Prediction |
polymorphism |
Model: simple_aae, prob: 0.999999999978411 (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) | chr6:32632818T>GN/A
show variant in all transcripts IGV
|
HGNC symbol | HLA-DQB1 |
Ensembl transcript ID | ENST00000399079 |
Genbank transcript ID | N/A |
UniProt peptide | P01920 |
alteration type | single base exchange |
alteration region | CDS |
DNA changes | c.136A>C cDNA.193A>C g.3343A>C |
AA changes | M46L Score: 15 explain score(s) |
position(s) of altered AA if AA alteration in CDS | 46 |
frameshift | no |
known variant | Reference ID: rs1130368
database | homozygous (G/G) | heterozygous | allele carriers |
1000G | 192 | 685 | 877 |
ExAC | 1588 | 13404 | 14992 |
|
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) | -2.798 | 0.001 | | -4.342 | 0 | (flanking) | 0.134 | 0.125 | 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 | 3338 | wt: 0.7836 / mu: 0.8056 (marginal change - not scored) | wt: GGATTTCGTGTTCCAGTTTAAGGGCATGTGCTACTTCACCA mu: GGATTTCGTGTTCCAGTTTAAGGGCCTGTGCTACTTCACCA | ttaa|GGGC | Acc increased | 3340 | wt: 0.22 / mu: 0.26 | wt: ATTTCGTGTTCCAGTTTAAGGGCATGTGCTACTTCACCAAC mu: ATTTCGTGTTCCAGTTTAAGGGCCTGTGCTACTTCACCAAC | aagg|GCAT |
|
distance from splice site | 27 |
Kozak consensus sequence altered? | N/A |
conservation protein level for non-synonymous changes | species | match | gene | aa | alignment | Human | | | 46 | S | P | E | D | F | V | F | Q | F | K | G | M | C | Y | F | T | N | G | T | E | R | V | R | L |
mutated | all conserved | | 46 | S | P | E | D | F | V | F | Q | F | K | G | L | C | Y | F | T | N | G | T | E | R | V | R |
Ptroglodytes | all identical | ENSPTRG00000018018 | 46 | S | P | E | D | F | V | Y | Q | F | K | G | M | C | Y | F | T | N | G | T | E | R | V | R |
Mmulatta | no homologue | | | |
Fcatus | no homologue | | | |
Mmusculus | not conserved | ENSMUSG00000073421 | 42 | S | E | R | H | F | V | Y | Q | F | M | G | E | C | Y | F | T | N | G | T | Q | R | I | R |
Ggallus | no homologue | | | |
Trubripes | no homologue | | | |
Drerio | not conserved | ENSDARG00000079105 | 34 | G | Y | Y | D | Y | I | - | - | - | K | Q | Q | C | F | YS | T | S | D | Y | S | D | M | V |
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 | 40 | 50 | STRAND | | lost | 47 | 47 | DISULFID | | might get lost (downstream of altered splice site) | 51 | 51 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | 51 | 54 | TURN | | might get lost (downstream of altered splice site) | 55 | 64 | STRAND | | might get lost (downstream of altered splice site) | 67 | 73 | STRAND | | might get lost (downstream of altered splice site) | 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 | 675 / 675 |
position (AA) of stopcodon in wt / mu AA sequence | 225 / 225 |
position of stopcodon in wt / mu cDNA | 732 / 732 |
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 | 58 / 58 |
chromosome | 6 |
strand | -1 |
last intron/exon boundary | 719 |
theoretical NMD boundary in CDS | 611 |
length of CDS | 675 |
coding sequence (CDS) position | 136 |
cDNA position (for ins/del: last normal base / first normal base) | 193 |
gDNA position (for ins/del: last normal base / first normal base) | 3343 |
chromosomal position (for ins/del: last normal base / first normal base) | 32632818 |
original gDNA sequence snippet | TCGTGTTCCAGTTTAAGGGCATGTGCTACTTCACCAACGGG |
altered gDNA sequence snippet | TCGTGTTCCAGTTTAAGGGCCTGTGCTACTTCACCAACGGG |
original cDNA sequence snippet | TCGTGTTCCAGTTTAAGGGCATGTGCTACTTCACCAACGGG |
altered cDNA sequence snippet | TCGTGTTCCAGTTTAAGGGCCTGTGCTACTTCACCAACGGG |
