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 3.42 s - this script 8.353189 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
HLA-DPA1polymorphism_automatic8.67968513951212e-07simple_aaeT259Psingle base exchangers1126769show file
HLA-DPA1polymorphism_automatic8.67968513951212e-07simple_aaeT259Psingle base exchangers1126769show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999132031486 (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
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:33036435T>GN/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.775A>C
cDNA.905A>C
g.12118A>C
AA changes T259P Score: 38 explain score(s)
position(s) of altered AA
if AA alteration in CDS
259
frameshift no
known variant Reference ID: rs1126769
databasehomozygous (G/G)heterozygousallele carriers
1000G56910521621
ExAC50611845423515
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.5540.995
0.5850.99
(flanking)-0.1950.981
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 21
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      259LRSGHDPRAQGTL*
mutated  not conserved    259LRSGHDPRAQGPL
Ptroglodytes  not conserved  ENSPTRG00000018029  259LRSGRDPRAQGPL
Mmulatta  not conserved  ENSMMUG00000019371  259LRSGRDPRAQGPL
Fcatus  not conserved  ENSFCAG00000012247  212RRPRH-PWVQGPL
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no alignment  ENSDARG00000001832  n/a
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no alignment  ENSXETG00000031520  n/a
protein features
start (aa)end (aa)featuredetails 
246260TOPO_DOMCytoplasmic (Potential).lost
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 775
cDNA position
(for ins/del: last normal base / first normal base)
905
gDNA position
(for ins/del: last normal base / first normal base)
12118
chromosomal position
(for ins/del: last normal base / first normal base)
33036435
original gDNA sequence snippet ATGACCCCCGGGCCCAGGGGACCCTGTGAAATACTGTAAAG
altered gDNA sequence snippet ATGACCCCCGGGCCCAGGGGCCCCTGTGAAATACTGTAAAG
original cDNA sequence snippet ATGACCCCCGGGCCCAGGGGACCCTGTGAAATACTGTAAAG
altered cDNA sequence snippet ATGACCCCCGGGCCCAGGGGCCCCTGTGAAATACTGTAAAG
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 QAFSFEAQGG LANIAILNNN LNTLIQRSNH TQATNDPPEV
TVFPKEPVEL GQPNTLICHI DKFFPPVLNV TWLCNGELVT EGVAESLFLP RTDYSFHKFH
YLTFVPSAED FYDCRVEHWG LDQPLLKHWE AQEPIQMPET TETVLCALGL VLGLVGIIVG
TVLIIKSLRS GHDPRAQGPL *
speed 1.94 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: 0.999999132031486 (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
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:33036435T>GN/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.775A>C
cDNA.806A>C
g.12118A>C
AA changes T259P Score: 38 explain score(s)
position(s) of altered AA
if AA alteration in CDS
259
frameshift no
known variant Reference ID: rs1126769
databasehomozygous (G/G)heterozygousallele carriers
1000G56910521621
ExAC50611845423515
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.5540.995
0.5850.99
(flanking)-0.1950.981
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 21
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      259LRSGHDPRAQGTL*
mutated  not conserved    259LRSGHDPRAQGPL
Ptroglodytes  not conserved  ENSPTRG00000018029  259LRSGRDPRAQGPL
Mmulatta  not conserved  ENSMMUG00000019371  259LRSGRDPRAQGPL
Fcatus  not conserved  ENSFCAG00000012247  212RRPRH-PWVQGPL
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no alignment  ENSDARG00000001832  n/a
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no alignment  ENSXETG00000031520  n/a
protein features
start (aa)end (aa)featuredetails 
246260TOPO_DOMCytoplasmic (Potential).lost
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 775
cDNA position
(for ins/del: last normal base / first normal base)
806
gDNA position
(for ins/del: last normal base / first normal base)
12118
chromosomal position
(for ins/del: last normal base / first normal base)
33036435
original gDNA sequence snippet ATGACCCCCGGGCCCAGGGGACCCTGTGAAATACTGTAAAG
altered gDNA sequence snippet ATGACCCCCGGGCCCAGGGGCCCCTGTGAAATACTGTAAAG
original cDNA sequence snippet ATGACCCCCGGGCCCAGGGGACCCTGTGAAATACTGTAAAG
altered cDNA sequence snippet ATGACCCCCGGGCCCAGGGGCCCCTGTGAAATACTGTAAAG
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 QAFSFEAQGG LANIAILNNN LNTLIQRSNH TQATNDPPEV
TVFPKEPVEL GQPNTLICHI DKFFPPVLNV TWLCNGELVT EGVAESLFLP RTDYSFHKFH
YLTFVPSAED FYDCRVEHWG LDQPLLKHWE AQEPIQMPET TETVLCALGL VLGLVGIIVG
TVLIIKSLRS GHDPRAQGPL *
speed 1.48 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