Prediction |
polymorphism |
Model: without_aae, prob: 0.00684955316770625 (classification due to TGP/ExAC,
real probability is shown anyway)
(explain) |
| Summary |
- homozygous in TGP or ExAC
- protein features (might be) affected
- splice site changes
|
hyperlink |
| analysed issue |
analysis result |
| name of alteration | no title |
| alteration (phys. location) | chr11:62951221C>GN/A
show variant in all transcripts IGV
|
| HGNC symbol | SLC22A10 |
| Ensembl transcript ID | ENST00000535888 |
| Genbank transcript ID | N/A |
| UniProt peptide | Q63ZE4 |
| alteration type | single base exchange |
| alteration region | intron |
| DNA changes | g.45883C>G |
| AA changes | N/A |
position(s) of altered AA
if AA alteration in CDS | N/A |
| frameshift | N/A |
| known variant | Reference ID: rs11231397
| database | homozygous (G/G) | heterozygous | allele carriers |
| 1000G | 459 | 1187 | 1646 |
| ExAC | 10521 | 11725 | 22246 |
|
| regulatory features | H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 0.435 | 0.763 | | -0.783 | 0.693 | | (flanking) | 1.495 | 0.716 |
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser |
| splice sites | splice site change before start ATG (at aa -135) | | effect | gDNA position | score | detection sequence | exon-intron border | | Acc marginally increased | 45873 | wt: 0.9139 / mu: 0.9214 (marginal change - not scored) | wt: TTCTTCATTCCATTCCTGTGTGCAGCTTTTCTAAGTTCCTT
mu: TTCTTCATTCCATTCCTGTGTGCAGCTTTTGTAAGTTCCTT | gtgt|GCAG | | Acc gained | 45882 | 0.64 | mu: CCATTCCTGTGTGCAGCTTTTGTAAGTTCCTTTAAGCCCTC | tttt|GTAA |
|
| distance from splice site | 16805 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | N/A |
| protein features | | start (aa) | end (aa) | feature | details | | | 1 | 15 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) | | 16 | 36 | TRANSMEM | Helical; (Potential). | might get lost (downstream of altered splice site) | | 37 | 145 | TOPO_DOM | Extracellular (Potential). | might get lost (downstream of altered splice site) | | 56 | 56 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 102 | 102 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 146 | 166 | TRANSMEM | Helical; (Potential). | might get lost (downstream of altered splice site) | | 167 | 193 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) | | 194 | 214 | TRANSMEM | Helical; (Potential). | might get lost (downstream of altered splice site) | | 215 | 230 | TOPO_DOM | Extracellular (Potential). | might get lost (downstream of altered splice site) | | 231 | 251 | TRANSMEM | Helical; (Potential). | might get lost (downstream of altered splice site) | | 252 | 259 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) | | 260 | 280 | TRANSMEM | Helical; (Potential). | might get lost (downstream of altered splice site) | | 281 | 349 | TOPO_DOM | Extracellular (Potential). | might get lost (downstream of altered splice site) | | 350 | 370 | TRANSMEM | Helical; (Potential). | might get lost (downstream of altered splice site) | | 371 | 377 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) | | 378 | 398 | TRANSMEM | Helical; (Potential). | might get lost (downstream of altered splice site) | | 399 | 406 | TOPO_DOM | Extracellular (Potential). | might get lost (downstream of altered splice site) | | 407 | 427 | TRANSMEM | Helical; (Potential). | might get lost (downstream of altered splice site) | | 428 | 436 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) | | 437 | 457 | TRANSMEM | Helical; (Potential). | might get lost (downstream of altered splice site) | | 458 | 472 | TOPO_DOM | Extracellular (Potential). | might get lost (downstream of altered splice site) | | 473 | 493 | TRANSMEM | Helical; (Potential). | might get lost (downstream of altered splice site) | | 494 | 495 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) | | 496 | 516 | TRANSMEM | Helical; (Potential). | might get lost (downstream of altered splice site) | | 517 | 541 | TOPO_DOM | Extracellular (Potential). | might get lost (downstream of altered splice site) |
|
| length of protein | N/A |
| AA sequence altered | N/A |
| position of stopcodon in wt / mu CDS | N/A |
| position (AA) of stopcodon in wt / mu AA sequence | N/A |
| position of stopcodon in wt / mu cDNA | N/A |
| poly(A) signal | N/A |
conservation
nucleotide level for all changes - no scoring up to now | N/A |
| position of start ATG in wt / mu cDNA | 541 / 541 |
| chromosome | 11 |
| strand | 1 |
| last intron/exon boundary | 1105 |
| theoretical NMD boundary in CDS | 514 |
| length of CDS | 444 |
| coding sequence (CDS) position | N/A |
cDNA position
(for ins/del: last normal base / first normal base) | N/A |
gDNA position
(for ins/del: last normal base / first normal base) | 45883 |
chromosomal position
(for ins/del: last normal base / first normal base) | 62951221 |
| original gDNA sequence snippet | CATTCCTGTGTGCAGCTTTTCTAAGTTCCTTTAAGCCCTCT |
| altered gDNA sequence snippet | CATTCCTGTGTGCAGCTTTTGTAAGTTCCTTTAAGCCCTCT |
| original cDNA sequence snippet | N/A |
| altered cDNA sequence snippet | N/A |
| wildtype AA sequence | MIIISNNSLP ITEWIRPNSK ALVVILSSGA LSIGQIILGG LAYVFRDWQT LHVVASVPFF
VFFLLSRWLV ESARWLIITN KLDEGLKALR KVARTNGIKN AEETLNIEVV RSTMQEELDA
AQTKTTVCDL FRNPSMRKRI CILVFLR* |
| mutated AA sequence | N/A |
| speed | 0.35 s |
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