Yum, tasty mutations...

MutationTaster - study a chromosomal position

MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 5 transcript(s)...
Querying Taster for transcript #1: ENST00000399082
Querying Taster for transcript #2: ENST00000399079
Querying Taster for transcript #3: ENST00000374943
Querying Taster for transcript #4: ENST00000434651
Querying Taster for transcript #5: ENST00000399084
MT speed 0 s - this script 9.292755 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
HLA-DQB1polymorphism_automatic1.28249633135624e-11simple_aaeaffectedG67Asingle base exchangers1063322show file
HLA-DQB1polymorphism_automatic2.12979633928967e-11simple_aaeaffectedG157Asingle base exchangers1063322show file
HLA-DQB1polymorphism_automatic2.12979633928967e-11simple_aaeaffectedG157Asingle base exchangers1063322show file
HLA-DQB1polymorphism_automatic2.12979633928967e-11simple_aaeaffectedG157Asingle base exchangers1063322show file
HLA-DQB1polymorphism_automatic2.12979633928967e-11simple_aaeaffectedG157Asingle base exchangers1063322show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

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
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC18865-496313902
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
PhyloPPhastCons
(flanking)0.170.003
-0.060.001
(flanking)-0.5190.002
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased6223wt: 0.61 / mu: 0.69wt: CTCGGTGACAGATTTCTATCCAGGCCAGATCAAAGTCCGGT
mu: CTCGGTGACAGATTTCTATCCAGCCCAGATCAAAGTCCGGT
 atcc|AGGC
Donor increased6224wt: 0.75 / mu: 0.88wt: TATCCAGGCCAGATC
mu: TATCCAGCCCAGATC
 TCCA|ggcc
Donor gained62290.40mu: AGCCCAGATCAAAGT CCCA|gatc
distance from splice site 91
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      67LLVCSVTDFYPGQIKVRWFRNDQE
mutated  not conserved    67VTDFYPAQIKVRWFRNDQ
Ptroglodytes  all identical  ENSPTRG00000018018  157LLVCSVTDFYPGQIKVRWFRNDQ
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000073421  153TLVCSVTDFYPAKIKVRWFRNGQ
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000079105  142VLLCSAYEFYPKKIKMSWLRDGK
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
33126REGIONBeta-1.lost
33230TOPO_DOMExtracellular (Potential).lost
6773STRANDlost
7476TURNmight get lost (downstream of altered splice site)
7881STRANDmight get lost (downstream of altered splice site)
8486HELIXmight get lost (downstream of altered splice site)
8794HELIXmight get lost (downstream of altered splice site)
97109HELIXmight get lost (downstream of altered splice site)
111111CONFLICTC -> S (in Ref. 71; AAD39697).might get lost (downstream of altered splice site)
111111DISULFIDmight get lost (downstream of altered splice site)
111119HELIXmight get lost (downstream of altered splice site)
113113CONFLICTH -> Q (in Ref. 22; AAF28315).might get lost (downstream of altered splice site)
122124HELIXmight get lost (downstream of altered splice site)
127220REGIONBeta-2.might get lost (downstream of altered splice site)
129233DOMAINIg-like C1-type.might get lost (downstream of altered splice site)
130134STRANDmight get lost (downstream of altered splice site)
141144STRANDmight get lost (downstream of altered splice site)
147157STRANDmight get lost (downstream of altered splice site)
149149DISULFIDmight get lost (downstream of altered splice site)
160165STRANDmight get lost (downstream of altered splice site)
168170STRANDmight get lost (downstream of altered splice site)
172176STRANDmight get lost (downstream of altered splice site)
173173CONFLICTG -> A (in Ref. 24; X76553/X76554).might get lost (downstream of altered splice site)
183185STRANDmight get lost (downstream of altered splice site)
187193STRANDmight get lost (downstream of altered splice site)
203208STRANDmight get lost (downstream of altered splice site)
205205DISULFIDmight get lost (downstream of altered splice site)
214214CONFLICTN -> T (in Ref. 8; AAA59770).might get lost (downstream of altered splice site)
216220STRANDmight get lost (downstream of altered splice site)
