Prediction |
polymorphism |
Model: simple_aae, prob: 0.99999999528558 (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) | chr6:32632745G>AN/A
show variant in all transcripts IGV
|
| HGNC symbol | HLA-DQB1 |
| Ensembl transcript ID | ENST00000434651 |
| Genbank transcript ID | NM_002123 |
| UniProt peptide | P01920 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.209C>T
cDNA.296C>T
g.3416C>T |
| AA changes | A70V Score: 64 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 70 |
| frameshift | no |
| known variant | Reference ID: rs1063318
| database | homozygous (A/A) | heterozygous | allele carriers |
| 1000G | 506 | 781 | 1287 |
| ExAC | 6826 | 14734 | 21560 |
|
| regulatory features | DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 0.72 | 0.656 | | -0.565 | 0.026 | | (flanking) | 0.388 | 0.016 |
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 | | Donor gained | 3409 | 0.53 | mu: GAGAGGAGTACGTGC | GAGG|agta |
|
| distance from splice site | 100 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 70 | V | T | R | Y | I | Y | N | R | E | E | Y | A | R | F | D | S | D | V | G | V | Y | R | A | V |
| mutated | not conserved | | 70 | | | R | Y | I | Y | N | R | E | E | Y | V | R | F | D | S | D | V | G | V | Y | R | A |
| Ptroglodytes | not conserved | ENSPTRG00000018018 | 70 | | | R | Y | I | Y | N | R | E | E | Y | V | R | F | D | S | D | V | G | V | Y | R | A |
| Mmulatta | no homologue | | | |
| Fcatus | no homologue | | | |
| Mmusculus | not conserved | ENSMUSG00000073421 | 65 | | | | | | | | R | E | E | Y | V | R | Y | D | S | D | V | G | E | H | R | A |
| Ggallus | no homologue | | | |
| Trubripes | no homologue | | | |
| Drerio | not conserved | ENSDARG00000079105 | 58 | L | A | S | Y | S | F | N | K | V | V | D | T | Q | F | N | S | S | V | G | K | | | |
| Dmelanogaster | no homologue | | | |
| Celegans | no homologue | | | |
| Xtropicalis | no homologue | | | |
|
| 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 | 786 / 786 |
| position (AA) of stopcodon in wt / mu AA sequence | 262 / 262 |
| position of stopcodon in wt / mu cDNA | 873 / 873 |
| 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 | 88 / 88 |
| chromosome | 6 |
| strand | -1 |
| last intron/exon boundary | 860 |
| theoretical NMD boundary in CDS | 722 |
| length of CDS | 786 |
| coding sequence (CDS) position | 209 |
cDNA position
(for ins/del: last normal base / first normal base) | 296 |
gDNA position
(for ins/del: last normal base / first normal base) | 3416 |
chromosomal position
(for ins/del: last normal base / first normal base) | 32632745 |
| original gDNA sequence snippet | CTATAACCGAGAGGAGTACGCGCGCTTCGACAGCGACGTGG |
| altered gDNA sequence snippet | CTATAACCGAGAGGAGTACGTGCGCTTCGACAGCGACGTGG |
| original cDNA sequence snippet | CTATAACCGAGAGGAGTACGCGCGCTTCGACAGCGACGTGG |
| altered cDNA sequence snippet | CTATAACCGAGAGGAGTACGTGCGCTTCGACAGCGACGTGG |
| wildtype AA sequence | MSWKKALRIP GDLRVATVTL MLAMLSSLLA EGRDSPEDFV FQFKGMCYFT NGTERVRLVT
RYIYNREEYA RFDSDVGVYR AVTPQGRPDA EYWNSQKEVL EGTRAELDTV CRHNYEVAFR
GILQRRVEPT VTISPSRTEA LNHHNLLVCS VTDFYPGQIK VRWFRNDQEE TAGVVSTPLI
RNGDWTFQIL VMLEMTPQRG DVYTCHVEHP SLQSPITVEW RAQSESAQSK MLSGVGGFVL
GLIFLGLGLI IRQRSQKGLL H* |
| mutated AA sequence | MSWKKALRIP GDLRVATVTL MLAMLSSLLA EGRDSPEDFV FQFKGMCYFT NGTERVRLVT
RYIYNREEYV RFDSDVGVYR AVTPQGRPDA EYWNSQKEVL EGTRAELDTV CRHNYEVAFR
GILQRRVEPT VTISPSRTEA LNHHNLLVCS VTDFYPGQIK VRWFRNDQEE TAGVVSTPLI
RNGDWTFQIL VMLEMTPQRG DVYTCHVEHP SLQSPITVEW RAQSESAQSK MLSGVGGFVL
GLIFLGLGLI IRQRSQKGLL H* |
| speed | 0.63 s |
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