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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 SGPL1 |
 Gene summary |
| Gene information | Gene symbol | SGPL1 | Gene ID | 8879 |
| Gene name | sphingosine-1-phosphate lyase 1 | |
| Synonyms | NPHS14|S1PL|SPL | |
| Cytomap | 10q22.1 | |
| Type of gene | protein-coding | |
| Description | sphingosine-1-phosphate lyase 1SP-lyase 1SPL 1hSPLsphingosine-1-phosphate aldolase | |
| Modification date | 20180523 | |
| UniProtAcc | O95470 | |
| Context | PubMed: SGPL1 [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 |
| SGPL1 | GO:0006631 | fatty acid metabolic process | 24809814 |
| SGPL1 | GO:0006672 | ceramide metabolic process | 14570870 |
| SGPL1 | GO:0030149 | sphingolipid catabolic process | 24809814 |
| SGPL1 | GO:0097190 | apoptotic signaling pathway | 14570870 |
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Exon skipping events across known transcript of Ensembl for SGPL1 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 SGPL1 |
| 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 SGPL1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_42204 | 10 | 72575725:72575882:72576566:72576636:72604229:72604395 | 72576566:72576636 | ENSG00000166224.12 | ENST00000373202.3 |
| exon_skip_42217 | 10 | 72576566:72576636:72604229:72604395:72610899:72610967 | 72604229:72604395 | ENSG00000166224.12 | ENST00000373202.3 |
| exon_skip_42223 | 10 | 72610899:72610967:72614464:72614612:72617370:72617447 | 72614464:72614612 | ENSG00000166224.12 | ENST00000373202.3,ENST00000299297.4 |
| exon_skip_42227 | 10 | 72628101:72628190:72629548:72629654:72630804:72630903 | 72629548:72629654 | ENSG00000166224.12 | ENST00000373202.3 |
| exon_skip_42228 | 10 | 72629548:72629654:72630804:72630903:72631593:72631743 | 72630804:72630903 | ENSG00000166224.12 | ENST00000373202.3 |
| exon_skip_42229 | 10 | 72630804:72630903:72631593:72631743:72633107:72633346 | 72631593:72631743 | ENSG00000166224.12 | ENST00000373202.3 |
| exon_skip_42231 | 10 | 72631593:72631743:72633107:72633346:72635158:72635305 | 72633107:72633346 | ENSG00000166224.12 | ENST00000373202.3 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for SGPL1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_42204 | 10 | 72575725:72575882:72576566:72576636:72604229:72604395 | 72576566:72576636 | ENSG00000166224.12 | ENST00000373202.3 |
| exon_skip_42217 | 10 | 72576566:72576636:72604229:72604395:72610899:72610967 | 72604229:72604395 | ENSG00000166224.12 | ENST00000373202.3 |
| exon_skip_42223 | 10 | 72610899:72610967:72614464:72614612:72617370:72617447 | 72614464:72614612 | ENSG00000166224.12 | ENST00000373202.3,ENST00000299297.4 |
| exon_skip_42227 | 10 | 72628101:72628190:72629548:72629654:72630804:72630903 | 72629548:72629654 | ENSG00000166224.12 | ENST00000373202.3 |
| exon_skip_42228 | 10 | 72629548:72629654:72630804:72630903:72631593:72631743 | 72630804:72630903 | ENSG00000166224.12 | ENST00000373202.3 |
| exon_skip_42229 | 10 | 72630804:72630903:72631593:72631743:72633107:72633346 | 72631593:72631743 | ENSG00000166224.12 | ENST00000373202.3 |
| exon_skip_42231 | 10 | 72631593:72631743:72633107:72633346:72635158:72635305 | 72633107:72633346 | ENSG00000166224.12 | ENST00000373202.3 |
| 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 SGPL1 |
| 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 |
| ENST00000373202 | 72576566 | 72576636 | 5CDS-5UTR |
| ENST00000373202 | 72604229 | 72604395 | Frame-shift |
| ENST00000373202 | 72614464 | 72614612 | Frame-shift |
| ENST00000373202 | 72629548 | 72629654 | Frame-shift |
| ENST00000373202 | 72633107 | 72633346 | Frame-shift |
| ENST00000373202 | 72630804 | 72630903 | In-frame |
| ENST00000373202 | 72631593 | 72631743 | 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 |
| ENST00000373202 | 72576566 | 72576636 | 5CDS-5UTR |
| ENST00000373202 | 72604229 | 72604395 | Frame-shift |
| ENST00000373202 | 72614464 | 72614612 | Frame-shift |
| ENST00000373202 | 72629548 | 72629654 | Frame-shift |
| ENST00000373202 | 72633107 | 72633346 | Frame-shift |
| ENST00000373202 | 72630804 | 72630903 | In-frame |