221230REGIONConnecting peptide.might get lost (downstream of altered splice site)
231251TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
252261TOPO_DOMCytoplasmic (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 1.21 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999978702 (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 ENST00000399079
Genbank transcript ID N/A
UniProt peptide P01920
alteration type single base exchange
alteration region CDS
DNA changes c.470G>C
cDNA.527G>C
g.6226G>C
AA changes G157A Score: 60 explain score(s)
position(s) of altered AA
if AA alteration in CDS
157
frameshift no
known variant Reference ID: rs1063322
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC18865-496313902
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
PhyloPPhastCons
(flanking)0.170.003
-0.060.001
(flanking)-0.5190.002
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased6223wt: 0.61 / mu: 0.69wt: CTCGGTGACAGATTTCTATCCAGGCCAGATCAAAGTCCGGT
mu: CTCGGTGACAGATTTCTATCCAGCCCAGATCAAAGTCCGGT
 atcc|AGGC
Donor increased6224wt: 0.75 / mu: 0.88wt: TATCCAGGCCAGATC
mu: TATCCAGCCCAGATC
 TCCA|ggcc
Donor gained62290.40mu: AGCCCAGATCAAAGT CCCA|gatc
distance from splice site 91
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      157LLVCSVTDFYPGQIKVRWFRNDQE
mutated  not conserved    157LLVCSVTDFYPAQIKVRWFRNDQ
Ptroglodytes  all identical  ENSPTRG00000018018  157LLVCSVTDFYPGQIKVRWFRNDQ
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000073421  152TLVCSVTDFYPAKIKVRWFRNGQ
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000079105  142VLLCSAYEFYPKKIKMSWLRDGK
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
33230TOPO_DOMExtracellular (Potential).lost
127220REGIONBeta-2.lost
129233DOMAINIg-like C1-type.lost
147157STRANDlost
160165STRANDmight get lost (downstream of altered splice site)
168170STRANDmight get lost (downstream of altered splice site)
172176STRANDmight get lost (downstream of altered splice site)
173173CONFLICTG -> A (in Ref. 24; X76553/X76554).might get lost (downstream of altered splice site)
183185STRANDmight get lost (downstream of altered splice site)
187193STRANDmight get lost (downstream of altered splice site)
203208STRANDmight get lost (downstream of altered splice site)
205205DISULFIDmight get lost (downstream of altered splice site)
214214CONFLICTN -> T (in Ref. 8; AAA59770).might get lost (downstream of altered splice site)
216220STRANDmight get lost (downstream of altered splice site)
221230REGIONConnecting peptide.might get lost (downstream of altered splice site)
231251TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
252261TOPO_DOMCytoplasmic (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 470
cDNA position
(for ins/del: last normal base / first normal base)
527
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 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 FQFKGMCYFT NGTERVRLVT
RYIYNREEYA RFDSDVGVYR AVTPQGRPDA EYWNSQKEVL EGTRAELDTV CRHNYEVAFR
GILQRRVEPT VTISPSRTEA LNHHNLLVCS VTDFYPAQIK VRWFRNDQEE TAGVVSTPLI
RNGDWTFQIL VMLEMTPQRG DVYTCHVEHP SLQSPITVEW RLLH*
speed 1.25 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999978702 (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 ENST00000374943
Genbank transcript ID NM_001243961
UniProt peptide P01920
alteration type single base exchange
alteration region CDS
DNA changes c.470G>C
cDNA.547G>C
g.6226G>C
AA changes G157A Score: 60 explain score(s)
position(s) of altered AA
if AA alteration in CDS
157
frameshift no
known variant Reference ID: rs1063322
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC18865-496313902
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
PhyloPPhastCons
(flanking)0.170.003
-0.060.001
(flanking)-0.5190.002
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased6223wt: 0.61 / mu: 0.69wt: CTCGGTGACAGATTTCTATCCAGGCCAGATCAAAGTCCGGT
mu: CTCGGTGACAGATTTCTATCCAGCCCAGATCAAAGTCCGGT
 atcc|AGGC
Donor increased6224wt: 0.75 / mu: 0.88wt: TATCCAGGCCAGATC
mu: TATCCAGCCCAGATC
 TCCA|ggcc
