Prediction |
polymorphism |
Model: simple_aae, prob: 0.999999999886167 (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) | chr6:32609105G>AN/A
show variant in all transcripts IGV
|
| HGNC symbol | HLA-DQA1 |
| Ensembl transcript ID | ENST00000343139 |
| Genbank transcript ID | NM_002122 |
| UniProt peptide | P01909 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.101G>A
cDNA.203G>A
g.13150G>A |
| AA changes | C34Y Score: 194 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 34 |
| frameshift | no |
| known variant | Reference ID: rs1129740
| database | homozygous (A/A) | heterozygous | allele carriers |
| 1000G | 817 | 986 | 1803 |
| ExAC | 19411 | -6055 | 13356 |
|
| regulatory features | H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
PolII, Polymerase, RNA Polymerase II |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 2.441 | 0.007 | | -0.375 | 0 | | (flanking) | -2.058 | 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 | 13153 | wt: 0.27 / mu: 0.41 | wt: TGACCACGTTGCCTCTTGTGGTGTAAACTTGTACCAGTTTT
mu: TGACCACGTTGCCTCTTATGGTGTAAACTTGTACCAGTTTT | gtgg|TGTA | | Donor marginally increased | 13154 | wt: 0.4641 / mu: 0.5466 (marginal change - not scored) | wt: TGTGGTGTAAACTTG
mu: TATGGTGTAAACTTG | TGGT|gtaa | | Acc gained | 13152 | 0.70 | mu: CTGACCACGTTGCCTCTTATGGTGTAAACTTGTACCAGTTT | tatg|GTGT |
|
| distance from splice site | 19 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 34 | G | E | D | I | V | A | D | H | V | A | S | C | G | V | N | L | Y | Q | F | Y | G | P | S | G |
| mutated | not conserved | | 34 | G | E | D | I | V | A | D | H | V | A | S | Y | G | V | N | L | Y | Q | F | Y | G | P | S |
| Ptroglodytes | no homologue | | | |
| Mmulatta | no alignment | ENSMMUG00000014605 | n/a | |
| Fcatus | no homologue | | | |
| Mmusculus | not conserved | ENSMUSG00000036594 | 34 | G | E | DD | I | E | A | D | H | V | G | T | Y | G | I | S | V | Y | Q | S | P | G | D | I |
| Ggallus | no homologue | | | |
| Trubripes | no homologue | | | |
| Drerio | not conserved | ENSDARG00000001832 | 29 | A | Q | - | - | - | A | E | H | - | - | - | - | - | - | R | D | F | Q | F | T | G | C | S |
| Dmelanogaster | no homologue | | | |
| Celegans | no homologue | | | |
| Xtropicalis | no alignment | ENSXETG00000031520 | n/a | |
|
| protein features | | start (aa) | end (aa) | feature | details | | | 24 | 119 | REGION | Alpha-1. | lost | | 24 | 216 | TOPO_DOM | Extracellular (Potential). | lost | | 29 | 40 | STRAND | | lost | | 41 | 44 | TURN | | might get lost (downstream of altered splice site) | | 45 | 52 | STRAND | | might get lost (downstream of altered splice site) | | 55 | 61 | STRAND | | might get lost (downstream of altered splice site) | | 62 | 65 | TURN | | might get lost (downstream of altered splice site) | | 66 | 71 | STRAND | | might get lost (downstream of altered splice site) | | 72 | 77 | HELIX | | might get lost (downstream of altered splice site) | | 81 | 101 | HELIX | | might get lost (downstream of altered splice site) | | 91 | 91 | CONFLICT | L -> H (in Ref. 4; AAA59760). | might get lost (downstream of altered splice site) | | 102 | 104 | TURN | | might get lost (downstream of altered splice site) | | 103 | 103 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 107 | 107 | CONFLICT | A -> P (in Ref. 16; AAA59754). | might get lost (downstream of altered splice site) | | 