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 4 transcript(s)...
Querying Taster for transcript #1: ENST00000503431
Querying Taster for transcript #2: ENST00000284440
Querying Taster for transcript #3: ENST00000508768
Querying Taster for transcript #4: ENST00000512788
MT speed 0 s - this script 4.256662 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
UCHL1polymorphism_automatic0.927317212070911simple_aaeaffectedS18Ysingle base exchangers5030732show file
UCHL1polymorphism_automatic0.927317212070911simple_aaeaffectedS18Ysingle base exchangers5030732show file
UCHL1polymorphism_automatic0.927317212070911simple_aaeaffectedS18Ysingle base exchangers5030732show file
UCHL1polymorphism_automatic0.927317212070911simple_aaeaffectedS18Ysingle base exchangers5030732show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.0726827879290891 (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 CM994452)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr4:41259633C>AN/A show variant in all transcripts   IGV
HGNC symbol UCHL1
Ensembl transcript ID ENST00000503431
Genbank transcript ID N/A
UniProt peptide P09936
alteration type single base exchange
alteration region CDS
DNA changes c.53C>A
cDNA.115C>A
g.1204C>A
AA changes S18Y Score: 144 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 18
frameshift no
known variant Reference ID: rs5030732
databasehomozygous (A/A)heterozygousallele carriers
1000G2637461009
ExAC116862337401

known disease mutation at this position, please check HGMD for details (HGMD ID CM994452)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
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
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0420.951
0.6340.953
(flanking)1.3190.955
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally decreased1196wt: 0.9949 / mu: 0.9941 (marginal change - not scored)wt: CGCCTTGTCTCCTCTCCGCAGGTGCTGTCCCGGCTGGGGGT
mu: CGCCTTGTCTCCTCTCCGCAGGTGCTGTACCGGCTGGGGGT		 gcag|GTGC
Acc marginally increased1194wt: 0.9748 / mu: 0.9793 (marginal change - not scored)wt: GCCGCCTTGTCTCCTCTCCGCAGGTGCTGTCCCGGCTGGGG
mu: GCCGCCTTGTCTCCTCTCCGCAGGTGCTGTACCGGCTGGGG		 ccgc|AGGT
Acc increased1207wt: 0.35 / mu: 0.46wt: CTCTCCGCAGGTGCTGTCCCGGCTGGGGGTCGCCGGCCAGT
mu: CTCTCCGCAGGTGCTGTACCGGCTGGGGGTCGCCGGCCAGT		 cccg|GCTG
distance from splice site 8
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      18EINPEMLNKVLSRLGVAGQWRFVD
mutated  not conserved    18EINPEMLNKVLYRLGVAGQWRFV
Ptroglodytes  all identical  ENSPTRG00000016009  18EINPEVSARVLSRLGVAGQWRFV
Mmulatta  all identical  ENSMMUG00000013071  18EINPEMLNKVLSRLGVAGQWRFV
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000029223  18EINPEMLNKVLAKLGVAGQWRFA
Ggallus  all identical  ENSGALG00000014261  19EINPEMLNKVLSRLGVSPGWRFV
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000026871  18EINPEMLNKVLSKLGVGSKWRFV
Dmelanogaster  not conserved  FBgn0010288  19ESNPEVLTKYIHKLGVSPAWSVT
Celegans  not conserved  F46E10.8  20ESNPSVINPMIEKMGVSGV-KTV
Xtropicalis  all conserved  ENSXETG00000021089  29LSEVLAQLGVLDGWKFV
protein features
start (aa)end (aa)featuredetails 
1019HELIXlost
2431STRANDmight get lost (downstream of altered splice site)
3640HELIXmight get lost (downstream of altered splice site)
4654STRANDmight get lost (downstream of altered splice site)
5770HELIXmight get lost (downstream of altered splice site)
7174TURNmight get lost (downstream of altered splice site)
7373MUTAGENQ->R: No effect on enzymatic parameters.might get lost (downstream of altered splice site)
8688STRANDmight get lost (downstream of altered splice site)
9090MUTAGENC->S: Abolishes enzymatic activity.might get lost (downstream of altered splice site)
9090ACT_SITENucleophile.might get lost (downstream of altered splice site)
90100HELIXmight get lost (downstream of altered splice site)
