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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 BCKDK |
 Gene summary |
| Gene information | Gene symbol | BCKDK | Gene ID | 10295 |
| Gene name | branched chain ketoacid dehydrogenase kinase | |
| Synonyms | BCKDKD|BDK | |
| Cytomap | 16p11.2 | |
| Type of gene | protein-coding | |
| Description | [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial3-methyl-2-oxobutanoate dehydrogenase [lipoamide] kinase, mitochondrialBCKD-kinaseBCKDHKINbranched chain alpha-ketoacid dehydrogenase kinase | |
| Modification date | 20180522 | |
| UniProtAcc | O14874 | |
| Context | PubMed: BCKDK [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 BCKDK 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 BCKDK |
| 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 BCKDK |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_135968 | 16 | 31121424:31121445:31121525:31121645:31121721:31121820 | 31121525:31121645 | ENSG00000103507.9 | ENST00000394950.3,ENST00000484226.2,ENST00000287507.3,ENST00000394951.1,ENST00000567530.1,ENST00000219794.6,ENST00000566568.1 |
| exon_skip_135970 | 16 | 31121730:31121820:31122008:31122082:31122411:31122540 | 31122008:31122082 | ENSG00000103507.9 | ENST00000394950.3,ENST00000287507.3,ENST00000394951.1,ENST00000219794.6 |
| exon_skip_135974 | 16 | 31122008:31122082:31122411:31122540:31122620:31122710 | 31122411:31122540 | ENSG00000103507.9 | ENST00000394950.3,ENST00000394951.1,ENST00000219794.6 |
| exon_skip_135975 | 16 | 31122411:31122540:31122620:31122710:31123189:31123348 | 31122620:31122710 | ENSG00000103507.9 | ENST00000394950.3,ENST00000394951.1,ENST00000567530.1,ENST00000219794.6,ENST00000566568.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for BCKDK |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_135968 | 16 | 31121424:31121445:31121525:31121645:31121721:31121820 | 31121525:31121645 | ENSG00000103507.9 | ENST00000394951.1,ENST00000567530.1,ENST00000394950.3,ENST00000287507.3,ENST00000219794.6,ENST00000566568.1,ENST00000484226.2 |
| exon_skip_135970 | 16 | 31121730:31121820:31122008:31122082:31122411:31122540 | 31122008:31122082 | ENSG00000103507.9 | ENST00000394951.1,ENST00000394950.3,ENST00000287507.3,ENST00000219794.6 |
| exon_skip_135974 | 16 | 31122008:31122082:31122411:31122540:31122620:31122710 | 31122411:31122540 | ENSG00000103507.9 | ENST00000394951.1,ENST00000394950.3,ENST00000219794.6 |
| exon_skip_135975 | 16 | 31122411:31122540:31122620:31122710:31123189:31123348 | 31122620:31122710 | ENSG00000103507.9 | ENST00000394951.1,ENST00000567530.1,ENST00000394950.3,ENST00000219794.6,ENST00000566568.1 |
| 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 BCKDK |
| 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 |
| ENST00000219794 | 31122008 | 31122082 | Frame-shift |
| ENST00000394951 | 31122008 | 31122082 | Frame-shift |
| ENST00000219794 | 31121525 | 31121645 | In-frame |
| ENST00000394951 | 31121525 | 31121645 | In-frame |
| ENST00000219794 | 31122411 | 31122540 | In-frame |
| ENST00000394951 | 31122411 | 31122540 | In-frame |
| ENST00000219794 | 31122620 | 31122710 | In-frame |
| ENST00000394951 | 31122620 | 31122710 | 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 |
| ENST00000219794 | 31122008 | 31122082 | Frame-shift |
| ENST00000394951 | 31122008 | 31122082 | Frame-shift |
| ENST00000219794 | 31121525 | 31121645 | In-frame |
| ENST00000394951 | 31121525 | 31121645 | In-frame |
| ENST00000219794 | 31122411 | 31122540 | In-frame |
| ENST00000394951 | 31122411 | 31122540 | In-frame |
| ENST00000219794 | 31122620 | 31122710 | In-frame |
| ENST00000394951 | 31122620 | 31122710 | In-frame |
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Infer the effects of exon skipping event on protein functional features for BCKDK |
| 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 |
| ENST00000219794 | 2143 | 412 | 31121525 | 31121645 | 787 | 906 | 141 | 181 |
| ENST00000394951 | 2181 | 412 | 31121525 | 31121645 | 1047 | 1166 | 141 | 181 |
| ENST00000219794 | 2143 | 412 | 31122411 | 31122540 | 1080 | 1208 | 239 | 281 |
| ENST00000394951 | 2181 | 412 | 31122411 | 31122540 | 1340 | 1468 | 239 | 281 |
| ENST00000219794 | 2143 | 412 | 31122620 | 31122710 | 1209 | 1298 | 282 | 311 |
| ENST00000394951 | 2181 | 412 | 31122620 | 31122710 | 1469 | 1558 | 282 | 311 |