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 RLLH* |
mutated AA sequence | MSWKKALRIP GDLRVATVTL MLAMLSSLLA EGRDSPEDFV FQFKGLCYFT NGTERVRLVT RYIYNREEYA RFDSDVGVYR AVTPQGRPDA EYWNSQKEVL EGTRAELDTV CRHNYEVAFR GILQRRVEPT VTISPSRTEA LNHHNLLVCS VTDFYPGQIK VRWFRNDQEE TAGVVSTPLI RNGDWTFQIL VMLEMTPQRG DVYTCHVEHP SLQSPITVEW RLLH* |
speed | 1.22 s |
|
|
Prediction |
polymorphism |
Model: simple_aae, prob: 0.999999999978411 (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) | chr6:32632818T>GN/A
show variant in all transcripts IGV
|
HGNC symbol | HLA-DQB1 |
Ensembl transcript ID | ENST00000374943 |
Genbank transcript ID | NM_001243961 |
UniProt peptide | P01920 |
alteration type | single base exchange |
alteration region | CDS |
DNA changes | c.136A>C cDNA.213A>C g.3343A>C |
AA changes | M46L Score: 15 explain score(s) |
position(s) of altered AA if AA alteration in CDS | 46 |
frameshift | no |
known variant | Reference ID: rs1130368
database | homozygous (G/G) | heterozygous | allele carriers |
1000G | 192 | 685 | 877 |
ExAC | 1588 | 13404 | 14992 |
|
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) | -2.798 | 0.001 | | -4.342 | 0 | (flanking) | 0.134 | 0.125 | 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 | 3338 | wt: 0.7836 / mu: 0.8056 (marginal change - not scored) | wt: GGATTTCGTGTTCCAGTTTAAGGGCATGTGCTACTTCACCA mu: GGATTTCGTGTTCCAGTTTAAGGGCCTGTGCTACTTCACCA | ttaa|GGGC | Acc increased | 3340 | wt: 0.22 / mu: 0.26 | wt: ATTTCGTGTTCCAGTTTAAGGGCATGTGCTACTTCACCAAC mu: ATTTCGTGTTCCAGTTTAAGGGCCTGTGCTACTTCACCAAC | aagg|GCAT |
|
distance from splice site | 27 |
Kozak consensus sequence altered? | N/A |
conservation protein level for non-synonymous changes | species | match | gene | aa | alignment | Human | | | 46 | S | P | E | D | F | V | F | Q | F | K | G | M | C | Y | F | T | N | G | T | E | R | V | R | L |
mutated | all conserved | | 46 | S | P | E | D | F | V | F | Q | F | K | G | L | C | Y | F | T | N | G | T | E | R | V | R |
Ptroglodytes | all identical | ENSPTRG00000018018 | 46 | S | P | E | D | F | V | Y | Q | F | K | G | M | C | Y | F | T | N | G | T | E | R | V | R |
Mmulatta | no homologue | | | |
Fcatus | no homologue | | | |
Mmusculus | not conserved | ENSMUSG00000073421 | 42 | S | E | R | H | F | V | Y | Q | F | M | G | E | C | Y | F | T | N | G | T | Q | R | I | R |
Ggallus | no homologue | | | |
Trubripes | no homologue | | | |
Drerio | not conserved | ENSDARG00000079105 | 34 | G | Y | Y | D | Y | I | - | - | - | K | Q | Q | C | F | YS | T | S | D | Y | S | D | M | V |
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 | 40 | 50 | STRAND | | lost | 47 | 47 | DISULFID | | might get lost (downstream of altered splice site) | 51 | 51 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | 51 | 54 | TURN | | might get lost (downstream of altered splice site) | 55 | 64 | STRAND | | might get lost (downstream of altered splice site) | 67 | 73 | STRAND | | might get lost (downstream of altered splice site) | 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 | 810 / 810 |
position (AA) of stopcodon in wt / mu AA sequence | 270 / 270 |
position of stopcodon in wt / mu cDNA | 887 / 887 |
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 | 78 / 78 |
chromosome | 6 |
strand | -1 |
last intron/exon boundary | 874 |
theoretical NMD boundary in CDS | 746 |
length of CDS | 810 |
coding sequence (CDS) position | 136 |
cDNA position (for ins/del: last normal base / first normal base) | 213 |
gDNA position (for ins/del: last normal base / first normal base) | 3343 |
