43052657:43052894 | ENSG00000101076.12 | ENST00000316673.4,ENST00000457232.1,ENST00000372920.1,ENST00000316099.4,ENST00000415691.2 |
| exon_skip_352151 | 20 | 43052657:43052894:43056974:43057097:43058162:43058311 | 43056974:43057097 | ENSG00000101076.12 | ENST00000457232.1,ENST00000415691.2 |
| exon_skip_352153 | 20 | 43052657:43052894:43056974:43057127:43058162:43058311 | 43056974:43057127 | ENSG00000101076.12 | ENST00000316673.4,ENST00000372920.1,ENST00000316099.4 |
| PSI values of skipped exons in GTEx. |
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| * Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for HNF4A |
| Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000316099 | 43036020 | 43036115 | Frame-shift |
| ENST00000316099 | 43047064 | 43047152 | Frame-shift |
| ENST00000316099 | 43048360 | 43048516 | In-frame |
| ENST00000316099 | 43052657 | 43052894 | In-frame |
| ENST00000316099 | 43056974 | 43057127 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000316099 | 43036020 | 43036115 | Frame-shift |
| ENST00000316099 | 43047064 | 43047152 | Frame-shift |
| ENST00000316099 | 43048360 | 43048516 | In-frame |
| ENST00000316099 | 43052657 | 43052894 | In-frame |
| ENST00000316099 | 43056974 | 43057127 | In-frame |
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Infer the effects of exon skipping event on protein functional features for HNF4A |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
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| Loci of skipped exons in TCGA 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 |
| ENST00000316099 | 4711 | 474 | 43048360 | 43048516 | 826 | 981 | 245 | 297 |
| ENST00000316099 | 4711 | 474 | 43052657 | 43052894 | 982 | 1218 | 297 | 376 |
| ENST00000316099 | 4711 | 474 | 43056974 | 43057127 | 1219 | 1371 | 376 | 427 |
| Loci of skipped exons in GTEx 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 |
| ENST00000316099 | 4711 | 474 | 43048360 | 43048516 | 826 | 981 | 245 | 297 |
| ENST00000316099 | 4711 | 474 | 43052657 | 43052894 | 982 | 1218 | 297 | 376 |
| ENST00000316099 | 4711 | 474 | 43056974 | 43057127 | 1219 | 1371 | 376 | 427 |
| Lost protein functional features of individual exon skipping events in TCGA. |
| 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 |
| Lost protein functional features of individual exon skipping events in GTEx. |
| 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 |
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SNVs in the skipped exons for HNF4A |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
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| - Differential PSIs between mutated versus non-mutated samples. |
| - Non-synonymous mutations located in the skipped exons in TCGA. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| STAD | TCGA-BR-4183-01 | exon_skip_352133 | 43019098 | 43019319 | 43019236 | 43019236 | Frame_Shift_Del | A | - | p.K2fs |
| LUAD | TCGA-62-A46P-01 | exon_skip_352144 | 43036021 | 43036115 | 43036056 | 43036056 | Frame_Shift_Del | G | - | p.R109fs |
| STAD | TCGA-BR-4257-01 | exon_skip_352145 | 43047065 | 43047152 | 43047140 | 43047140 | Frame_Shift_Del | G | - | p.D241fs |
| STAD | TCGA-BR-4257-01 | exon_skip_352145 | 43047065 | 43047152 | 43047140 | 43047140 | Frame_Shift_Del | G | - | p.V242fs |
| LIHC | TCGA-BC-A3KG-01 | exon_skip_352146 | 43048361 | 43048516 | 43048503 | 43048503 | Frame_Shift_Del | C | - | p.I293fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_352148 | 43052658 | 43052894 | 43052725 | 43052725 | Frame_Shift_Del | G | - | p.E320fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_352151 | 43056975 | 43057097 | 43057006 | 43057006 | Frame_Shift_Del | C | - | p.H387fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_352153 | 43056975 | 43057127 | 43057006 | 43057006 | Frame_Shift_Del | C | - | p.H387fs |
| KIRP | TCGA-MH-A560-01 | exon_skip_352148 | 43052658 | 43052894 | 43052875 | 43052876 | Frame_Shift_Ins | - | C | p.L363fs |
| KIRP | TCGA-MH-A560-01 | exon_skip_352148 | 43052658 | 43052894 | 43052875 | 43052876 | Frame_Shift_Ins | - | C | p.L370fs |
| SKCM | TCGA-D9-A6EC-06 | exon_skip_352148 | 43052658 | 43052894 | 43052705 | 43052705 | Nonsense_Mutation | C | T | p.Q292X |
| SKCM | TCGA-D9-A6EC-06 | exon_skip_352148 | 43052658 | 43052894 | 43052705 | 43052705 | Nonsense_Mutation | C | T | p.Q314* |
| SKCM | TCGA-D3-A1Q6-06 | exon_skip_352148 | 43052658 | 43052894 | 43052831 | 43052831 | Nonsense_Mutation | C | T | p.Q334X |
| SKCM | TCGA-D3-A1Q6-06 | exon_skip_352148 | 43052658 | 43052894 | 43052831 | 43052831 | Nonsense_Mutation | C | T | p.Q356* |
| STAD | TCGA-CG-5723-01 | exon_skip_352153 | 43056975 | 43057127 | 43057109 | 43057109 | Nonsense_Mutation | C | T | p.R422* |
| STAD | TCGA-CG-5723-01 | exon_skip_352153 | 43056975 | 43057127 | 43057109 | 43057109 | Nonsense_Mutation | C | T | p.R422X |
