Prediction |
disease causing |
Model: simple_aae, prob: 0.999999999998726 (classification due to ClinVar,
real probability is shown anyway)
(explain) |
Summary |
- amino acid sequence changed
- known disease mutation at this position (HGMD CM960425)
- known disease mutation: rs8421 (pathogenic)
- protein features (might be) affected
- splice site changes
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hyperlink |
analysed issue |
analysis result |
name of alteration | no title |
alteration (phys. location) | chr1:150776679C>GN/A
show variant in all transcripts IGV
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HGNC symbol | CTSK |
Ensembl transcript ID | ENST00000271651 |
Genbank transcript ID | NM_000396 |
UniProt peptide | P43235 |
alteration type | single base exchange |
alteration region | CDS |
DNA changes | c.436G>C cDNA.547G>C g.4121G>C |
AA changes | G146R Score: 125 explain score(s) |
position(s) of altered AA if AA alteration in CDS | 146 |
frameshift | no |
known variant | Reference ID: rs74315302
Allele 'G' was neither found in ExAC nor 1000G. known disease mutation: rs8421 (pathogenic for Pyknodysostosis|Inborn genetic diseases|not provided) dbSNP
NCBI variation viewer known disease mutation at this position, please check HGMD for details (HGMD ID CM960425)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960425) known disease mutation at this position, please check HGMD for details (HGMD ID CM960425)
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regulatory features | H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation |
phyloP / phastCons | | PhyloP | PhastCons |
(flanking) | 5.582 | 1 | | 5.582 | 1 | (flanking) | 0.675 | 1 | 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 | Acc marginally increased | 4112 | wt: 0.7301 / mu: 0.7975 (marginal change - not scored) | wt: GTGGTTCCTGTTGGGCTTTTAGCTCTGTGGGTGCCCTGGAG mu: GTGGTTCCTGTTGGGCTTTTAGCTCTGTGCGTGCCCTGGAG | ttta|GCTC | Acc increased | 4118 | wt: 0.26 / mu: 0.44 | wt: CCTGTTGGGCTTTTAGCTCTGTGGGTGCCCTGGAGGGCCAA mu: CCTGTTGGGCTTTTAGCTCTGTGCGTGCCCTGGAGGGCCAA | tctg|TGGG | Acc marginally increased | 4121 | wt: 0.9601 / mu: 0.9673 (marginal change - not scored) | wt: GTTGGGCTTTTAGCTCTGTGGGTGCCCTGGAGGGCCAACTC mu: GTTGGGCTTTTAGCTCTGTGCGTGCCCTGGAGGGCCAACTC | gtgg|GTGC | Acc marginally increased | 4116 | wt: 0.5809 / mu: 0.5906 (marginal change - not scored) | wt: TTCCTGTTGGGCTTTTAGCTCTGTGGGTGCCCTGGAGGGCC mu: TTCCTGTTGGGCTTTTAGCTCTGTGCGTGCCCTGGAGGGCC | gctc|TGTG | Donor increased | 4126 | wt: 0.61 / mu: 0.82 | wt: GGTGCCCTGGAGGGC mu: CGTGCCCTGGAGGGC | TGCC|ctgg | Donor increased | 4112 | wt: 0.23 / mu: 0.44 | wt: CTTTTAGCTCTGTGG mu: CTTTTAGCTCTGTGC | TTTA|gctc | Acc gained | 4123 | 0.84 | mu: TGGGCTTTTAGCTCTGTGCGTGCCCTGGAGGGCCAACTCAA | gcgt|GCCC | Acc gained | 4128 | 0.51 | mu: TTTTAGCTCTGTGCGTGCCCTGGAGGGCCAACTCAAGAAGA | ccct|GGAG |
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distance from splice site | 37 |
Kozak consensus sequence altered? | N/A |
conservation protein level for non-synonymous changes | species | match | gene | aa | alignment | Human | | | 146 | Q | C | G | S | C | W | A | F | S | S | V | G | A | L | E | G | Q | L | K | K | K | T | G | K |
mutated | not conserved | | 146 | Q | C | G | S | C | W | A | F | S | S | V | R | A | L | E | G | Q | L | K | K | K | T | G |
Ptroglodytes | all identical | ENSPTRG00000001265 | 146 | Q | C | G | S | C | W | A | F | S | S | V | G | A | L | E | G | Q | L | K | K | K | T | G |
Mmulatta | all identical | ENSMMUG00000000537 | 146 | Q | C | G | S | C | W | A | F | S | S | V | G | A | L | E | G | Q | L | K | K | K | T | G |
Fcatus | all identical | ENSFCAG00000003643 | 147 | Q | C | G | S | C | W | A | F | S | S | V | G | A | L | E | G | Q | L | K | K | K | T | G |
Mmusculus | all identical | ENSMUSG00000028111 | 146 | Q | C | G | S | C | W | A | F | S | S | A | G | A | L | E | G | Q | L | K | K | K | T | G |
Ggallus | no homologue | | | |
Trubripes | all identical | ENSTRUG00000000525 | 152 | Q | C | G | S | C | W | A | F | S | S | A | G | A | L | E | G | M | Q | A | K | K | T | G |
Drerio | all identical | ENSDARG00000040251 | 149 | | | | | | | A | F | S | S | V | G | A | L | E | G | Q | L | M | K | T | K | G |
Dmelanogaster | all identical | FBgn0013770 | 185 | H | C | G | S | C | W | A | F | S | S | T | G | A | L | E | G | Q | H | F | R | K | S | G |
