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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 SMPD1 |
 Gene summary |
| Gene information | Gene symbol | SMPD1 | Gene ID | 6609 |
| Gene name | sphingomyelin phosphodiesterase 1 | |
| Synonyms | ASM|ASMASE|NPD | |
| Cytomap | 11p15.4 | |
| Type of gene | protein-coding | |
| Description | sphingomyelin phosphodiesteraseacid sphingomyelinasesphingomyelin phosphodiesterase 1, acid lysosomal | |
| Modification date | 20180523 | |
| UniProtAcc | P17405 | |
| Context | PubMed: SMPD1 [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 |
| SMPD1 | GO:0006685 | sphingomyelin catabolic process | 18815062 |
| SMPD1 | GO:0046513 | ceramide biosynthetic process | 18815062 |
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Exon skipping events across known transcript of Ensembl for SMPD1 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 SMPD1 |
| 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 SMPD1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_56603 | 11 | 6411811:6412146:6412613:6413386:6414846:6414923 | 6412613:6413386 | ENSG00000166311.5 | ENST00000533123.1 |
| exon_skip_56606 | 11 | 6412613:6412733:6414445:6414617:6414846:6414923 | 6414445:6414617 | ENSG00000166311.5 | ENST00000531303.1 |
| exon_skip_56610 | 11 | 6412613:6413386:6413422:6413426:6414846:6414923 | 6413422:6413426 | ENSG00000166311.5 | ENST00000356761.2 |
| exon_skip_56611 | 11 | 6412616:6413386:6414445:6414617:6414846:6414923 | 6414445:6414617 | ENSG00000166311.5 | ENST00000527275.1,ENST00000342245.4 |
| exon_skip_56613 | 11 | 6412616:6413386:6414846:6414923:6415125:6415271 | 6414846:6414923 | ENSG00000166311.5 | ENST00000533123.1 |
| exon_skip_56614 | 11 | 6413422:6413426:6414445:6414617:6414846:6414923 | 6414445:6414617 | ENSG00000166311.5 | ENST00000534405.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for SMPD1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_56606 | 11 | 6412613:6412733:6414445:6414617:6414846:6414923 | 6414445:6414617 | ENSG00000166311.5 | ENST00000531303.1 |
| exon_skip_56610 | 11 | 6412613:6413386:6413422:6413426:6414846:6414923 | 6413422:6413426 | ENSG00000166311.5 | ENST00000356761.2 |
| exon_skip_56611 | 11 | 6412616:6413386:6414445:6414617:6414846:6414923 | 6414445:6414617 | ENSG00000166311.5 | ENST00000342245.4,ENST00000527275.1 |
| exon_skip_56613 | 11 | 6412616:6413386:6414846:6414923:6415125:6415271 | 6414846:6414923 | ENSG00000166311.5 | ENST00000533123.1 |
| exon_skip_56614 | 11 | 6413422:6413426:6414445:6414617:6414846:6414923 | 6414445:6414617 | ENSG00000166311.5 | ENST00000534405.1 |
| 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 SMPD1 |
| 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 |
| ENST00000342245 | 6414445 | 6414617 | 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 |
| ENST00000342245 | 6414445 | 6414617 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for SMPD1 |
| 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 SMPD1 |
| - 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-HU-A4GT-01 | exon_skip_56603 | 6412614 | 6413386 | 6412854 | 6412854 | Frame_Shift_Del | C | - | p.P187fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_56603 | 6412614 | 6413386 | 6413286 | 6413286 | Frame_Shift_Del | C | - | p.P332fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_56603 | 6412614 | 6413386 | 6413286 | 6413286 | Frame_Shift_Del | C | - | p.P332fs |
| STAD | TCGA-B7-A5TI-01 | exon_skip_56603 | 6412614 | 6413386 | 6413286 | 6413286 | Frame_Shift_Del | C | - | p.P332fs |
| STAD | TCGA-BR-8591-01 | exon_skip_56603 | 6412614 | 6413386 | 6413286 | 6413286 | Frame_Shift_Del | C | - | p.P330fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_56603 | 6412614 | 6413386 | 6413347 | 6413347 | Frame_Shift_Del | G | - | p.W351fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_56614 exon_skip_56611 exon_skip_56606 | 6414446 | 6414617 | 6414450 | 6414450 | Frame_Shift_Del | G | - | p.G367fs |
| PAAD | TCGA-HZ-8001-01 | exon_skip_56603 | 6412614 | 6413386 | 6412853 | 6412854 | Frame_Shift_Ins | - | C | p.PP186fs |