Donor gained62290.40mu: AGCCCAGATCAAAGT CCCA|gatc
distance from splice site 91
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      157LLVCSVTDFYPGQIKVRWFRNDQE
mutated  not conserved    157LLVCSVTDFYPAQIKVRWFRNDQ
Ptroglodytes  all identical  ENSPTRG00000018018  157LLVCSVTDFYPGQIKVRWFRNDQ
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000073421  152TLVCSVTDFYPAKIKVRWFRNGQ
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000079105  142VLLCSAYEFYPKKIKMSWLRDGK
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
33230TOPO_DOMExtracellular (Potential).lost
127220REGIONBeta-2.lost
129233DOMAINIg-like C1-type.lost
147157STRANDlost
160165STRANDmight get lost (downstream of altered splice site)
168170STRANDmight get lost (downstream of altered splice site)
172176STRANDmight get lost (downstream of altered splice site)
173173CONFLICTG -> A (in Ref. 24; X76553/X76554).might get lost (downstream of altered splice site)
183185STRANDmight get lost (downstream of altered splice site)
187193STRANDmight get lost (downstream of altered splice site)
203208STRANDmight get lost (downstream of altered splice site)
205205DISULFIDmight get lost (downstream of altered splice site)
214214CONFLICTN -> T (in Ref. 8; AAA59770).might get lost (downstream of altered splice site)
216220STRANDmight get lost (downstream of altered splice site)
221230REGIONConnecting peptide.might get lost (downstream of altered splice site)
231251TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
252261TOPO_DOMCytoplasmic (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 470
cDNA position
(for ins/del: last normal base / first normal base)
547
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 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 FQFKGMCYFT NGTERVRLVT
RYIYNREEYA RFDSDVGVYR AVTPQGRPDA EYWNSQKEVL EGTRAELDTV CRHNYEVAFR
GILQRRVEPT VTISPSRTEA LNHHNLLVCS VTDFYPAQIK VRWFRNDQEE TAGVVSTPLI
RNGDWTFQIL VMLEMTPQRG DVYTCHVEHP SLQSPITVEW RAQSESAQSK MLSGVGGFVL
GLIFLGLGLI IRQRSQKGPQ GPPPAGLLH*
speed 1.12 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999978702 (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 ENST00000434651
Genbank transcript ID NM_002123
UniProt peptide P01920
alteration type single base exchange
alteration region CDS
DNA changes c.470G>C
cDNA.557G>C
g.6226G>C
AA changes G157A Score: 60 explain score(s)
position(s) of altered AA
if AA alteration in CDS
157
frameshift no
known variant Reference ID: rs1063322
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC18865-496313902
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
PhyloPPhastCons
(flanking)0.170.003
-0.060.001
(flanking)-0.5190.002
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased6223wt: 0.61 / mu: 0.69wt: CTCGGTGACAGATTTCTATCCAGGCCAGATCAAAGTCCGGT
mu: CTCGGTGACAGATTTCTATCCAGCCCAGATCAAAGTCCGGT
 atcc|AGGC
Donor increased6224wt: 0.75 / mu: 0.88wt: TATCCAGGCCAGATC
mu: TATCCAGCCCAGATC
 TCCA|ggcc
Donor gained62290.40mu: AGCCCAGATCAAAGT CCCA|gatc
distance from splice site 91
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      157LLVCSVTDFYPGQIKVRWFRNDQE
mutated  not conserved    157LLVCSVTDFYPAQIKVRWFRNDQ
Ptroglodytes  all identical  ENSPTRG00000018018  157LLVCSVTDFYPGQIKVRWFRNDQ
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000073421  152TLVCSVTDFYPAKIKVRWFRNGQ
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000079105  142VLLCSAYEFYPKKIKMSWLRDGK
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
33230TOPO_DOMExtracellular (Potential).lost
127220REGIONBeta-2.lost
129233DOMAINIg-like C1-type.lost
147157STRANDlost
160165STRANDmight get lost (downstream of altered splice site)
168170STRANDmight get lost (downstream of altered splice site)
172176STRANDmight get lost (downstream of altered splice site)
173173CONFLICTG -> A (in Ref. 24; X76553/X76554).might get lost (downstream of altered splice site)
183185STRANDmight get lost (downstream of altered splice site)
187193STRANDmight get lost (downstream of altered splice site)