| ENST00000373202 | 72631593 | 72631743 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SGPL1 |
| 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 |
| ENST00000373202 | 5762 | 568 | 72630804 | 72630903 | 1011 | 1109 | 270 | 303 |
| ENST00000373202 | 5762 | 568 | 72631593 | 72631743 | 1110 | 1259 | 303 | 353 |
| 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 |
| ENST00000373202 | 5762 | 568 | 72630804 | 72630903 | 1011 | 1109 | 270 | 303 |
| ENST00000373202 | 5762 | 568 | 72631593 | 72631743 | 1110 | 1259 | 303 | 353 |
| 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 |
| O95470 | 270 | 303 | 280 | 286 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Q6R |
| O95470 | 270 | 303 | 1 | 568 | Chain | ID=PRO_0000147012;Note=Sphingosine-1-phosphate lyase 1 |
| O95470 | 270 | 303 | 269 | 273 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Q6R |
| O95470 | 270 | 303 | 298 | 308 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Q6R |
| O95470 | 270 | 303 | 62 | 568 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O95470 | 270 | 303 | 290 | 292 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Q6R |
| O95470 | 303 | 353 | 312 | 316 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Q6R |
| O95470 | 303 | 353 | 344 | 349 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Q6R |
| O95470 | 303 | 353 | 1 | 568 | Chain | ID=PRO_0000147012;Note=Sphingosine-1-phosphate lyase 1 |
| O95470 | 303 | 353 | 298 | 308 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Q6R |
| O95470 | 303 | 353 | 320 | 323 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Q6R |
| O95470 | 303 | 353 | 353 | 353 | Modified residue | Note=N6-(pyridoxal phosphate)lysine%3B alternate |
| O95470 | 303 | 353 | 353 | 353 | Modified residue | Note=N6-acetyllysine%3B alternate;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| O95470 | 303 | 353 | 317 | 317 | Mutagenesis | Note=Almost no sphinganine-1-phosphate aldolase activity. C->S;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11018465;Dbxref=PMID:11018465 |
| O95470 | 303 | 353 | 353 | 353 | Mutagenesis | Note=Loss of sphinganine-1-phosphate aldolase activity. K->L;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:14570870;Dbxref=PMID:14570870 |
| O95470 | 303 | 353 | 346 | 346 | Natural variant | ID=VAR_079215;Note=In NPHS1%3B decreased protein abundance in cells of patients homozygous for the mutation%3B increased aggregation%3B decreased sphinganine-1-phosphate aldolase activity. S->I;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:2816533 |
| O95470 | 303 | 353 | 62 | 568 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O95470 | 303 | 353 | 317 | 319 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Q6R |
| O95470 | 303 | 353 | 324 | 330 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Q6R |
| 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 |
| O95470 | 270 | 303 | 280 | 286 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Q6R |
| O95470 | 270 | 303 | 1 | 568 | Chain | ID=PRO_0000147012;Note=Sphingosine-1-phosphate lyase 1 |
| O95470 | 270 | 303 | 269 | 273 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Q6R |
| O95470 | 270 | 303 | 298 | 308 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Q6R |
| O95470 | 270 | 303 | 62 | 568 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O95470 | 270 | 303 | 290 | 292 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Q6R |
| O95470 | 303 | 353 | 312 | 316 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Q6R |
| O95470 | 303 | 353 | 344 | 349 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Q6R |
| O95470 | 303 | 353 | 1 | 568 | Chain | ID=PRO_0000147012;Note=Sphingosine-1-phosphate lyase 1 |
| O95470 | 303 | 353 | 298 | 308 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Q6R |
| O95470 | 303 | 353 | 320 | 323 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Q6R |
| O95470 | 303 | 353 | 353 | 353 | Modified residue | Note=N6-(pyridoxal phosphate)lysine%3B alternate |
| O95470 | 303 | 353 | 353 | 353 | Modified residue | Note=N6-acetyllysine%3B alternate;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| O95470 | 303 | 353 | 317 | 317 | Mutagenesis | Note=Almost no sphinganine-1-phosphate aldolase activity. C->S;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11018465;Dbxref=PMID:11018465 |