112 | 204 | DOMAIN | Ig-like C1-type. | might get lost (downstream of altered splice site) | | 113 | 120 | STRAND | | might get lost (downstream of altered splice site) | | 120 | 203 | REGION | Alpha-2. | might get lost (downstream of altered splice site) | | 128 | 137 | STRAND | | might get lost (downstream of altered splice site) | | 132 | 132 | DISULFID | | might get lost (downstream of altered splice site) | | 143 | 143 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 143 | 148 | STRAND | | might get lost (downstream of altered splice site) | | 151 | 153 | STRAND | | might get lost (downstream of altered splice site) | | 156 | 156 | CONFLICT | G -> D (in Ref. 3; CAA25141). | might get lost (downstream of altered splice site) | | 157 | 159 | STRAND | | might get lost (downstream of altered splice site) | | 170 | 178 | STRAND | | might get lost (downstream of altered splice site) | | 186 | 191 | STRAND | | might get lost (downstream of altered splice site) | | 188 | 188 | DISULFID | | might get lost (downstream of altered splice site) | | 195 | 197 | STRAND | | might get lost (downstream of altered splice site) | | 199 | 203 | STRAND | | might get lost (downstream of altered splice site) | | 204 | 216 | REGION | Connecting peptide. | might get lost (downstream of altered splice site) | | 213 | 213 | CONFLICT | E -> D (in Ref. 16; AAA59754). | might get lost (downstream of altered splice site) | | 217 | 239 | TRANSMEM | Helical; (Potential). | might get lost (downstream of altered splice site) | | 240 | 254 | TOPO_DOM | Cytoplasmic. | might get lost (downstream of altered splice site) |
|
| length of protein | normal |
| AA sequence altered | yes |
| position of stopcodon in wt / mu CDS | 768 / 768 |
| position (AA) of stopcodon in wt / mu AA sequence | 256 / 256 |
| position of stopcodon in wt / mu cDNA | 870 / 870 |
| 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 | 103 / 103 |
| chromosome | 6 |
| strand | 1 |
| last intron/exon boundary | 891 |
| theoretical NMD boundary in CDS | 738 |
| length of CDS | 768 |
| coding sequence (CDS) position | 101 |
cDNA position
(for ins/del: last normal base / first normal base) | 203 |
gDNA position
(for ins/del: last normal base / first normal base) | 13150 |
chromosomal position
(for ins/del: last normal base / first normal base) | 32609105 |
| original gDNA sequence snippet | AGCTGACCACGTTGCCTCTTGTGGTGTAAACTTGTACCAGT |
| altered gDNA sequence snippet | AGCTGACCACGTTGCCTCTTATGGTGTAAACTTGTACCAGT |
| original cDNA sequence snippet | GGCTGACCACGTTGCCTCTTGTGGTGTAAACTTGTACCAGT |
| altered cDNA sequence snippet | GGCTGACCACGTTGCCTCTTATGGTGTAAACTTGTACCAGT |
| wildtype AA sequence | MILNKALLLG ALALTTVMSP CGGEDIVADH VASCGVNLYQ FYGPSGQYTH EFDGDEQFYV
DLERKETAWR WPEFSKFGGF DPQGALRNMA VAKHNLNIMI KRYNSTAATN EVPEVTVFSK
SPVTLGQPNT LICLVDNIFP PVVNITWLSN GQSVTEGVSE TSFLSKSDHS FFKISYLTFL
PSADEIYDCK VEHWGLDQPL LKHWEPEIPA PMSELTETVV CALGLSVGLM GIVVGTVFII
QGLRSVGASR HQGPL* |
| mutated AA sequence | MILNKALLLG ALALTTVMSP CGGEDIVADH VASYGVNLYQ FYGPSGQYTH EFDGDEQFYV
DLERKETAWR WPEFSKFGGF DPQGALRNMA VAKHNLNIMI KRYNSTAATN EVPEVTVFSK
SPVTLGQPNT LICLVDNIFP PVVNITWLSN GQSVTEGVSE TSFLSKSDHS FFKISYLTFL
PSADEIYDCK VEHWGLDQPL LKHWEPEIPA PMSELTETVV CALGLSVGLM GIVVGTVFII
QGLRSVGASR HQGPL* |
| speed | 1.18 s |
|
|
Prediction |
polymorphism |
