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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 CACNA1D |
 Gene summary |
| Gene information | Gene symbol | CACNA1D | Gene ID | 776 |
| Gene name | calcium voltage-gated channel subunit alpha1 D | |
| Synonyms | CACH3|CACN4|CACNL1A2|CCHL1A2|Cav1.3|PASNA|SANDD | |
| Cytomap | 3p21.1 | |
| Type of gene | protein-coding | |
| Description | voltage-dependent L-type calcium channel subunit alpha-1Dcalcium channel, L type, alpha-1 polypeptidecalcium channel, neuroendocrine/brain-type, alpha 1 subunitcalcium channel, voltage-dependent, L type, alpha 1D subunitvoltage-gated calcium channel a | |
| Modification date | 20180523 | |
| UniProtAcc | Q01668 | |
| Context | PubMed: CACNA1D [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 |
| CACNA1D | GO:0006816 | calcium ion transport | 11160515 |
| CACNA1D | GO:0051928 | positive regulation of calcium ion transport | 1309651 |
| CACNA1D | GO:0070509 | calcium ion import | 1309651 |
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Exon skipping events across known transcript of Ensembl for CACNA1D 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 CACNA1D |
| 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 CACNA1D |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_375232 | 3 | 53700427:53700562:53707049:53707153:53736667:53736837 | 53707049:53707153 | ENSG00000157388.9 | ENST00000350061.5,ENST00000422281.2,ENST00000481478.1 |
| exon_skip_375233 | 3 | 53700427:53700562:53707739:53707843:53736667:53736837 | 53707739:53707843 | ENSG00000157388.9 | ENST00000288139.4,ENST00000481085.1 |
| exon_skip_375236 | 3 | 53752331:53752415:53752708:53752768:53753781:53753808 | 53752708:53752768 | ENSG00000157388.9 | ENST00000288139.4,ENST00000481478.1 |
| exon_skip_375237 | 3 | 53752327:53752415:53753781:53753808:53756340:53756485 | 53753781:53753808 | ENSG00000157388.9 | ENST00000350061.5,ENST00000422281.2,ENST00000481085.1 |
| exon_skip_375238 | 3 | 53757460:53757686:53757818:53758026:53760905:53761026 | 53757818:53758026 | ENSG00000157388.9 | ENST00000350061.5,ENST00000422281.2,ENST00000288139.4,ENST00000481478.1 |
| exon_skip_375239 | 3 | 53766042:53766109:53766841:53766989:53769400:53769530 | 53766841:53766989 | ENSG00000157388.9 | ENST00000350061.5,ENST00000422281.2,ENST00000288139.4,ENST00000481478.1 |
| exon_skip_375247 | 3 | 53796024:53796108:53803999:53804044:53804450:53804579 | 53803999:53804044 | ENSG00000157388.9 | ENST00000350061.5,ENST00000288139.4 |
| exon_skip_375250 | 3 | 53796024:53796108:53804450:53804579:53806859:53806925 | 53804450:53804579 | ENSG00000157388.9 | ENST00000422281.2,ENST00000540742.1 |
| exon_skip_375252 | 3 | 53796577:53796661:53803999:53804044:53804450:53804579 | 53803999:53804044 | ENSG00000157388.9 | ENST00000481478.1 |
| exon_skip_375255 | 3 | 53810629:53810757:53810886:53810983:53814052:53814155 | 53810886:53810983 | ENSG00000157388.9 | ENST00000350061.5,ENST00000422281.2,ENST00000288139.4,ENST00000481478.1,ENST00000540742.1 |
| exon_skip_375256 | 3 | 53815592:53815694:53820848:53820979:53834275:53834392 | 53820848:53820979 | ENSG00000157388.9 | ENST00000350061.5,ENST00000422281.2,ENST00000288139.4,ENST00000481478.1 |
| exon_skip_375259 | 3 | 53835340:53835452:53836173:53836200:53837449:53837599 | 53836173:53836200 | ENSG00000157388.9 | ENST00000350061.5,ENST00000288139.4,ENST00000481478.1,ENST00000544977.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for CACNA1D |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_375232 | 3 | 53700427:53700562:53707049:53707153:53736667:53736837 | 53707049:53707153 | ENSG00000157388.9 | ENST00000350061.5,ENST00000422281.2,ENST00000481478.1 |
| exon_skip_375233 | 3 | 53700427:53700562:53707739:53707843:53736667:53736837 | 53707739:53707843 | ENSG00000157388.9 | ENST00000288139.4,ENST00000481085.1 |
