Prediction |
polymorphism |
Model: simple_aae, prob: 0.999999999987175 (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) | chr6:32629935C>GN/A
show variant in all transcripts IGV
|
HGNC symbol | HLA-DQB1 |
Ensembl transcript ID | ENST00000399082 |
Genbank transcript ID | N/A |
UniProt peptide | P01920 |
alteration type | single base exchange |
alteration region | CDS |
DNA changes | c.200G>C cDNA.245G>C g.6226G>C |
AA changes | G67A Score: 60 explain score(s) |
position(s) of altered AA if AA alteration in CDS | 67 |
frameshift | no |
known variant | Reference ID: rs1063322
database | homozygous (G/G) | heterozygous | allele carriers |
1000G | - | - | - |
ExAC | 18865 | -4963 | 13902 |
|
regulatory features | H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation PolII, Polymerase, RNA Polymerase II |
phyloP / phastCons | | PhyloP | PhastCons |
(flanking) | 0.17 | 0.003 | | -0.06 | 0.001 | (flanking) | -0.519 | 0.002 | 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 | 6223 | wt: 0.61 / mu: 0.69 | wt: CTCGGTGACAGATTTCTATCCAGGCCAGATCAAAGTCCGGT mu: CTCGGTGACAGATTTCTATCCAGCCCAGATCAAAGTCCGGT | atcc|AGGC | Donor increased | 6224 | wt: 0.75 / mu: 0.88 | wt: TATCCAGGCCAGATC mu: TATCCAGCCCAGATC | TCCA|ggcc | Donor gained | 6229 | 0.40 | mu: AGCCCAGATCAAAGT | CCCA|gatc |
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distance from splice site | 91 |
Kozak consensus sequence altered? | N/A |
conservation protein level for non-synonymous changes | species | match | gene | aa | alignment | Human | | | 67 | L | L | V | C | S | V | T | D | F | Y | P | G | Q | I | K | V | R | W | F | R | N | D | Q | E |
mutated | not conserved | | 67 | | | | | | V | T | D | F | Y | P | A | Q | I | K | V | R | W | F | R | N | D | Q |
Ptroglodytes | all identical | ENSPTRG00000018018 | 157 | L | L | V | C | S | V | T | D | F | Y | P | G | Q | I | K | V | R | W | F | R | N | D | Q |
Mmulatta | no homologue | | | |
Fcatus | no homologue | | | |
Mmusculus | not conserved | ENSMUSG00000073421 | 153 | T | L | V | C | S | V | T | D | F | Y | P | A | K | I | K | V | R | W | F | R | N | G | Q |
Ggallus | no homologue | | | |
Trubripes | no homologue | | | |
Drerio | not conserved | ENSDARG00000079105 | 142 | V | L | L | C | S | A | Y | E | F | Y | P | K | K | I | K | M | S | W | L | R | D | G | K |
Dmelanogaster | no homologue | | | |
Celegans | no homologue | | | |
Xtropicalis | no homologue | | | |
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protein features | start (aa) | end (aa) | feature | details | | 33 | 126 | REGION | Beta-1. | lost | 33 | 230 | TOPO_DOM | Extracellular (Potential). | lost | 67 | 73 | STRAND | | lost | 74 | 76 | TURN | | might get lost (downstream of altered splice site) | 78 | 81 | STRAND | | might get lost (downstream of altered splice site) | 84 | 86 | HELIX | | might get lost (downstream of altered splice site) | 87 | 94 | HELIX | | might get lost (downstream of altered splice site) | 97 | 109 | HELIX | | might get lost (downstream of altered splice site) | 111 | 111 | CONFLICT | C -> S (in Ref. 71; AAD39697). | might get lost (downstream of altered splice site) | 111 | 111 | DISULFID | | might get lost (downstream of altered splice site) | 111 | 119 | HELIX | | might get lost (downstream of altered splice site) | 113 | 113 | CONFLICT | H -> Q (in Ref. 22; AAF28315). | might get lost (downstream of altered splice site) | 122 | 124 | HELIX | | might get lost (downstream of altered splice site) | 127 | 220 | REGION | Beta-2. | might get lost (downstream of altered splice site) | 129 | 233 | DOMAIN | Ig-like C1-type. | might get lost (downstream of altered splice site) | 130 | 134 | STRAND | | might get lost (downstream of altered splice site) | 141 | 144 | STRAND | | might get lost (downstream of altered splice site) | 147 | 157 | STRAND | | might get lost (downstream of altered splice site) | 149 | 149 | DISULFID | | might get lost (downstream of altered splice site) | 160 | 165 | STRAND | | might get lost (downstream of altered splice site) | 168 | 170 | STRAND | | might get lost (downstream of altered splice site) | 172 | 176 | STRAND | | might get lost (downstream of altered splice site) | 173 | 173 | CONFLICT | G -> A (in Ref. 24; X76553/X76554). | might get lost (downstream of altered splice site) | 183 | 185 | STRAND | | might get lost (downstream of altered splice site) | 187 | 193 | STRAND | | might get lost (downstream of altered splice site) | 203 | 208 | STRAND | | might get lost (downstream of altered splice site) | 205 | 205 | DISULFID | | might get lost (downstream of altered splice site) | 214 | 214 | CONFLICT | N -> T (in Ref. 8; AAA59770). | might get lost (downstream of altered splice site) | 216 | 220 | STRAND | | might get lost (downstream of altered splice site) | 221 | 230 | REGION | Connecting peptide. | might get lost (downstream of altered splice site) | 231 | 251 | TRANSMEM | Helical; (Potential). | might get lost (downstream of altered splice site) | 252 | 261 | 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 | 405 / 405 |
position (AA) of stopcodon in wt / mu AA sequence | 135 / 135 |
position of stopcodon in wt / mu cDNA | 450 / 450 |
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 | 46 / 46 |
chromosome | 6 |
strand | -1 |
last intron/exon boundary | 437 |
theoretical NMD boundary in CDS | 341 |
length of CDS | 405 |
coding sequence (CDS) position | 200 |
cDNA position (for ins/del: last normal base / first normal base) | 245 |
gDNA position (for ins/del: last normal base / first normal base) | 6226 |
chromosomal position (for ins/del: last normal base / first normal base) | 32629935 |
original gDNA sequence snippet | GGTGACAGATTTCTATCCAGGCCAGATCAAAGTCCGGTGGT |
altered gDNA sequence snippet | GGTGACAGATTTCTATCCAGCCCAGATCAAAGTCCGGTGGT |
original cDNA sequence snippet | GGTGACAGATTTCTATCCAGGCCAGATCAAAGTCCGGTGGT |
altered cDNA sequence snippet | GGTGACAGATTTCTATCCAGCCCAGATCAAAGTCCGGTGGT |
wildtype AA sequence | MSWKKALRIP GDLRVATVTL MLAMLSSLLA EGRDSPVEPT VTISPSRTEA LNHHNLLVCS VTDFYPGQIK VRWFRNDQEE TAGVVSTPLI RNGDWTFQIL VMLEMTPQRG DVYTCHVEHP SLQSPITVEW RLLH* |
mutated AA sequence | MSWKKALRIP GDLRVATVTL MLAMLSSLLA EGRDSPVEPT VTISPSRTEA LNHHNLLVCS VTDFYPAQIK VRWFRNDQEE TAGVVSTPLI RNGDWTFQIL VMLEMTPQRG DVYTCHVEHP SLQSPITVEW RLLH* |
speed | 0.32 s |
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