Model: simple_aae, prob: 0.999999999886167 (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) | chr6:32609105G>AN/A
show variant in all transcripts IGV
|
| HGNC symbol | HLA-DQA1 |
| Ensembl transcript ID | ENST00000395364 |
| Genbank transcript ID | N/A |
| UniProt peptide | P01909 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.101G>A
cDNA.203G>A
g.13150G>A |
| AA changes | C34Y Score: 194 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 34 |
| frameshift | no |
| known variant | Reference ID: rs1129740
| database | homozygous (A/A) | heterozygous | allele carriers |
| 1000G | 817 | 986 | 1803 |
| ExAC | 19411 | -6055 | 13356 |
|
| regulatory features | H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
PolII, Polymerase, RNA Polymerase II |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 2.441 | 0.007 | | -0.375 | 0 | | (flanking) | -2.058 | 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 | 13153 | wt: 0.27 / mu: 0.41 | wt: TGACCACGTTGCCTCTTGTGGTGTAAACTTGTACCAGTTTT
mu: TGACCACGTTGCCTCTTATGGTGTAAACTTGTACCAGTTTT | gtgg|TGTA | | Donor marginally increased | 13154 | wt: 0.4641 / mu: 0.5466 (marginal change - not scored) | wt: TGTGGTGTAAACTTG
mu: TATGGTGTAAACTTG | TGGT|gtaa | | Acc gained | 13152 | 0.70 | mu: CTGACCACGTTGCCTCTTATGGTGTAAACTTGTACCAGTTT | tatg|GTGT |
|
| distance from splice site | 19 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 34 | G | E | D | I | V | A | D | H | V | A | S | C | G | V | N | L | Y | Q | F | Y | G | P | S | G |
| mutated | not conserved | | 34 | G | E | D | I | V | A | D | H | V | A | S | Y | G | V | N | L | Y | Q | F | Y | G | P | S |
| Ptroglodytes | no homologue | | | |
| Mmulatta | no alignment | ENSMMUG00000014605 | n/a | |
| Fcatus | no homologue | | | |
| Mmusculus | not conserved | ENSMUSG00000036594 | 34 | G | E | DD | I | E | A | D | H | V | G | T | Y | G | I | S | V | Y | Q | S | P | G | D | I |
| Ggallus | no homologue | | | |
| Trubripes | no homologue | | | |
| Drerio | not conserved | ENSDARG00000001832 | 29 | A | Q | - | - | - | A | E | H | - | - | - | - | - | - | R | D | F | Q | F | T | G | C | S |
| Dmelanogaster | no homologue | | | |
| Celegans | no homologue | | | |
| Xtropicalis | no alignment | ENSXETG00000031520 | n/a | |
|
| protein features | | start (aa) | end (aa) | feature | details | | | 24 | 119 | REGION | Alpha-1. | lost | | 24 | 216 | TOPO_DOM | Extracellular (Potential). | lost | | 29 | 40 | STRAND | | lost | | 41 | 44 | TURN | | might get lost (downstream of altered splice site) | | 45 | 52 | STRAND | | might get lost (downstream of altered splice site) | | 55 | 61 | STRAND | | might get lost (downstream of altered splice site) | | 62 | 65 | TURN | | might get lost (downstream of altered splice site) | | 66 | 71 | STRAND | | might get lost (downstream of altered splice site) | | 72 | 77 | HELIX | | might get lost (downstream of altered splice site) | | 81 | 101 | HELIX | | might get lost (downstream of altered splice site) | | 91 | 91 | CONFLICT | L -> H (in Ref. 4; AAA59760). | might get lost (downstream of altered splice site) | | 102 | 104 | TURN | | might get lost (downstream of altered splice site) | | 103 | 103 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 107 | 107 | CONFLICT | A -> P (in Ref. 16; AAA59754). | might get lost (downstream of altered splice site) | | 112 | 204 | DOMAIN | Ig-like C1-type. | might get lost (downstream of altered splice