Prediction |
disease causing |
Model: without_aae, prob: 1 (classification due to ClinVar,
real probability is shown anyway)
(explain) |
| Summary |
- known disease mutation at this position (HGMD CM992118)
- known disease mutation: rs18279 (pathogenic)
- protein features (might be) affected
- splice site changes
|
hyperlink |
| analysed issue |
analysis result |
| name of alteration | no title |
| alteration (phys. location) | chr1:229568470A>GN/A
show variant in all transcripts IGV
|
| HGNC symbol | ACTA1 |
| Ensembl transcript ID | ENST00000366682 |
| Genbank transcript ID | N/A |
| UniProt peptide | P68133 |
| alteration type | single base exchange |
| alteration region | intron |
| DNA changes | g.1376T>C |
| AA changes | N/A |
position(s) of altered AA
if AA alteration in CDS | N/A |
| frameshift | N/A |
| known variant | Reference ID: rs121909519
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs18279 (pathogenic for Nemaline myopathy 3) dbSNP
NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM992118)
known disease mutation at this position, please check HGMD for details (HGMD ID CM992118)
known disease mutation at this position, please check HGMD for details (HGMD ID CM992118)
|
| regulatory features | H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | -0.821 | 0.771 | | 4.659 | 1 | | (flanking) | 5.64 | 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 increased | 1373 | wt: 0.46 / mu: 0.62 | wt: GCACCACACCTTCTACAACGAGCTTCGCGTGGCTCCCGAGG
mu: GCACCACACCTTCTACAACGAGCCTCGCGTGGCTCCCGAGG | acga|GCTT | | Acc increased | 1370 | wt: 0.24 / mu: 0.34 | wt: CTGGCACCACACCTTCTACAACGAGCTTCGCGTGGCTCCCG
mu: CTGGCACCACACCTTCTACAACGAGCCTCGCGTGGCTCCCG | acaa|CGAG | | Donor marginally increased | 1373 | wt: 0.8504 / mu: 0.9218 (marginal change - not scored) | wt: CAACGAGCTTCGCGT
mu: CAACGAGCCTCGCGT | ACGA|gctt | | Donor increased | 1368 | wt: 0.38 / mu: 0.47 | wt: TTCTACAACGAGCTT
mu: TTCTACAACGAGCCT | CTAC|aacg |
|
| distance from splice site | 48 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | N/A |
| protein features | | start (aa) | end (aa) | feature | details | | | 81 | 93 | HELIX | | might get lost (downstream of altered splice site) | | 93 | 93 | MOD_RES | Phosphotyrosine. | might get lost (downstream of altered splice site) | | 100 | 102 | HELIX | | might get lost (downstream of altered splice site) | | 105 | 109 | STRAND | | might get lost (downstream of altered splice site) | | 115 | 127 | HELIX | | might get lost (downstream of altered splice site) | | 132 | 138 | STRAND | | might get lost (downstream of altered splice site) | | 139 | 146 | HELIX | | might get lost (downstream of altered splice site) | | 154 | 157 | STRAND | | might get lost (downstream of altered splice site) | | 162 | 165 | STRAND | | might get lost (downstream of altered splice site) | | 174 | 176 | HELIX | | might get lost (downstream of altered splice site) | | 178 | 180 | STRAND | | might get lost (downstream of altered splice site) | | 186 | 197 | HELIX | | might get lost (downstream of altered splice site) | | 193 | 193 | MOD_RES | N6-acetyllysine. | might get lost (downstream of altered splice site) | | 205 | 218 | HELIX | | might get lost (downstream of altered splice site) | | 225 | 234 | HELIX | | might get lost (downstream of altered splice site) | | 240 | 243 | STRAND | | might get lost (downstream of altered splice site) | | 242 | 242 | MOD_RES | Phosphotyrosine (By similarity). | might get lost (downstream of altered splice site) | | 249 | 252 | STRAND | | might get lost (downstream of altered splice site) | | 255 | 264 | HELIX | | might get lost (downstream of altered splice site) | | 266 | 268 | HELIX | | might get lost (downstream of altered splice site) | | 277 | 284 | HELIX | | might get lost (downstream of altered splice site) | | 289 | 291 | TURN | | might get lost (downstream of altered splice site) | | 292 | 297 | HELIX | | might get lost (downstream of altered splice site) | | 299 | 302 | STRAND | | might get lost (downstream of altered splice site) | | 312 | 320 | HELIX | | might get lost (downstream of altered splice site) | | 328 | 328 | MOD_RES | N6-acetyllysine. | might get lost (downstream of altered splice site) | | 330 | 330 | MOD_RES | N6-acetyllysine. | might get lost (downstream of altered splice site) | | 335 | 338 | TURN | | might get lost (downstream of altered splice site) | | 340 | 342 | TURN | | might get lost (downstream of altered splice site) | | 347 | 350 | HELIX | | might get lost (downstream of altered splice site) | | 354 | 357 | HELIX | | might get lost (downstream of altered splice site) | | 358 | 360 | STRAND | | might get lost (downstream of altered splice site) | | 361 | 366 | HELIX | | might get lost (downstream of altered splice site) | | 371 | 375 | HELIX | | 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 | 104 / 104 |
| chromosome | 1 |
| strand | -1 |
| last intron/exon boundary | 989 |
| theoretical NMD boundary in CDS | 835 |
| length of CDS | 1029 |
| 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) | 1376 |
chromosomal position
(for ins/del: last normal base / first normal base) | 229568470 |
| original gDNA sequence snippet | CCACACCTTCTACAACGAGCTTCGCGTGGCTCCCGAGGAGC |
| altered gDNA sequence snippet | CCACACCTTCTACAACGAGCCTCGCGTGGCTCCCGAGGAGC |
| original cDNA sequence snippet | N/A |
| altered cDNA sequence snippet | N/A |
| wildtype AA sequence | MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA
QSKRGILTLK YPIEHGIITK ANREKMTQIM FETFNVPAMY VAIQAVLSLY ASGRTTGIVL
DSGDGVTHNV PIYEGYALPH AIMRLDLAGR DLTDYLMKIL TERGYSFVTT AEREIVRDIK
EKLCYVALDF ENEMATAASS SSLEKSYELP DGQVITIGNE RFRCPETLFQ PSFIGMESAG
IHETTYNSIM KCDIDIRKDL YANNVMSGGT TMYPGIADRM QKEITALAPS TMKIKIIAPP
ERKYSVWIGG SILASLSTFQ QMWITKQEYD EAGPSIVHRK CF* |
| mutated AA sequence | N/A |
| speed | 0.78 s |
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