9797MUTAGENH->Q,N: 2-fold increase in affinity for ubiquitin ethyl ester, slight reduction in enzymatic activity.might get lost (downstream of altered splice site)
101105TURNmight get lost (downstream of altered splice site)
113120HELIXmight get lost (downstream of altered splice site)
121123TURNmight get lost (downstream of altered splice site)
124124SITESusceptible to oxidation.might get lost (downstream of altered splice site)
126134HELIXmight get lost (downstream of altered splice site)
137147HELIXmight get lost (downstream of altered splice site)
160168STRANDmight get lost (downstream of altered splice site)
161161MUTAGENH->D: 10000-fold decrease in enzymatic activity; no change in affinity for ubiquitin ethyl ester.might get lost (downstream of altered splice site)
161161MUTAGENH->K,Q,N,Y: Abolishes enzymatic activity.might get lost (downstream of altered splice site)
161161ACT_SITEProton donor.might get lost (downstream of altered splice site)
171175STRANDmight get lost (downstream of altered splice site)
176176SITEImportant for enzyme activity.might get lost (downstream of altered splice site)
176176MUTAGEND->N: 6-fold decrease in affinity for ubiquitin ethyl ester; 97.5% decrease in enzymatic activity.might get lost (downstream of altered splice site)
179179SITESusceptible to oxidation.might get lost (downstream of altered splice site)
179181STRANDmight get lost (downstream of altered splice site)
183187STRANDmight get lost (downstream of altered splice site)
190192HELIXmight get lost (downstream of altered splice site)
193207HELIXmight get lost (downstream of altered splice site)
204204MUTAGENF->A: Almost complete loss of activity.might get lost (downstream of altered splice site)
211213HELIXmight get lost (downstream of altered splice site)
211216REGIONInteraction with ubiquitin.might get lost (downstream of altered splice site)
215221STRANDmight get lost (downstream of altered splice site)
220220SITESusceptible to oxidation.might get lost (downstream of altered splice site)
220220LIPIDS-farnesyl cysteine.might get lost (downstream of altered splice site)
221223PROPEPRemoved in mature form (Probable). /FTId=PRO_0000414311.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 672 / 672
position (AA) of stopcodon in wt / mu AA sequence 224 / 224
position of stopcodon in wt / mu cDNA 734 / 734
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 63 / 63
chromosome 4
strand 1
last intron/exon boundary 648
theoretical NMD boundary in CDS 535
length of CDS 672
coding sequence (CDS) position 53
cDNA position
(for ins/del: last normal base / first normal base)		 115
gDNA position
(for ins/del: last normal base / first normal base)		 1204
chromosomal position
(for ins/del: last normal base / first normal base)		 41259633
original gDNA sequence snippet CTCCTCTCCGCAGGTGCTGTCCCGGCTGGGGGTCGCCGGCC
altered gDNA sequence snippet CTCCTCTCCGCAGGTGCTGTACCGGCTGGGGGTCGCCGGCC
original cDNA sequence snippet GATGCTGAACAAAGTGCTGTCCCGGCTGGGGGTCGCCGGCC
altered cDNA sequence snippet GATGCTGAACAAAGTGCTGTACCGGCTGGGGGTCGCCGGCC
wildtype AA sequence MQLKPMEINP EMLNKVLSRL GVAGQWRFVD VLGLEEESLG SVPAPACALL LLFPLTAQHE
NFRKKQIEEL KGQEVSPKVY FMKQTIGNSC GTIGLIHAVA NNQDKLGFED GSVLKQFLSE
TEKMSPEDRA KCFEKNEAIQ AAHDAVAQEG QCRVDDKVNF HFILFNNVDG HLYELDGRMP
FPVNHGASSE DTLLKDAAKV CREFTEREQG EVRFSAVALC KAA*
mutated AA sequence MQLKPMEINP EMLNKVLYRL GVAGQWRFVD VLGLEEESLG SVPAPACALL LLFPLTAQHE
NFRKKQIEEL KGQEVSPKVY FMKQTIGNSC GTIGLIHAVA NNQDKLGFED GSVLKQFLSE
TEKMSPEDRA KCFEKNEAIQ AAHDAVAQEG QCRVDDKVNF HFILFNNVDG HLYELDGRMP
FPVNHGASSE DTLLKDAAKV CREFTEREQG EVRFSAVALC KAA*
speed 0.74 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: 0.0726827879290891 (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 CM994452)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr4:41259633C>AN/A show variant in all transcripts   IGV