site) | | 113 | 120 | STRAND | | might get lost (downstream of altered splice site) | | 120 | 203 | REGION | Alpha-2. | might get lost (downstream of altered splice site) | | 128 | 137 | STRAND | | might get lost (downstream of altered splice site) | | 132 | 132 | DISULFID | | might get lost (downstream of altered splice site) | | 143 | 143 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 143 | 148 | STRAND | | might get lost (downstream of altered splice site) | | 151 | 153 | STRAND | | might get lost (downstream of altered splice site) | | 156 | 156 | CONFLICT | G -> D (in Ref. 3; CAA25141). | might get lost (downstream of altered splice site) | | 157 | 159 | STRAND | | might get lost (downstream of altered splice site) | | 170 | 178 | STRAND | | might get lost (downstream of altered splice site) | | 186 | 191 | STRAND | | might get lost (downstream of altered splice site) | | 188 | 188 | DISULFID | | might get lost (downstream of altered splice site) | | 195 | 197 | STRAND | | might get lost (downstream of altered splice site) | | 199 | 203 | STRAND | | might get lost (downstream of altered splice site) | | 204 | 216 | REGION | Connecting peptide. | might get lost (downstream of altered splice site) | | 213 | 213 | CONFLICT | E -> D (in Ref. 16; AAA59754). | might get lost (downstream of altered splice site) | | 217 | 239 | TRANSMEM | Helical; (Potential). | might get lost (downstream of altered splice site) | | 240 | 254 | TOPO_DOM | Cytoplasmic. | might get lost (downstream of altered splice site) |
|
| length of protein | normal |
| AA sequence altered | yes |
| position of stopcodon in wt / mu CDS | 768 / 768 |
| position (AA) of stopcodon in wt / mu AA sequence | 256 / 256 |
| position of stopcodon in wt / mu cDNA | 870 / 870 |
| 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 | 103 / 103 |
| chromosome | 6 |
| strand | 1 |
| last intron/exon boundary | 891 |
| theoretical NMD boundary in CDS | 738 |
| length of CDS | 768 |
| coding sequence (CDS) position | 101 |
cDNA position
(for ins/del: last normal base / first normal base) | 203 |
gDNA position
(for ins/del: last normal base / first normal base) | 13150 |
chromosomal position
(for ins/del: last normal base / first normal base) | 32609105 |
| original gDNA sequence snippet | AGCTGACCACGTTGCCTCTTGTGGTGTAAACTTGTACCAGT |
| altered gDNA sequence snippet | AGCTGACCACGTTGCCTCTTATGGTGTAAACTTGTACCAGT |
| original cDNA sequence snippet | GGCTGACCACGTTGCCTCTTGTGGTGTAAACTTGTACCAGT |
| altered cDNA sequence snippet | GGCTGACCACGTTGCCTCTTATGGTGTAAACTTGTACCAGT |
| wildtype AA sequence | MILNKALLLG ALALTTVMSP CGGEDIVADH VASCGVNLYQ FYGPSGQYTH EFDGDEQFYV
DLERKETAWR WPEFSKFGGF DPQGALRNMA VAKHNLNIMI KRYNSTAATN EVPEVTVFSK
SPVTLGQPNT LICLVDNIFP PVVNITWLSN GQSVTEGVSE TSFLSKSDHS FFKISYLTFL
PSADEIYDCK VEHWGLDQPL LKHWEPEIPA PMSELTETVV CALGLSVGLM GIVVGTVFII
QGLRSVGASR HQGPL* |
| mutated AA sequence | MILNKALLLG ALALTTVMSP CGGEDIVADH VASYGVNLYQ FYGPSGQYTH EFDGDEQFYV
DLERKETAWR WPEFSKFGGF DPQGALRNMA VAKHNLNIMI KRYNSTAATN EVPEVTVFSK
SPVTLGQPNT LICLVDNIFP PVVNITWLSN GQSVTEGVSE TSFLSKSDHS FFKISYLTFL
PSADEIYDCK VEHWGLDQPL LKHWEPEIPA PMSELTETVV CALGLSVGLM GIVVGTVFII
QGLRSVGASR HQGPL* |
| speed | 1.20 s |
|
|
Prediction |
polymorphism |
Model: simple_aae, prob: 0.999999999886167 (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) | chr6:32609105G>AN/A
show variant in all transcripts IGV
