| Basic Information ▶ | |
| VISDB ID | TVIS20064958 |
|---|---|
| Fusion Name | HPV-SMPDL3A integration |
| Validated | No |
| Curated Way | Curated |
| Method | High-throughput Viral Integration Detection method |
| Wet Assay | Yes |
| Sample ID | - |
| Sample Name | S032 |
| Sample Type | Tumor |
| Age | 57 = 59; >57 = 50 |
| Gender | - |
| Disease Information ▶ | |
| Disease Name | Oropharyngeal squamous cell carcinoma |
| Disease Abbreviation | OPSCC |
| Cancer | Yes |
| Literature ▶ | |
| PubMed ID | 38279874 |
| Journal | Clinical and Translational Medicine |
| Published Year | 2024 |
| Human Genome ▶ | |
| Human Genome Version Description | GRCh37/hg19 |
| Human Genome RefSeq Accession | GCF_000001405.13 |
| Human Chromosome | chr6 |
| Cytogenetic Band | q22.31 |
| Human Strand | - |
| Human Integration Location Type | intronic |
| Hg19 Start | 123120538 |
| Hg19 End | 123120538 |
| Hg38 Start | 122799393 |
| Hg38 End | 122799393 |
| Junction Sequence | AGATGTAATATCAGATGACGAGGACGAAAATGCAACAGACACAGGGTCGGATATGGTAGATTTTATTGATACACAAGGAACATTTTGTGAACAGGCAGAGCTAGAGACAGCACAGGCATTGTTCCATGCGCAGGAGAACTGGAAAGCACTGCCATAAATAGAAAACAATATTTATAAAATATCTTAAGCCTGGGCCTCAATAAT |
| Target Gene ▶ | |
| Target Gene | SMPDL3A, ENSG00000294893 |
| Nearby Gene | - |
| Distance | - |
| Virus Information ▶ | |
| Virus Name | Human Papillomavirus |
| Virus Subtype Name | HPV18 |
| Virus Genome Accession | GQ180789 |
| TaxonomyID | 10566 |
| Virus Abbreviation | HPV |
| Virus Genome | Human papillomavirus type 18 isolate CU13, complete genome |
| Virus Genome Length | 7857 bp |
| Virus Breakpoint1 | 1134 |
| Virus Breakpoint2 | - |
| Virus Gene Name | HpV18gp3_E1 |
| Virus Region Type | - |
| Integrated Virus Sequence | - |
| ViMIC ID | - |
| Predicted VIS Effect ▶ | |
| Region | intron |
| Impact | intronic_insertion |
| Transcript | Transcript 1: ENST00000726593.1, Transcript 2: ENST00000726594.1, Transcript 3: ENST00000539041.5, Transcript 4: ENST00000894534.1, Transcript 5: ENST00000894535.1, Transcript 6: ENST00000368440.5, Transcript 7: ENST00000894536.1, Transcript 8: ENST00000894537.1 |
| Transcript 1 Gene Id | ENSG00000294893.1 |
| Transcript 1 Gene Name | ENSG00000294893 |
| Transcript 2 Gene Id | ENSG00000294893.1 |
| Transcript 2 Gene Name | ENSG00000294893 |
| Transcript 3 Gene Id | ENSG00000172594.14 |
| Transcript 3 Gene Name | SMPDL3A |
| Transcript 4 Gene Id | ENSG00000172594.14 |
| Transcript 4 Gene Name | SMPDL3A |
| Transcript 5 Gene Id | ENSG00000172594.14 |
| Transcript 5 Gene Name | SMPDL3A |
| Transcript 6 Gene Id | ENSG00000172594.14 |
| Transcript 6 Gene Name | SMPDL3A |
| Transcript 7 Gene Id | ENSG00000172594.14 |
| Transcript 7 Gene Name | SMPDL3A |
| Transcript 8 Gene Id | ENSG00000172594.14 |
| Transcript 8 Gene Name | SMPDL3A |
| SpliceAI Score | |
| Delta Scores | Acceptor Gain: 0.010 | Acceptor Loss: 0.020 | Donor Gain: 0.000 | Donor Loss: 0.010 |
| Delta Score Max | 0.020 |
| Delta Position at Max | -2046 |
| Delta Score Flag | LOW |
| Gene | SMPDL3A |
| AlphaGenome Analysis | |
| Chromosome | chr6 |
Center for Precision Health
McWilliams School of Biomedical Informatics at UTHealth Houston
7000 Fannin Street, Suite 600, Houston, TX 77030
Email: Zhongming Zhao, Ph.D