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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000419277
Querying Taster for transcript #2: ENST00000428995
MT speed 0 s - this script 3.393935 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
HLA-DPA1polymorphism_automatic0simple_aaeaffectedQ81Rsingle base exchangers1042178show file
HLA-DPA1polymorphism_automatic0simple_aaeaffectedQ81Rsingle base exchangers1042178show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 1 (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) chr6:33037522T>CN/A show variant in all transcripts   IGV
HGNC symbol HLA-DPA1
Ensembl transcript ID ENST00000419277
Genbank transcript ID NM_001242524
UniProt peptide P20036
alteration type single base exchange
alteration region CDS
DNA changes c.242A>G
cDNA.372A>G
g.11031A>G
AA changes Q81R Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 81
frameshift no
known variant Reference ID: rs1042178
databasehomozygous (C/C)heterozygousallele carriers
1000G56810601628
ExAC50651851623581
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.5670
-1.3880
(flanking)-0.1650.002
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased11041wt: 0.61 / mu: 0.70wt: GAGTTTGGCCAAGCCTTTTCCTTTGAGGCTCAGGGCGGGCT
mu: GAGTTTGGCCGAGCCTTTTCCTTTGAGGCTCAGGGCGGGCT		 ttcc|TTTG
distance from splice site 105
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      81KETVWHLEEFGQAFSFEAQGGLAN
mutated  all conserved    81KETVWHLEEFGRAFSFEAQGGLA
Ptroglodytes  all conserved  ENSPTRG00000018029  81KETVWHLEEFGRAFSFEAQGGLA
Mmulatta  all conserved  ENSMMUG00000019371  81KETVWHLEEFGRAFSFEAQGGLA
Fcatus  not conserved  ENSFCAG00000012247  47KETIWHLPEFIHAFNFDAWRGIA
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000001832  65KEGVVIAPDFADPLSFPGGYETGVA
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no alignment  ENSXETG00000031520  n/a
protein features
start (aa)end (aa)featuredetails 
29115REGIONAlpha-1.lost
29222TOPO_DOMExtracellular (Potential).lost
87106HELIXmight get lost (downstream of altered splice site)
107110TURNmight get lost (downstream of altered splice site)
109109CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
116209REGIONAlpha-2.might get lost (downstream of altered splice site)
118210DOMAINIg-like C1-type.might get lost (downstream of altered splice site)
119126STRANDmight get lost (downstream of altered splice site)
134145STRANDmight get lost (downstream of altered splice site)
138138DISULFIDBy similarity.might get lost (downstream of altered splice site)
149149CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
149154STRANDmight get lost (downstream of altered splice site)
163165STRANDmight get lost (downstream of altered splice site)
176184STRANDmight get lost (downstream of altered splice site)
192197STRANDmight get lost (downstream of altered splice site)
194194DISULFIDBy similarity.might get lost (downstream of altered splice site)
205209STRANDmight get lost (downstream of altered splice site)
210222REGIONConnecting peptide.might get lost (downstream of altered splice site)
223245TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
237237CONFLICTI -> F (in Ref. 7; CAA25143).might get lost (downstream of altered splice site)
246260TOPO_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 783 / 783
position (AA) of stopcodon in wt / mu AA sequence 261 / 261
position of stopcodon in wt / mu cDNA 913 / 913
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 131 / 131
chromosome 6
strand -1
last intron/exon boundary 926
theoretical NMD boundary in CDS 745
length of CDS 783
coding sequence (CDS) position 242
cDNA position
(for ins/del: last normal base / first normal base)		 372
gDNA position
(for ins/del: last normal base / first normal base)		 11031
chromosomal position
(for ins/del: last normal base / first normal base)		 33037522
original gDNA sequence snippet GCATCTGGAGGAGTTTGGCCAAGCCTTTTCCTTTGAGGCTC
altered gDNA sequence snippet GCATCTGGAGGAGTTTGGCCGAGCCTTTTCCTTTGAGGCTC
original cDNA sequence snippet GCATCTGGAGGAGTTTGGCCAAGCCTTTTCCTTTGAGGCTC
altered cDNA sequence snippet GCATCTGGAGGAGTTTGGCCGAGCCTTTTCCTTTGAGGCTC
wildtype AA sequence MRPEDRMFHI RAVILRALSL AFLLSLRGAG AIKADHVSTY AAFVQTHRPT GEFMFEFDED
EMFYVDLDKK ETVWHLEEFG QAFSFEAQGG LANIAILNNN LNTLIQRSNH TQATNDPPEV
TVFPKEPVEL GQPNTLICHI DKFFPPVLNV TWLCNGELVT EGVAESLFLP RTDYSFHKFH
YLTFVPSAED FYDCRVEHWG LDQPLLKHWE AQEPIQMPET TETVLCALGL VLGLVGIIVG
TVLIIKSLRS GHDPRAQGTL *
mutated AA sequence MRPEDRMFHI RAVILRALSL AFLLSLRGAG AIKADHVSTY AAFVQTHRPT GEFMFEFDED
EMFYVDLDKK ETVWHLEEFG RAFSFEAQGG LANIAILNNN LNTLIQRSNH TQATNDPPEV