HGNC symbol UCHL1
Ensembl transcript ID ENST00000284440
Genbank transcript ID NM_004181
UniProt peptide P09936
alteration type single base exchange
alteration region CDS
DNA changes c.53C>A
cDNA.197C>A
g.1204C>A
AA changes S18Y Score: 144 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 18
frameshift no
known variant Reference ID: rs5030732
databasehomozygous (A/A)heterozygousallele carriers
1000G2637461009
ExAC116862337401

known disease mutation at this position, please check HGMD for details (HGMD ID CM994452)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
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
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0420.951
0.6340.953
(flanking)1.3190.955
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally decreased1196wt: 0.9949 / mu: 0.9941 (marginal change - not scored)wt: CGCCTTGTCTCCTCTCCGCAGGTGCTGTCCCGGCTGGGGGT
mu: CGCCTTGTCTCCTCTCCGCAGGTGCTGTACCGGCTGGGGGT		 gcag|GTGC
Acc marginally increased1194wt: 0.9748 / mu: 0.9793 (marginal change - not scored)wt: GCCGCCTTGTCTCCTCTCCGCAGGTGCTGTCCCGGCTGGGG
mu: GCCGCCTTGTCTCCTCTCCGCAGGTGCTGTACCGGCTGGGG		 ccgc|AGGT
Acc increased1207wt: 0.35 / mu: 0.46wt: CTCTCCGCAGGTGCTGTCCCGGCTGGGGGTCGCCGGCCAGT
mu: CTCTCCGCAGGTGCTGTACCGGCTGGGGGTCGCCGGCCAGT		 cccg|GCTG
distance from splice site 8
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      18EINPEMLNKVLSRLGVAGQWRFVD
mutated  not conserved    18EINPEMLNKVLYRLGVAGQWRFV
Ptroglodytes  all identical  ENSPTRG00000016009  18EINPEVSARVLSRLGVAGQWRFV
Mmulatta  all identical  ENSMMUG00000013071  18EINPEMLNKVLSRLGVAGQWRFV
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000029223  18EINPEMLNKVLAKLGVAGQWRFA
Ggallus  all identical  ENSGALG00000014261  19EINPEMLNKVLSRLGVSPGWRFV
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000026871  18EINPEMLNKVLSKLGVGSKWRFV
Dmelanogaster  not conserved  FBgn0010288  19ESNPEVLTKYIHKLGVSPAWSVT
Celegans  not conserved  F46E10.8  20ESNPSVINPMIEKMGVSGV-KTV
Xtropicalis  all conserved  ENSXETG00000021089  29LSEVLAQLGVLDGWKFV
protein features
start (aa)end (aa)featuredetails 
1019HELIXlost
2431STRANDmight get lost (downstream of altered splice site)
3640HELIXmight get lost (downstream of altered splice site)
4654STRANDmight get lost (downstream of altered splice site)
5770HELIXmight get lost (downstream of altered splice site)
7174TURNmight get lost (downstream of altered splice site)
7373MUTAGENQ->R: No effect on enzymatic parameters.might get lost (downstream of altered splice site)
8688STRANDmight get lost (downstream of altered splice site)
9090MUTAGENC->S: Abolishes enzymatic activity.might get lost (downstream of altered splice site)
9090ACT_SITENucleophile.might get lost (downstream of altered splice site)
90100HELIXmight get lost (downstream of altered splice site)
9797MUTAGENH->Q,N: 2-fold increase in affinity for ubiquitin ethyl ester, slight reduction in enzymatic activity.might get lost (downstream of altered splice site)
101105TURNmight get lost (downstream of altered splice site)
113120HELIXmight get lost (downstream of altered splice site)
121123TURNmight get lost (downstream of altered splice site)
124124SITESusceptible to oxidation.might get lost (downstream of altered splice site)
126134HELIXmight get lost (downstream of altered splice site)
137147HELIXmight get lost (downstream of altered splice site)
160168STRANDmight get lost (downstream of altered splice site)
161161MUTAGENH->D: 10000-fold decrease in enzymatic activity; no change in affinity for ubiquitin ethyl ester.might get lost (downstream of altered splice site)
161161MUTAGENH->K,Q,N,Y: Abolishes enzymatic activity.might get lost (downstream of altered splice site)
161161ACT_SITEProton donor.might get lost (downstream of altered splice site)
171175STRANDmight get lost (downstream of altered splice site)
