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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 GGCX |
 Gene summary |
| Gene information | Gene symbol | GGCX | Gene ID | 2677 |
| Gene name | gamma-glutamyl carboxylase | |
| Synonyms | VKCFD1 | |
| Cytomap | 2p11.2 | |
| Type of gene | protein-coding | |
| Description | vitamin K-dependent gamma-carboxylasepeptidyl-glutamate 4-carboxylase | |
| Modification date | 20180519 | |
| UniProtAcc | P38435 | |
| Context | PubMed: GGCX [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 |
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Exon skipping events across known transcript of Ensembl for GGCX 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 GGCX |
| 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 GGCX |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_340759 | 2 | 85778959:85779104:85779538:85779690:85780061:85780193 | 85779538:85779690 | ENSG00000115486.7 | ENST00000233838.4,ENST00000430215.3 |
| exon_skip_340761 | 2 | 85780354:85780620:85781265:85781429:85782606:85782713 | 85781265:85781429 | ENSG00000115486.7 | ENST00000233838.4,ENST00000430215.3 |
| exon_skip_340769 | 2 | 85782606:85782713:85783304:85783383:85785562:85785728 | 85783304:85783383 | ENSG00000115486.7 | ENST00000233838.4,ENST00000430215.3 |
| exon_skip_340770 | 2 | 85782606:85782713:85783304:85783383:85785661:85785785 | 85783304:85783383 | ENSG00000115486.7 | ENST00000423570.1 |
| exon_skip_340777 | 2 | 85783340:85783383:85785562:85785728:85786039:85786198 | 85785562:85785728 | ENSG00000115486.7 | ENST00000233838.4,ENST00000430215.3 |
| exon_skip_340778 | 2 | 85783340:85783383:85785562:85785785:85786039:85786198 | 85785562:85785785 | ENSG00000115486.7 | ENST00000428479.3 |
| exon_skip_340785 | 2 | 85786128:85786198:85787937:85788108:85788508:85788596 | 85787937:85788108 | ENSG00000115486.7 | ENST00000496962.1,ENST00000423570.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for GGCX |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_340759 | 2 | 85778959:85779104:85779538:85779690:85780061:85780193 | 85779538:85779690 | ENSG00000115486.7 | ENST00000233838.4,ENST00000430215.3 |
| exon_skip_340761 | 2 | 85780354:85780620:85781265:85781429:85782606:85782713 | 85781265:85781429 | ENSG00000115486.7 | ENST00000233838.4,ENST00000430215.3 |
| exon_skip_340769 | 2 | 85782606:85782713:85783304:85783383:85785562:85785728 | 85783304:85783383 | ENSG00000115486.7 | ENST00000233838.4,ENST00000430215.3 |
| exon_skip_340770 | 2 | 85782606:85782713:85783304:85783383:85785661:85785785 | 85783304:85783383 | ENSG00000115486.7 | ENST00000423570.1 |
| exon_skip_340777 | 2 | 85783340:85783383:85785562:85785728:85786039:85786198 | 85785562:85785728 | ENSG00000115486.7 | ENST00000233838.4,ENST00000430215.3 |
| exon_skip_340778 | 2 | 85783340:85783383:85785562:85785785:85786039:85786198 | 85785562:85785785 | ENSG00000115486.7 | ENST00000428479.3 |
| exon_skip_340785 | 2 | 85786128:85786198:85787937:85788108:85788508:85788596 | 85787937:85788108 | ENSG00000115486.7 | ENST00000423570.1,ENST00000496962.1 |
| 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 GGCX |
| 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 |
| ENST00000233838 | 85779538 | 85779690 | Frame-shift |
| ENST00000233838 | 85781265 | 85781429 | Frame-shift |
| ENST00000233838 | 85783304 | 85783383 | Frame-shift |
| ENST00000233838 | 85785562 | 85785728 | Frame-shift |
| 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 |
| ENST00000233838 | 85779538 | 85779690 | Frame-shift |
| ENST00000233838 | 85781265 | 85781429 | Frame-shift |
| ENST00000233838 | 85783304 | 85783383 | Frame-shift |
| ENST00000233838 | 85785562 | 85785728 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for GGCX |
| 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 |
| 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 |
| 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 GGCX |
| - 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 |
| HNSC | TCGA-CV-7438-01 | exon_skip_340759 | 85779539 | 85779690 | 85779683 | 85779683 | Frame_Shift_Del | G | - | p.T432fs |
| OV | TCGA-23-1118-01 | exon_skip_340777 | 85785563 | 85785728 | 85785630 | 85785643 | Frame_Shift_Del | TCCATGATGTCTTG | - | p.D153fs |
