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: ENST00000367233
Querying Taster for transcript #2: ENST00000367231
Querying Taster for transcript #3: ENST00000367230
MT speed 0 s - this script 3.638629 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
MTRF1Lpolymorphism_automatic1.01151975684388e-10simple_aaeT38Asingle base exchangers3818125show file
MTRF1Lpolymorphism_automatic1.01151975684388e-10simple_aaeT38Asingle base exchangers3818125show file
MTRF1Lpolymorphism_automatic1.01151975684388e-10simple_aaeT38Asingle base exchangers3818125show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999898848 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:153323709T>CN/A show variant in all transcripts   IGV
HGNC symbol MTRF1L
Ensembl transcript ID ENST00000367233
Genbank transcript ID NM_019041
UniProt peptide Q9UGC7
alteration type single base exchange
alteration region CDS
DNA changes c.112A>G
cDNA.112A>G
g.112A>G
AA changes T38A Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 38
frameshift no
known variant Reference ID: rs3818125
databasehomozygous (C/C)heterozygousallele carriers
1000G108411342218
ExAC66981053717235
regulatory features ZBTB33, Transcription Factor, ZBTB33 Transcription Factor Binding
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
Gabp, Transcription Factor, Gabp TF binding
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
H2AZ, Histone, Histone 2A variant Z
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
E2F4, Transcription Factor, E2F4 Transcription Factor Binding
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Cmyc, Transcription Factor, Cmyc TF binding
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
CTCF, Transcription Factor, CCCTC-binding factor
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3980.237
-0.0720.244
(flanking)0.4160.523
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 112
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      38SSGSPPLEELFTRGGPLRTFLERQ
mutated  not conserved    38SSGSPPLEELFARGGPLRTFLER
Ptroglodytes  not conserved  ENSPTRG00000018722  38SSGSPPLEELFARGGPLRTFLER
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000019774  38----PPSEELLARGGPLRAFLER
Ggallus  not conserved  ENSGALG00000013609  30SA-RPRLDELFAIPSLSRLLKAR
Trubripes  no alignment  ENSTRUG00000001172  n/a
Drerio  no homologue    
Dmelanogaster  no alignment  FBgn0032486  n/a
Celegans  no alignment  W03F8.3  n/a
Xtropicalis  no homologue    
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1143 / 1143
position (AA) of stopcodon in wt / mu AA sequence 381 / 381
position of stopcodon in wt / mu cDNA 1143 / 1143
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 1 / 1
chromosome 6
strand -1
last intron/exon boundary 943
theoretical NMD boundary in CDS 892
length of CDS 1143
coding sequence (CDS) position 112
cDNA position
(for ins/del: last normal base / first normal base)		 112
gDNA position
(for ins/del: last normal base / first normal base)		 112
chromosomal position
(for ins/del: last normal base / first normal base)		 153323709
original gDNA sequence snippet CGCCGCTGGAGGAGCTGTTCACCCGGGGCGGGCCCTTGCGG
altered gDNA sequence snippet CGCCGCTGGAGGAGCTGTTCGCCCGGGGCGGGCCCTTGCGG
original cDNA sequence snippet CGCCGCTGGAGGAGCTGTTCACCCGGGGCGGGCCCTTGCGG
altered cDNA sequence snippet CGCCGCTGGAGGAGCTGTTCGCCCGGGGCGGGCCCTTGCGG
wildtype AA sequence MRSRVLWGAA RWLWPRRAVG PARRPLSSGS PPLEELFTRG GPLRTFLERQ AGSEAHLKVR
RPELLAVIKL LNEKERELRE TEHLLHDENE DLRKLAENEI TLCQKEITQL KHQIILLLVP
SEETDENDLI LEVTAGVGGQ EAMLFTSEIF DMYQQYAAFK RWHFETLEYF PSELGGLRHA
SASIGGSEAY RHMKFEGGVH RVQRVPKTEK QGRVHTSTMT VAILPQPTEI NLVINPKDLR
IDTKRASGAG GQHVNTTDSA VRIVHLPTGV VSECQQERSQ LKNKELAMTK LRAKLYSMHL
