Prediction |
polymorphism |
Model: simple_aae, prob: 0.999999999999827 (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) | chr1:152882982C>GN/A
show variant in all transcripts IGV
|
| HGNC symbol | IVL |
| Ensembl transcript ID | ENST00000368764 |
| Genbank transcript ID | NM_005547 |
| UniProt peptide | P07476 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.709C>G
cDNA.773C>G
g.1962C>G |
| AA changes | Q237E Score: 29 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 237 |
| frameshift | no |
| known variant | Reference ID: rs7520711
| database | homozygous (G/G) | heterozygous | allele carriers |
| 1000G | 580 | 965 | 1545 |
| ExAC | - | - | - |
|
| regulatory features | N/A |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | -0.573 | 0 | | -0.891 | 0 | | (flanking) | -1.12 | 0 |
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 | 1961 | wt: 0.36 / mu: 0.98 | wt: CTCCCACAGCAGCAG
mu: CTCCCAGAGCAGCAG | CCCA|cagc | | Donor marginally increased | 1966 | wt: 0.2168 / mu: 0.2226 (marginal change - not scored) | wt: ACAGCAGCAGGAGGG
mu: AGAGCAGCAGGAGGG | AGCA|gcag | | Donor gained | 1958 | 0.54 | mu: GAGCTCCCAGAGCAG | GCTC|ccag |
|
| distance from splice site | 728 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 237 | P | E | Q | Q | E | G | Q | L | E | L | P | Q | Q | Q | E | G | Q | L | E | L | S | E | Q | Q |
| mutated | all conserved | | 237 | P | E | Q | Q | E | G | Q | L | E | L | P | E | Q | Q | E | | | | | | | | |
| Ptroglodytes | all conserved | ENSPTRG00000030382 | 204 | L | E | Q | Q | K | G | Q | L | E | L | P | E | Q | Q | E | | | | | | | | |
| Mmulatta | no homologue | | | |
| Fcatus | no homologue | | | |
| Mmusculus | not conserved | ENSMUSG00000049128 | 210 | | | | | | | | | | I | P | G | E | K | Q | Q | E | L | H | L | G | Q | R |
| Ggallus | no homologue | | | |
| Trubripes | no homologue | | | |
| Drerio | no homologue | | | |
| Dmelanogaster | all identical | FBgn0031820 | 347 | | | Q | P | V | N | KNTAIG | V | Q | I | Q | Q | S | Q | EPLG | G | T | L | P | T | R | Q | K |
| Celegans | all identical | Y75B8A.8 | 191 | Q | F | Q | R | Q | Q | Q | - | - | - | Q | Q | Q | Q | Q | L | Q | Q | N | P | Q | N | Q |
| Xtropicalis | no homologue | | | |
|
| protein features | | start (aa) | end (aa) | feature | details | | | 153 | 542 | REGION | 39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD]. | lost | | 233 | 242 | REPEAT | 9. | lost | | 243 | 252 | REPEAT | 10. | might get lost (downstream of altered splice site) | | 253 | 262 | REPEAT | 11. | might get lost (downstream of altered splice site) | | 263 | 272 | REPEAT | 12. | might get lost (downstream of altered splice site) | | 273 | 282 | REPEAT | 13. | might get lost (downstream of altered splice site) | | 283 | 292 | REPEAT | 14. | might get lost (downstream of altered splice site) | | 293 | 302 | REPEAT | 15. | might get lost (downstream of altered splice site) | | 303 | 312 | REPEAT | 16. | might get lost (downstream of altered splice site) | | 313 | 318 | HELIX | | might get lost (downstream of altered splice site) | | 313 | 322 | REPEAT | 17. | might get lost (downstream of altered splice site) | | 323 | 328 | HELIX | | might get lost (downstream of altered splice site) | | 323 | 332 | REPEAT | 18. | might get lost (downstream of altered splice site) | | 333 | 338 | HELIX | | might get lost (downstream of altered splice site) | | 333 | 342 | REPEAT | 19. | might get lost (downstream of altered splice site) | | 343 | 348 | HELIX | | might get lost (downstream of altered splice site) | | 343 | 352 | REPEAT | 20. | might get lost (downstream of altered splice site) | | 353 | 358 | HELIX | | might get lost (downstream of altered splice site) | | 353 | 362 | REPEAT | 21. | might get lost (downstream of altered splice site) | | 363 | 372 | REPEAT | 22. | might get lost (downstream of altered splice site) | | 373 | 382 | REPEAT | 23. | might get lost (downstream of altered splice site) | | 383 | 392 | REPEAT | 24; approximate. | might