Prediction |
polymorphism |
Model: simple_aae, prob: 0.9999763771291 (classification due to TGP/ExAC,
real probability is shown anyway)
(explain) |
| Summary |
- amino acid sequence changed
- 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 | SLC22A25 |
| Ensembl transcript ID | ENST00000403374 |
| Genbank transcript ID | N/A |
| UniProt peptide | Q6T423 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.401G>C
cDNA.705G>C
g.45904G>C |
| AA changes | R134T Score: 71 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 134 |
| frameshift | no |
| 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 | | effect | gDNA position | score | wt detection sequence | exon-intron border | | Donor increased | 45908 | wt: 0.68 / mu: 0.83 | wt: AGAAAAGCTGCACAC
mu: ACAAAAGCTGCACAC | AAAA|gctg | | Donor marginally increased | 45895 | wt: 0.9228 / mu: 0.9770 (marginal change - not scored) | wt: CTTAAAGGAACTTAG
mu: CTTAAAGGAACTTAC | TAAA|ggaa |
|
| distance from splice site | 56 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 134 | N | N | K | P | E | E | G | L | K | E | L | R | K | A | A | H | R | N | G | M | K | N | A | E |
| mutated | not conserved | | 134 | N | N | K | P | E | E | G | L | K | E | L | T | K | A | A | H | R | N | G | M | K | N | A |
| Ptroglodytes | no homologue | | | |
| Mmulatta | no homologue | | | |
| Fcatus | no homologue | | | |
| Mmusculus | no homologue | | | |
| Ggallus | no homologue | | | |
| Trubripes | not conserved | ENSTRUG00000000413 | 306 | | R | R | S | D | K | A | L | K | N | L | H | R | V | A | R | I | N | G | K | P | I | N |
| Drerio | no homologue | | | |
| Dmelanogaster | no homologue | | | |
| Celegans | no homologue | | | |
| Xtropicalis | no homologue | | | |
|
| protein features | | start (aa) | end (aa) | feature | details | | | 31 | 145 | TOPO_DOM | Extracellular (Potential). | lost | | 146 | 166 | TRANSMEM | Helical; Name=2; (Potential). | might get lost (downstream of altered splice site) | | 167 | 177 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) | | 178 | 198 | TRANSMEM | Helical; Name=3; (Potential). | might get lost (downstream of altered splice site) | | 199 | 204 | TOPO_DOM | Extracellular (Potential). | might get lost (downstream of altered splice site) | | 205 | 225 | TRANSMEM | Helical; Name=4; (Potential). | might get lost (downstream of altered splice site) | | 226 | 234 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) | | 235 | 255 | TRANSMEM | Helical; Name=5; (Potential). | might get lost (downstream of altered splice site) | | 256 | 259 | TOPO_DOM | Extracellular (Potential). | might get lost (downstream of altered splice site) | | 260 | 280 | TRANSMEM | Helical; Name=6; (Potential). | might get lost (downstream of altered splice site) | | 281 | 349 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) | | 350 | 370 | TRANSMEM | Helical; Name=7; (Potential). | might get lost (downstream of altered splice site) | | 371 | 377 | TOPO_DOM | Extracellular (Potential). | might get lost (downstream of altered splice site) | | 378 | 398 | TRANSMEM | Helical; Name=8; (Potential). | might get lost (downstream of altered splice site) | | 399 | 406 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) | | 407 | 427 | TRANSMEM | Helical; Name=9; (Potential). | might get lost (downstream of altered splice site) | | 428 | 434 | TOPO_DOM | Extracellular (Potential). | might get lost (downstream of altered splice site) | | 435 | 455 | TRANSMEM | Helical; Name=10; (Potential). | might get lost (downstream of altered splice site) | | 456 | 470 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) | | 471 | 491 | TRANSMEM | Helical; Name=11; (Potential). | might get lost (downstream of altered splice site) | | 492 | 494 | TOPO_DOM | Extracellular (Potential). | might get lost (downstream of altered splice site) | | 495 | 515 | TRANSMEM | Helical; Name=12; (Potential). | might get lost (downstream of altered splice site) | | 516 | 547 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) |
|
| length of protein | normal |
| AA sequence altered | yes |
| position of stopcodon in wt / mu CDS | 705 / 705 |
| position (AA) of stopcodon in wt / mu AA sequence | 235 / 235 |
| position of stopcodon in wt / mu cDNA | 1009 / 1009 |
| 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 | 305 / 305 |
| chromosome | 11 |
| strand | -1 |
| last intron/exon boundary | 1642 |
| theoretical NMD boundary in CDS | 1287 |
| length of CDS | 705 |
| coding sequence (CDS) position | 401 |
cDNA position
(for ins/del: last normal base / first normal base) | 705 |
gDNA position
(for ins/del: last normal base / first normal base) | 45904 |
chromosomal position
(for ins/del: last normal base / first normal base) | 62951221 |
| original gDNA sequence snippet | AGAGGGCTTAAAGGAACTTAGAAAAGCTGCACACAGGAATG |
| altered gDNA sequence snippet | AGAGGGCTTAAAGGAACTTACAAAAGCTGCACACAGGAATG |
| original cDNA sequence snippet | AGAGGGCTTAAAGGAACTTAGAAAAGCTGCACACAGGAATG |
| altered cDNA sequence snippet | AGAGGGCTTAAAGGAACTTACAAAAGCTGCACACAGGAATG |
| wildtype AA sequence | MNMFGRKFVL RWSYLQLAIV GTCAAFAPTI LVYCSLRFLA GAATFSIIVN TVLLIVEWIT
HQFCAMALTL TLCAASIGHI TLGSLAFVIR DQCILQLVMS APCFVFFLFS RWLAESARWL
IINNKPEEGL KELRKAAHRN GMKNAEDILT MEVLKSTMKQ ELEAAQKKHS LCELLRIPNI
CKRICFLSFV RSAGVCWRST PDPVCLGITS GGCRTAKIPA CSFLWKLHFR GAPA* |
| mutated AA sequence | MNMFGRKFVL RWSYLQLAIV GTCAAFAPTI LVYCSLRFLA GAATFSIIVN TVLLIVEWIT
HQFCAMALTL TLCAASIGHI TLGSLAFVIR DQCILQLVMS APCFVFFLFS RWLAESARWL
IINNKPEEGL KELTKAAHRN GMKNAEDILT MEVLKSTMKQ ELEAAQKKHS LCELLRIPNI
CKRICFLSFV RSAGVCWRST PDPVCLGITS GGCRTAKIPA CSFLWKLHFR GAPA* |
| speed | 0.39 s |
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