EEEINKRQNA RKIQIGSKGR SEKIRTYNFP QNRVTDHRIN KTLHDLETFM QGDYLLDELV
QSLKEYADYE SLVEIISQKV *
mutated AA sequence MRSRVLWGAA RWLWPRRAVG PARRPLSSGS PPLEELFARG GPLRTFLERQ AGSEAHLKVR
RPELLAVIKL LNEKERELRE TEHLLHDENE DLRKLAENEI TLCQKEITQL KHQIILLLVP
SEETDENDLI LEVTAGVGGQ EAMLFTSEIF DMYQQYAAFK RWHFETLEYF PSELGGLRHA
SASIGGSEAY RHMKFEGGVH RVQRVPKTEK QGRVHTSTMT VAILPQPTEI NLVINPKDLR
IDTKRASGAG GQHVNTTDSA VRIVHLPTGV VSECQQERSQ LKNKELAMTK LRAKLYSMHL
EEEINKRQNA RKIQIGSKGR SEKIRTYNFP QNRVTDHRIN KTLHDLETFM QGDYLLDELV
QSLKEYADYE SLVEIISQKV *
speed 0.83 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: 0.999999999898848 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:153323709T>CN/A show variant in all transcripts   IGV
HGNC symbol MTRF1L
Ensembl transcript ID ENST00000367231
Genbank transcript ID NM_001114184
UniProt peptide Q9UGC7
alteration type single base exchange
alteration region CDS
DNA changes c.112A>G
cDNA.112A>G
g.112A>G
AA changes T38A Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 38
frameshift no
known variant Reference ID: rs3818125
databasehomozygous (C/C)heterozygousallele carriers
1000G108411342218
ExAC66981053717235
regulatory features ZBTB33, Transcription Factor, ZBTB33 Transcription Factor Binding
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
Gabp, Transcription Factor, Gabp TF binding
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
H2AZ, Histone, Histone 2A variant Z
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
E2F4, Transcription Factor, E2F4 Transcription Factor Binding
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Cmyc, Transcription Factor, Cmyc TF binding
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
CTCF, Transcription Factor, CCCTC-binding factor
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3980.237
-0.0720.244
(flanking)0.4160.523
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 112
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      38SSGSPPLEELFTRGGPLRTFLERQ
mutated  not conserved    38SSGSPPLEELFARGGPLRTFLER
Ptroglodytes  not conserved  ENSPTRG00000018722  38SSGSPPLEELFARGGPLRTFLER
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000019774  38----PPSEELLARGGPLRAFLER
Ggallus  not conserved  ENSGALG00000013609  30SA-RPRLDELFAIPSLSRLLKAR
Trubripes  no alignment  ENSTRUG00000001172  n/a
Drerio  no homologue    
Dmelanogaster  no alignment  FBgn0032486  n/a
Celegans  no alignment  W03F8.3  n/a
Xtropicalis  no homologue    
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 816 / 816
position (AA) of stopcodon in wt / mu AA sequence 272 / 272
position of stopcodon in wt / mu cDNA 816 / 816
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 1 / 1
chromosome 6
strand -1
last intron/exon boundary 806
theoretical NMD boundary in CDS 755
length of CDS 816
coding sequence (CDS) position 112
cDNA position
(for ins/del: last normal base / first normal base)		 112
gDNA position
(for ins/del: last normal base / first normal base)		 112
chromosomal position
(for ins/del: last normal base / first normal base)		 153323709
original gDNA sequence snippet CGCCGCTGGAGGAGCTGTTCACCCGGGGCGGGCCCTTGCGG
altered gDNA sequence snippet CGCCGCTGGAGGAGCTGTTCGCCCGGGGCGGGCCCTTGCGG
original cDNA sequence snippet CGCCGCTGGAGGAGCTGTTCACCCGGGGCGGGCCCTTGCGG
altered cDNA sequence snippet CGCCGCTGGAGGAGCTGTTCGCCCGGGGCGGGCCCTTGCGG
wildtype AA sequence MRSRVLWGAA RWLWPRRAVG PARRPLSSGS PPLEELFTRG GPLRTFLERQ AGSEAHLKVR
RPELLAVIKL LNEKERELRE TEHLLHDENE DLRKLAENEI TLCQKEITQL KHQIILLLVP
SEETDENDLI LEVTAGVGGQ EAMLFTSEIF DMYQQYAAFK RWHFETLEYF PSELGGLRHA
SASIGGSEAY RHMKFEGGVH RVQRVPKTEK QGRVHTSTMT VAILPQPTEI NLVINPKDLR
IDTKRASGAG GQHVNTTDSA VRIVHLPTDW K*
mutated AA sequence MRSRVLWGAA RWLWPRRAVG PARRPLSSGS PPLEELFARG GPLRTFLERQ AGSEAHLKVR