176176SITEImportant for enzyme activity.might get lost (downstream of altered splice site)
176176MUTAGEND->N: 6-fold decrease in affinity for ubiquitin ethyl ester; 97.5% decrease in enzymatic activity.might get lost (downstream of altered splice site)
179179SITESusceptible to oxidation.might get lost (downstream of altered splice site)
179181STRANDmight get lost (downstream of altered splice site)
183187STRANDmight get lost (downstream of altered splice site)
190192HELIXmight get lost (downstream of altered splice site)
193207HELIXmight get lost (downstream of altered splice site)
204204MUTAGENF->A: Almost complete loss of activity.might get lost (downstream of altered splice site)
211213HELIXmight get lost (downstream of altered splice site)
211216REGIONInteraction with ubiquitin.might get lost (downstream of altered splice site)
215221STRANDmight get lost (downstream of altered splice site)
220220SITESusceptible to oxidation.might get lost (downstream of altered splice site)
220220LIPIDS-farnesyl cysteine.might get lost (downstream of altered splice site)
221223PROPEPRemoved in mature form (Probable). /FTId=PRO_0000414311.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 672 / 672
position (AA) of stopcodon in wt / mu AA sequence 224 / 224
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 145 / 145
chromosome 4
strand 1
last intron/exon boundary 730
theoretical NMD boundary in CDS 535
length of CDS 672
coding sequence (CDS) position 53
cDNA position
(for ins/del: last normal base / first normal base)		 197
gDNA position
(for ins/del: last normal base / first normal base)		 1204
chromosomal position
(for ins/del: last normal base / first normal base)		 41259633
original gDNA sequence snippet CTCCTCTCCGCAGGTGCTGTCCCGGCTGGGGGTCGCCGGCC
altered gDNA sequence snippet CTCCTCTCCGCAGGTGCTGTACCGGCTGGGGGTCGCCGGCC
original cDNA sequence snippet GATGCTGAACAAAGTGCTGTCCCGGCTGGGGGTCGCCGGCC
altered cDNA sequence snippet GATGCTGAACAAAGTGCTGTACCGGCTGGGGGTCGCCGGCC
wildtype AA sequence MQLKPMEINP EMLNKVLSRL GVAGQWRFVD VLGLEEESLG SVPAPACALL LLFPLTAQHE
NFRKKQIEEL KGQEVSPKVY FMKQTIGNSC GTIGLIHAVA NNQDKLGFED GSVLKQFLSE
TEKMSPEDRA KCFEKNEAIQ AAHDAVAQEG QCRVDDKVNF HFILFNNVDG HLYELDGRMP
FPVNHGASSE DTLLKDAAKV CREFTEREQG EVRFSAVALC KAA*
mutated AA sequence MQLKPMEINP EMLNKVLYRL GVAGQWRFVD VLGLEEESLG SVPAPACALL LLFPLTAQHE
NFRKKQIEEL KGQEVSPKVY FMKQTIGNSC GTIGLIHAVA NNQDKLGFED GSVLKQFLSE
TEKMSPEDRA KCFEKNEAIQ AAHDAVAQEG QCRVDDKVNF HFILFNNVDG HLYELDGRMP
FPVNHGASSE DTLLKDAAKV CREFTEREQG EVRFSAVALC KAA*
speed 0.71 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: 0.0726827879290891 (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 CM994452)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr4:41259633C>AN/A show variant in all transcripts   IGV
HGNC symbol UCHL1
Ensembl transcript ID ENST00000508768
Genbank transcript ID N/A
UniProt peptide P09936
alteration type single base exchange
alteration region CDS
DNA changes c.53C>A
cDNA.90C>A
g.1204C>A
AA changes S18Y Score: 144 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 18
frameshift no
known variant Reference ID: rs5030732
databasehomozygous (A/A)heterozygousallele carriers
1000G2637461009
ExAC116862337401

known disease mutation at this position, please check HGMD for details (HGMD ID CM994452)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
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
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0420.951
0.6340.953
(flanking)1.3190.955
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally decreased1196wt: 0.9949 / mu: 0.9941 (marginal change - not scored)wt: CGCCTTGTCTCCTCTCCGCAGGTGCTGTCCCGGCTGGGGGT
mu: CGCCTTGTCTCCTCTCCGCAGGTGCTGTACCGGCTGGGGGT		 gcag|GTGC
Acc marginally increased1194wt: 0.9748 / mu: 0.9793 (marginal change - not scored)wt: GCCGCCTTGTCTCCTCTCCGCAGGTGCTGTCCCGGCTGGGG