| exon_skip_375236 | 3 | 53752331:53752415:53752708:53752768:53753781:53753808 | 53752708:53752768 | ENSG00000157388.9 | ENST00000288139.4,ENST00000481478.1 |
| exon_skip_375237 | 3 | 53752327:53752415:53753781:53753808:53756340:53756485 | 53753781:53753808 | ENSG00000157388.9 | ENST00000350061.5,ENST00000422281.2,ENST00000481085.1 |
| exon_skip_375238 | 3 | 53757460:53757686:53757818:53758026:53760905:53761026 | 53757818:53758026 | ENSG00000157388.9 | ENST00000350061.5,ENST00000288139.4,ENST00000422281.2,ENST00000481478.1 |
| exon_skip_375239 | 3 | 53766042:53766109:53766841:53766989:53769400:53769530 | 53766841:53766989 | ENSG00000157388.9 | ENST00000350061.5,ENST00000288139.4,ENST00000422281.2,ENST00000481478.1 |
| exon_skip_375247 | 3 | 53796024:53796108:53803999:53804044:53804450:53804579 | 53803999:53804044 | ENSG00000157388.9 | ENST00000350061.5,ENST00000288139.4 |
| exon_skip_375252 | 3 | 53796577:53796661:53803999:53804044:53804450:53804579 | 53803999:53804044 | ENSG00000157388.9 | ENST00000481478.1 |
| exon_skip_375255 | 3 | 53810629:53810757:53810886:53810983:53814052:53814155 | 53810886:53810983 | ENSG00000157388.9 | ENST00000350061.5,ENST00000288139.4,ENST00000422281.2,ENST00000481478.1,ENST00000540742.1 |
| exon_skip_375256 | 3 | 53815592:53815694:53820848:53820979:53834275:53834392 | 53820848:53820979 | ENSG00000157388.9 | ENST00000350061.5,ENST00000288139.4,ENST00000422281.2,ENST00000481478.1 |
| exon_skip_375259 | 3 | 53835340:53835452:53836173:53836200:53837449:53837599 | 53836173:53836200 | ENSG00000157388.9 | ENST00000350061.5,ENST00000288139.4,ENST00000481478.1,ENST00000544977.1 |
| 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 CACNA1D |
| 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 |
| ENST00000350061 | 53707049 | 53707153 | Frame-shift |
| ENST00000350061 | 53757818 | 53758026 | Frame-shift |
| ENST00000350061 | 53766841 | 53766989 | Frame-shift |
| ENST00000350061 | 53810886 | 53810983 | Frame-shift |
| ENST00000350061 | 53820848 | 53820979 | Frame-shift |
| ENST00000350061 | 53753781 | 53753808 | In-frame |
| ENST00000350061 | 53803999 | 53804044 | In-frame |
| ENST00000350061 | 53836173 | 53836200 | 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 |
| ENST00000350061 | 53707049 | 53707153 | Frame-shift |
| ENST00000350061 | 53757818 | 53758026 | Frame-shift |
| ENST00000350061 | 53766841 | 53766989 | Frame-shift |
| ENST00000350061 | 53810886 | 53810983 | Frame-shift |
| ENST00000350061 | 53820848 | 53820979 | Frame-shift |
| ENST00000350061 | 53753781 | 53753808 | In-frame |
| ENST00000350061 | 53803999 | 53804044 | In-frame |
| ENST00000350061 | 53836173 | 53836200 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CACNA1D |
| 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 |
| ENST00000350061 | 7653 | 2161 | 53803999 | 53804044 | 4382 | 4426 | 1290 | 1305 |
| 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 |
| ENST00000350061 | 7653 | 2161 | 53803999 | 53804044 | 4382 | 4426 | 1290 | 1305 |
| 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 |
| Q01668 | 1290 | 1305 | 1291 | 1305 | Alternative sequence | ID=VSP_046743;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:18482979;Dbxref=PMID:18482979 |
| Q01668 | 1290 | 1305 | 1 | 2161 | Chain | ID=PRO_0000053933;Note=Voltage-dependent L-type calcium channel subunit alpha-1D |
| Q01668 | 1290 | 1305 | 1192 | 1467 | Repeat | Note=IV |
| Q01668 | 1290 | 1305 | 1289 | 1290 | Sequence conflict | Note=Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q01668 | 1290 | 1305 | 1289 | 1313 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| 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 |
| Q01668 | 1290 | 1305 | 1291 | 1305 | Alternative sequence | ID=VSP_046743;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:18482979;Dbxref=PMID:18482979 |