RPELLAVIKL LNEKERELRE TEHLLHDENE DLRKLAENEI TLCQKEITQL KHQIILLLVP
SEETDENDLI LEVTAGVGGQ EAMLFTSEIF DMYQQYAAFK RWHFETLEYF PSELGGLRHA
SASIGGSEAY RHMKFEGGVH RVQRVPKTEK QGRVHTSTMT VAILPQPTEI NLVINPKDLR
IDTKRASGAG GQHVNTTDSA VRIVHLPTDW K*
speed 0.90 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: 0.999999999898848 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:153323709T>CN/A show variant in all transcripts   IGV
HGNC symbol MTRF1L
Ensembl transcript ID ENST00000367230
Genbank transcript ID N/A
UniProt peptide Q9UGC7
alteration type single base exchange
alteration region CDS
DNA changes c.112A>G
cDNA.112A>G
g.112A>G
AA changes T38A Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 38
frameshift no
known variant Reference ID: rs3818125
databasehomozygous (C/C)heterozygousallele carriers
1000G108411342218
ExAC66981053717235
regulatory features ZBTB33, Transcription Factor, ZBTB33 Transcription Factor Binding
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
Gabp, Transcription Factor, Gabp TF binding
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
H2AZ, Histone, Histone 2A variant Z
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
E2F4, Transcription Factor, E2F4 Transcription Factor Binding
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Cmyc, Transcription Factor, Cmyc TF binding
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
CTCF, Transcription Factor, CCCTC-binding factor
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3980.237
-0.0720.244
(flanking)0.4160.523
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 112
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      38SSGSPPLEELFTRGGPLRTFLERQ
mutated  not conserved    38SSGSPPLEELFARGGPLRTFLER
Ptroglodytes  not conserved  ENSPTRG00000018722  38SSGSPPLEELFARGGPLRTFLER
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000019774  38----PPSEELLARGGPLRAFLER
Ggallus  not conserved  ENSGALG00000013609  30SA-RPRLDELFAIPSLSRLLKAR
Trubripes  no alignment  ENSTRUG00000001172  n/a
Drerio  no homologue    
Dmelanogaster  no alignment  FBgn0032486  n/a
Celegans  no alignment  W03F8.3  n/a
Xtropicalis  no homologue    
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 708 / 708
position (AA) of stopcodon in wt / mu AA sequence 236 / 236
position of stopcodon in wt / mu cDNA 708 / 708
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 1 / 1
chromosome 6
strand -1
last intron/exon boundary 698
theoretical NMD boundary in CDS 647
length of CDS 708
coding sequence (CDS) position 112
cDNA position
(for ins/del: last normal base / first normal base)		 112
gDNA position
(for ins/del: last normal base / first normal base)		 112
chromosomal position
(for ins/del: last normal base / first normal base)		 153323709
original gDNA sequence snippet CGCCGCTGGAGGAGCTGTTCACCCGGGGCGGGCCCTTGCGG
altered gDNA sequence snippet CGCCGCTGGAGGAGCTGTTCGCCCGGGGCGGGCCCTTGCGG
original cDNA sequence snippet CGCCGCTGGAGGAGCTGTTCACCCGGGGCGGGCCCTTGCGG
altered cDNA sequence snippet CGCCGCTGGAGGAGCTGTTCGCCCGGGGCGGGCCCTTGCGG
wildtype AA sequence MRSRVLWGAA RWLWPRRAVG PARRPLSSGS PPLEELFTRG GPLRTFLERQ AGSEAHLKVR
RPELLAVIKL LNEKERELRE TEHLLHDENE DLRKLAENEI TLCQKEITQL KHQIILLLVP
SEETDENDLI LEVTAGVGGG LRHASASIGG SEAYRHMKFE GGVHRVQRVP KTEKQGRVHT
STMTVAILPQ PTEINLVINP KDLRIDTKRA SGAGGQHVNT TDSAVRIVHL PTDWK*
mutated AA sequence MRSRVLWGAA RWLWPRRAVG PARRPLSSGS PPLEELFARG GPLRTFLERQ AGSEAHLKVR
RPELLAVIKL LNEKERELRE TEHLLHDENE DLRKLAENEI TLCQKEITQL KHQIILLLVP
SEETDENDLI LEVTAGVGGG LRHASASIGG SEAYRHMKFE GGVHRVQRVP KTEKQGRVHT
STMTVAILPQ PTEINLVINP KDLRIDTKRA SGAGGQHVNT TDSAVRIVHL PTDWK*
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

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