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: ENST00000418931
Querying Taster for transcript #2: ENST00000411942
Querying Taster for transcript #3: ENST00000535465
MT speed 4.65 s - this script 8.183139 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
HLA-DPB1polymorphism_automatic1.46405110257319e-12simple_aaeM105Vsingle base exchangers1042151show file
HLA-DPB1polymorphism_automatic1.46405110257319e-12simple_aaeM105Vsingle base exchangers1042151show file
HLA-DPB1polymorphism_automatic1.46405110257319e-12simple_aaeM105Vsingle base exchangers1042151show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999998536 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM131322)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:33048661A>GN/A show variant in all transcripts   IGV
HGNC symbol HLA-DPB1
Ensembl transcript ID ENST00000418931
Genbank transcript ID NM_002121
UniProt peptide P04440
alteration type single base exchange
alteration region CDS
DNA changes c.313A>G
cDNA.429A>G
g.4959A>G
AA changes M105V Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS
105
frameshift no
known variant Reference ID: rs1042151
databasehomozygous (G/G)heterozygousallele carriers
1000G1928801072
ExAC21551808420239

known disease mutation at this position, please check HGMD for details (HGMD ID CM131322)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.1610
-1.5710
(flanking)-0.1870.001
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 52
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      105ILEEKRAVPDRMCRHNYELGGPMT
mutated  all conserved    105ILEEKRAVPDRVCRHNYELGGPM
Ptroglodytes  all identical  ENSPTRG00000018030  105LLEEKRAVPDRMCRHNYELNEAV
Mmulatta  all identical  ENSMMUG00000019367  82LLEEMRAVVDTMCRYNYELDEAV
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000079105  95YLHQLKAQVDTFCRHNAQIWDSA
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
30121REGIONBeta-1.lost
30225TOPO_DOMExtracellular (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 777 / 777
position (AA) of stopcodon in wt / mu AA sequence 259 / 259
position of stopcodon in wt / mu cDNA 893 / 893
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 117 / 117
chromosome 6
strand 1
last intron/exon boundary 898
theoretical NMD boundary in CDS 731
length of CDS 777
coding sequence (CDS) position 313
cDNA position
(for ins/del: last normal base / first normal base)
429
gDNA position
(for ins/del: last normal base / first normal base)
4959
chromosomal position
(for ins/del: last normal base / first normal base)
33048661
original gDNA sequence snippet AGCGGGCAGTGCCGGACAGGATGTGCAGACACAACTACGAG
altered gDNA sequence snippet AGCGGGCAGTGCCGGACAGGGTGTGCAGACACAACTACGAG
original cDNA sequence snippet AGCGGGCAGTGCCGGACAGGATGTGCAGACACAACTACGAG
altered cDNA sequence snippet AGCGGGCAGTGCCGGACAGGGTGTGCAGACACAACTACGAG
wildtype AA sequence MMVLQVSAAP RTVALTALLM VLLTSVVQGR ATPENYLFQG RQECYAFNGT QRFLERYIYN
REEFARFDSD VGEFRAVTEL GRPAAEYWNS QKDILEEKRA VPDRMCRHNY ELGGPMTLQR
RVQPRVNVSP SKKGPLQHHN LLVCHVTDFY PGSIQVRWFL NGQEETAGVV STNLIRNGDW
TFQILVMLEM TPQQGDVYTC QVEHTSLDSP VTVEWKAQSD SARSKTLTGA GGFVLGLIIC
GVGIFMHRRS KKVQRGSA*
mutated AA sequence MMVLQVSAAP RTVALTALLM VLLTSVVQGR ATPENYLFQG RQECYAFNGT QRFLERYIYN
REEFARFDSD VGEFRAVTEL GRPAAEYWNS QKDILEEKRA VPDRVCRHNY ELGGPMTLQR
RVQPRVNVSP SKKGPLQHHN LLVCHVTDFY PGSIQVRWFL NGQEETAGVV STNLIRNGDW
TFQILVMLEM TPQQGDVYTC QVEHTSLDSP VTVEWKAQSD SARSKTLTGA GGFVLGLIIC
GVGIFMHRRS KKVQRGSA*
speed 1.65 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: 0.999999999998536 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM131322)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:33048661A>GN/A show variant in all transcripts   IGV
HGNC symbol HLA-DPB1
Ensembl transcript ID ENST00000411942
Genbank transcript ID N/A
UniProt peptide P04440
alteration type single base exchange
alteration region CDS
DNA changes c.313A>G
cDNA.383A>G
g.4959A>G
AA changes M105V Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS
105
frameshift no
known variant Reference ID: rs1042151
databasehomozygous (G/G)heterozygousallele carriers
1000G1928801072
ExAC21551808420239

