Prediction |
polymorphism |
Model: simple_aae, prob: 0.999999999999507 (classification due to TGP/ExAC,
real probability is shown anyway)
(explain) |
| Summary |
- amino acid sequence changed
- homozygous in TGP or ExAC
- known disease mutation at this position (HGMD CM108210)
- protein features (might be) affected
- splice site changes
|
hyperlink |
| analysed issue |
analysis result |
| name of alteration | no title |
| alteration (phys. location) | chr1:116310967T>CN/A
show variant in all transcripts IGV
|
| HGNC symbol | CASQ2 |
| Ensembl transcript ID | ENST00000456138 |
| Genbank transcript ID | N/A |
| UniProt peptide | O14958 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.196A>G
cDNA.369A>G
g.436A>G |
| AA changes | T66A Score: 58 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 66 |
| frameshift | no |
| known variant | Reference ID: rs4074536
| database | homozygous (C/C) | heterozygous | allele carriers |
| 1000G | 444 | 1121 | 1565 |
| ExAC | 6950 | 18867 | 25817 |
known disease mutation at this position, please check HGMD for details (HGMD ID CM108210)
|
| regulatory features | H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 1.431 | 0.007 | | 0.922 | 0.005 | | (flanking) | -2.02 | 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 | | Acc marginally increased | 431 | wt: 0.4968 / mu: 0.5255 (marginal change - not scored) | wt: TGAGCCGGTGTCTTCAGATAAGGTCACGCAAAAACAGTTCC
mu: TGAGCCGGTGTCTTCAGATAAGGTCGCGCAAAAACAGTTCC | ataa|GGTC | | Acc increased | 427 | wt: 0.23 / mu: 0.26 | wt: ACCATGAGCCGGTGTCTTCAGATAAGGTCACGCAAAAACAG
mu: ACCATGAGCCGGTGTCTTCAGATAAGGTCGCGCAAAAACAG | tcag|ATAA | | Donor marginally increased | 441 | wt: 0.8750 / mu: 0.8841 (marginal change - not scored) | wt: ACGCAAAAACAGTTC
mu: GCGCAAAAACAGTTC | GCAA|aaac |
|
| distance from splice site | 39 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | |
| protein features | | start (aa) | end (aa) | feature | details | | | 49 | 66 | STRAND | | lost | | 67 | 67 | CONFLICT | Q -> P (in Ref. 1; BAA23494). | might get lost (downstream of altered splice site) | | 67 | 84 | HELIX | | might get lost (downstream of altered splice site) | | 85 | 97 | STRAND | | might get lost (downstream of altered splice site) | | 98 | 103 | HELIX | | might get lost (downstream of altered splice site) | | 104 | 130 | STRAND | | might get lost (downstream of altered splice site) | | 131 | 141 | HELIX | | might get lost (downstream of altered splice site) | | 142 | 152 | STRAND | | might get lost (downstream of altered splice site) | | 153 | 158 | HELIX | | might get lost (downstream of altered splice site) | | 159 | 176 | STRAND | | might get lost (downstream of altered splice site) | | 175 | 175 | CONFLICT | D -> G (in Ref. 2; BAG35873). | might get lost (downstream of altered splice site) | | 177 | 188 | HELIX | | might get lost (downstream of altered splice site) | | 189 | 200 | STRAND | | might get lost (downstream of altered splice site) | | 201 | 207 | HELIX | | might get lost (downstream of altered splice site) | | 208 | 217 | STRAND | | might get lost (downstream of altered splice site) | | 219 | 223 | STRAND | | might get lost (downstream of altered splice site) | | 