| 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 |
| ENST00000219794 | 2143 | 412 | 31121525 | 31121645 | 787 | 906 | 141 | 181 |
| ENST00000394951 | 2181 | 412 | 31121525 | 31121645 | 1047 | 1166 | 141 | 181 |
| ENST00000219794 | 2143 | 412 | 31122411 | 31122540 | 1080 | 1208 | 239 | 281 |
| ENST00000394951 | 2181 | 412 | 31122411 | 31122540 | 1340 | 1468 | 239 | 281 |
| ENST00000219794 | 2143 | 412 | 31122620 | 31122710 | 1209 | 1298 | 282 | 311 |
| ENST00000394951 | 2181 | 412 | 31122620 | 31122710 | 1469 | 1558 | 282 | 311 |
| 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 |
| O14874 | 141 | 181 | 31 | 412 | Chain | ID=PRO_0000023452;Note=[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase%2C mitochondrial |
| O14874 | 141 | 181 | 31 | 412 | Chain | ID=PRO_0000023452;Note=[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase%2C mitochondrial |
| O14874 | 141 | 181 | 159 | 404 | Domain | Note=Histidine kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00107 |
| O14874 | 141 | 181 | 159 | 404 | Domain | Note=Histidine kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00107 |
| O14874 | 141 | 181 | 174 | 174 | Natural variant | ID=VAR_072184;Note=In BCKDKD%3B partial loss of kinase activity. R->G;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24449431;Dbxref=PMID:24449431 |
| O14874 | 141 | 181 | 174 | 174 | Natural variant | ID=VAR_072184;Note=In BCKDKD%3B partial loss of kinase activity. R->G;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24449431;Dbxref=PMID:24449431 |
| O14874 | 239 | 281 | 31 | 412 | Chain | ID=PRO_0000023452;Note=[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase%2C mitochondrial |
| O14874 | 239 | 281 | 31 | 412 | Chain | ID=PRO_0000023452;Note=[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase%2C mitochondrial |
| O14874 | 239 | 281 | 159 | 404 | Domain | Note=Histidine kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00107 |
| O14874 | 239 | 281 | 159 | 404 | Domain | Note=Histidine kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00107 |
| O14874 | 282 | 311 | 282 | 311 | Alternative sequence | ID=VSP_054604;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| O14874 | 282 | 311 | 282 | 311 | Alternative sequence | ID=VSP_054604;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| O14874 | 282 | 311 | 31 | 412 | Chain | ID=PRO_0000023452;Note=[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase%2C mitochondrial |
| O14874 | 282 | 311 | 31 | 412 | Chain | ID=PRO_0000023452;Note=[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase%2C mitochondrial |
| O14874 | 282 | 311 | 159 | 404 | Domain | Note=Histidine kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00107 |
| O14874 | 282 | 311 | 159 | 404 | Domain | Note=Histidine kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00107 |
| 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 |
| O14874 | 141 | 181 | 31 | 412 | Chain | ID=PRO_0000023452;Note=[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase%2C mitochondrial |
| O14874 | 141 | 181 | 31 | 412 | Chain | ID=PRO_0000023452;Note=[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase%2C mitochondrial |
| O14874 | 141 | 181 | 159 | 404 | Domain | Note=Histidine kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00107 |
| O14874 | 141 | 181 | 159 | 404 | Domain | Note=Histidine kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00107 |
| O14874 | 141 | 181 | 174 | 174 | Natural variant | ID=VAR_072184;Note=In BCKDKD%3B partial loss of kinase activity. R->G;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24449431;Dbxref=PMID:24449431 |
| O14874 | 141 | 181 | 174 | 174 | Natural variant | ID=VAR_072184;Note=In BCKDKD%3B partial loss of kinase activity. R->G;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24449431;Dbxref=PMID:24449431 |
| O14874 | 239 | 281 | 31 | 412 | Chain | ID=PRO_0000023452;Note=[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase%2C mitochondrial |
| O14874 | 239 | 281 | 31 | 412 | Chain | ID=PRO_0000023452;Note=[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase%2C mitochondrial |
| O14874 | 239 | 281 | 159 | 404 | Domain | Note=Histidine kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00107 |
| O14874 | 239 | 281 | 159 | 404 | Domain | Note=Histidine kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00107 |
