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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 HPS1 |
 Gene summary |
| Gene information | Gene symbol | HPS1 | Gene ID | 3257 |
| Gene name | HPS1, biogenesis of lysosomal organelles complex 3 subunit 1 | |
| Synonyms | BLOC3S1|HPS | |
| Cytomap | 10q24.2 | |
| Type of gene | protein-coding | |
| Description | Hermansky-Pudlak syndrome 1 proteinHermansky-Pudlak syndrome 1 protein isoform | |
| Modification date | 20180519 | |
| UniProtAcc | Q92902 | |
| Context | PubMed: HPS1 [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 |
| HPS1 | GO:1903232 | melanosome assembly | 23084991 |
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Exon skipping events across known transcript of Ensembl for HPS1 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 HPS1 |
| 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 HPS1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_52880 | 10 | 100176771:100177483:100177931:100178014:100179801:100179915 | 100177931:100178014 | ENSG00000107521.14 | ENST00000361490.4,ENST00000325103.6,ENST00000467246.1 |
| exon_skip_52883 | 10 | 100183636:100183644:100184069:100184131:100185297:100185477 | 100184069:100184131 | ENSG00000107521.14 | ENST00000361490.4,ENST00000497527.1,ENST00000325103.6,ENST00000467246.1,ENST00000478087.1,ENST00000359632.3,ENST00000470095.1 |
| exon_skip_52888 | 10 | 100185297:100185477:100185574:100185742:100186971:100187021 | 100185574:100185742 | ENSG00000107521.14 | ENST00000361490.4,ENST00000325103.6,ENST00000467246.1,ENST00000359632.3 |
| exon_skip_52889 | 10 | 100185662:100185742:100186971:100187021:100189329:100189399 | 100186971:100187021 | ENSG00000107521.14 | ENST00000361490.4,ENST00000325103.6,ENST00000467246.1,ENST00000498219.1,ENST00000359632.3 |
| exon_skip_52891 | 10 | 100189329:100189399:100189547:100189646:100190327:100190421 | 100189547:100189646 | ENSG00000107521.14 | ENST00000338546.5,ENST00000361490.4,ENST00000325103.6 |
| exon_skip_52894 | 10 | 100190327:100190427:100190887:100191048:100193696:100193848 | 100190887:100191048 | ENSG00000107521.14 | ENST00000467246.1,ENST00000478087.1 |
| exon_skip_52895 | 10 | 100190327:100190427:100190887:100191048:100193739:100193848 | 100190887:100191048 | ENSG00000107521.14 | ENST00000338546.5,ENST00000361490.4,ENST00000414009.1,ENST00000325103.6,ENST00000480020.1 |
| exon_skip_52897 | 10 | 100193739:100193848:100195028:100195171:100195391:100195529 | 100195028:100195171 | ENSG00000107521.14 | ENST00000338546.5,ENST00000361490.4,ENST00000325103.6,ENST00000467246.1 |
| exon_skip_52901 | 10 | 100195391:100195529:100202880:100202997:100205056:100205161 | 100202880:100202997 | ENSG00000107521.14 | ENST00000338546.5,ENST00000361490.4,ENST00000325103.6,ENST00000467246.1,ENST00000474873.1,ENST00000498219.1,ENST00000480020.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for HPS1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_52880 | 10 | 100176771:100177483:100177931:100178014:100179801:100179915 | 100177931:100178014 | ENSG00000107521.14 | ENST00000361490.4,ENST00000325103.6,ENST00000467246.1 |
| exon_skip_52883 | 10 | 100183636:100183644:100184069:100184131:100185297:100185477 | 100184069:100184131 | ENSG00000107521.14 | ENST00000361490.4,ENST00000325103.6,ENST00000467246.1,ENST00000359632.3,ENST00000478087.1,ENST00000470095.1,ENST00000497527.1 |
| exon_skip_52888 | 10 | 100185297:100185477:100185574:100185742:100186971:100187021 | 100185574:100185742 | ENSG00000107521.14 | ENST00000361490.4,ENST00000325103.6,ENST00000467246.1,ENST00000359632.3 |
| exon_skip_52889 | 10 | 100185662:100185742:100186971:100187021:100189329:100189399 | 100186971:100187021 | ENSG00000107521.14 | ENST00000361490.4,ENST00000325103.6,ENST00000467246.1,ENST00000359632.3,ENST00000498219.1 |
