Prediction |
polymorphism |
Model: simple_aae, prob: 0.995981849418459 (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) | chr15:40903684A>GN/A
show variant in all transcripts IGV
|
| HGNC symbol | KNL1 |
| Ensembl transcript ID | ENST00000527044 |
| Genbank transcript ID | N/A |
| UniProt peptide | Q8NG31 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.253A>G
cDNA.628A>G
g.17467A>G |
| AA changes | T85A Score: 58 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 85 |
| frameshift | no |
| known variant | Reference ID: rs12911738
| database | homozygous (G/G) | heterozygous | allele carriers |
| 1000G | 1368 | 796 | 2164 |
| ExAC | 3321 | 1687 | 5008 |
|
| regulatory features | H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 0.042 | 0.998 | | 1.182 | 0.999 | | (flanking) | 1.137 | 0.998 |
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser |
| splice sites | alteration within used splice site, likely to disturb normal splicing
| effect | gDNA position | score | detection sequence | exon-intron border | | Acceptor lost | 17464 | sequence motif lost | - | wt: acag|AAAC
mu: acag.AAGC | | Acc increased | 17460 | wt: 0.35 / mu: 0.46 | wt: ATTTTAATTTTATTTTTAGAAACAGAAACAGGAGAAAATCT
mu: ATTTTAATTTTATTTTTAGAAACAGAAGCAGGAGAAAATCT | agaa|ACAG | | Acc increased | 17459 | wt: 0.67 / mu: 0.78 | wt: AATTTTAATTTTATTTTTAGAAACAGAAACAGGAGAAAATC
mu: AATTTTAATTTTATTTTTAGAAACAGAAGCAGGAGAAAATC | taga|AACA | | Acc marginally increased | 17457 | wt: 0.9416 / mu: 0.9627 (marginal change - not scored) | wt: TTAATTTTAATTTTATTTTTAGAAACAGAAACAGGAGAAAA
mu: TTAATTTTAATTTTATTTTTAGAAACAGAAGCAGGAGAAAA | ttta|GAAA | | Donor increased | 17461 | wt: 0.70 / mu: 0.99 | wt: TAGAAACAGAAACAG
mu: TAGAAACAGAAGCAG | GAAA|caga |
|
| distance from splice site | 3 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 85 | M | K | I | V | R | K | S | E | M | E | E | T | G | E | N | L | L | L | I | Q | N | K | K | L |
| mutated | not conserved | | 85 | M | K | I | V | R | K | S | E | M | E | E | A | G | E | N | L | L | L | I | Q | N | K | K |
| Ptroglodytes | no homologue | | | |
| Mmulatta | no homologue | | | |
| Fcatus | no homologue | | | |
| Mmusculus | all conserved | ENSMUSG00000027326 | 85 | M | K | T | E | R | N | S | E | I | - | - | S | G | M | N | T | L | L | | | | | |
| Ggallus | no homologue | | | |
| Trubripes | no alignment | ENSTRUG00000013401 | n/a | |
| Drerio | all identical | ENSDARG00000070239 | 366 | Y | F | S | E | E | D | N | A | M | E | M | T | G | V | S | D | I | S | V | R | N | K | D |
| Dmelanogaster | no homologue | | | |
| Celegans | no homologue | | | |
| Xtropicalis | no homologue | | | |
|
| protein features | | start (aa) | end (aa) | feature | details | | | 1 | 728 | REGION | Interaction with BUB1 and BUB1B. | lost | | 205 | 211 | HELIX | | might get lost (downstream of altered splice site) | | 241 | 250 | HELIX | | might get lost (downstream of altered splice site) | | 505 | 505 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 513 | 513 | MOD_RES | Phosphothreonine. | might get lost (downstream of altered splice site) | | 539 | 539 | MOD_RES | Phosphothreonine. | might get lost (downstream of altered splice site) | | 578 | 578 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 601 | 601 | MOD_RES | Phosphothreonine. | might get lost (downstream of altered splice site) | | 682 | 682 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 765 | 765 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 767 | 767 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 855 | 1201 | REGION | 2 X 104 AA approximate repeats. | might get lost (downstream of altered splice site) | | 885 | 989 | REPEAT | 1. | might get lost (downstream of altered splice site) | | 954 | 954 | MOD_RES | Phosphothreonine. | might get lost (downstream of altered splice site) | | 956 | 956 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 1039 | 1039 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 1042 | 1042 | MOD_RES | Phosphothreonine. | might get lost (downstream of altered splice site) | | 1076 | 1076 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 1099 | 1201 | REPEAT | 2. | might get lost (downstream of altered splice site) | | 1232 | 1232 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 1332 | 1332 | CONFLICT | P -> A (in Ref. 2; BAC05691). | might get lost (downstream of altered splice site) | | 1357 | 1357 | CONFLICT | N -> H (in Ref. 2; BAC05691). | might get lost (downstream of altered splice site) | | 1720 | 1720 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 1756 | 1756 | CONFLICT | N -> Y (in Ref. 2; BAC05691). | might get lost (downstream of altered splice site) | | 1773 | 1773 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 1789 | 1803 | MOTIF | Nuclear localization signal (Potential). | might get lost (downstream of altered splice site) | | 1818 | 1819 | SITE | Breakpoint for translocation to form MLL- CASC5. | might get lost (downstream of altered splice site) | | 1834 | 2316 | REGION | Necessary for kinetochore localization and for interaction with NSL1 and DSN1. | might get lost (downstream of altered splice site) | | 1845 | 1845 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 1869 | 1869 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 1879 | 1879 | MOD_RES | Phosphothreonine. | might get lost (downstream of altered splice site) | | 1942 | 2133 | COILED | Potential. | might get lost (downstream of altered splice site) |
|
| length of protein | normal |
| AA sequence altered | yes |
| position of stopcodon in wt / mu CDS | 342 / 342 |
| position (AA) of stopcodon in wt / mu AA sequence | 114 / 114 |
| position of stopcodon in wt / mu cDNA | 717 / 717 |
| 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 | 376 / 376 |
| chromosome | 15 |
| strand | 1 |
| last intron/exon boundary | 692 |
| theoretical NMD boundary in CDS | 266 |
| length of CDS | 342 |
| coding sequence (CDS) position | 253 |
cDNA position
(for ins/del: last normal base / first normal base) | 628 |
gDNA position
(for ins/del: last normal base / first normal base) | 17467 |
chromosomal position
(for ins/del: last normal base / first normal base) | 40903684 |
| original gDNA sequence snippet | TTTTATTTTTAGAAACAGAAACAGGAGAAAATCTTCTTTTG |
| altered gDNA sequence snippet | TTTTATTTTTAGAAACAGAAGCAGGAGAAAATCTTCTTTTG |
| original cDNA sequence snippet | GAAAGTCAGAAATGGAAGAAACAGGAGAAAATCTTCTTTTG |
| altered cDNA sequence snippet | GAAAGTCAGAAATGGAAGAAGCAGGAGAAAATCTTCTTTTG |
| wildtype AA sequence | MDGVSSEANE ENDNIERPVR RRHSSILKPP RSPLQDLRGG NERVQESNAL RNKKNSRRVS
FADTIKVFQT ESHMKIVRKS EMEETGENLL LIQNKKLEDN YCEITVFNYR TYP* |
| mutated AA sequence | MDGVSSEANE ENDNIERPVR RRHSSILKPP RSPLQDLRGG NERVQESNAL RNKKNSRRVS
FADTIKVFQT ESHMKIVRKS EMEEAGENLL LIQNKKLEDN YCEITVFNYR TYP* |
| speed | 1.05 s |
|
|