|
| HGNC symbol | HLA-DQA1 |
| Ensembl transcript ID | ENST00000395363 |
| Genbank transcript ID | N/A |
| UniProt peptide | P01909 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.101G>A
cDNA.159G>A
g.13150G>A |
| AA changes | C34Y Score: 194 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 34 |
| frameshift | no |
| known variant | Reference ID: rs1129740
| database | homozygous (A/A) | heterozygous | allele carriers |
| 1000G | 817 | 986 | 1803 |
| ExAC | 19411 | -6055 | 13356 |
|
| regulatory features | H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
PolII, Polymerase, RNA Polymerase II |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 2.441 | 0.007 | | -0.375 | 0 | | (flanking) | -2.058 | 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 | 13153 | wt: 0.27 / mu: 0.41 | wt: TGACCACGTTGCCTCTTGTGGTGTAAACTTGTACCAGTTTT
mu: TGACCACGTTGCCTCTTATGGTGTAAACTTGTACCAGTTTT | gtgg|TGTA | | Donor marginally increased | 13154 | wt: 0.4641 / mu: 0.5466 (marginal change - not scored) | wt: TGTGGTGTAAACTTG
mu: TATGGTGTAAACTTG | TGGT|gtaa | | Acc gained | 13152 | 0.70 | mu: CTGACCACGTTGCCTCTTATGGTGTAAACTTGTACCAGTTT | tatg|GTGT |
|
| distance from splice site | 19 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 34 | G | E | D | I | V | A | D | H | V | A | S | C | G | V | N | L | Y | Q | F | Y | G | P | S | G |
| mutated | not conserved | | 34 | G | E | D | I | V | A | D | H | V | A | S | Y | G | V | N | L | Y | Q | F | Y | G | P | S |
| Ptroglodytes | no homologue | | | |
| Mmulatta | no alignment | ENSMMUG00000014605 | n/a | |
| Fcatus | no homologue | | | |
| Mmusculus | not conserved | ENSMUSG00000036594 | 34 | G | E | DD | I | E | A | D | H | V | G | T | Y | G | I | S | V | Y | Q | S | P | G | D | I |
| Ggallus | no homologue | | | |
| Trubripes | no homologue | | | |
| Drerio | not conserved | ENSDARG00000001832 | 29 | A | Q | - | - | - | A | E | H | - | - | - | - | - | - | R | D | F | Q | F | T | G | C | S |
| Dmelanogaster | no homologue | | | |
| Celegans | no homologue | | | |
| Xtropicalis | no alignment | ENSXETG00000031520 | n/a | |
|
| protein features | | start (aa) | end (aa) | feature | details | | | 24 | 119 | REGION | Alpha-1. | lost | | 24 | 216 | TOPO_DOM | Extracellular (Potential). | lost | | 29 | 40 | STRAND | | lost | | 41 | 44 | TURN | | might get lost (downstream of altered splice site) | | 45 | 52 | STRAND | | might get lost (downstream of altered splice site) | | 55 | 61 | STRAND | | might get lost (downstream of altered splice site) | | 62 | 65 | TURN | | might get lost (downstream of altered splice site) | | 66 | 71 | STRAND | | might get lost (downstream of altered splice site) | | 72 | 77 | HELIX | | might get lost (downstream of altered splice site) | | 81 | 101 | HELIX | | might get lost (downstream of altered splice site) | | 91 | 91 | CONFLICT | L -> H (in Ref. 4; AAA59760). | might get lost (downstream of altered splice site) | | 102 | 104 | TURN | | might get lost (downstream of altered splice site) | | 103 | 103 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 107 | 107 | CONFLICT | A -> P (in Ref. 16; AAA59754). | might get lost (downstream of altered splice site) | | 112 | 204 | DOMAIN | Ig-like C1-type. | might get lost (downstream of altered splice site) | | 113 | 120 | STRAND | | might get lost (downstream of altered splice site) | | 120 | 203 | REGION | Alpha-2. | might get lost (downstream of altered splice site) | | 128 | 137 | STRAND | | might get lost (downstream of altered splice site) | | 132 | 132 | DISULFID | | might get lost (downstream of altered splice site) | | 143 | 143 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 143 | 148 | STRAND | | might get lost (downstream of altered splice site) | | 151 | 153 | STRAND | | might get lost (downstream of altered splice site) | | 156 | 156 | CONFLICT | G -> D (in Ref. 3; CAA25141). | might get lost (downstream of altered splice site) | | 157 | 159 | STRAND | | might get lost (downstream of altered splice site) | | 170 | 178 | STRAND | | might get lost (downstream of altered splice site) | | 186 | 191 | STRAND | | might get lost (downstream of altered splice site) | | 188 | 188 | DISULFID | | might get lost (downstream of altered splice site) | | 195 | 197 | STRAND | | might get lost (downstream of altered splice site) | | 199 | 203 | STRAND | | might get lost (downstream of altered splice site) | | 204 | 216 | REGION | Connecting peptide. | might get lost (downstream of altered splice site) | | 213 | 213 | CONFLICT | E -> D (in Ref. 16; AAA59754). | might get lost (downstream of altered splice site) | | 217 | 239 | TRANSMEM | Helical; (Potential). | might get lost (downstream of altered splice site) | | 240 | 254 | TOPO_DOM | Cytoplasmic. | might get lost (downstream of altered splice site) |
|
| length of protein | normal |
| AA sequence altered | yes |
| position of stopcodon in wt / mu CDS | 768 / 768 |
| position (AA) of stopcodon in wt / mu AA sequence | 256 / 256 |
| position of stopcodon in wt / mu cDNA | 826 / 826 |
| 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 | 59 / 59 |
| chromosome | 6 |
| strand | 1 |
| last intron/exon boundary | 847 |
| theoretical NMD boundary in CDS | 738 |
| length of CDS | 768 |
| coding sequence (CDS) position | 101 |
cDNA position
(for ins/del: last normal base / first normal base) | 159 |
gDNA position
(for ins/del: last normal base / first normal base) | 13150 |
chromosomal position
(for ins/del: last normal base / first normal base) | 32609105 |
| original gDNA sequence snippet | AGCTGACCACGTTGCCTCTTGTGGTGTAAACTTGTACCAGT |
| altered gDNA sequence snippet | AGCTGACCACGTTGCCTCTTATGGTGTAAACTTGTACCAGT |
| original cDNA sequence snippet | GGCTGACCACGTTGCCTCTTGTGGTGTAAACTTGTACCAGT |
| altered cDNA sequence snippet | GGCTGACCACGTTGCCTCTTATGGTGTAAACTTGTACCAGT |
| wildtype AA sequence | MILNKALLLG ALALTTVMSP CGGEDIVADH VASCGVNLYQ FYGPSGQYTH EFDGDEQFYV
DLERKETAWR WPEFSKFGGF DPQGALRNMA VAKHNLNIMI KRYNSTAATN EVPEVTVFSK
SPVTLGQPNT LICLVDNIFP PVVNITWLSN GQSVTEGVSE TSFLSKSDHS FFKISYLTFL
PSADEIYDCK VEHWGLDQPL LKHWEPEIPA PMSELTETVV CALGLSVGLM GIVVGTVFII
QGLRSVGASR HQGPL* |
| mutated AA sequence | MILNKALLLG ALALTTVMSP CGGEDIVADH VASYGVNLYQ FYGPSGQYTH EFDGDEQFYV
DLERKETAWR WPEFSKFGGF DPQGALRNMA VAKHNLNIMI KRYNSTAATN EVPEVTVFSK
SPVTLGQPNT LICLVDNIFP PVVNITWLSN GQSVTEGVSE TSFLSKSDHS FFKISYLTFL
PSADEIYDCK VEHWGLDQPL LKHWEPEIPA PMSELTETVV CALGLSVGLM GIVVGTVFII
QGLRSVGASR HQGPL* |
| speed | 0.44 s |
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Prediction |
polymorphism |
Model: simple_aae, prob: 0.999999999886167 (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) | chr6:32609105G>AN/A
show variant in all transcripts IGV