| exon_skip_52891 | 10 | 100189329:100189399:100189547:100189646:100190327:100190421 | 100189547:100189646 | ENSG00000107521.14 | ENST00000361490.4,ENST00000325103.6,ENST00000338546.5 |
| exon_skip_52894 | 10 | 100190327:100190427:100190887:100191048:100193696:100193848 | 100190887:100191048 | ENSG00000107521.14 | ENST00000467246.1,ENST00000478087.1 |
| exon_skip_52895 | 10 | 100190327:100190427:100190887:100191048:100193739:100193848 | 100190887:100191048 | ENSG00000107521.14 | ENST00000361490.4,ENST00000325103.6,ENST00000338546.5,ENST00000414009.1,ENST00000480020.1 |
| exon_skip_52897 | 10 | 100193739:100193848:100195028:100195171:100195391:100195529 | 100195028:100195171 | ENSG00000107521.14 | ENST00000361490.4,ENST00000325103.6,ENST00000467246.1,ENST00000338546.5 |
| exon_skip_52901 | 10 | 100195391:100195529:100202880:100202997:100205056:100205161 | 100202880:100202997 | ENSG00000107521.14 | ENST00000361490.4,ENST00000325103.6,ENST00000467246.1,ENST00000498219.1,ENST00000338546.5,ENST00000480020.1,ENST00000474873.1 |
| 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 HPS1 |
| 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 |
| ENST00000325103 | 100177931 | 100178014 | Frame-shift |
| ENST00000361490 | 100177931 | 100178014 | Frame-shift |
| ENST00000325103 | 100184069 | 100184131 | Frame-shift |
| ENST00000361490 | 100184069 | 100184131 | Frame-shift |
| ENST00000325103 | 100186971 | 100187021 | Frame-shift |
| ENST00000361490 | 100186971 | 100187021 | Frame-shift |
| ENST00000325103 | 100190887 | 100191048 | Frame-shift |
| ENST00000361490 | 100190887 | 100191048 | Frame-shift |
| ENST00000325103 | 100195028 | 100195171 | Frame-shift |
| ENST00000361490 | 100195028 | 100195171 | Frame-shift |
| ENST00000325103 | 100185574 | 100185742 | In-frame |
| ENST00000361490 | 100185574 | 100185742 | In-frame |
| ENST00000325103 | 100189547 | 100189646 | In-frame |
| ENST00000361490 | 100189547 | 100189646 | In-frame |
| ENST00000325103 | 100202880 | 100202997 | In-frame |
| ENST00000361490 | 100202880 | 100202997 | 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 |
| ENST00000325103 | 100177931 | 100178014 | Frame-shift |
| ENST00000361490 | 100177931 | 100178014 | Frame-shift |
| ENST00000325103 | 100184069 | 100184131 | Frame-shift |
| ENST00000361490 | 100184069 | 100184131 | Frame-shift |
| ENST00000325103 | 100186971 | 100187021 | Frame-shift |
| ENST00000361490 | 100186971 | 100187021 | Frame-shift |
| ENST00000325103 | 100190887 | 100191048 | Frame-shift |
| ENST00000361490 | 100190887 | 100191048 | Frame-shift |
| ENST00000325103 | 100195028 | 100195171 | Frame-shift |
| ENST00000361490 | 100195028 | 100195171 | Frame-shift |
| ENST00000325103 | 100185574 | 100185742 | In-frame |
| ENST00000361490 | 100185574 | 100185742 | In-frame |
| ENST00000325103 | 100189547 | 100189646 | In-frame |
| ENST00000361490 | 100189547 | 100189646 | In-frame |
| ENST00000325103 | 100202880 | 100202997 | In-frame |
| ENST00000361490 | 100202880 | 100202997 | In-frame |
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Infer the effects of exon skipping event on protein functional features for HPS1 |
| 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 |
| ENST00000325103 | 3720 | 700 | 100202880 | 100202997 | 235 | 351 | 0 | 39 |
| ENST00000361490 | 3695 | 700 | 100202880 | 100202997 | 210 | 326 | 0 | 39 |
| ENST00000325103 | 3720 | 700 | 100189547 | 100189646 | 1003 | 1101 | 256 | 289 |
| ENST00000361490 | 3695 | 700 | 100189547 | 100189646 | 978 | 1076 | 256 | 289 |
| ENST00000325103 | 3720 | 700 | 100185574 | 100185742 | 1222 | 1389 | 329 | 385 |
| ENST00000361490 | 3695 | 700 | 100185574 | 100185742 | 1197 | 1364 | 329 | 385 |
| 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 |
| ENST00000325103 | 3720 | 700 | 100202880 | 100202997 | 235 | 351 | 0 | 39 |
| ENST00000361490 | 3695 | 700 | 100202880 | 100202997 | 210 | 326 | 0 | 39 |
| ENST00000325103 | 3720 | 700 | 100189547 | 100189646 | 1003 | 1101 | 256 | 289 |
