Prediction |
polymorphism |
Model: simple_aae, prob: 0.999999999927918 (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) | chr6:31379807C>TN/A
show variant in all transcripts IGV
|
| HGNC symbol | MICA |
| Ensembl transcript ID | ENST00000399172 |
| Genbank transcript ID | N/A |
| UniProt peptide | Q29983 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.568C>T
cDNA.662C>T
g.12247C>T |
| AA changes | R190W Score: 101 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 190 |
| frameshift | no |
| known variant | Reference ID: rs1051798
| database | homozygous (T/T) | heterozygous | allele carriers |
| 1000G | 348 | 1127 | 1475 |
| ExAC | 5298 | 22171 | 27469 |
|
| regulatory features | H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | -0.094 | 0.001 | | -2.673 | 0 | | (flanking) | -0.663 | 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 | 12247 | wt: 0.6265 / mu: 0.6347 (marginal change - not scored) | wt: GGGCTTCCAGCTTCTATCCCCGGAATATCATACTGACCTGG
mu: GGGCTTCCAGCTTCTATCCCTGGAATATCATACTGACCTGG | cccc|GGAA | | Acc increased | 12249 | wt: 0.44 / mu: 0.52 | wt: GCTTCCAGCTTCTATCCCCGGAATATCATACTGACCTGGCG
mu: GCTTCCAGCTTCTATCCCTGGAATATCATACTGACCTGGCG | ccgg|AATA | | Acc marginally increased | 12248 | wt: 0.8416 / mu: 0.8428 (marginal change - not scored) | wt: GGCTTCCAGCTTCTATCCCCGGAATATCATACTGACCTGGC
mu: GGCTTCCAGCTTCTATCCCTGGAATATCATACTGACCTGGC | cccg|GAAT | | Acc increased | 12245 | wt: 0.25 / mu: 0.56 | wt: CAGGGCTTCCAGCTTCTATCCCCGGAATATCATACTGACCT
mu: CAGGGCTTCCAGCTTCTATCCCTGGAATATCATACTGACCT | atcc|CCGG | | Donor marginally increased | 12245 | wt: 0.2960 / mu: 0.3063 (marginal change - not scored) | wt: CTATCCCCGGAATAT
mu: CTATCCCTGGAATAT | ATCC|ccgg |
|
| distance from splice site | 84 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 190 | T | V | T | C | R | A | S | S | F | Y | P | R | N | I | I | L | T | W | R | Q | D | G | V | S |
| mutated | not conserved | | 190 | | | T | C | R | A | S | S | F | Y | P | W | N | I | I | L | T | W | R | Q | D | G | V |
| Ptroglodytes | all identical | ENSPTRG00000017957 | 233 | T | V | T | C | W | A | S | S | F | Y | P | R | N | I | T | L | T | W | R | | | | |
| Mmulatta | not conserved | ENSMMUG00000006609 | 233 | T | V | T | C | R | A | S | G | F | Y | P | G | N | I | T | L | T | W | R | Q | D | | |
| Fcatus | no homologue | | | |
| Mmusculus | no homologue | | | |
| Ggallus | no homologue | | | |
| Trubripes | no homologue | | | |
| Drerio | no homologue | | | |
| Dmelanogaster | no homologue | | | |
| Celegans | no homologue | | | |
| Xtropicalis | all identical | ENSXETG00000030689 | 225 | K | L | H | 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 | | 177 | 196 | HELIX | | lost | | 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 | 870 / 870 |
| position (AA) of stopcodon in wt / mu AA sequence | 290 / 290 |
| position of stopcodon in wt / mu cDNA | 964 / 964 |
| 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 | 95 / 95 |
| chromosome | 6 |
| strand | 1 |
| last intron/exon boundary | 994 |
| theoretical NMD boundary in CDS | 849 |
| length of CDS | 870 |
| coding sequence (CDS) position | 568 |
cDNA position
(for ins/del: last normal base / first normal base) | 662 |
gDNA position
(for ins/del: last normal base / first normal base) | 12247 |
chromosomal position
(for ins/del: last normal base / first normal base) | 31379807 |
| original gDNA sequence snippet | GGGCTTCCAGCTTCTATCCCCGGAATATCATACTGACCTGG |
| altered gDNA sequence snippet | GGGCTTCCAGCTTCTATCCCTGGAATATCATACTGACCTGG |
| original cDNA sequence snippet | GGGCTTCCAGCTTCTATCCCCGGAATATCATACTGACCTGG |
| altered cDNA sequence snippet | GGGCTTCCAGCTTCTATCCCTGGAATATCATACTGACCTGG |
| wildtype AA sequence | MGLGPVFLLL AGIFPFAPPG AAAEPHSLRY NLTVLSWDGS VQSGFLAEVH LDGQPFLRYD
RQKCRAKPQG QWAEDVLGNK TWDRETRDLT GNGKDLRMTL AHIKDQKEVP QSSRAQTLAM
NVRNFLKEDA MKTKTHYHAM HADCLQELRR YLESGVVLRR TVPPMVNVTR SEASEGNITV
TCRASSFYPR NIILTWRQDG VSLSHDTQQW GDVLPDGNGT YQTWVATRIC RGEEQRFTCY
MEHSGNHSTH PVPSGKVLVL QSHWQTFHVS AVAAGCCYFC YYYFLCPLL* |
| mutated AA sequence | MGLGPVFLLL AGIFPFAPPG AAAEPHSLRY NLTVLSWDGS VQSGFLAEVH LDGQPFLRYD
RQKCRAKPQG QWAEDVLGNK TWDRETRDLT GNGKDLRMTL AHIKDQKEVP QSSRAQTLAM
NVRNFLKEDA MKTKTHYHAM HADCLQELRR YLESGVVLRR TVPPMVNVTR SEASEGNITV
TCRASSFYPW NIILTWRQDG VSLSHDTQQW GDVLPDGNGT YQTWVATRIC RGEEQRFTCY
MEHSGNHSTH PVPSGKVLVL QSHWQTFHVS AVAAGCCYFC YYYFLCPLL* |
| speed | 1.35 s |
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