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| HGNC symbol | HLA-DQA1 |
| Ensembl transcript ID | ENST00000374949 |
| Genbank transcript ID | N/A |
| UniProt peptide | P01909 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.101G>A
cDNA.140G>A
g.13150G>A |
| AA changes | C34Y Score: 194 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 34 |
| frameshift | no |
| known variant | Reference ID: rs1129740
| database | homozygous (A/A) | heterozygous | allele carriers |
| 1000G | 817 | 986 | 1803 |
| ExAC | 19411 | -6055 | 13356 |
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| regulatory features | H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
PolII, Polymerase, RNA Polymerase II |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 2.441 | 0.007 | | -0.375 | 0 | | (flanking) | -2.058 | 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 | 13153 | wt: 0.27 / mu: 0.41 | wt: TGACCACGTTGCCTCTTGTGGTGTAAACTTGTACCAGTTTT
mu: TGACCACGTTGCCTCTTATGGTGTAAACTTGTACCAGTTTT | gtgg|TGTA | | Donor marginally increased | 13154 | wt: 0.4641 / mu: 0.5466 (marginal change - not scored) | wt: TGTGGTGTAAACTTG
mu: TATGGTGTAAACTTG | TGGT|gtaa | | Acc gained | 13152 | 0.70 | mu: CTGACCACGTTGCCTCTTATGGTGTAAACTTGTACCAGTTT | tatg|GTGT |
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| distance from splice site | 19 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 34 | G | E | D | I | V | A | D | H | V | A | S | C | G | V | N | L | Y | Q | F | Y | G | P | S | G |
| mutated | not conserved | | 34 | G | E | D | I | V | A | D | H | V | A | S | Y | G | V | N | L | Y | Q | F | Y | G | P | S |
| Ptroglodytes | no homologue | | | |
| Mmulatta | no alignment | ENSMMUG00000014605 | n/a | |
| Fcatus | no homologue | | | |
| Mmusculus | not conserved | ENSMUSG00000036594 | 34 | G | E | DD | I | E | A | D | H | V | G | T | Y | G | I | S | V | Y | Q | S | P | G | D | I |
| Ggallus | no homologue | | | |
| Trubripes | no homologue | | | |
| Drerio | not conserved | ENSDARG00000001832 | 29 | A | Q | - | - | - | A | E | H | - | - | - | - | - | - | R | D | F | Q | F | T | G | C | S |
| Dmelanogaster | no homologue | | | |
| Celegans | no homologue | | | |
| Xtropicalis | no alignment | ENSXETG00000031520 | n/a | |
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| protein features | | start (aa) | end (aa) | feature | details | | | 24 | 119 | REGION | Alpha-1. | lost | | 24 | 216 | TOPO_DOM | Extracellular (Potential). | lost | | 29 | 40 | STRAND | | lost | | 41 | 44 | TURN | | might get lost (downstream of altered splice site) | | 45 | 52 | STRAND | | might get lost (downstream of altered splice site) | | 55 | 61 | STRAND | | might get lost (downstream of altered splice site) | | 62 | 65 | TURN | | might get lost (downstream of altered splice site) | | 66 | 71 | STRAND | | might get lost (downstream of altered splice site) | | 72 | 77 | HELIX | | might get lost (downstream of altered splice site) | | 81 | 101 | HELIX | | might get lost (downstream of altered splice site) | | 91 | 91 | CONFLICT | L -> H (in Ref. 4; AAA59760). | might get lost (downstream of altered splice site) | | 102 | 104 | TURN | | might get lost (downstream of altered splice site) | | 103 | 103 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 107 | 107 | CONFLICT | A -> P (in Ref. 16; AAA59754). | might get lost (downstream of altered splice site) | | 112 | 204 | DOMAIN | Ig-like C1-type. | might get lost (downstream of altered splice site) | | 113 | 120 | STRAND | | might get lost (downstream of altered splice site) | | 120 | 203 | REGION | Alpha-2. | might get lost (downstream of altered splice site) | | 128 | 137 | STRAND | | might get lost (downstream of altered splice site) | | 132 | 132 | DISULFID | | might get lost (downstream of altered splice site) | | 143 | 143 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 143 | 148 | STRAND | | might get lost (downstream of altered splice site) | | 151 | 153 | STRAND | | might get lost (downstream of altered splice site) | | 156 | 156 | CONFLICT | G -> D (in Ref. 3; CAA25141). | might get lost (downstream of altered splice site) | | 157 | 159 | STRAND | | might get lost (downstream of altered splice site) | | 170 | 178 | STRAND | | might get lost (downstream of altered splice site) | | 186 | 191 | STRAND | | might get lost (downstream of altered splice site) | | 188 | 188 | DISULFID | | might get lost (downstream of altered splice site) | | 195 | 197 | STRAND | | might get lost (downstream of altered splice site) | | 199 | 203 | STRAND | | might get lost (downstream of altered splice site) | | 204 | 216 | REGION | Connecting peptide. | might get lost (downstream of altered splice site) | | 213 | 213 | CONFLICT | E -> D (in Ref. 16; AAA59754). | might get lost (downstream of altered splice site) | | 217 | 239 | TRANSMEM | Helical; (Potential). | might get lost (downstream of altered splice site) | | 240 | 254 | TOPO_DOM | Cytoplasmic. | might get lost (downstream of altered splice site) |
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| length of protein | normal |
| AA sequence altered | yes |
| position of stopcodon in wt / mu CDS | 768 / 768 |
| position (AA) of stopcodon in wt / mu AA sequence | 256 / 256 |
| position of stopcodon in wt / mu cDNA | 807 / 807 |
| 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 | 40 / 40 |
| chromosome | 6 |
| strand | 1 |
| last intron/exon boundary | 653 |
| theoretical NMD boundary in CDS | 563 |
| length of CDS | 768 |
| coding sequence (CDS) position | 101 |
cDNA position
(for ins/del: last normal base / first normal base) | 140 |
gDNA position
(for ins/del: last normal base / first normal base) | 13150 |
chromosomal position
(for ins/del: last normal base / first normal base) | 32609105 |
| original gDNA sequence snippet | AGCTGACCACGTTGCCTCTTGTGGTGTAAACTTGTACCAGT |
| altered gDNA sequence snippet | AGCTGACCACGTTGCCTCTTATGGTGTAAACTTGTACCAGT |
| original cDNA sequence snippet | GGCTGACCACGTTGCCTCTTGTGGTGTAAACTTGTACCAGT |
| altered cDNA sequence snippet | GGCTGACCACGTTGCCTCTTATGGTGTAAACTTGTACCAGT |
| wildtype AA sequence | MILNKALLLG ALALTTVMSP CGGEDIVADH VASCGVNLYQ FYGPSGQYTH EFDGDEQFYV
DLERKETAWR WPEFSKFGGF DPQGALRNMA VAKHNLNIMI KRYNSTAATN EVPEVTVFSK
SPVTLGQPNT LICLVDNIFP PVVNITWLSN GQSVTEGVSE TSFLSKSDHS FFKISYLTFL
PSADEIYDCK VEHWGLDQPL LKHWEPEIPA PMSELTETVV CALGLSVGLM GIVVGTVFII
QGLRSVGASR HQGPL* |
| mutated AA sequence | MILNKALLLG ALALTTVMSP CGGEDIVADH VASYGVNLYQ FYGPSGQYTH EFDGDEQFYV
DLERKETAWR WPEFSKFGGF DPQGALRNMA VAKHNLNIMI KRYNSTAATN EVPEVTVFSK
SPVTLGQPNT LICLVDNIFP PVVNITWLSN GQSVTEGVSE TSFLSKSDHS FFKISYLTFL
PSADEIYDCK VEHWGLDQPL LKHWEPEIPA PMSELTETVV CALGLSVGLM GIVVGTVFII
QGLRSVGASR HQGPL* |
| speed | 0.96 s |
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