| PAAD | TCGA-IB-7893-01 | exon_skip_56603 | 6412614 | 6413386 | 6412853 | 6412854 | Frame_Shift_Ins | - | C | p.PP186fs |
| LGG | TCGA-DU-7014-01 | exon_skip_56603 | 6412614 | 6413386 | 6412859 | 6412860 | Frame_Shift_Ins | - | A | p.T189fs |
| UCEC | TCGA-AP-A0LP-01 | exon_skip_56614 exon_skip_56611 exon_skip_56606 | 6414446 | 6414617 | 6414449 | 6414450 | Frame_Shift_Ins | - | G | p.I365fs |
| LIHC | TCGA-BC-A112-01 | exon_skip_56614 exon_skip_56611 exon_skip_56606 | 6414446 | 6414617 | 6414580 | 6414581 | Frame_Shift_Ins | - | G | p.G409fs |
| CESC | TCGA-Q1-A73O-01 | exon_skip_56603 | 6412614 | 6413386 | 6412747 | 6412747 | Nonsense_Mutation | C | G | p.S151* |
| SKCM | TCGA-ER-A19P-06 | exon_skip_56614 exon_skip_56611 exon_skip_56606 | 6414446 | 6414617 | 6414574 | 6414574 | Nonsense_Mutation | G | A | p.W407* |
| UCEC | TCGA-AX-A063-01 | exon_skip_56614 exon_skip_56611 exon_skip_56606 | 6414446 | 6414617 | 6414606 | 6414606 | Nonsense_Mutation | C | T | p.R418* |
| UCEC | TCGA-BS-A0UJ-01 | exon_skip_56613 | 6414847 | 6414923 | 6414846 | 6414846 | Splice_Site | G | A | e4-1 |
| - 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 |
| SET2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 6412614 | 6413386 | 6412708 | 6412708 | Missense_Mutation | A | G | p.H138R |
| A431_SKIN | 6412614 | 6413386 | 6412718 | 6412718 | Missense_Mutation | G | C | p.E141D |
| OVK18_OVARY | 6412614 | 6413386 | 6412744 | 6412744 | Missense_Mutation | G | T | p.R150L |
| JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 6412614 | 6413386 | 6412750 | 6412750 | Missense_Mutation | T | C | p.V152A |
| C84_LARGE_INTESTINE | 6412614 | 6413386 | 6412893 | 6412893 | Missense_Mutation | G | T | p.V200F |
| NCIH1573_LUNG | 6412614 | 6413386 | 6412993 | 6412993 | Missense_Mutation | C | G | p.S233C |
| SKUT1_SOFT_TISSUE | 6412614 | 6413386 | 6413028 | 6413028 | Missense_Mutation | T | C | p.Y245H |
| VCAP_PROSTATE | 6412614 | 6413386 | 6413028 | 6413028 | Missense_Mutation | T | C | p.Y245H |
| EN_ENDOMETRIUM | 6412614 | 6413386 | 6413047 | 6413047 | Missense_Mutation | A | G | p.K251R |
| OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 6412614 | 6413386 | 6413086 | 6413086 | Missense_Mutation | G | A | p.S264N |
| MZ7MEL_SKIN | 6412614 | 6413386 | 6413139 | 6413139 | Missense_Mutation | C | T | p.P282S |
| SNU46_UPPER_AERODIGESTIVE_TRACT | 6412614 | 6413386 | 6413142 | 6413142 | Missense_Mutation | G | C | p.A283P |
| KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 6412614 | 6413386 | 6413157 | 6413157 | Missense_Mutation | C | T | p.H288Y |
| NB5_AUTONOMIC_GANGLIA | 6412614 | 6413386 | 6413167 | 6413167 | Missense_Mutation | G | T | p.R291L |
| COV434_OVARY | 6412614 | 6413386 | 6413191 | 6413191 | Missense_Mutation | C | A | p.T299N |
| REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 6412614 | 6413386 | 6413332 | 6413332 | Missense_Mutation | C | T | p.A346V |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SMPD1 |
| 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 SMPD1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SMPD1 |
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RelatedDrugs for SMPD1 |
| 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 |
| P17405 | DB00381 | Amlodipine | Sphingomyelin phosphodiesterase | small molecule | approved | |
| P17405 | DB01151 | Desipramine | Sphingomyelin phosphodiesterase | small molecule | approved|investigational | |
| P17405 | DB00477 | Chlorpromazine | Sphingomyelin phosphodiesterase | small molecule | approved|investigational|vet_approved |
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RelatedDiseases for SMPD1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| SMPD1 | C0268243 | Niemann-Pick Disease, Type B | 25 | CTD_human;ORPHANET;UNIPROT |
| SMPD1 | C0268242 | Niemann-Pick Disease, Type A | 20 | CTD_human;ORPHANET;UNIPROT |
| SMPD1 | C0027626 | Neoplasm Invasiveness | 1 | CTD_human |
| SMPD1 | C0028064 | Niemann-Pick Diseases | 1 | CTD_human |
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