| ENST00000361490 | 3695 | 700 | 100189547 | 100189646 | 978 | 1076 | 256 | 289 |
| ENST00000325103 | 3720 | 700 | 100185574 | 100185742 | 1222 | 1389 | 329 | 385 |
| ENST00000361490 | 3695 | 700 | 100185574 | 100185742 | 1197 | 1364 | 329 | 385 |
| 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 |
| Q92902 | 0 | 39 | 1 | 700 | Chain | ID=PRO_0000084047;Note=Hermansky-Pudlak syndrome 1 protein |
| Q92902 | 0 | 39 | 1 | 700 | Chain | ID=PRO_0000084047;Note=Hermansky-Pudlak syndrome 1 protein |
| Q92902 | 0 | 39 | 34 | 39 | Compositional bias | Note=Poly-Glu |
| Q92902 | 0 | 39 | 34 | 39 | Compositional bias | Note=Poly-Glu |
| Q92902 | 256 | 289 | 257 | 289 | Alternative sequence | ID=VSP_004289;Note=In isoform II. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q92902 | 256 | 289 | 257 | 289 | Alternative sequence | ID=VSP_004289;Note=In isoform II. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q92902 | 256 | 289 | 1 | 700 | Chain | ID=PRO_0000084047;Note=Hermansky-Pudlak syndrome 1 protein |
| Q92902 | 256 | 289 | 1 | 700 | Chain | ID=PRO_0000084047;Note=Hermansky-Pudlak syndrome 1 protein |
| Q92902 | 256 | 289 | 283 | 283 | Natural variant | ID=VAR_005290;Note=G->W;Dbxref=dbSNP:rs11592273 |
| Q92902 | 256 | 289 | 283 | 283 | Natural variant | ID=VAR_005290;Note=G->W;Dbxref=dbSNP:rs11592273 |
| Q92902 | 329 | 385 | 325 | 700 | Alternative sequence | ID=VSP_004291;Note=In isoform III. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:9579545;Dbxref=PMID:15489334,PMID:9579545 |
| Q92902 | 329 | 385 | 325 | 700 | Alternative sequence | ID=VSP_004291;Note=In isoform III. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:9579545;Dbxref=PMID:15489334,PMID:9579545 |
| Q92902 | 329 | 385 | 1 | 700 | Chain | ID=PRO_0000084047;Note=Hermansky-Pudlak syndrome 1 protein |
| Q92902 | 329 | 385 | 1 | 700 | Chain | ID=PRO_0000084047;Note=Hermansky-Pudlak syndrome 1 protein |
| 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 |
| Q92902 | 0 | 39 | 1 | 700 | Chain | ID=PRO_0000084047;Note=Hermansky-Pudlak syndrome 1 protein |
| Q92902 | 0 | 39 | 1 | 700 | Chain | ID=PRO_0000084047;Note=Hermansky-Pudlak syndrome 1 protein |
| Q92902 | 0 | 39 | 34 | 39 | Compositional bias | Note=Poly-Glu |
| Q92902 | 0 | 39 | 34 | 39 | Compositional bias | Note=Poly-Glu |
| Q92902 | 256 | 289 | 257 | 289 | Alternative sequence | ID=VSP_004289;Note=In isoform II. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q92902 | 256 | 289 | 257 | 289 | Alternative sequence | ID=VSP_004289;Note=In isoform II. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q92902 | 256 | 289 | 1 | 700 | Chain | ID=PRO_0000084047;Note=Hermansky-Pudlak syndrome 1 protein |
| Q92902 | 256 | 289 | 1 | 700 | Chain | ID=PRO_0000084047;Note=Hermansky-Pudlak syndrome 1 protein |
| Q92902 | 256 | 289 | 283 | 283 | Natural variant | ID=VAR_005290;Note=G->W;Dbxref=dbSNP:rs11592273 |
| Q92902 | 256 | 289 | 283 | 283 | Natural variant | ID=VAR_005290;Note=G->W;Dbxref=dbSNP:rs11592273 |
| Q92902 | 329 | 385 | 325 | 700 | Alternative sequence | ID=VSP_004291;Note=In isoform III. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:9579545;Dbxref=PMID:15489334,PMID:9579545 |
| Q92902 | 329 | 385 | 325 | 700 | Alternative sequence | ID=VSP_004291;Note=In isoform III. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:9579545;Dbxref=PMID:15489334,PMID:9579545 |
| Q92902 | 329 | 385 | 1 | 700 | Chain | ID=PRO_0000084047;Note=Hermansky-Pudlak syndrome 1 protein |
| Q92902 | 329 | 385 | 1 | 700 | Chain | ID=PRO_0000084047;Note=Hermansky-Pudlak syndrome 1 protein |
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SNVs in the skipped exons for HPS1 |
| - 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-A1EG-01 | exon_skip_52888 | 100185575 | 100185742 | 100185680 | 100185680 | Frame_Shift_Del | C | - | p.R350fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_52888 | 100185575 | 100185742 | 100185686 | 100185686 | Frame_Shift_Del | G | - | p.P348fs |