get lost (downstream of altered splice site) | | 393 | 402 | REPEAT | 25. | might get lost (downstream of altered splice site) | | 403 | 412 | REPEAT | 26. | might get lost (downstream of altered splice site) | | 413 | 422 | REPEAT | 27. | might get lost (downstream of altered splice site) | | 423 | 432 | REPEAT | 28. | might get lost (downstream of altered splice site) | | 433 | 442 | REPEAT | 29. | might get lost (downstream of altered splice site) | | 443 | 452 | REPEAT | 30. | might get lost (downstream of altered splice site) | | 453 | 462 | REPEAT | 31. | might get lost (downstream of altered splice site) | | 463 | 472 | REPEAT | 32. | might get lost (downstream of altered splice site) | | 473 | 482 | REPEAT | 33. | might get lost (downstream of altered splice site) | | 483 | 492 | REPEAT | 34. | might get lost (downstream of altered splice site) | | 493 | 502 | REPEAT | 35. | might get lost (downstream of altered splice site) | | 496 | 496 | CROSSLNK | Isoglutamyl lysine isopeptide (Gln-Lys) (interchain with K-? in other proteins). | might get lost (downstream of altered splice site) | | 503 | 512 | REPEAT | 36; approximate. | might get lost (downstream of altered splice site) | | 513 | 522 | REPEAT | 37. | might get lost (downstream of altered splice site) | | 523 | 532 | REPEAT | 38. | might get lost (downstream of altered splice site) | | 533 | 542 | REPEAT | 39; approximate. | might get lost (downstream of altered splice site) |
|
| length of protein | normal |
| AA sequence altered | yes |
| position of stopcodon in wt / mu CDS | 1758 / 1758 |
| position (AA) of stopcodon in wt / mu AA sequence | 586 / 586 |
| position of stopcodon in wt / mu cDNA | 1822 / 1822 |
| 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 | 65 / 65 |
| chromosome | 1 |
| strand | 1 |
| last intron/exon boundary | 46 |
| theoretical NMD boundary in CDS | cannot be calculated, too little distance between start ATG and last intron/exon boundary |
| length of CDS | 1758 |
| coding sequence (CDS) position | 709 |
cDNA position
(for ins/del: last normal base / first normal base) | 773 |
gDNA position
(for ins/del: last normal base / first normal base) | 1962 |
chromosomal position
(for ins/del: last normal base / first normal base) | 152882982 |
| original gDNA sequence snippet | AGGGGCAGCTGGAGCTCCCACAGCAGCAGGAGGGGCAGCTG |
| altered gDNA sequence snippet | AGGGGCAGCTGGAGCTCCCAGAGCAGCAGGAGGGGCAGCTG |
| original cDNA sequence snippet | AGGGGCAGCTGGAGCTCCCACAGCAGCAGGAGGGGCAGCTG |
| altered cDNA sequence snippet | AGGGGCAGCTGGAGCTCCCAGAGCAGCAGGAGGGGCAGCTG |
| wildtype AA sequence | MSQQHTLPVT LSPALSQELL KTVPPPVNTH QEQMKQPTPL PPPCQKVPVE LPVEVPSKQE
EKHMTAVKGL PEQECEQQQK EPQEQELQQQ HWEQHEEYQK AENPEQQLKQ EKTQRDQQLN
KQLEEEKKLL DQQLDQELVK RDEQLGMKKE QLLELPEQQE GHLKHLEQQE GQLKHPEQQE
GQLELPEQQE GQLELPEQQE GQLELPEQQE GQLELPEQQE GQLELPEQQE GQLELPQQQE
GQLELSEQQE GQLELSEQQE GQLKHLEHQE GQLEVPEEQM GQLKYLEQQE GQLKHLDQQE
KQPELPEQQM GQLKHLEQQE GQPKHLEQQE GQLEQLEEQE GQLKHLEQQE GQLEHLEHQE
GQLGLPEQQV LQLKQLEKQQ GQPKHLEEEE GQLKHLVQQE GQLKHLVQQE GQLEQQERQV
EHLEQQVGQL KHLEEQEGQL KHLEQQQGQL EVPEQQVGQP KNLEQEEKQL ELPEQQEGQV
KHLEKQEAQL ELPEQQVGQP KHLEQQEKHL EHPEQQDGQL KHLEQQEGQL KDLEQQKGQL
EQPVFAPAPG QVQDIQPALP TKGEVLLPVE HQQQKQEVQW PPKHK* |
| mutated AA sequence | MSQQHTLPVT LSPALSQELL KTVPPPVNTH QEQMKQPTPL PPPCQKVPVE LPVEVPSKQE
EKHMTAVKGL PEQECEQQQK EPQEQELQQQ HWEQHEEYQK AENPEQQLKQ EKTQRDQQLN
KQLEEEKKLL DQQLDQELVK RDEQLGMKKE QLLELPEQQE GHLKHLEQQE GQLKHPEQQE
GQLELPEQQE GQLELPEQQE GQLELPEQQE GQLELPEQQE GQLELPEQQE GQLELPEQQE
GQLELSEQQE GQLELSEQQE GQLKHLEHQE GQLEVPEEQM GQLKYLEQQE GQLKHLDQQE
KQPELPEQQM GQLKHLEQQE GQPKHLEQQE GQLEQLEEQE GQLKHLEQQE GQLEHLEHQE
GQLGLPEQQV LQLKQLEKQQ GQPKHLEEEE GQLKHLVQQE GQLKHLVQQE GQLEQQERQV
EHLEQQVGQL KHLEEQEGQL KHLEQQQGQL EVPEQQVGQP KNLEQEEKQL ELPEQQEGQV
KHLEKQEAQL ELPEQQVGQP KHLEQQEKHL EHPEQQDGQL KHLEQQEGQL KDLEQQKGQL
EQPVFAPAPG QVQDIQPALP TKGEVLLPVE HQQQKQEVQW PPKHK* |
| speed | 0.58 s |
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