| Q01668 | 1290 | 1305 | 1 | 2161 | Chain | ID=PRO_0000053933;Note=Voltage-dependent L-type calcium channel subunit alpha-1D |
| Q01668 | 1290 | 1305 | 1192 | 1467 | Repeat | Note=IV |
| Q01668 | 1290 | 1305 | 1289 | 1290 | Sequence conflict | Note=Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q01668 | 1290 | 1305 | 1289 | 1313 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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SNVs in the skipped exons for CACNA1D |
| - 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 |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_375238 | 53757819 | 53758026 | 53758010 | 53758010 | Frame_Shift_Del | T | - | p.L716fs |
| COAD | TCGA-DM-A1DA-01 | exon_skip_375239 | 53766842 | 53766989 | 53766889 | 53766892 | Frame_Shift_Del | GCCG | - | p.840_841del |
| STAD | TCGA-BR-4201-01 | exon_skip_375239 | 53766842 | 53766989 | 53766932 | 53766932 | Frame_Shift_Del | A | - | p.E855fs |
| STAD | TCGA-BR-4201-01 | exon_skip_375239 | 53766842 | 53766989 | 53766932 | 53766932 | Frame_Shift_Del | A | - | p.E875fs |
| UCEC | TCGA-DI-A0WH-01 | exon_skip_375239 | 53766842 | 53766989 | 53766932 | 53766932 | Frame_Shift_Del | A | - | p.E855fs |
| KIRC | TCGA-B0-4698-01 | exon_skip_375239 | 53766842 | 53766989 | 53766941 | 53766941 | Frame_Shift_Del | C | - | p.A878fs |
| UCEC | TCGA-D1-A17F-01 | exon_skip_375250 | 53804451 | 53804579 | 53804484 | 53804484 | Frame_Shift_Del | T | - | p.F1317fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_375255 | 53810887 | 53810983 | 53810896 | 53810896 | Frame_Shift_Del | A | - | p.I1520fs |
| KIRC | TCGA-B8-A54F-01 | exon_skip_375236 | 53752709 | 53752768 | 53752717 | 53752717 | Nonsense_Mutation | G | A | p.W496X |
| ESCA | TCGA-LN-A9FP-01 | exon_skip_375239 | 53766842 | 53766989 | 53766862 | 53766862 | Nonsense_Mutation | G | T | p.E852* |
| ESCA | TCGA-LN-A9FP-01 | exon_skip_375239 | 53766842 | 53766989 | 53766862 | 53766862 | Nonsense_Mutation | G | T | p.E852X |
| UCEC | TCGA-AX-A05Z-01 | exon_skip_375256 | 53820849 | 53820979 | 53820926 | 53820926 | Nonsense_Mutation | G | T | p.E1644* |
| UCEC | TCGA-AX-A0J0-01 | exon_skip_375256 | 53820849 | 53820979 | 53820926 | 53820926 | Nonsense_Mutation | G | T | p.E1644* |
| OV | TCGA-25-2399-01 | exon_skip_375237 | 53753782 | 53753808 | 53753780 | 53753780 | Splice_Site | A | G | p.C493_splice |
| ESCA | TCGA-L5-A4OR-01 | exon_skip_375239 | 53766842 | 53766989 | 53766990 | 53766990 | Splice_Site | G | A | . |
| ESCA | TCGA-L5-A4OR-01 | exon_skip_375239 | 53766842 | 53766989 | 53766990 | 53766990 | Splice_Site | G | A | e20+1 |
| - 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 |
| NCIH1339_LUNG | 53707050 | 53707153 | 53707065 | 53707065 | Missense_Mutation | G | A | p.G378R |
| CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 53707050 | 53707153 | 53707122 | 53707122 | Missense_Mutation | G | A | p.V397I |
| U698M_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 53707050 | 53707153 | 53707141 | 53707141 | Missense_Mutation | G | C | p.G403A |
| BECKER_CENTRAL_NERVOUS_SYSTEM | 53757819 | 53758026 | 53757874 | 53757874 | Missense_Mutation | A | G | p.I650V |
| SW684_SOFT_TISSUE | 53757819 | 53758026 | 53757881 | 53757881 | Missense_Mutation | C | T | p.S652L |
| 647V_URINARY_TRACT | 53757819 | 53758026 | 53757892 | 53757892 | Missense_Mutation | C | A | p.L656M |
| KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 53757819 | 53758026 | 53757896 | 53757896 | Missense_Mutation | T | C | p.L657P |
| HCT15_LARGE_INTESTINE | 53757819 | 53758026 | 53757914 | 53757914 | Missense_Mutation | T | C | p.I663T |
| MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 53757819 | 53758026 | 53757986 | 53757986 | Missense_Mutation | C | T | p.T687I |
