Prediction |
polymorphism |
Model: without_aae, prob: 2.47075679079387e-08 (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) | chr4:39064162A>CN/A
show variant in all transcripts IGV
|
| HGNC symbol | KLHL5 |
| Ensembl transcript ID | ENST00000508137 |
| Genbank transcript ID | NM_001171654 |
| UniProt peptide | Q96PQ7 |
| alteration type | single base exchange |
| alteration region | intron |
| DNA changes | g.17504A>C |
| AA changes | N/A |
position(s) of altered AA
if AA alteration in CDS | N/A |
| frameshift | N/A |
| known variant | Reference ID: rs2711941
| database | homozygous (C/C) | heterozygous | allele carriers |
| 1000G | 1393 | 902 | 2295 |
| ExAC | - | - | - |
|
| regulatory features | H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 1.17 | 0.96 | | 0.584 | 0.986 | | (flanking) | 1.091 | 0.996 |
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser |
| splice sites | splice site change before start ATG (at aa -12) | | effect | gDNA position | score | detection sequence | exon-intron border | | Acc marginally increased | 17513 | wt: 0.8705 / mu: 0.9553 (marginal change - not scored) | wt: TTCCTTTACATATTTTTGTTGTGTACAGCAGGGCATATACT
mu: TTCCTTTACATCTTTTTGTTGTGTACAGCAGGGCATATACT | gttg|TGTA | | Acc increased | 17511 | wt: 0.46 / mu: 0.92 | wt: TTTTCCTTTACATATTTTTGTTGTGTACAGCAGGGCATATA
mu: TTTTCCTTTACATCTTTTTGTTGTGTACAGCAGGGCATATA | ttgt|TGTG | | Acc marginally increased | 17500 | wt: 0.6897 / mu: 0.7142 (marginal change - not scored) | wt: AATGTGATTTATTTTCCTTTACATATTTTTGTTGTGTACAG
mu: AATGTGATTTATTTTCCTTTACATCTTTTTGTTGTGTACAG | ttta|CATA | | Acc marginally increased | 17502 | wt: 0.8826 / mu: 0.8993 (marginal change - not scored) | wt: TGTGATTTATTTTCCTTTACATATTTTTGTTGTGTACAGCA
mu: TGTGATTTATTTTCCTTTACATCTTTTTGTTGTGTACAGCA | taca|TATT | | Acc increased | 17496 | wt: 0.43 / mu: 0.59 | wt: TATGAATGTGATTTATTTTCCTTTACATATTTTTGTTGTGT
mu: TATGAATGTGATTTATTTTCCTTTACATCTTTTTGTTGTGT | ttcc|TTTA | | Acc marginally increased | 17509 | wt: 0.9724 / mu: 0.9952 (marginal change - not scored) | wt: TATTTTCCTTTACATATTTTTGTTGTGTACAGCAGGGCATA
mu: TATTTTCCTTTACATCTTTTTGTTGTGTACAGCAGGGCATA | tttt|GTTG | | Acc marginally increased | 17505 | wt: 0.9645 / mu: 0.9690 (marginal change - not scored) | wt: GATTTATTTTCCTTTACATATTTTTGTTGTGTACAGCAGGG
mu: GATTTATTTTCCTTTACATCTTTTTGTTGTGTACAGCAGGG | atat|TTTT | | Acc increased | 17506 | wt: 0.45 / mu: 0.96 | wt: ATTTATTTTCCTTTACATATTTTTGTTGTGTACAGCAGGGC
mu: ATTTATTTTCCTTTACATCTTTTTGTTGTGTACAGCAGGGC | tatt|TTTG | | Acc increased | 17510 | wt: 0.80 / mu: 0.92 | wt: ATTTTCCTTTACATATTTTTGTTGTGTACAGCAGGGCATAT
mu: ATTTTCCTTTACATCTTTTTGTTGTGTACAGCAGGGCATAT | tttg|TTGT | | Acc increased | 17514 | wt: 0.81 / mu: 0.90 | wt: TCCTTTACATATTTTTGTTGTGTACAGCAGGGCATATACTT
mu: TCCTTTACATCTTTTTGTTGTGTACAGCAGGGCATATACTT | ttgt|GTAC | | Acc marginally increased | 17499 | wt: 0.7974 / mu: 0.8121 (marginal change - not scored) | wt: GAATGTGATTTATTTTCCTTTACATATTTTTGTTGTGTACA