mu: GCCGCCTTGTCTCCTCTCCGCAGGTGCTGTACCGGCTGGGG		 ccgc|AGGT
Acc increased1207wt: 0.35 / mu: 0.46wt: CTCTCCGCAGGTGCTGTCCCGGCTGGGGGTCGCCGGCCAGT
mu: CTCTCCGCAGGTGCTGTACCGGCTGGGGGTCGCCGGCCAGT		 cccg|GCTG
distance from splice site 8
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      18EINPEMLNKVLSRLGVAGQWRFVD
mutated  not conserved    18EINPEMLNKVLYRLGVAGQWRFV
Ptroglodytes  all identical  ENSPTRG00000016009  18EINPEVSARVLSRLGVAGQWRFV
Mmulatta  all identical  ENSMMUG00000013071  18EINPEMLNKVLSRLGVAGQWRFV
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000029223  18EINPEMLNKVLAKLGVAGQWRFA
Ggallus  all identical  ENSGALG00000014261  19EINPEMLNKVLSRLGVSPGWRFV
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000026871  18EINPEMLNKVLSKLGVGSKWRFV
Dmelanogaster  not conserved  FBgn0010288  19ESNPEVLTKYIHKLGVSPAWSVT
Celegans  not conserved  F46E10.8  20ESNPSVINPMIEKMGVSGV-KTV
Xtropicalis  all conserved  ENSXETG00000021089  29LSEVLAQLGVLDGWKFV
protein features
start (aa)end (aa)featuredetails 
1019HELIXlost
2431STRANDmight get lost (downstream of altered splice site)
3640HELIXmight get lost (downstream of altered splice site)
4654STRANDmight get lost (downstream of altered splice site)
5770HELIXmight get lost (downstream of altered splice site)
7174TURNmight get lost (downstream of altered splice site)
7373MUTAGENQ->R: No effect on enzymatic parameters.might get lost (downstream of altered splice site)
8688STRANDmight get lost (downstream of altered splice site)
9090MUTAGENC->S: Abolishes enzymatic activity.might get lost (downstream of altered splice site)
9090ACT_SITENucleophile.might get lost (downstream of altered splice site)
90100HELIXmight get lost (downstream of altered splice site)
9797MUTAGENH->Q,N: 2-fold increase in affinity for ubiquitin ethyl ester, slight reduction in enzymatic activity.might get lost (downstream of altered splice site)
101105TURNmight get lost (downstream of altered splice site)
113120HELIXmight get lost (downstream of altered splice site)
121123TURNmight get lost (downstream of altered splice site)
124124SITESusceptible to oxidation.might get lost (downstream of altered splice site)
126134HELIXmight get lost (downstream of altered splice site)
137147HELIXmight get lost (downstream of altered splice site)
160168STRANDmight get lost (downstream of altered splice site)
161161MUTAGENH->D: 10000-fold decrease in enzymatic activity; no change in affinity for ubiquitin ethyl ester.might get lost (downstream of altered splice site)
161161MUTAGENH->K,Q,N,Y: Abolishes enzymatic activity.might get lost (downstream of altered splice site)
161161ACT_SITEProton donor.might get lost (downstream of altered splice site)
171175STRANDmight get lost (downstream of altered splice site)
176176SITEImportant for enzyme activity.might get lost (downstream of altered splice site)
176176MUTAGEND->N: 6-fold decrease in affinity for ubiquitin ethyl ester; 97.5% decrease in enzymatic activity.might get lost (downstream of altered splice site)
179179SITESusceptible to oxidation.might get lost (downstream of altered splice site)
179181STRANDmight get lost (downstream of altered splice site)
183187STRANDmight get lost (downstream of altered splice site)
190192HELIXmight get lost (downstream of altered splice site)
193207HELIXmight get lost (downstream of altered splice site)
204204MUTAGENF->A: Almost complete loss of activity.might get lost (downstream of altered splice site)
211213HELIXmight get lost (downstream of altered splice site)
211216REGIONInteraction with ubiquitin.might get lost (downstream of altered splice site)
215221STRANDmight get lost (downstream of altered splice site)
220220SITESusceptible to oxidation.might get lost (downstream of altered splice site)
220220LIPIDS-farnesyl cysteine.might get lost (downstream of altered splice site)