| O95470 | 303 | 353 | 353 | 353 | Mutagenesis | Note=Loss of sphinganine-1-phosphate aldolase activity. K->L;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:14570870;Dbxref=PMID:14570870 |
| O95470 | 303 | 353 | 346 | 346 | Natural variant | ID=VAR_079215;Note=In NPHS1%3B decreased protein abundance in cells of patients homozygous for the mutation%3B increased aggregation%3B decreased sphinganine-1-phosphate aldolase activity. S->I;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:2816533 |
| O95470 | 303 | 353 | 62 | 568 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O95470 | 303 | 353 | 317 | 319 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Q6R |
| O95470 | 303 | 353 | 324 | 330 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4Q6R |
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SNVs in the skipped exons for SGPL1 |
| - 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-G3-A3CJ-01 | exon_skip_42228 | 72630805 | 72630903 | 72630888 | 72630888 | Frame_Shift_Del | C | - | p.V298fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_42231 | 72633108 | 72633346 | 72633122 | 72633122 | Frame_Shift_Del | A | - | p.P358fs |
| BRCA | TCGA-AN-A0FZ-01 | exon_skip_42217 | 72604230 | 72604395 | 72604349 | 72604349 | Nonsense_Mutation | G | A | p.W49* |
| LUSC | TCGA-22-5473-01 | exon_skip_42223 | 72614465 | 72614612 | 72614558 | 72614558 | Nonsense_Mutation | C | T | p.Q119* |
| BLCA | TCGA-K4-A6MB-01 | exon_skip_42231 | 72633108 | 72633346 | 72633171 | 72633171 | Nonsense_Mutation | C | T | p.Q375* |
| - 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 |
| CW2_LARGE_INTESTINE | 72614465 | 72614612 | 72614485 | 72614485 | Missense_Mutation | G | T | p.K94N |
| JEG3_PLACENTA | 72614465 | 72614612 | 72614536 | 72614536 | Missense_Mutation | G | T | p.E111D |
| DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 72629549 | 72629654 | 72629554 | 72629554 | Missense_Mutation | C | A | p.A237D |
| HCC2450_LUNG | 72629549 | 72629654 | 72629556 | 72629556 | Missense_Mutation | C | T | p.P238S |
| SW1463_LARGE_INTESTINE | 72629549 | 72629654 | 72629560 | 72629560 | Missense_Mutation | A | C | p.Q239P |
| BC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 72629549 | 72629654 | 72629628 | 72629628 | Missense_Mutation | A | G | p.T262A |
| MERO84_LUNG | 72629549 | 72629654 | 72629629 | 72629629 | Missense_Mutation | C | T | p.T262M |
| JHUEM7_ENDOMETRIUM | 72629549 | 72629654 | 72629634 | 72629634 | Missense_Mutation | A | G | p.M264V |
| HEC251_ENDOMETRIUM | 72630805 | 72630903 | 72630880 | 72630880 | Missense_Mutation | G | T | p.D296Y |
| SNU1040_LARGE_INTESTINE | 72631594 | 72631743 | 72631630 | 72631630 | Missense_Mutation | G | A | p.A316T |
| RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 72631594 | 72631743 | 72631654 | 72631654 | Missense_Mutation | G | A | p.V324I |
| SNU1040_LARGE_INTESTINE | 72633108 | 72633346 | 72633117 | 72633117 | Missense_Mutation | G | A | p.A357T |
| OC316_OVARY | 72633108 | 72633346 | 72633183 | 72633183 | Missense_Mutation | G | A | p.D379N |
| OC314_OVARY | 72633108 | 72633346 | 72633183 | 72633183 | Missense_Mutation | G | A | p.D379N |
| RT4_URINARY_TRACT | 72604230 | 72604395 | 72604247 | 72604247 | Nonsense_Mutation | C | A | p.Y15* |
| JSC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 72614465 | 72614612 | 72614558 | 72614558 | Nonsense_Mutation | C | T | p.Q119* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SGPL1 |
| 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 SGPL1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SGPL1 |
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RelatedDrugs for SGPL1 |
| 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 |
| O95470 | DB00114 | Pyridoxal phosphate | Sphingosine-1-phosphate lyase 1 {ECO:0000305} | small molecule | approved|investigational|nutraceutical |
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RelatedDiseases for SGPL1 |
| 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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