chromosomal position (for ins/del: last normal base / first normal base) | 32632818 |
original gDNA sequence snippet | TCGTGTTCCAGTTTAAGGGCATGTGCTACTTCACCAACGGG |
altered gDNA sequence snippet | TCGTGTTCCAGTTTAAGGGCCTGTGCTACTTCACCAACGGG |
original cDNA sequence snippet | TCGTGTTCCAGTTTAAGGGCATGTGCTACTTCACCAACGGG |
altered cDNA sequence snippet | TCGTGTTCCAGTTTAAGGGCCTGTGCTACTTCACCAACGGG |
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 IRQRSQKGPQ GPPPAGLLH* |
mutated AA sequence | MSWKKALRIP GDLRVATVTL MLAMLSSLLA EGRDSPEDFV FQFKGLCYFT NGTERVRLVT RYIYNREEYA RFDSDVGVYR AVTPQGRPDA EYWNSQKEVL EGTRAELDTV CRHNYEVAFR GILQRRVEPT VTISPSRTEA LNHHNLLVCS VTDFYPGQIK VRWFRNDQEE TAGVVSTPLI RNGDWTFQIL VMLEMTPQRG DVYTCHVEHP SLQSPITVEW RAQSESAQSK MLSGVGGFVL GLIFLGLGLI IRQRSQKGPQ GPPPAGLLH* |
speed | 1.01 s |
|
|
Prediction |
polymorphism |
Model: simple_aae, prob: 0.999999999978411 (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) | chr6:32632818T>GN/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.136A>C cDNA.223A>C g.3343A>C |
AA changes | M46L Score: 15 explain score(s) |
position(s) of altered AA if AA alteration in CDS | 46 |
frameshift | no |
known variant | Reference ID: rs1130368
database | homozygous (G/G) | heterozygous | allele carriers |
1000G | 192 | 685 | 877 |
ExAC | 1588 | 13404 | 14992 |
|
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) | -2.798 | 0.001 | | -4.342 | 0 | (flanking) | 0.134 | 0.125 | 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 | 3338 | wt: 0.7836 / mu: 0.8056 (marginal change - not scored) | wt: GGATTTCGTGTTCCAGTTTAAGGGCATGTGCTACTTCACCA mu: GGATTTCGTGTTCCAGTTTAAGGGCCTGTGCTACTTCACCA | ttaa|GGGC | Acc increased | 3340 | wt: 0.22 / mu: 0.26 | wt: ATTTCGTGTTCCAGTTTAAGGGCATGTGCTACTTCACCAAC mu: ATTTCGTGTTCCAGTTTAAGGGCCTGTGCTACTTCACCAAC | aagg|GCAT |
|
distance from splice site | 27 |
Kozak consensus sequence altered? | N/A |
conservation protein level for non-synonymous changes | species | match | gene | aa | alignment | Human | | | 46 | S | P | E | D | F | V | F | Q | F | K | G | M | C | Y | F | T | N | G | T | E | R | V | R | L |
mutated | all conserved | | 46 | S | P | E | D | F | V | F | Q | F | K | G | L | C | Y | F | T | N | G | T | E | R | V | R |
Ptroglodytes | all identical | ENSPTRG00000018018 | 46 | S | P | E | D | F | V | Y | Q | F | K | G | M | C | Y | F | T | N | G | T | E | R | V | R |
Mmulatta | no homologue | | | |
Fcatus | no homologue | | | |
Mmusculus | not conserved | ENSMUSG00000073421 | 42 | S | E | R | H | F | V | Y | Q | F | M | G | E | C | Y | F | T | N | G | T | Q | R | I | R |
Ggallus | no homologue | | | |
Trubripes | no homologue | | | |
Drerio | not conserved | ENSDARG00000079105 | 34 | G | Y | Y | D | Y | I | - | - | - | K | Q | Q | C | F | YS | T | S | D | Y | S | D | M | V |
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 | 40 | 50 | STRAND | | lost | 47 | 47 | DISULFID | | might get lost (downstream of altered splice site) | 51 | 51 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | 51 | 54 | TURN | | might get lost (downstream of altered splice site) | 55 | 64 | STRAND | | might get lost (downstream of altered splice site) | 67 | 73 | STRAND | | might get lost (downstream of altered splice site) | 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 | 136 |
cDNA position (for ins/del: last normal base / first normal base) | 223 |
gDNA position (for ins/del: last normal base / first normal base) | 3343 |
chromosomal position (for ins/del: last normal base / first normal base) | 32632818 |
