Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000544021
Querying Taster for transcript #2: ENST00000266556
MT speed 0 s - this script 3.918143 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
TAPBPLpolymorphism_automatic7.77224300474444e-08simple_aaeaffectedA42Vsingle base exchangers2041385show file
TAPBPLpolymorphism_automatic0.045918613137283without_aaeaffectedsingle base exchangers2041385show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.99999992227757 (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) chr12:6562293C>TN/A show variant in all transcripts   IGV
HGNC symbol TAPBPL
Ensembl transcript ID ENST00000266556
Genbank transcript ID NM_018009
UniProt peptide Q9BX59
alteration type single base exchange
alteration region CDS
DNA changes c.125C>T
cDNA.290C>T
g.1438C>T
AA changes A42V Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 42
frameshift no
known variant Reference ID: rs2041385
databasehomozygous (T/T)heterozygousallele carriers
1000G1398621001
ExAC27001487017570
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K4ac, Histone, Histone 3 Lysine 4 Acetylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9310.702
-0.7770.005
(flanking)-1.4330
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased1436wt: 0.42 / mu: 0.75wt: GTGGTCCTAGACTGCTTCCTGGCGAAGGACGGTGCGCACCG
mu: GTGGTCCTAGACTGCTTCCTGGTGAAGGACGGTGCGCACCG		 cctg|GCGA
Donor marginally increased1436wt: 0.9965 / mu: 0.9967 (marginal change - not scored)wt: TTCCTGGCGAAGGAC
mu: TTCCTGGTGAAGGAC		 CCTG|gcga
distance from splice site 61
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      42RAVDVVLDCFLAKDGAHRGALASS
mutated  not conserved    42RAVDVVLDCFLVKDGAHRGALAS
Ptroglodytes  all identical  ENSPTRG00000004573  42RAVDVVLDCFLAKDSAHRGALAS
Mmulatta  all identical  ENSMMUG00000014266  42RAVDVVLDCFLAKDGGHRGALAS
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000038213  42QPTDIILDCFLVTEDRHRGAFAS
Ggallus  not conserved  ENSGALG00000014428  72RRVDVVLGCSYVWEGGLSRAFGG
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000058351  48DVVLSCSLIEEGGGMGGMGG
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
19405TOPO_DOMLumenal (Potential).lost
4242CONFLICTA -> V (in Ref. 2; BAB41077 and 4; AAH15017).lost
146146CONFLICTM -> V (in Ref. 2; BAA91465/BAB41077 and 4; AAH15017).might get lost (downstream of altered splice site)
165165CONFLICTT -> A (in Ref. 2; BAA91465/BAB41077 and 4; AAH15017).might get lost (downstream of altered splice site)
169169CONFLICTA -> V (in Ref. 2; BAB41077 and 4; AAH15017).might get lost (downstream of altered splice site)
181297DOMAINIg-like V-type.might get lost (downstream of altered splice site)
212212DISULFIDBy similarity.might get lost (downstream of altered splice site)
283283DISULFIDBy similarity.might get lost (downstream of altered splice site)
304394DOMAINIg-like C1-type.might get lost (downstream of altered splice site)
321321DISULFIDBy similarity.might get lost (downstream of altered splice site)
382382DISULFIDBy similarity.might get lost (downstream of altered splice site)
406426TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
427468TOPO_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 1407 / 1407
position (AA) of stopcodon in wt / mu AA sequence 469 / 469
position of stopcodon in wt / mu cDNA 1572 / 1572
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 166 / 166
chromosome 12
strand 1
last intron/exon boundary 1457
theoretical NMD boundary in CDS 1241
length of CDS 1407
coding sequence (CDS) position 125
cDNA position
(for ins/del: last normal base / first normal base)		 290
gDNA position
(for ins/del: last normal base / first normal base)		 1438
chromosomal position
(for ins/del: last normal base / first normal base)		 6562293
original gDNA sequence snippet GGTCCTAGACTGCTTCCTGGCGAAGGACGGTGCGCACCGTG
altered gDNA sequence snippet GGTCCTAGACTGCTTCCTGGTGAAGGACGGTGCGCACCGTG
original cDNA sequence snippet GGTCCTAGACTGCTTCCTGGCGAAGGACGGTGCGCACCGTG
altered cDNA sequence snippet GGTCCTAGACTGCTTCCTGGTGAAGGACGGTGCGCACCGTG