| JHUEM7_ENDOMETRIUM | 53757819 | 53758026 | 53758012 | 53758012 | Missense_Mutation | C | A | p.L696I |
| NCIH647_LUNG | 53766842 | 53766989 | 53766845 | 53766846 | Missense_Mutation | GG | AA | p.G826E |
| HEPG2_LIVER | 53766842 | 53766989 | 53766877 | 53766877 | Missense_Mutation | C | T | p.P837S |
| C3A_LIVER | 53766842 | 53766989 | 53766877 | 53766877 | Missense_Mutation | C | T | p.P837S |
| UACC812_BREAST | 53766842 | 53766989 | 53766899 | 53766899 | Missense_Mutation | G | A | p.R844H |
| JHUEM7_ENDOMETRIUM | 53766842 | 53766989 | 53766905 | 53766905 | Missense_Mutation | G | A | p.R846Q |
| SNU1040_LARGE_INTESTINE | 53804451 | 53804579 | 53804469 | 53804469 | Missense_Mutation | A | G | p.R1312G |
| KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 53804451 | 53804579 | 53804490 | 53804490 | Missense_Mutation | C | T | p.R1319C |
| HSC3_UPPER_AERODIGESTIVE_TRACT | 53804451 | 53804579 | 53804509 | 53804509 | Missense_Mutation | G | A | p.R1325Q |
| SUM159PT_BREAST | 53810887 | 53810983 | 53810912 | 53810912 | Missense_Mutation | G | T | p.V1506F |
| NCIH1563_LUNG | 53810887 | 53810983 | 53810918 | 53810918 | Missense_Mutation | C | G | p.L1508V |
| YAMATO_SOFT_TISSUE | 53810887 | 53810983 | 53810972 | 53810972 | Missense_Mutation | G | A | p.V1526I |
| ES5_BONE | 53820849 | 53820979 | 53820946 | 53820946 | Missense_Mutation | G | T | p.K1630N |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CACNA1D |
| 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 CACNA1D |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CACNA1D |
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RelatedDrugs for CACNA1D |
| 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 |
| Q01668 | DB00401 | Nisoldipine | Voltage-dependent L-type calcium channel subunit alpha-1D | small molecule | approved | |
| Q01668 | DB00661 | Verapamil | Voltage-dependent L-type calcium channel subunit alpha-1D | small molecule | approved | |
| Q01668 | DB00898 | Ethanol | Voltage-dependent L-type calcium channel subunit alpha-1D | small molecule | approved | |
| Q01668 | DB01115 | Nifedipine | Voltage-dependent L-type calcium channel subunit alpha-1D | small molecule | approved | |
| Q01668 | DB04855 | Dronedarone | Voltage-dependent L-type calcium channel subunit alpha-1D | small molecule | approved | |
| Q01668 | DB00270 | Isradipine | Voltage-dependent L-type calcium channel subunit alpha-1D | small molecule | approved|investigational | |
| Q01668 | DB00393 | Nimodipine | Voltage-dependent L-type calcium channel subunit alpha-1D | small molecule | approved|investigational | |
| Q01668 | DB00568 | Cinnarizine | Voltage-dependent L-type calcium channel subunit alpha-1D | small molecule | approved|investigational | |
| Q01668 | DB00622 | Nicardipine | Voltage-dependent L-type calcium channel subunit alpha-1D | small molecule | approved|investigational | |
| Q01668 | DB01023 | Felodipine | Voltage-dependent L-type calcium channel subunit alpha-1D | small molecule | approved|investigational | |
| Q01668 | DB01054 | Nitrendipine | Voltage-dependent L-type calcium channel subunit alpha-1D | small molecule | approved|investigational | |
| Q01668 | DB04920 | Clevidipine | Voltage-dependent L-type calcium channel subunit alpha-1D | small molecule | approved|investigational |
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RelatedDiseases for CACNA1D |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| CACNA1D | C0001430 | Adenoma | 2 | CTD_human |
| CACNA1D | C0011053 | Deafness | 1 | CTD_human;HPO |
| CACNA1D | C0020428 | Hyperaldosteronism | 1 | CTD_human;HPO |
| CACNA1D | C0525045 | Mood Disorders | 1 | PSYGENET |
| CACNA1D | C3809609 | PRIMARY ALDOSTERONISM, SEIZURES, AND NEUROLOGIC ABNORMALITIES | 1 | ORPHANET;UNIPROT |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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