original gDNA sequence snippet | TCGTGTTCCAGTTTAAGGGCATGTGCTACTTCACCAACGGG |
altered gDNA sequence snippet | TCGTGTTCCAGTTTAAGGGCCTGTGCTACTTCACCAACGGG |
original cDNA sequence snippet | TCGTGTTCCAGTTTAAGGGCATGTGCTACTTCACCAACGGG |
altered cDNA sequence snippet | TCGTGTTCCAGTTTAAGGGCCTGTGCTACTTCACCAACGGG |
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 FQFKGLCYFT NGTERVRLVT RYIYNREEYA RFDSDVGVYR AVTPQGRPDA EYWNSQKEVL EGTRAELDTV CRHNYEVAFR GILQRRVEPT VTISPSRTEA LNHHNLLVCS VTDFYPGQIK VRWFRNDQEE TAGVVSTPLI RNGDWTFQIL VMLEMTPQRG DVYTCHVEHP SLQSPITVEW RAQSESAQSK MLSGVGGFVL GLIFLGLGLI IRQRSQKGLL H* |
speed | 0.84 s |
|
|
Prediction |
polymorphism |
Model: simple_aae, prob: 0.999999999978411 (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) | chr6:32632818T>GN/A
show variant in all transcripts IGV
|
HGNC symbol | HLA-DQB1 |
Ensembl transcript ID | ENST00000399084 |
Genbank transcript ID | N/A |
UniProt peptide | P01920 |
alteration type | single base exchange |
alteration region | CDS |
DNA changes | c.136A>C cDNA.315A>C g.3343A>C |
AA changes | M46L Score: 15 explain score(s) |
position(s) of altered AA if AA alteration in CDS | 46 |
frameshift | no |
known variant | Reference ID: rs1130368
database | homozygous (G/G) | heterozygous | allele carriers |
1000G | 192 | 685 | 877 |
ExAC | 1588 | 13404 | 14992 |
|
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) | -2.798 | 0.001 | | -4.342 | 0 | (flanking) | 0.134 | 0.125 | 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 | 3338 | wt: 0.7836 / mu: 0.8056 (marginal change - not scored) | wt: GGATTTCGTGTTCCAGTTTAAGGGCATGTGCTACTTCACCA mu: GGATTTCGTGTTCCAGTTTAAGGGCCTGTGCTACTTCACCA | ttaa|GGGC | Acc increased | 3340 | wt: 0.22 / mu: 0.26 | wt: ATTTCGTGTTCCAGTTTAAGGGCATGTGCTACTTCACCAAC mu: ATTTCGTGTTCCAGTTTAAGGGCCTGTGCTACTTCACCAAC | aagg|GCAT |
|
distance from splice site | 27 |
Kozak consensus sequence altered? | N/A |
conservation protein level for non-synonymous changes | species | match | gene | aa | alignment | Human | | | 46 | S | P | E | D | F | V | F | Q | F | K | G | M | C | Y | F | T | N | G | T | E | R | V | R | L |
mutated | all conserved | | 46 | S | P | E | D | F | V | F | Q | F | K | G | L | C | Y | F | T | N | G | T | E | R | V | R |
Ptroglodytes | all identical | ENSPTRG00000018018 | 46 | S | P | E | D | F | V | Y | Q | F | K | G | M | C | Y | F | T | N | G | T | E | R | V | R |
Mmulatta | no homologue | | | |
Fcatus | no homologue | | | |
Mmusculus | not conserved | ENSMUSG00000073421 | 42 | S | E | R | H | F | V | Y | Q | F | M | G | E | C | Y | F | T | N | G | T | Q | R | I | R |
Ggallus | no homologue | | | |
Trubripes | no homologue | | | |
Drerio | not conserved | ENSDARG00000079105 | 34 | G | Y | Y | D | Y | I | - | - | - | K | Q | Q | C | F | YS | T | S | D | Y | S | D | M | V |
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 | 40 | 50 | STRAND | | lost | 47 | 47 | DISULFID | | might get lost (downstream of altered splice site) | 51 | 51 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | 51 | 54 | TURN | | might get lost (downstream of altered splice site) | 55 | 64 | STRAND | | might get lost (downstream of altered splice site) | 67 | 73 | STRAND | | might get lost (downstream of altered splice site) | 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 | 965 / 965 |
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 | 180 / 180 |
chromosome | 6 |
strand | -1 |
last intron/exon boundary | 952 |
theoretical NMD boundary in CDS | 722 |
length of CDS | 786 |
coding sequence (CDS) position | 136 |