wildtype AA sequence MGTQEGWCLL LCLALSGAAE TKPHPAEGQW RAVDVVLDCF LAKDGAHRGA LASSEDRARA
SLVLKQVPVL DDGSLEDFTD FQGGTLAQDD PPIIFEASVD LVQIPQAEAL LHADCSGKEV
TCEISRYFLQ MTETTVKTAA WFMANMQVSG GGPSISLVMK TPRVTKNEAL WHPTLNLPLS
PQGTVRTAVE FQVMTQTQSL SFLLGSSASL DCGFSMAPGL DLISVEWRLQ HKGRGQLVYS
WTAGQGQAVR KGATLEPAQL GMARDASLTL PGLTIQDEGT YICQITTSLY RAQQIIQLNI
QASPKVRLSL ANEALLPTLI CDIAGYYPLD VVVTWTREEL GGSPAQVSGA SFSSLRQSVA
GTYSISSSLT AEPGSAGATY TCQVTHISLE EPLGASTQVV PPERRTALGV IFASSLFLLA
LMFLGLQRRQ APTGLGLLQA ERWETTSCAD TQSSHLHEDR TARVSQPS*
mutated AA sequence MGTQEGWCLL LCLALSGAAE TKPHPAEGQW RAVDVVLDCF LVKDGAHRGA LASSEDRARA
SLVLKQVPVL DDGSLEDFTD FQGGTLAQDD PPIIFEASVD LVQIPQAEAL LHADCSGKEV
TCEISRYFLQ MTETTVKTAA WFMANMQVSG GGPSISLVMK TPRVTKNEAL WHPTLNLPLS
PQGTVRTAVE FQVMTQTQSL SFLLGSSASL DCGFSMAPGL DLISVEWRLQ HKGRGQLVYS
WTAGQGQAVR KGATLEPAQL GMARDASLTL PGLTIQDEGT YICQITTSLY RAQQIIQLNI
QASPKVRLSL ANEALLPTLI CDIAGYYPLD VVVTWTREEL GGSPAQVSGA SFSSLRQSVA
GTYSISSSLT AEPGSAGATY TCQVTHISLE EPLGASTQVV PPERRTALGV IFASSLFLLA
LMFLGLQRRQ APTGLGLLQA ERWETTSCAD TQSSHLHEDR TARVSQPS*
speed 1.30 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: 0.954081386862717 (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) chr12:6562293C>TN/A show variant in all transcripts   IGV
HGNC symbol TAPBPL
Ensembl transcript ID ENST00000544021
Genbank transcript ID N/A
UniProt peptide Q9BX59
alteration type single base exchange
alteration region intron
DNA changes g.1438C>T
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs2041385
databasehomozygous (T/T)heterozygousallele carriers
1000G1398621001
ExAC27001487017570
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K4ac, Histone, Histone 3 Lysine 4 Acetylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9310.702
-0.7770.005
(flanking)-1.4330
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased1436wt: 0.42 / mu: 0.75wt: GTGGTCCTAGACTGCTTCCTGGCGAAGGACGGTGCGCACCG
mu: GTGGTCCTAGACTGCTTCCTGGTGAAGGACGGTGCGCACCG		 cctg|GCGA
Donor marginally increased1436wt: 0.9965 / mu: 0.9967 (marginal change - not scored)wt: TTCCTGGCGAAGGAC
mu: TTCCTGGTGAAGGAC		 CCTG|gcga
distance from splice site 320
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
19405TOPO_DOMLumenal (Potential).might get lost (downstream of altered splice site)
4242CONFLICTA -> V (in Ref. 2; BAB41077 and 4; AAH15017).might get lost (downstream of altered splice site)
146146CONFLICTM -> V (in Ref. 2; BAA91465/BAB41077 and 4; AAH15017).might get lost (downstream of altered splice site)
165165CONFLICTT -> A (in Ref. 2; BAA91465/BAB41077 and 4; AAH15017).might get lost (downstream of altered splice site)
169169CONFLICTA -> V (in Ref. 2; BAB41077 and 4; AAH15017).might get lost (downstream of altered splice site)
181297DOMAINIg-like V-type.might get lost (downstream of altered splice site)
212212DISULFIDBy similarity.might get lost (downstream of altered splice site)
283283DISULFIDBy similarity.might get lost (downstream of altered splice site)
304394DOMAINIg-like C1-type.might get lost (downstream of altered splice site)
321321DISULFIDBy similarity.might get lost (downstream of altered splice site)
382382DISULFIDBy similarity.might get lost (downstream of altered splice site)
406426TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
427468TOPO_DOMCytoplasmic (Potential).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 178 / 178
chromosome 12
strand 1
last intron/exon boundary 726
theoretical NMD boundary in CDS 498
length of CDS 558
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)		 1438
chromosomal position
(for ins/del: last normal base / first normal base)		 6562293
original gDNA sequence snippet GGTCCTAGACTGCTTCCTGGCGAAGGACGGTGCGCACCGTG
altered gDNA sequence snippet GGTCCTAGACTGCTTCCTGGTGAAGGACGGTGCGCACCGTG
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MGTQEGWCLL LCLALSGAAE TMDLVQIPQA EALLHADCSG KEVTCEISRY FLQMTETTVK
TAAWFMANMQ VSGGGPSISL VMKTPRVTKN EALWHPTLNL PLSPQGTVRT AVEFQVMTQT
QSLSFLLGSS ASLDCGFSMA PGLDLISVEW RLQHKGRGRG DLHLPDHHLS VPSSADHPAQ
HPSFP*
mutated AA sequence N/A
speed 0.62 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