Celegans | all identical | T03E6.7 | 151 | | | | | | | | | | | T | G | A | L | E | G | Q | H | A | R | K | L | G |
Xtropicalis | all identical | ENSXETG00000008929 | 153 | I | C | G | S | C | W | A | F | S | S | V | G | A | L | E | G | Q | L | M | K | K | T | G |
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protein features | start (aa) | end (aa) | feature | details | | 139 | 156 | HELIX | | lost | 164 | 170 | HELIX | | might get lost (downstream of altered splice site) | 170 | 170 | DISULFID | | might get lost (downstream of altered splice site) | 176 | 178 | HELIX | | might get lost (downstream of altered splice site) | 177 | 177 | DISULFID | | might get lost (downstream of altered splice site) | 182 | 192 | HELIX | | might get lost (downstream of altered splice site) | 195 | 197 | STRAND | | might get lost (downstream of altered splice site) | 198 | 200 | TURN | | might get lost (downstream of altered splice site) | 210 | 210 | DISULFID | | might get lost (downstream of altered splice site) | 214 | 216 | HELIX | | might get lost (downstream of altered splice site) | 217 | 219 | STRAND | | might get lost (downstream of altered splice site) | 224 | 226 | STRAND | | might get lost (downstream of altered splice site) | 232 | 241 | HELIX | | might get lost (downstream of altered splice site) | 245 | 249 | STRAND | | might get lost (downstream of altered splice site) | 254 | 257 | HELIX | | might get lost (downstream of altered splice site) | 261 | 264 | STRAND | | might get lost (downstream of altered splice site) | 269 | 269 | DISULFID | | might get lost (downstream of altered splice site) | 276 | 276 | ACT_SITE | By similarity. | might get lost (downstream of altered splice site) | 276 | 286 | STRAND | | might get lost (downstream of altered splice site) | 289 | 295 | STRAND | | might get lost (downstream of altered splice site) | 296 | 296 | ACT_SITE | By similarity. | might get lost (downstream of altered splice site) | 300 | 302 | STRAND | | might get lost (downstream of altered splice site) | 303 | 305 | TURN | | might get lost (downstream of altered splice site) | 307 | 316 | STRAND | | might get lost (downstream of altered splice site) | 317 | 319 | HELIX | | might get lost (downstream of altered splice site) | 318 | 318 | DISULFID | | might get lost (downstream of altered splice site) | 320 | 322 | TURN | | might get lost (downstream of altered splice site) | 325 | 327 | STRAND | | 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 | 990 / 990 |
position (AA) of stopcodon in wt / mu AA sequence | 330 / 330 |
position of stopcodon in wt / mu cDNA | 1101 / 1101 |
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 | 112 / 112 |
chromosome | 1 |
strand | -1 |
last intron/exon boundary | 1002 |
theoretical NMD boundary in CDS | 840 |
length of CDS | 990 |
coding sequence (CDS) position | 436 |
cDNA position (for ins/del: last normal base / first normal base) | 547 |
gDNA position (for ins/del: last normal base / first normal base) | 4121 |
chromosomal position (for ins/del: last normal base / first normal base) | 150776679 |
original gDNA sequence snippet | GTTGGGCTTTTAGCTCTGTGGGTGCCCTGGAGGGCCAACTC |
altered gDNA sequence snippet | GTTGGGCTTTTAGCTCTGTGCGTGCCCTGGAGGGCCAACTC |
original cDNA sequence snippet | GTTGGGCTTTTAGCTCTGTGGGTGCCCTGGAGGGCCAACTC |
altered cDNA sequence snippet | GTTGGGCTTTTAGCTCTGTGCGTGCCCTGGAGGGCCAACTC |
wildtype AA sequence | MWGLKVLLLP VVSFALYPEE ILDTHWELWK KTHRKQYNNK VDEISRRLIW EKNLKYISIH NLEASLGVHT YELAMNHLGD MTSEEVVQKM TGLKVPLSHS RSNDTLYIPE WEGRAPDSVD YRKKGYVTPV KNQGQCGSCW AFSSVGALEG QLKKKTGKLL NLSPQNLVDC VSENDGCGGG YMTNAFQYVQ KNRGIDSEDA YPYVGQEESC MYNPTGKAAK CRGYREIPEG NEKALKRAVA RVGPVSVAID ASLTSFQFYS KGVYYDESCN SDNLNHAVLA VGYGIQKGNK HWIIKNSWGE NWGNKGYILM ARNKNNACGI ANLASFPKM* |
mutated AA sequence | MWGLKVLLLP VVSFALYPEE ILDTHWELWK KTHRKQYNNK VDEISRRLIW EKNLKYISIH NLEASLGVHT YELAMNHLGD MTSEEVVQKM TGLKVPLSHS RSNDTLYIPE WEGRAPDSVD YRKKGYVTPV KNQGQCGSCW AFSSVRALEG QLKKKTGKLL NLSPQNLVDC VSENDGCGGG YMTNAFQYVQ KNRGIDSEDA YPYVGQEESC MYNPTGKAAK CRGYREIPEG NEKALKRAVA RVGPVSVAID ASLTSFQFYS KGVYYDESCN SDNLNHAVLA VGYGIQKGNK HWIIKNSWGE NWGNKGYILM ARNKNNACGI ANLASFPKM* |
speed | 0.88 s |
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