| LIHC | TCGA-ZP-A9D2-01 | exon_skip_352148 | 43052658 | 43052894 | 43052656 | 43052656 | Splice_Site | A | T | . |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
| - 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 |
| CROAP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 43036021 | 43036115 | 43036037 | 43036037 | Missense_Mutation | G | A | p.V103M |
| HCT15_LARGE_INTESTINE | 43036021 | 43036115 | 43036063 | 43036063 | Missense_Mutation | G | T | p.Q111H |
| HEC6_ENDOMETRIUM | 43048361 | 43048516 | 43048411 | 43048411 | Missense_Mutation | C | T | p.R263W |
| SNU1040_LARGE_INTESTINE | 43048361 | 43048516 | 43048411 | 43048411 | Missense_Mutation | C | T | p.R263W |
| R262_CENTRAL_NERVOUS_SYSTEM | 43048361 | 43048516 | 43048429 | 43048429 | Missense_Mutation | C | T | p.L269F |
| NCIH1373_LUNG | 43048361 | 43048516 | 43048444 | 43048444 | Missense_Mutation | C | A | p.L274M |
| EGI1_BILIARY_TRACT | 43052658 | 43052894 | 43052694 | 43052694 | Missense_Mutation | G | A | p.R310Q |
| A3KAW_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 43052658 | 43052894 | 43052700 | 43052700 | Missense_Mutation | G | A | p.R312H |
| SW1783_CENTRAL_NERVOUS_SYSTEM | 43052658 | 43052894 | 43052700 | 43052700 | Missense_Mutation | G | A | p.R312H |
| SAT_UPPER_AERODIGESTIVE_TRACT | 43052658 | 43052894 | 43052742 | 43052742 | Missense_Mutation | G | C | p.R326P |
| SNU1040_LARGE_INTESTINE | 43052658 | 43052894 | 43052756 | 43052756 | Missense_Mutation | C | T | p.R331C |
| NCIH1436_LUNG | 43052658 | 43052894 | 43052762 | 43052762 | Missense_Mutation | C | A | p.R333S |
| CORL321_PLEURA | 43056975 | 43057097 | 43056981 | 43056981 | Missense_Mutation | C | A | p.P379H |
| CORL321_PLEURA | 43056975 | 43057127 | 43056981 | 43056981 | Missense_Mutation | C | A | p.P379H |
| ATN1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 43056975 | 43057097 | 43056999 | 43056999 | Missense_Mutation | C | T | p.A385V |
| ATN1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 43056975 | 43057127 | 43056999 | 43056999 | Missense_Mutation | C | T | p.A385V |
| KNS42_CENTRAL_NERVOUS_SYSTEM | 43056975 | 43057097 | 43056999 | 43056999 | Missense_Mutation | C | T | p.A385V |
| KNS42_CENTRAL_NERVOUS_SYSTEM | 43056975 | 43057127 | 43056999 | 43056999 | Missense_Mutation | C | T | p.A385V |
| CP66MEL_SKIN | 43056975 | 43057097 | 43057027 | 43057027 | Missense_Mutation | G | A | p.M394I |
| CP66MEL_SKIN | 43056975 | 43057127 | 43057027 | 43057027 | Missense_Mutation | G | A | p.M394I |
| ATN1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 43056975 | 43057097 | 43057038 | 43057038 | Missense_Mutation | T | C | p.M398T |
| ATN1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 43056975 | 43057127 | 43057038 | 43057038 | Missense_Mutation | T | C | p.M398T |
| KNS42_CENTRAL_NERVOUS_SYSTEM | 43056975 | 43057097 | 43057038 | 43057038 | Missense_Mutation | T | C | p.M398T |
| KNS42_CENTRAL_NERVOUS_SYSTEM | 43056975 | 43057127 | 43057038 | 43057038 | Missense_Mutation | T | C | p.M398T |
| MOLT3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 43056975 | 43057097 | 43057055 | 43057055 | Missense_Mutation | G | A | p.V404I |
| MOLT3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 43056975 | 43057127 | 43057055 | 43057055 | Missense_Mutation | G | A | p.V404I |
| MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 43056975 | 43057097 | 43057055 | 43057055 | Missense_Mutation | G | A | p.V404I |
| MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 43056975 | 43057127 | 43057055 | 43057055 | Missense_Mutation | G | A | p.V404I |
| HEC265_ENDOMETRIUM | 43056975 | 43057097 | 43057056 | 43057056 | Missense_Mutation | T | C | p.V404A |
| HEC265_ENDOMETRIUM | 43056975 | 43057127 | 43057056 | 43057056 | Missense_Mutation | T | C | p.V404A |
| BICR16_UPPER_AERODIGESTIVE_TRACT | 43036021 | 43036115 | 43036085 | 43036085 | Nonsense_Mutation | A | T | p.K119* |
| NCIH513_PLEURA | 43048361 | 43048516 | 43048435 | 43048435 | Nonsense_Mutation | G | T | p.E271* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for HNF4A |
| sQTL information located at the skipped exons. |
| Exon skip ID | Chromosome | Three exons | Skippped exon | ENST | Cancer type | SNP id | Location | DNA change (ref/var) | P-value |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for HNF4A |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for HNF4A |
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RelatedDrugs for HNF4A |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for HNF4A |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| HNF4A | C1852093 | Maturity-Onset Diabetes of the Young, Type 1 | 5 | CTD_human;UNIPROT |
| HNF4A | C0011860 | Diabetes Mellitus, Non-Insulin-Dependent | 4 | CTD_human;ORPHANET;UNIPROT |
| HNF4A | C4014962 | FANCONI RENOTUBULAR SYNDROME 4 WITH MATURITY-ONSET DIABETES OF THE YOUNG | 2 | UNIPROT |
| HNF4A | C0009324 | Ulcerative Colitis | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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