203208STRANDmight get lost (downstream of altered splice site)
205205DISULFIDmight get lost (downstream of altered splice site)
214214CONFLICTN -> T (in Ref. 8; AAA59770).might get lost (downstream of altered splice site)
216220STRANDmight get lost (downstream of altered splice site)
221230REGIONConnecting peptide.might get lost (downstream of altered splice site)
231251TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
252261TOPO_DOMCytoplasmic (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 470
cDNA position
(for ins/del: last normal base / first normal base)
557
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 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
RYIYNREEYA RFDSDVGVYR AVTPQGRPDA EYWNSQKEVL EGTRAELDTV CRHNYEVAFR
GILQRRVEPT VTISPSRTEA LNHHNLLVCS VTDFYPAQIK VRWFRNDQEE TAGVVSTPLI
RNGDWTFQIL VMLEMTPQRG DVYTCHVEHP SLQSPITVEW RAQSESAQSK MLSGVGGFVL
GLIFLGLGLI IRQRSQKGLL H*
speed 1.86 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
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Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999978702 (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 ENST00000399084
Genbank transcript ID N/A
UniProt peptide P01920
alteration type single base exchange
alteration region CDS
DNA changes c.470G>C
cDNA.649G>C
g.6226G>C
AA changes G157A Score: 60 explain score(s)
position(s) of altered AA
if AA alteration in CDS
157
frameshift no
known variant Reference ID: rs1063322
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC18865-496313902
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
PhyloPPhastCons
(flanking)0.170.003
-0.060.001
(flanking)-0.5190.002
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased6223wt: 0.61 / mu: 0.69wt: CTCGGTGACAGATTTCTATCCAGGCCAGATCAAAGTCCGGT
mu: CTCGGTGACAGATTTCTATCCAGCCCAGATCAAAGTCCGGT
 atcc|AGGC
Donor increased6224wt: 0.75 / mu: 0.88wt: TATCCAGGCCAGATC
mu: TATCCAGCCCAGATC
 TCCA|ggcc
Donor gained62290.40mu: AGCCCAGATCAAAGT CCCA|gatc
distance from splice site 91
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      157LLVCSVTDFYPGQIKVRWFRNDQE
mutated  not conserved    157LLVCSVTDFYPAQIKVRWFRNDQ
Ptroglodytes  all identical  ENSPTRG00000018018  157LLVCSVTDFYPGQIKVRWFRNDQ
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000073421  152TLVCSVTDFYPAKIKVRWFRNGQ
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000079105  142VLLCSAYEFYPKKIKMSWLRDGK
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
33230TOPO_DOMExtracellular (Potential).lost
127220REGIONBeta-2.lost
129233DOMAINIg-like C1-type.lost
147157STRANDlost
160165STRANDmight get lost (downstream of altered splice site)
168170STRANDmight get lost (downstream of altered splice site)
172176STRANDmight get lost (downstream of altered splice site)
173173CONFLICTG -> A (in Ref. 24; X76553/X76554).might get lost (downstream of altered splice site)
183185STRANDmight get lost (downstream of altered splice site)
187193STRANDmight get lost (downstream of altered splice site)
203208STRANDmight get lost (downstream of altered splice site)
205205DISULFIDmight get lost (downstream of altered splice site)
214214CONFLICTN -> T (in Ref. 8; AAA59770).might get lost (downstream of altered splice site)
216220STRANDmight get lost (downstream of altered splice site)
221230REGIONConnecting peptide.might get lost (downstream of altered splice site)
231251TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
252261TOPO_DOMCytoplasmic (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 470
cDNA position
(for ins/del: last normal base / first normal base)
649
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 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
RYIYNREEYA RFDSDVGVYR AVTPQGRPDA EYWNSQKEVL EGTRAELDTV CRHNYEVAFR
GILQRRVEPT VTISPSRTEA LNHHNLLVCS VTDFYPAQIK VRWFRNDQEE TAGVVSTPLI
RNGDWTFQIL VMLEMTPQRG DVYTCHVEHP SLQSPITVEW RAQSESAQSK MLSGVGGFVL
GLIFLGLGLI IRQRSQKGLL H*
speed 1.34 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
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Problems