229 | 233 | STRAND | | might get lost (downstream of altered splice site) | | 234 | 243 | HELIX | | might get lost (downstream of altered splice site) | | 248 | 252 | STRAND | | might get lost (downstream of altered splice site) | | 256 | 261 | HELIX | | might get lost (downstream of altered splice site) | | 262 | 278 | STRAND | | might get lost (downstream of altered splice site) | | 279 | 294 | HELIX | | might get lost (downstream of altered splice site) | | 295 | 298 | STRAND | | might get lost (downstream of altered splice site) | | 300 | 307 | STRAND | | might get lost (downstream of altered splice site) | | 312 | 320 | HELIX | | might get lost (downstream of altered splice site) | | 321 | 328 | STRAND | | might get lost (downstream of altered splice site) | | 330 | 351 | STRAND | | might get lost (downstream of altered splice site) | | 335 | 335 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 356 | 361 | HELIX | | might get lost (downstream of altered splice site) | | 356 | 399 | COMPBIAS | Asp/Glu-rich (acidic). | might get lost (downstream of altered splice site) | | 362 | 369 | STRAND | | might get lost (downstream of altered splice site) | | 385 | 385 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 393 | 393 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) |
|
| length of protein | normal |
| AA sequence altered | yes |
| position of stopcodon in wt / mu CDS | 987 / 987 |
| position (AA) of stopcodon in wt / mu AA sequence | 329 / 329 |
| position of stopcodon in wt / mu cDNA | 1160 / 1160 |
| 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 | 174 / 174 |
| chromosome | 1 |
| strand | -1 |
| last intron/exon boundary | 975 |
| theoretical NMD boundary in CDS | 751 |
| length of CDS | 987 |
| coding sequence (CDS) position | 196 |
cDNA position
(for ins/del: last normal base / first normal base) | 369 |
gDNA position
(for ins/del: last normal base / first normal base) | 436 |
chromosomal position
(for ins/del: last normal base / first normal base) | 116310967 |
| original gDNA sequence snippet | CGGTGTCTTCAGATAAGGTCACGCAAAAACAGTTCCAACTG |
| altered gDNA sequence snippet | CGGTGTCTTCAGATAAGGTCGCGCAAAAACAGTTCCAACTG |
| original cDNA sequence snippet | CGGTGTCTTCAGATAAGGTCACGCAAAAACAGTTCCAACTG |
| altered cDNA sequence snippet | CGGTGTCTTCAGATAAGGTCGCGCAAAAACAGTTCCAACTG |
| wildtype AA sequence | MKRTHLFIVG IYFLSSCRAE EGLNFPTYDG KDRVVSLSEK NFKQVLKKYD LLCLYYHEPV
SSDKVTQKQF QLKEIVLELV AQVLEHKAIG FVMVDAKKEA KLAKKLDYKA FEEAAEHFQP
YIKFFATFDK GVAKKLSLKM NEVDFYEPFM DEPIAIPNKP YTEEELVEFV KEHQRPTLRR
LRPEEMFETW EDDLNGIHIV AFAEKSDPDG YEFLEILKQV ARDNTDNPDL SILWIDPDDF
PLLVAYWEKT FKIDLFRPQI GVVNVTDADS VWMEIPDDDD LPTAEELEDW IEDVLSGKIN
TEDDDEDDDD DDNSDEEDND DSDDDDDE* |
| mutated AA sequence | MKRTHLFIVG IYFLSSCRAE EGLNFPTYDG KDRVVSLSEK NFKQVLKKYD LLCLYYHEPV
SSDKVAQKQF QLKEIVLELV AQVLEHKAIG FVMVDAKKEA KLAKKLDYKA FEEAAEHFQP
YIKFFATFDK GVAKKLSLKM NEVDFYEPFM DEPIAIPNKP YTEEELVEFV KEHQRPTLRR
LRPEEMFETW EDDLNGIHIV AFAEKSDPDG YEFLEILKQV ARDNTDNPDL SILWIDPDDF
PLLVAYWEKT FKIDLFRPQI GVVNVTDADS VWMEIPDDDD LPTAEELEDW IEDVLSGKIN
TEDDDEDDDD DDNSDEEDND DSDDDDDE* |
| speed | 0.14 s |
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