Prediction |
polymorphism |
Model: simple_aae, prob: 0.999999999929229 (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) | chr17:39274518C>TN/A
show variant in all transcripts IGV
|
HGNC symbol | KRTAP4-11 |
Ensembl transcript ID | ENST00000391413 |
Genbank transcript ID | NM_033059 |
UniProt peptide | Q9BYQ6 |
alteration type | single base exchange |
alteration region | CDS |
DNA changes | c.50G>A cDNA.89G>A g.89G>A |
AA changes | R17Q Score: 43 explain score(s) |
position(s) of altered AA if AA alteration in CDS | 17 |
frameshift | no |
known variant | Reference ID: rs9897031
database | homozygous (T/T) | heterozygous | allele carriers |
1000G | 1293 | 858 | 2151 |
ExAC | 29933 | -27099 | 2834 |
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regulatory features | H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation |
phyloP / phastCons | | PhyloP | PhastCons |
(flanking) | 1.418 | 0.195 | | -0.378 | 0.199 | (flanking) | 1.665 | 0.282 | 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 | 85 | wt: 0.80 / mu: 0.99 | wt: GCTGTGGCCGAGACC mu: GCTGTGGCCAAGACC | TGTG|gccg |
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distance from splice site | 89 |
Kozak consensus sequence altered? | N/A |
conservation protein level for non-synonymous changes | species | match | gene | aa | alignment | Human | | | 17 | C | G | S | V | C | S | H | Q | G | C | G | R | D | L | C | Q | E | T | C | C | R | P | S | C |
mutated | all conserved | | 17 | C | G | S | V | C | S | H | Q | G | C | G | Q | D | L | C | Q | E | T | C | C | R | P | S |
Ptroglodytes | all conserved | ENSPTRG00000030937 | 17 | C | G | S | V | C | S | H | Q | G | C | G | Q | D | L | C | Q | E | T | C | C | H | P | S |
Mmulatta | no homologue | | | |
Fcatus | no homologue | | | |
Mmusculus | all conserved | ENSMUSG00000069718 | 17 | C | G | S | V | C | S | E | E | G | C | G | Q | G | - | - | - | - | - | C | C | Q | P | S |
Ggallus | no homologue | | | |
Trubripes | no homologue | | | |
Drerio | no homologue | | | |
Dmelanogaster | no homologue | | | |
Celegans | no homologue | | | |
Xtropicalis | no homologue | | | |
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protein features | start (aa) | end (aa) | feature | details | | 5 | 163 | REGION | 27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC]. | lost | 17 | 17 | CONFLICT | R -> Q (in Ref. 1; CAC27583 and 3; AAI26132/AAI30563). | lost | 24 | 28 | REPEAT | 2. | might get lost (downstream of altered splice site) | 29 | 33 | REPEAT | 3. | might get lost (downstream of altered splice site) | 34 | 38 | REPEAT | 4. | might get lost (downstream of altered splice site) | 44 | 48 | REPEAT | 5. | might get lost (downstream of altered splice site) | 49 | 53 | REPEAT | 6. | might get lost (downstream of altered splice site) | 54 | 58 | REPEAT | 7. | might get lost (downstream of altered splice site) | 59 | 63 | REPEAT | 8. | might get lost (downstream of altered splice site) | 64 | 68 | REPEAT | 9. | might get lost (downstream of altered splice site) | 69 | 73 | REPEAT | 10. | might get lost (downstream of altered splice site) | 74 | 78 | REPEAT | 11. | might get lost (downstream of altered splice site) | 79 | 83 | REPEAT | 12. | might get lost (downstream of altered splice site) | 84 | 88 | REPEAT | 13. | might get lost (downstream of altered splice site) | 89 | 93 | REPEAT | 14. | might get lost (downstream of altered splice site) | 94 | 98 | REPEAT | 15. | might get lost (downstream of altered splice site) | 99 | 103 | REPEAT | 16. | might get lost (downstream of altered splice site) | 104 | 108 | REPEAT | 17. | might get lost (downstream of altered splice site) | 109 | 113 | REPEAT | 18. | might get lost (downstream of altered splice site) | 114 | 118 | REPEAT | 19. | might get lost (downstream of altered splice site) | 119 | 123 | REPEAT | 20. | might get lost (downstream of altered splice site) | 124 | 128 | REPEAT | 21. | might get lost (downstream of altered splice site) | 129 | 133 | REPEAT | 22. | might get lost (downstream of altered splice site) | 134 | 138 | REPEAT | 23. | might get lost (downstream of altered splice site) | 144 | 148 | REPEAT | 24. | might get lost (downstream of altered splice site) | 149 | 153 | REPEAT | 25. | might get lost (downstream of altered splice site) | 154 | 158 | REPEAT | 26. | might get lost (downstream of altered splice site) | 159 | 163 | REPEAT | 27. | might get lost (downstream of altered splice site) | 167 | 167 | CONFLICT | R -> G (in Ref. 1; CAC27583 and 3; AAI26132/AAI30563). | might get lost (downstream of altered splice site) |
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length of protein | normal |
AA sequence altered | yes |
position of stopcodon in wt / mu CDS | 588 / 588 |
position (AA) of stopcodon in wt / mu AA sequence | 196 / 196 |
position of stopcodon in wt / mu cDNA | 627 / 627 |
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 | 40 / 40 |
chromosome | 17 |
strand | -1 |
last intron/exon boundary | 1 |
theoretical NMD boundary in CDS | cannot be calculated, too little distance between start ATG and last intron/exon boundary |
length of CDS | 588 |
coding sequence (CDS) position | 50 |
cDNA position (for ins/del: last normal base / first normal base) | 89 |
gDNA position (for ins/del: last normal base / first normal base) | 89 |
chromosomal position (for ins/del: last normal base / first normal base) | 39274518 |
original gDNA sequence snippet | CTCTCACCAAGGCTGTGGCCGAGACCTCTGCCAGGAGACCT |
altered gDNA sequence snippet | CTCTCACCAAGGCTGTGGCCAAGACCTCTGCCAGGAGACCT |
original cDNA sequence snippet | CTCTCACCAAGGCTGTGGCCGAGACCTCTGCCAGGAGACCT |
altered cDNA sequence snippet | CTCTCACCAAGGCTGTGGCCAAGACCTCTGCCAGGAGACCT |
wildtype AA sequence | MVNSCCGSVC SHQGCGRDLC QETCCRPSCC ETTCCRTTYC RPSCCVSSCC RPQCCQSVCC QPTCCRPRCC ISSCCRPSCC VSSCCKPQCC QSMCCQPTCC RPRCCISSCC RPSCCVSSCC RPQCCQSVCC QPTCCHPSCS ISSCCRPSCC ESSCCRPCCC LRPVCGRVSC HTTCYRPTCV ISSCPRPLCC ASSCC* |
mutated AA sequence | MVNSCCGSVC SHQGCGQDLC QETCCRPSCC ETTCCRTTYC RPSCCVSSCC RPQCCQSVCC QPTCCRPRCC ISSCCRPSCC VSSCCKPQCC QSMCCQPTCC RPRCCISSCC RPSCCVSSCC RPQCCQSVCC QPTCCHPSCS ISSCCRPSCC ESSCCRPCCC LRPVCGRVSC HTTCYRPTCV ISSCPRPLCC ASSCC* |
speed | 0.55 s |
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