| O14874 | 282 | 311 | 282 | 311 | Alternative sequence | ID=VSP_054604;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| O14874 | 282 | 311 | 282 | 311 | Alternative sequence | ID=VSP_054604;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| O14874 | 282 | 311 | 31 | 412 | Chain | ID=PRO_0000023452;Note=[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase%2C mitochondrial |
| O14874 | 282 | 311 | 31 | 412 | Chain | ID=PRO_0000023452;Note=[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase%2C mitochondrial |
| O14874 | 282 | 311 | 159 | 404 | Domain | Note=Histidine kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00107 |
| O14874 | 282 | 311 | 159 | 404 | Domain | Note=Histidine kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00107 |
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SNVs in the skipped exons for BCKDK |
| - 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. |
BCKDK_STAD_exon_skip_135968_psi_boxplot.png |
| - 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 |
| UCEC | TCGA-BK-A0CA-01 | exon_skip_135974 | 31122412 | 31122540 | 31122472 | 31122473 | Frame_Shift_Ins | - | G | p.A259fs |
| UCEC | TCGA-D1-A160-01 | exon_skip_135970 | 31122009 | 31122082 | 31122051 | 31122051 | Nonsense_Mutation | A | T | p.K229* |
| STAD | TCGA-HU-A4GH-01 | exon_skip_135968 | 31121526 | 31121645 | 31121524 | 31121524 | Splice_Site | A | T | . |
| STAD | TCGA-HU-A4GH-01 | exon_skip_135968 | 31121526 | 31121645 | 31121524 | 31121524 | Splice_Site | A | T | p.I142_splice |
| KIRP | TCGA-5P-A9JU-01 | exon_skip_135968 | 31121526 | 31121645 | 31121525 | 31121525 | Splice_Site | G | T | . |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-HU-A4GH-01 |
| Cancer type: STAD | |
| ESID: exon_skip_135968 | |
| Skipped exon start: 31121526 | |
| Skipped exon end: 31121645 | |
| Mutation start: 31121524 | |
| Mutation end: 31121524 | |
| Mutation type: Splice_Site | |
| Reference seq: A | |
| Mutation seq: T | |
| AAchange: . | |
| Sample: TCGA-HU-A4GH-01 |
| Cancer type: STAD | |
| ESID: exon_skip_135968 | |
| Skipped exon start: 31121526 | |
| Skipped exon end: 31121645 | |
| Mutation start: 31121524 | |
| Mutation end: 31121524 | |
| Mutation type: Splice_Site | |
| Reference seq: A | |
| Mutation seq: T | |
| AAchange: p.I142_splice | |
exon_skip_135968_STAD_TCGA-HU-A4GH-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 |
| 639V_URINARY_TRACT | 31121526 | 31121645 | 31121583 | 31121583 | Missense_Mutation | G | A | p.D161N |
| ANGMCSS_CENTRAL_NERVOUS_SYSTEM | 31121526 | 31121645 | 31121631 | 31121631 | Missense_Mutation | C | T | p.R177W |
| ISHIKAWAHERAKLIO02ER_ENDOMETRIUM | 31122009 | 31122082 | 31122033 | 31122033 | Missense_Mutation | A | G | p.T223A |
| RL952_ENDOMETRIUM | 31122412 | 31122540 | 31122414 | 31122414 | Missense_Mutation | G | A | p.R240H |
| HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 31122412 | 31122540 | 31122441 | 31122441 | Missense_Mutation | C | T | p.A249V |
| P32ISH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 31122412 | 31122540 | 31122459 | 31122459 | Missense_Mutation | A | G | p.N255S |
| CROAP3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 31122621 | 31122710 | 31122626 | 31122626 | Missense_Mutation | C | T | p.T284I |
| AN3CA_ENDOMETRIUM | 31122621 | 31122710 | 31122674 | 31122674 | Missense_Mutation | T | C | p.I300T |
| SNU1040_LARGE_INTESTINE | 31122621 | 31122710 | 31122682 | 31122682 | Missense_Mutation | G | A | p.A303T |
| SNU1040_LARGE_INTESTINE | 31122621 | 31122710 | 31122686 | 31122686 | Missense_Mutation | A | G | p.N304S |
| UMUC5_URINARY_TRACT | 31122621 | 31122710 | 31122708 | 31122708 | Missense_Mutation | C | G | p.I311M |
| SNU1040_LARGE_INTESTINE | 31122412 | 31122540 | 31122539 | 31122539 | Splice_Site | A | T | p.R282* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for BCKDK |
| 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 BCKDK |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for BCKDK |
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RelatedDrugs for BCKDK |
| 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 BCKDK |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| BCKDK | C3554078 | BRANCHED-CHAIN KETO ACID DEHYDROGENASE KINASE DEFICIENCY | 2 | ORPHANET;UNIPROT |
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