TVFPKEPVEL GQPNTLICHI DKFFPPVLNV TWLCNGELVT EGVAESLFLP RTDYSFHKFH
YLTFVPSAED FYDCRVEHWG LDQPLLKHWE AQEPIQMPET TETVLCALGL VLGLVGIIVG
TVLIIKSLRS GHDPRAQGTL *
speed 0.76 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: 1 (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) chr6:33037522T>CN/A show variant in all transcripts   IGV
HGNC symbol HLA-DPA1
Ensembl transcript ID ENST00000428995
Genbank transcript ID N/A
UniProt peptide P20036
alteration type single base exchange
alteration region CDS
DNA changes c.242A>G
cDNA.273A>G
g.11031A>G
AA changes Q81R Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 81
frameshift no
known variant Reference ID: rs1042178
databasehomozygous (C/C)heterozygousallele carriers
1000G56810601628
ExAC50651851623581
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.5670
-1.3880
(flanking)-0.1650.002
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased11041wt: 0.61 / mu: 0.70wt: GAGTTTGGCCAAGCCTTTTCCTTTGAGGCTCAGGGCGGGCT
mu: GAGTTTGGCCGAGCCTTTTCCTTTGAGGCTCAGGGCGGGCT		 ttcc|TTTG
distance from splice site 105
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      81KETVWHLEEFGQAFSFEAQGGLAN
mutated  all conserved    81KETVWHLEEFGRAFSFEAQGGLA
Ptroglodytes  all conserved  ENSPTRG00000018029  81KETVWHLEEFGRAFSFEAQGGLA
Mmulatta  all conserved  ENSMMUG00000019371  81KETVWHLEEFGRAFSFEAQGGLA
Fcatus  not conserved  ENSFCAG00000012247  47KETIWHLPEFIHAFNFDAWRGIA
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000001832  65KEGVVIAPDFADPLSFPGGYETGVA
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no alignment  ENSXETG00000031520  n/a
protein features
start (aa)end (aa)featuredetails 
29115REGIONAlpha-1.lost
29222TOPO_DOMExtracellular (Potential).lost
87106HELIXmight get lost (downstream of altered splice site)
107110TURNmight get lost (downstream of altered splice site)
109109CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
116209REGIONAlpha-2.might get lost (downstream of altered splice site)
118210DOMAINIg-like C1-type.might get lost (downstream of altered splice site)
119126STRANDmight get lost (downstream of altered splice site)
134145STRANDmight get lost (downstream of altered splice site)
138138DISULFIDBy similarity.might get lost (downstream of altered splice site)
149149CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
149154STRANDmight get lost (downstream of altered splice site)
163165STRANDmight get lost (downstream of altered splice site)
176184STRANDmight get lost (downstream of altered splice site)
192197STRANDmight get lost (downstream of altered splice site)
194194DISULFIDBy similarity.might get lost (downstream of altered splice site)
205209STRANDmight get lost (downstream of altered splice site)
210222REGIONConnecting peptide.might get lost (downstream of altered splice site)
223245TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
237237CONFLICTI -> F (in Ref. 7; CAA25143).might get lost (downstream of altered splice site)
246260TOPO_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 783 / 783
position (AA) of stopcodon in wt / mu AA sequence 261 / 261
position of stopcodon in wt / mu cDNA 814 / 814
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 32 / 32
chromosome 6
strand -1
last intron/exon boundary 827
theoretical NMD boundary in CDS 745
length of CDS 783
coding sequence (CDS) position 242
cDNA position
(for ins/del: last normal base / first normal base)		 273
gDNA position
(for ins/del: last normal base / first normal base)		 11031
chromosomal position
(for ins/del: last normal base / first normal base)		 33037522
original gDNA sequence snippet GCATCTGGAGGAGTTTGGCCAAGCCTTTTCCTTTGAGGCTC
altered gDNA sequence snippet GCATCTGGAGGAGTTTGGCCGAGCCTTTTCCTTTGAGGCTC
original cDNA sequence snippet GCATCTGGAGGAGTTTGGCCAAGCCTTTTCCTTTGAGGCTC
altered cDNA sequence snippet GCATCTGGAGGAGTTTGGCCGAGCCTTTTCCTTTGAGGCTC
wildtype AA sequence MRPEDRMFHI RAVILRALSL AFLLSLRGAG AIKADHVSTY AAFVQTHRPT GEFMFEFDED
EMFYVDLDKK ETVWHLEEFG QAFSFEAQGG LANIAILNNN LNTLIQRSNH TQATNDPPEV
TVFPKEPVEL GQPNTLICHI DKFFPPVLNV TWLCNGELVT EGVAESLFLP RTDYSFHKFH
YLTFVPSAED FYDCRVEHWG LDQPLLKHWE AQEPIQMPET TETVLCALGL VLGLVGIIVG
TVLIIKSLRS GHDPRAQGTL *
mutated AA sequence MRPEDRMFHI RAVILRALSL AFLLSLRGAG AIKADHVSTY AAFVQTHRPT GEFMFEFDED
EMFYVDLDKK ETVWHLEEFG RAFSFEAQGG LANIAILNNN LNTLIQRSNH TQATNDPPEV
TVFPKEPVEL GQPNTLICHI DKFFPPVLNV TWLCNGELVT EGVAESLFLP RTDYSFHKFH
YLTFVPSAED FYDCRVEHWG LDQPLLKHWE AQEPIQMPET TETVLCALGL VLGLVGIIVG
TVLIIKSLRS GHDPRAQGTL *
speed 0.64 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

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