mu: GAATGTGATTTATTTTCCTTTACATCTTTTTGTTGTGTACA | cttt|ACAT | | Acc increased | 17508 | wt: 0.40 / mu: 0.81 | wt: TTATTTTCCTTTACATATTTTTGTTGTGTACAGCAGGGCAT
mu: TTATTTTCCTTTACATCTTTTTGTTGTGTACAGCAGGGCAT | tttt|TGTT | | Donor marginally increased | 17509 | wt: 0.8305 / mu: 0.8890 (marginal change - not scored) | wt: ATTTTTGTTGTGTAC
mu: CTTTTTGTTGTGTAC | TTTT|gttg | | Acc gained | 17512 | 0.40 | mu: TTTCCTTTACATCTTTTTGTTGTGTACAGCAGGGCATATAC | tgtt|GTGT |
|
| distance from splice site | 13423 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | N/A |
| protein features | | start (aa) | end (aa) | feature | details | | | 220 | 287 | DOMAIN | BTB. | might get lost (downstream of altered splice site) | | 323 | 323 | CONFLICT | L -> P (in Ref. 2; BAA91845). | might get lost (downstream of altered splice site) | | 435 | 435 | CONFLICT | Q -> R (in Ref. 1; AAL08584). | might get lost (downstream of altered splice site) | | 468 | 514 | REPEAT | Kelch 1. | might get lost (downstream of altered splice site) | | 515 | 561 | REPEAT | Kelch 2. | might get lost (downstream of altered splice site) | | 563 | 608 | REPEAT | Kelch 3. | might get lost (downstream of altered splice site) | | 594 | 594 | CONFLICT | M -> K (in Ref. 2; BAA91845). | might get lost (downstream of altered splice site) | | 609 | 655 | REPEAT | Kelch 4. | might get lost (downstream of altered splice site) | | 657 | 708 | REPEAT | Kelch 5. | might get lost (downstream of altered splice site) | | 695 | 695 | CONFLICT | S -> G (in Ref. 2; BAA92121). | might get lost (downstream of altered splice site) | | 709 | 754 | REPEAT | Kelch 6. | 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 | 78 / 78 |
| chromosome | 4 |
| strand | 1 |
| last intron/exon boundary | 1728 |
| theoretical NMD boundary in CDS | 1600 |
| length of CDS | 1707 |
| 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) | 17504 |
chromosomal position
(for ins/del: last normal base / first normal base) | 39064162 |
| original gDNA sequence snippet | TGATTTATTTTCCTTTACATATTTTTGTTGTGTACAGCAGG |
| altered gDNA sequence snippet | TGATTTATTTTCCTTTACATCTTTTTGTTGTGTACAGCAGG |
| original cDNA sequence snippet | N/A |
| altered cDNA sequence snippet | N/A |
| wildtype AA sequence | MEPCTSDEFF QALNHAEQTF KKMENYLRHK QLCDVILVAG DRRIPAHRLV LSSVSDYFAA
MFTNDVREAR QEEIKMEGVE PNSLWSLIQY AYTGRLELKE DNIECLLSTA CLLQLSQVVE
ACCKFLMKQL HPSNCLGIRS FADAQGCTDL HKVAHNYTME HFMEVIRNQE FVLLPASEIA
KLLASDDMNI PNEETILNAL LTWVRHDLEQ RRKDLSKLLA YIRLPLLAPQ FLADMENNVL
FRDDIECQKL IMEAMKYHLL PERRPMLQSP RTKPRKSTVG TLFAVGGMDS TKGATSIEKY
DLRTNMWTPV ANMNGRRLQF GVAVLDDKLY VVGGRDGLKT LNTVECYNPK TKTWSVMPPM
STHRHGLGVA VLEGPMYAVG GHDGWSYLNT VERWDPQARQ WNFVATMSTP RSTVGVAVLS
GKLYAVGGRD GSSCLKSVEC FDPHTNKWTL CAQMSKRRGG VGVTTWNGLL YAIGGHDAPA
SNLTSRLSDC VERYDPKTDM WTAVASMSIS RDAVGVCLLG DKLYAVGGYD GQAYLNTVEA
YDPQTNEWTQ VAPLCLGRAG ACVVTVKL* |
| mutated AA sequence | N/A |
| speed | 0.86 s |
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