| COAD | TCGA-AD-6889-01 | exon_skip_52889 | 100186972 | 100187021 | 100186987 | 100186988 | Frame_Shift_Del | GG | - | p.324_325del |
| COAD | TCGA-AY-6197-01 | exon_skip_52889 | 100186972 | 100187021 | 100186987 | 100186987 | Frame_Shift_Del | G | - | p.M325fs |
| COAD | TCGA-G4-6588-01 | exon_skip_52889 | 100186972 | 100187021 | 100186987 | 100186987 | Frame_Shift_Del | G | - | p.M325fs |
| READ | TCGA-EI-6507-01 | exon_skip_52889 | 100186972 | 100187021 | 100186987 | 100186987 | Frame_Shift_Del | G | - | p.M325fs |
| SKCM | TCGA-FW-A3I3-06 | exon_skip_52889 | 100186972 | 100187021 | 100186987 | 100186987 | Frame_Shift_Del | G | - | p.P324fs |
| UCEC | TCGA-D1-A101-01 | exon_skip_52889 | 100186972 | 100187021 | 100186987 | 100186987 | Frame_Shift_Del | G | - | p.P324fs |
| COAD | TCGA-A6-6781-01 | exon_skip_52889 | 100186972 | 100187021 | 100186986 | 100186987 | Frame_Shift_Ins | - | G | p.M325fs |
| COAD | TCGA-AA-A00E-01 | exon_skip_52889 | 100186972 | 100187021 | 100186986 | 100186987 | Frame_Shift_Ins | - | G | p.M325fs |
| COAD | TCGA-CM-6674-01 | exon_skip_52889 | 100186972 | 100187021 | 100186986 | 100186987 | Frame_Shift_Ins | - | G | p.M325fs |
| BRCA | TCGA-E9-A1NI-01 | exon_skip_52891 | 100189548 | 100189646 | 100189562 | 100189563 | Frame_Shift_Ins | - | C | p.S284fs |
| UCEC | TCGA-D1-A103-01 | exon_skip_52883 | 100184070 | 100184131 | 100184123 | 100184123 | Nonsense_Mutation | C | T | p.W448* |
| BLCA | TCGA-GU-A767-01 | exon_skip_52897 | 100195029 | 100195171 | 100195123 | 100195123 | Nonsense_Mutation | C | A | p.E102* |
| BLCA | TCGA-5N-A9KI-01 | exon_skip_52901 | 100202881 | 100202997 | 100202940 | 100202940 | Nonsense_Mutation | G | A | p.Q20* |
| - 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 |
| RKO_LARGE_INTESTINE | 100186972 | 100187021 | 100186987 | 100186989 | In_Frame_Del | GGG | - | p.P324del |
| MN60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 100177932 | 100178014 | 100177959 | 100177959 | Missense_Mutation | A | G | p.I638T |
| DU145_PROSTATE | 100184070 | 100184131 | 100184105 | 100184105 | Missense_Mutation | C | A | p.K454N |
| SNU1040_LARGE_INTESTINE | 100185575 | 100185742 | 100185663 | 100185663 | Missense_Mutation | T | C | p.N356S |
| CAOV3_OVARY | 100185575 | 100185742 | 100185693 | 100185693 | Missense_Mutation | G | A | p.S346F |
| HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 100190888 | 100191048 | 100190939 | 100190939 | Missense_Mutation | G | A | p.A206V |
| IGROV1_OVARY | 100190888 | 100191048 | 100190954 | 100190954 | Missense_Mutation | C | T | p.R201Q |
| SNU1040_LARGE_INTESTINE | 100195029 | 100195171 | 100195107 | 100195107 | Missense_Mutation | C | T | p.R107Q |
| UMUC3_URINARY_TRACT | 100202881 | 100202997 | 100202928 | 100202928 | Missense_Mutation | C | G | p.E24Q |
| EB2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 100202881 | 100202997 | 100202988 | 100202988 | Missense_Mutation | C | T | p.V4I |
| EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 100202881 | 100202997 | 100202988 | 100202988 | Missense_Mutation | C | T | p.V4I |
| RF48_STOMACH | 100202881 | 100202997 | 100202993 | 100202993 | Missense_Mutation | T | C | p.K2R |
| KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 100195029 | 100195171 | 100195090 | 100195090 | Nonsense_Mutation | T | A | p.K113* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for HPS1 |
| 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 HPS1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for HPS1 |
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RelatedDrugs for HPS1 |
| 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 HPS1 |
| 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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