| OV | TCGA-23-1118-01 | exon_skip_340778 | 85785563 | 85785785 | 85785630 | 85785643 | Frame_Shift_Del | TCCATGATGTCTTG | - | p.D153fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_340777 | 85785563 | 85785728 | 85785645 | 85785645 | Frame_Shift_Del | C | - | p.D153fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_340778 | 85785563 | 85785785 | 85785645 | 85785645 | Frame_Shift_Del | C | - | p.D153fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_340785 | 85787938 | 85788108 | 85788002 | 85788002 | Frame_Shift_Del | C | - | p.R50fs |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-23-1118-01 |
| Cancer type: OV | |
| ESID: exon_skip_340777 | |
| Skipped exon start: 85785563 | |
| Skipped exon end: 85785728 | |
| Mutation start: 85785630 | |
| Mutation end: 85785643 | |
| Mutation type: Frame_Shift_Del | |
| Reference seq: TCCATGATGTCTTG | |
| Mutation seq: - | |
| AAchange: p.D153fs | |
| Sample: TCGA-23-1118-01 |
| Cancer type: OV | |
| ESID: exon_skip_340778 | |
| Skipped exon start: 85785563 | |
| Skipped exon end: 85785785 | |
| Mutation start: 85785630 | |
| Mutation end: 85785643 | |
| Mutation type: Frame_Shift_Del | |
| Reference seq: TCCATGATGTCTTG | |
| Mutation seq: - | |
| AAchange: p.D153fs | |
exon_skip_340777_OV_TCGA-23-1118-01.png | |
exon_skip_340778_OV_TCGA-23-1118-01.png | |
 | Sample: TCGA-23-1118-01 |
| Cancer type: OV | |
| ESID: exon_skip_340777 | |
| Skipped exon start: 85785563 | |
| Skipped exon end: 85785728 | |
| Mutation start: 85785630 | |
| Mutation end: 85785643 | |
| Mutation type: Frame_Shift_Del | |
| Reference seq: TCCATGATGTCTTG | |
| Mutation seq: - | |
| AAchange: p.D153fs | |
| Sample: TCGA-23-1118-01 |
| Cancer type: OV | |
| ESID: exon_skip_340778 | |
| Skipped exon start: 85785563 | |
| Skipped exon end: 85785785 | |
| Mutation start: 85785630 | |
| Mutation end: 85785643 | |
| Mutation type: Frame_Shift_Del | |
| Reference seq: TCCATGATGTCTTG | |
| Mutation seq: - | |
| AAchange: p.D153fs | |
| exon_skip_340777_OV_TCGA-23-1118-01.png | |
| exon_skip_340778_OV_TCGA-23-1118-01.png | |
| - 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 |
| VMRCRCW_KIDNEY | 85787938 | 85788108 | 85788101 | 85788103 | In_Frame_Del | TAC | - | p.V17del |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 85779539 | 85779690 | 85779620 | 85779620 | Missense_Mutation | C | A | p.R453L |
| SNU1040_LARGE_INTESTINE | 85779539 | 85779690 | 85779620 | 85779620 | Missense_Mutation | C | T | p.R453H |
| DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 85779539 | 85779690 | 85779620 | 85779620 | Missense_Mutation | C | A | p.R453L |
| OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 85779539 | 85779690 | 85779620 | 85779620 | Missense_Mutation | C | A | p.R453L |
| RERFLCAD2_LUNG | 85779539 | 85779690 | 85779633 | 85779633 | Missense_Mutation | T | A | p.T449S |
| MHHPREB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 85781266 | 85781429 | 85781323 | 85781323 | Missense_Mutation | T | C | p.I278V |
| PL18_PANCREAS | 85781266 | 85781429 | 85781346 | 85781346 | Missense_Mutation | A | G | p.L270P |
| SNU719_STOMACH | 85781266 | 85781429 | 85781413 | 85781413 | Missense_Mutation | C | T | p.E248K |
| RL952_ENDOMETRIUM | 85787938 | 85788108 | 85787943 | 85787943 | Missense_Mutation | A | T | p.L70H |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for GGCX |
| 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 GGCX |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for GGCX |
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RelatedDrugs for GGCX |
| 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 |
| P38435 | DB00036 | Coagulation factor VIIa Recombinant Human | Vitamin K-dependent gamma-carboxylase | biotech | approved | |
| P38435 | DB01022 | Phylloquinone | Vitamin K-dependent gamma-carboxylase | small molecule | approved|investigational | |
| P38435 | DB00055 | Drotrecogin alfa | Vitamin K-dependent gamma-carboxylase | biotech | approved|investigational|withdrawn | |
| P38435 | DB00142 | Glutamic Acid | Vitamin K-dependent gamma-carboxylase | small molecule | approved|nutraceutical | |
| P38435 | DB00170 | Menadione | Vitamin K-dependent gamma-carboxylase | small molecule | approved|nutraceutical |
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RelatedDiseases for GGCX |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| GGCX | C1848534 | VITAMIN K-DEPENDENT CLOTTING FACTORS, COMBINED DEFICIENCY OF, 1 | 4 | CTD_human;ORPHANET;UNIPROT |
| GGCX | C0005779 | Blood Coagulation Disorders | 1 | CTD_human |
| GGCX | C1835813 | Pseudoxanthoma Elasticum-Like Disorder with Multiple Coagulation Factor Deficiency | 1 | CTD_human;ORPHANET;UNIPROT |
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