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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000437316
Querying Taster for transcript #2: ENST00000435145
Querying Taster for transcript #3: ENST00000411527
MT speed 3.89 s - this script 6.020408 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
HLA-DQB2polymorphism_automatic1.0639000791457e-10simple_aaeaffectedI230Vsingle base exchangers9276570show file
HLA-DQB2polymorphism_automatic1.0639000791457e-10simple_aaeaffectedI230Vsingle base exchangers9276570show file
HLA-DQB2polymorphism_automatic2.56030363490201e-05without_aaeaffectedsingle base exchangers9276570show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999999989361 (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) chr6:32725619T>CN/A show variant in all transcripts   IGV
HGNC symbol HLA-DQB2
Ensembl transcript ID ENST00000437316
Genbank transcript ID N/A
UniProt peptide P05538
alteration type single base exchange
alteration region CDS
DNA changes c.688A>G
cDNA.752A>G
g.5693A>G
AA changes I230V Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS
230
frameshift no
known variant Reference ID: rs9276570
databasehomozygous (C/C)heterozygousallele carriers
1000G33319292262
ExAC34852579729282
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.1760.118
-1.0120.001
(flanking)-5.0320
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased5687wt: 0.29 / mu: 0.98wt: TGCTGAGTGGCATTG
mu: TGCTGAGTGGCGTTG
 CTGA|gtgg
distance from splice site 42
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      230SESAQSKMLSGIGGFVLGLIFLGL
mutated  all conserved    230SESAQSKMLSGVGGFVLGLIFL
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000073421  231SESAWSKMLSGIGGCVLGVI
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000079105  220SESDRNKFAIGASGLVLGIIIAI
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
33229TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
127229REGIONBeta-2.might get lost (downstream of altered splice site)
230250TRANSMEMHelical; (Potential).lost
251268TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
266268CONFLICTLLH -> HLL (in Ref. 2; CAA60790).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 795 / 795
position (AA) of stopcodon in wt / mu AA sequence 265 / 265
position of stopcodon in wt / mu cDNA 859 / 859
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 65 / 65
chromosome 6
strand -1
last intron/exon boundary 846
theoretical NMD boundary in CDS 731
length of CDS 795
coding sequence (CDS) position 688
cDNA position
(for ins/del: last normal base / first normal base)
752
gDNA position
(for ins/del: last normal base / first normal base)
5693
chromosomal position
(for ins/del: last normal base / first normal base)
32725619
original gDNA sequence snippet AGAGCAAGATGCTGAGTGGCATTGGAGGCTTCGTGCTGGGG
altered gDNA sequence snippet AGAGCAAGATGCTGAGTGGCGTTGGAGGCTTCGTGCTGGGG
original cDNA sequence snippet AGAGCAAGATGCTGAGTGGCATTGGAGGCTTCGTGCTGGGG
altered cDNA sequence snippet AGAGCAAGATGCTGAGTGGCGTTGGAGGCTTCGTGCTGGGG
wildtype AA sequence MALQIPGGFW AAAVTVMLVM LSTPVAEARD FPKDFLVQFK GMCYFTNGTE RVRGVARYIY
NREEYGRFDS DVGEFQAVTE LGRSIEDWNN YKDFLEQERA AVDKVCRHNY EAELRTTLQR
QVEPTVTISP SRTEALNHHN LLVCSVTDFY PAQIKVRWFR NDQEETAGVV STSLIRNGDW
TFQILVMLEI TPQRGDIYTC QVEHPSLQSP ITVEWRAQSE SAQSKMLSGI GGFVLGLIFL
GLGLIIRHRG QKGPRGPPPA GLLH*
mutated AA sequence MALQIPGGFW AAAVTVMLVM LSTPVAEARD FPKDFLVQFK GMCYFTNGTE RVRGVARYIY
NREEYGRFDS DVGEFQAVTE LGRSIEDWNN YKDFLEQERA AVDKVCRHNY EAELRTTLQR
QVEPTVTISP SRTEALNHHN LLVCSVTDFY PAQIKVRWFR NDQEETAGVV STSLIRNGDW
TFQILVMLEI TPQRGDIYTC QVEHPSLQSP ITVEWRAQSE SAQSKMLSGV GGFVLGLIFL
GLGLIIRHRG QKGPRGPPPA GLLH*
speed 1.47 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: 0.99999999989361 (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) chr6:32725619T>CN/A show variant in all transcripts   IGV
HGNC symbol HLA-DQB2
Ensembl transcript ID ENST00000435145
Genbank transcript ID N/A
UniProt peptide P05538
alteration type single base exchange
alteration region CDS
DNA changes c.688A>G
cDNA.750A>G
g.5693A>G
AA changes I230V Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS
230
frameshift no
known variant Reference ID: rs9276570
databasehomozygous (C/C)heterozygousallele carriers
1000G33319292262
ExAC34852579729282
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.1760.118
-1.0120.001
(flanking)-5.0320
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased5687wt: 0.29 / mu: 0.98wt: TGCTGAGTGGCATTG
