Prediction |
polymorphism |
Model: simple_aae, prob: 0.999999999999972 (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 CM1314936)
- protein features (might be) affected
- splice site changes
|
hyperlink |
| analysed issue |
analysis result |
| name of alteration | no title |
| alteration (phys. location) | chr6:31379817T>CN/A
show variant in all transcripts IGV
|
| HGNC symbol | MICA |
| Ensembl transcript ID | ENST00000376222 |
| Genbank transcript ID | N/A |
| UniProt peptide | Q29983 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.293T>C
cDNA.1445T>C
g.12257T>C |
| AA changes | I98T Score: 89 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 98 |
| frameshift | no |
| known variant | Reference ID: rs1140700
| database | homozygous (C/C) | heterozygous | allele carriers |
| 1000G | 910 | 1097 | 2007 |
| ExAC | 14124 | 4519 | 18643 |
known disease mutation at this position, please check HGMD for details (HGMD ID CM1314936)
|
| regulatory features | H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | -0.558 | 0 | | -0.931 | 0 | | (flanking) | -1.181 | 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 increased | 12249 | wt: 0.44 / mu: 0.49 | wt: GCTTCCAGCTTCTATCCCCGGAATATCATACTGACCTGGCG
mu: GCTTCCAGCTTCTATCCCCGGAATATCACACTGACCTGGCG | ccgg|AATA | | Acc marginally increased | 12248 | wt: 0.8416 / mu: 0.8431 (marginal change - not scored) | wt: GGCTTCCAGCTTCTATCCCCGGAATATCATACTGACCTGGC
mu: GGCTTCCAGCTTCTATCCCCGGAATATCACACTGACCTGGC | cccg|GAAT |
|
| distance from splice site | 94 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 98 | C | R | A | S | S | F | Y | P | R | N | I | I | L | T | W | R | Q | D | G | V | S | L | S | H |
| mutated | not conserved | | 98 | C | R | A | S | S | F | Y | P | R | N | I | T | L | T | W | R | Q | D | G | V | S | L | S |
| Ptroglodytes | not conserved | ENSPTRG00000017957 | 236 | C | W | A | S | S | F | Y | P | R | N | I | T | L | T | W | R | Q | D | G | I | S | L | S |
| Mmulatta | not conserved | ENSMMUG00000006609 | 236 | | | A | S | G | F | Y | P | G | N | I | T | L | T | W | R | Q | D | G | V | S | L | S |
| Fcatus | no homologue | | | |
| Mmusculus | no homologue | | | |
| Ggallus | no homologue | | | |
| Trubripes | no homologue | | | |
| Drerio | no homologue | | | |
| Dmelanogaster | no homologue | | | |
| Celegans | no homologue | | | |
| Xtropicalis | not conserved | ENSXETG00000030689 | 228 | C | R | V | Y | G | F | Y | P | R | D | V | E | V | K | W | I | K | | | | | | |
|
| protein features | | start (aa) | end (aa) | feature | details | | | 24 | 307 | TOPO_DOM | Extracellular (Potential). | lost | | 82 | 101 | HELIX | | lost | | 109 | 121 | STRAND | | might get lost (downstream of altered splice site) | | 119 | 119 | DISULFID | | might get lost (downstream of altered splice site) | | 127 | 135 | STRAND | | might get lost (downstream of altered splice site) | | 138 | 144 | STRAND | | might get lost (downstream of altered splice site) | | 145 | 148 | TURN | | might get lost (downstream of altered splice site) | | 149 | 151 | STRAND | | might get lost (downstream of altered splice site) | | 156 | 170 | HELIX | | might get lost (downstream of altered splice site) | | 177 | 196 | HELIX | | might get lost (downstream of altered splice site) | | 187 | 187 | DISULFID | | might get lost (downstream of altered splice site) | | 207 | 296 | DOMAIN | Ig-like C1-type. | might get lost (downstream of altered splice site) | | 208 | 213 | STRAND | | might get lost (downstream of altered splice site) | | 210 | 210 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 217 | 233 | STRAND | | might get lost (downstream of altered splice site) | | 220 | 220 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 225 | 225 | DISULFID | | might get lost (downstream of altered splice site) | | 236 | 241 | STRAND | | might get lost (downstream of altered splice site) | | 248 | 250 | TURN | | might get lost (downstream of altered splice site) | | 251 | 253 | STRAND | | might get lost (downstream of altered splice site) | | 260 | 262 | STRAND | | might get lost (downstream of altered splice site) | | 261 | 261 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 264 | 273 | STRAND | | might get lost (downstream of altered splice site) | | 277 | 279 | HELIX | | might get lost (downstream of altered splice site) | | 280 | 286 | STRAND | | might get lost (downstream of altered splice site) | | 282 | 282 | DISULFID | | might get lost (downstream of altered splice site) | | 289 | 294 | STRAND | | might get lost (downstream of altered splice site) | | 308 | 328 | TRANSMEM | Helical; (Potential). | might get lost (downstream of altered splice site) | | 329 | 383 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) |
|
| length of protein | normal |
| AA sequence altered | yes |
| position of stopcodon in wt / mu CDS | 585 / 585 |
| position (AA) of stopcodon in wt / mu AA sequence | 195 / 195 |
| position of stopcodon in wt / mu cDNA | 1737 / 1737 |
| 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 | 1153 / 1153 |
| chromosome | 6 |
| strand | 1 |
| last intron/exon boundary | 1767 |
| theoretical NMD boundary in CDS | 564 |
| length of CDS | 585 |
| coding sequence (CDS) position | 293 |
cDNA position
(for ins/del: last normal base / first normal base) | 1445 |
gDNA position
(for ins/del: last normal base / first normal base) | 12257 |
chromosomal position
(for ins/del: last normal base / first normal base) | 31379817 |
| original gDNA sequence snippet | CTTCTATCCCCGGAATATCATACTGACCTGGCGTCAGGATG |
| altered gDNA sequence snippet | CTTCTATCCCCGGAATATCACACTGACCTGGCGTCAGGATG |
| original cDNA sequence snippet | CTTCTATCCCCGGAATATCATACTGACCTGGCGTCAGGATG |
| altered cDNA sequence snippet | CTTCTATCCCCGGAATATCACACTGACCTGGCGTCAGGATG |
| wildtype AA sequence | MGQRDQGLDR ERKGPQDDPG SYQGPERRNF LKEDAMKTKT HYHAMHADCL QELRRYLESG
VVLRRTVPPM VNVTRSEASE GNITVTCRAS SFYPRNIILT WRQDGVSLSH DTQQWGDVLP
DGNGTYQTWV ATRICRGEEQ RFTCYMEHSG NHSTHPVPSG KVLVLQSHWQ TFHVSAVAAG
CCYFCYYYFL CPLL* |
| mutated AA sequence | MGQRDQGLDR ERKGPQDDPG SYQGPERRNF LKEDAMKTKT HYHAMHADCL QELRRYLESG
VVLRRTVPPM VNVTRSEASE GNITVTCRAS SFYPRNITLT WRQDGVSLSH DTQQWGDVLP
DGNGTYQTWV ATRICRGEEQ RFTCYMEHSG NHSTHPVPSG KVLVLQSHWQ TFHVSAVAAG
CCYFCYYYFL CPLL* |
| speed | 0.29 s |
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