cDNA position (for ins/del: last normal base / first normal base) | 315 |
gDNA position (for ins/del: last normal base / first normal base) | 3343 |
chromosomal position (for ins/del: last normal base / first normal base) | 32632818 |
original gDNA sequence snippet | TCGTGTTCCAGTTTAAGGGCATGTGCTACTTCACCAACGGG |
altered gDNA sequence snippet | TCGTGTTCCAGTTTAAGGGCCTGTGCTACTTCACCAACGGG |
original cDNA sequence snippet | TCGTGTTCCAGTTTAAGGGCATGTGCTACTTCACCAACGGG |
altered cDNA sequence snippet | TCGTGTTCCAGTTTAAGGGCCTGTGCTACTTCACCAACGGG |
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 FQFKGLCYFT NGTERVRLVT RYIYNREEYA RFDSDVGVYR AVTPQGRPDA EYWNSQKEVL EGTRAELDTV CRHNYEVAFR GILQRRVEPT VTISPSRTEA LNHHNLLVCS VTDFYPGQIK VRWFRNDQEE TAGVVSTPLI RNGDWTFQIL VMLEMTPQRG DVYTCHVEHP SLQSPITVEW RAQSESAQSK MLSGVGGFVL GLIFLGLGLI IRQRSQKGLL H* |
speed | 1.28 s |
|
|
Prediction |
polymorphism |
Model: without_aae, prob: 0.999994251922821 (classification due to TGP/ExAC,
real probability is shown anyway)
(explain) |
Summary |
- 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) | chr6:32632818T>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 | intron |
DNA changes | g.3343A>C |
AA changes | N/A |
position(s) of altered AA if AA alteration in CDS | N/A |
frameshift | N/A |
known variant | Reference ID: rs1130368
database | homozygous (G/G) | heterozygous | allele carriers |
1000G | 192 | 685 | 877 |
ExAC | 1588 | 13404 | 14992 |
|
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) | -2.798 | 0.001 | | -4.342 | 0 | (flanking) | 0.134 | 0.125 | 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 | 3338 | wt: 0.7836 / mu: 0.8056 (marginal change - not scored) | wt: GGATTTCGTGTTCCAGTTTAAGGGCATGTGCTACTTCACCA mu: GGATTTCGTGTTCCAGTTTAAGGGCCTGTGCTACTTCACCA | ttaa|GGGC | Acc increased | 3340 | wt: 0.22 / mu: 0.26 | wt: ATTTCGTGTTCCAGTTTAAGGGCATGTGCTACTTCACCAAC mu: ATTTCGTGTTCCAGTTTAAGGGCCTGTGCTACTTCACCAAC | aagg|GCAT |
|
distance from splice site | 1458 |
Kozak consensus sequence altered? | N/A |
conservation protein level for non-synonymous changes | N/A |
protein features | start (aa) | end (aa) | feature | details | | 33 | 126 | REGION | Beta-1. | might get lost (downstream of altered splice site) | 33 | 230 | TOPO_DOM | Extracellular (Potential). | might get lost (downstream of altered splice site) | 40 | 50 | STRAND | | might get lost (downstream of altered splice site) | 47 | 47 | DISULFID | | might get lost (downstream of altered splice site) | 51 | 51 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | 51 | 54 | TURN | | might get lost (downstream of altered splice site) | 55 | 64 | STRAND | | might get lost (downstream of altered splice site) | 67 | 73 | STRAND | | might get lost (downstream of altered splice site) | 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 | 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 | 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 | 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) | 3343 |
chromosomal position (for ins/del: last normal base / first normal base) | 32632818 |
original gDNA sequence snippet | TCGTGTTCCAGTTTAAGGGCATGTGCTACTTCACCAACGGG |
altered gDNA sequence snippet | TCGTGTTCCAGTTTAAGGGCCTGTGCTACTTCACCAACGGG |
original cDNA sequence snippet | N/A |
altered cDNA sequence snippet | N/A |
wildtype AA sequence | MSWKKALRIP GDLRVATVTL MLAMLSSLLA EGRDSPVEPT VTISPSRTEA LNHHNLLVCS VTDFYPGQIK VRWFRNDQEE TAGVVSTPLI RNGDWTFQIL VMLEMTPQRG DVYTCHVEHP SLQSPITVEW RLLH* |
mutated AA sequence | N/A |
speed | 1.01 s |
|
|