mu: TGCTGAGTGGCGTTG
 CTGA|gtgg
distance from splice site 42
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      230SESAQSKMLSGIGGFVLGLIFLGL
mutated  all conserved    230SESAQSKMLSGVGGFVLGLIFL
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000073421  231SESAWSKMLSGIGGCVLGVI
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000079105  220SESDRNKFAIGASGLVLGIIIAI
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
33229TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
127229REGIONBeta-2.might get lost (downstream of altered splice site)
230250TRANSMEMHelical; (Potential).lost
251268TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
266268CONFLICTLLH -> HLL (in Ref. 2; CAA60790).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 828 / 828
position (AA) of stopcodon in wt / mu AA sequence 276 / 276
position of stopcodon in wt / mu cDNA 890 / 890
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 63 / 63
chromosome 6
strand -1
last intron/exon boundary 820
theoretical NMD boundary in CDS 707
length of CDS 828
coding sequence (CDS) position 688
cDNA position
(for ins/del: last normal base / first normal base)
750
gDNA position
(for ins/del: last normal base / first normal base)
5693
chromosomal position
(for ins/del: last normal base / first normal base)
32725619
original gDNA sequence snippet AGAGCAAGATGCTGAGTGGCATTGGAGGCTTCGTGCTGGGG
altered gDNA sequence snippet AGAGCAAGATGCTGAGTGGCGTTGGAGGCTTCGTGCTGGGG
original cDNA sequence snippet AGAGCAAGATGCTGAGTGGCATTGGAGGCTTCGTGCTGGGG
altered cDNA sequence snippet AGAGCAAGATGCTGAGTGGCGTTGGAGGCTTCGTGCTGGGG
wildtype AA sequence MALQIPGGFW AAAVTVMLVM LSTPVAEARD FPKDFLVQFK GMCYFTNGTE RVRGVARYIY
NREEYGRFDS DVGEFQAVTE LGRSIEDWNN YKDFLEQERA AVDKVCRHNY EAELRTTLQR
QVEPTVTISP SRTEALNHHN LLVCSVTDFY PAQIKVRWFR NDQEETAGVV STSLIRNGDW
TFQILVMLEI TPQRGDIYTC QVEHPSLQSP ITVEWRAQSE SAQSKMLSGI GGFVLGLIFL
GLGLIIRHRG QKGPRGPPPA GNISAMIQSG ERAQA*
mutated AA sequence MALQIPGGFW AAAVTVMLVM LSTPVAEARD FPKDFLVQFK GMCYFTNGTE RVRGVARYIY
NREEYGRFDS DVGEFQAVTE LGRSIEDWNN YKDFLEQERA AVDKVCRHNY EAELRTTLQR
QVEPTVTISP SRTEALNHHN LLVCSVTDFY PAQIKVRWFR NDQEETAGVV STSLIRNGDW
TFQILVMLEI TPQRGDIYTC QVEHPSLQSP ITVEWRAQSE SAQSKMLSGV GGFVLGLIFL
GLGLIIRHRG QKGPRGPPPA GNISAMIQSG ERAQA*
speed 1.50 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: without_aae, prob: 0.999974396963651 (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) chr6:32725619T>CN/A show variant in all transcripts   IGV
HGNC symbol HLA-DQB2
Ensembl transcript ID ENST00000411527
Genbank transcript ID NM_001198858
UniProt peptide P05538
alteration type single base exchange
alteration region intron
DNA changes g.5693A>G
AA changes N/A
position(s) of altered AA
if AA alteration in CDS
N/A
frameshift N/A
known variant Reference ID: rs9276570
databasehomozygous (C/C)heterozygousallele carriers
1000G33319292262
ExAC34852579729282
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.1760.118
-1.0120.001
(flanking)-5.0320
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased5687wt: 0.29 / mu: 0.98wt: TGCTGAGTGGCATTG
mu: TGCTGAGTGGCGTTG
 CTGA|gtgg
distance from splice site 538
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
N/A
protein features
start (aa)end (aa)featuredetails 
33229TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
127229REGIONBeta-2.might get lost (downstream of altered splice site)
128216DOMAINIg-like C1-type.might get lost (downstream of altered splice site)
230250TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
251268TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
266268CONFLICTLLH -> HLL (in Ref. 2; CAA60790).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 21 / 21
chromosome 6
strand -1
last intron/exon boundary 691
theoretical NMD boundary in CDS 620
length of CDS 684
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)
5693
chromosomal position
(for ins/del: last normal base / first normal base)
32725619
original gDNA sequence snippet AGAGCAAGATGCTGAGTGGCATTGGAGGCTTCGTGCTGGGG
altered gDNA sequence snippet AGAGCAAGATGCTGAGTGGCGTTGGAGGCTTCGTGCTGGGG
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MALQIPGGFW AAAVTVMLVM LSTPVAEARD FPKDFLVQFK GMCYFTNGTE RVRGVARYIY
NREEYGRFDS DVGEFQAVTE LGRSIEDWNN YKDFLEQERA AVDKVCRHNY EAELRTTLQR
QVEPTVTISP SRTEALNHHN LLVCSVTDFY PAQIKVRWFR NDQEETAGVV STSLIRNGDW
TFQILVMLEI TPQRGDIYTC QVEHPSLQSP ITVEWRPRGP PPAGLLH*
mutated AA sequence N/A
speed 0.92 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

Problems