known disease mutation at this position, please check HGMD for details (HGMD ID CM131322)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.1610
-1.5710
(flanking)-0.1870.001
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 52
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      105ILEEKRAVPDRMCRHNYELGGPMT
mutated  all conserved    105ILEEKRAVPDRVCRHNYELGGPM
Ptroglodytes  all identical  ENSPTRG00000018030  105LLEEKRAVPDRMCRHNYELNEAV
Mmulatta  all identical  ENSMMUG00000019367  82LLEEMRAVVDTMCRYNYELDEAV
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000079105  95YLHQLKAQVDTFCRHNAQIWDSA
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
30121REGIONBeta-1.lost
30225TOPO_DOMExtracellular (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 687 / 687
position (AA) of stopcodon in wt / mu AA sequence 229 / 229
position of stopcodon in wt / mu cDNA 757 / 757
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 71 / 71
chromosome 6
strand 1
last intron/exon boundary 762
theoretical NMD boundary in CDS 641
length of CDS 687
coding sequence (CDS) position 313
cDNA position
(for ins/del: last normal base / first normal base)
383
gDNA position
(for ins/del: last normal base / first normal base)
4959
chromosomal position
(for ins/del: last normal base / first normal base)
33048661
original gDNA sequence snippet AGCGGGCAGTGCCGGACAGGATGTGCAGACACAACTACGAG
altered gDNA sequence snippet AGCGGGCAGTGCCGGACAGGGTGTGCAGACACAACTACGAG
original cDNA sequence snippet AGCGGGCAGTGCCGGACAGGATGTGCAGACACAACTACGAG
altered cDNA sequence snippet AGCGGGCAGTGCCGGACAGGGTGTGCAGACACAACTACGAG
wildtype AA sequence MMVLQVSAAP RTVALTALLM VLLTSVVQGR ATPENYLFQG RQECYAFNGT QRFLERYIYN
REEFARFDSD VGEFRAVTEL GRPAAEYWNS QKDILEEKRA VPDRMCRHNY ELGGPMTLQR
RGSIQVRWFL NGQEETAGVV STNLIRNGDW TFQILVMLEM TPQQGDVYTC QVEHTSLDSP
VTVEWKAQSD SARSKTLTGA GGFVLGLIIC GVGIFMHRRS KKVQRGSA*
mutated AA sequence MMVLQVSAAP RTVALTALLM VLLTSVVQGR ATPENYLFQG RQECYAFNGT QRFLERYIYN
REEFARFDSD VGEFRAVTEL GRPAAEYWNS QKDILEEKRA VPDRVCRHNY ELGGPMTLQR
RGSIQVRWFL NGQEETAGVV STNLIRNGDW TFQILVMLEM TPQQGDVYTC QVEHTSLDSP
VTVEWKAQSD SARSKTLTGA GGFVLGLIIC GVGIFMHRRS KKVQRGSA*
speed 1.64 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: 0.999999999998536 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM131322)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:33048661A>GN/A show variant in all transcripts   IGV
HGNC symbol HLA-DPB1
Ensembl transcript ID ENST00000535465
Genbank transcript ID N/A
UniProt peptide P04440
alteration type single base exchange
alteration region CDS
DNA changes c.313A>G
cDNA.389A>G
g.4959A>G
AA changes M105V Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS
105
frameshift no
known variant Reference ID: rs1042151
databasehomozygous (G/G)heterozygousallele carriers
1000G1928801072
ExAC21551808420239

known disease mutation at this position, please check HGMD for details (HGMD ID CM131322)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.1610
-1.5710
(flanking)-0.1870.001
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 213
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      105ILEEKRAVPDRMCRHNYELGGPMT
mutated  all conserved    105ILEEKRAVPDRVCRHNYELGGPM
Ptroglodytes  all identical  ENSPTRG00000018030  105LLEEKRAVPDRMCRHNYELNEAV
Mmulatta  all identical  ENSMMUG00000019367  82LLEEMRAVVDTMCRYNYELDEAV
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000079105  95YLHQLKAQVDTFCRHNAQI
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
30121REGIONBeta-1.lost
30225TOPO_DOMExtracellular (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 372 / 372
position (AA) of stopcodon in wt / mu AA sequence 124 / 124
position of stopcodon in wt / mu cDNA 448 / 448
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 77 / 77
chromosome 6
strand 1
last intron/exon boundary 802
theoretical NMD boundary in CDS 675
length of CDS 372
coding sequence (CDS) position 313
cDNA position
(for ins/del: last normal base / first normal base)
389
gDNA position
(for ins/del: last normal base / first normal base)
4959
chromosomal position
(for ins/del: last normal base / first normal base)
33048661
original gDNA sequence snippet AGCGGGCAGTGCCGGACAGGATGTGCAGACACAACTACGAG
altered gDNA sequence snippet AGCGGGCAGTGCCGGACAGGGTGTGCAGACACAACTACGAG
original cDNA sequence snippet AGCGGGCAGTGCCGGACAGGATGTGCAGACACAACTACGAG
altered cDNA sequence snippet AGCGGGCAGTGCCGGACAGGGTGTGCAGACACAACTACGAG
wildtype AA sequence MMVLQVSAAP RTVALTALLM VLLTSVVQGR ATPENYLFQG RQECYAFNGT QRFLERYIYN
REEFARFDSD VGEFRAVTEL GRPAAEYWNS QKDILEEKRA VPDRMCRHNY ELGGPMTLQR
RGE*
mutated AA sequence MMVLQVSAAP RTVALTALLM VLLTSVVQGR ATPENYLFQG RQECYAFNGT QRFLERYIYN
REEFARFDSD VGEFRAVTEL GRPAAEYWNS QKDILEEKRA VPDRVCRHNY ELGGPMTLQR
RGE*
speed 1.36 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

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