221223PROPEPRemoved in mature form (Probable). /FTId=PRO_0000414311.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 624 / 624
position (AA) of stopcodon in wt / mu AA sequence 208 / 208
position of stopcodon in wt / mu cDNA 661 / 661
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 38 / 38
chromosome 4
strand 1
last intron/exon boundary 575
theoretical NMD boundary in CDS 487
length of CDS 624
coding sequence (CDS) position 53
cDNA position
(for ins/del: last normal base / first normal base)		 90
gDNA position
(for ins/del: last normal base / first normal base)		 1204
chromosomal position
(for ins/del: last normal base / first normal base)		 41259633
original gDNA sequence snippet CTCCTCTCCGCAGGTGCTGTCCCGGCTGGGGGTCGCCGGCC
altered gDNA sequence snippet CTCCTCTCCGCAGGTGCTGTACCGGCTGGGGGTCGCCGGCC
original cDNA sequence snippet GATGCTGAACAAAGTGCTGTCCCGGCTGGGGGTCGCCGGCC
altered cDNA sequence snippet GATGCTGAACAAAGTGCTGTACCGGCTGGGGGTCGCCGGCC
wildtype AA sequence MQLKPMEINP EMLNKVLSRL GVAGQWRFVD VLGLEEESLG SVPAPACALL LLFPLTAQHE
NFRKKQIEEL KGQEVSPKVY FMKQTIGNSC GTIGLIHAVA NNQDKLGFED GSVLKQFLSE
TEKMSPEDRA KCFEKNEVDD KVNFHFILFN NVDGHLYELD GRMPFPVNHG ASSEDTLLKD
AAKVCREFTE REQGEVRFSA VALCKAA*
mutated AA sequence MQLKPMEINP EMLNKVLYRL GVAGQWRFVD VLGLEEESLG SVPAPACALL LLFPLTAQHE
NFRKKQIEEL KGQEVSPKVY FMKQTIGNSC GTIGLIHAVA NNQDKLGFED GSVLKQFLSE
TEKMSPEDRA KCFEKNEVDD KVNFHFILFN NVDGHLYELD GRMPFPVNHG ASSEDTLLKD
AAKVCREFTE REQGEVRFSA VALCKAA*
speed 0.70 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
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Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.0726827879290891 (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 CM994452)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr4:41259633C>AN/A show variant in all transcripts   IGV
HGNC symbol UCHL1
Ensembl transcript ID ENST00000512788
Genbank transcript ID N/A
UniProt peptide P09936
alteration type single base exchange
alteration region CDS
DNA changes c.53C>A
cDNA.85C>A
g.1204C>A
AA changes S18Y Score: 144 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 18
frameshift no
known variant Reference ID: rs5030732
databasehomozygous (A/A)heterozygousallele carriers
1000G2637461009
ExAC116862337401

known disease mutation at this position, please check HGMD for details (HGMD ID CM994452)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
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
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0420.951
0.6340.953
(flanking)1.3190.955
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally decreased1196wt: 0.9949 / mu: 0.9941 (marginal change - not scored)wt: CGCCTTGTCTCCTCTCCGCAGGTGCTGTCCCGGCTGGGGGT
mu: CGCCTTGTCTCCTCTCCGCAGGTGCTGTACCGGCTGGGGGT		 gcag|GTGC
Acc marginally increased1194wt: 0.9748 / mu: 0.9793 (marginal change - not scored)wt: GCCGCCTTGTCTCCTCTCCGCAGGTGCTGTCCCGGCTGGGG
mu: GCCGCCTTGTCTCCTCTCCGCAGGTGCTGTACCGGCTGGGG		 ccgc|AGGT
Acc increased1207wt: 0.35 / mu: 0.46wt: CTCTCCGCAGGTGCTGTCCCGGCTGGGGGTCGCCGGCCAGT
mu: CTCTCCGCAGGTGCTGTACCGGCTGGGGGTCGCCGGCCAGT		 cccg|GCTG
distance from splice site 8
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      18EINPEMLNKVLSRLGVAGQWRFVD
mutated  not conserved    18EINPEMLNKVLYRLGVAGQWRFV
Ptroglodytes  all identical  ENSPTRG00000016009  18EINPEVSARVLSRLGVAGQWRFV
Mmulatta  all identical  ENSMMUG00000013071  18EINPEMLNKVLSRLGVAGQWRFV
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000029223  18EINPEMLNKVLAKLGVAGQWRFA
Ggallus  all identical  ENSGALG00000014261  19EINPEMLNKVLSRLGVSPGWRFV
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000026871  18EINPEMLNKVLSKLGVGSKWRFV
Dmelanogaster  not conserved  FBgn0010288  19ESNPEVLTKYIHKLGVSPAWSVT
Celegans  not conserved  F46E10.8  20ESNPSVINPMIEKMGVSGV-KTV
Xtropicalis  all conserved  ENSXETG00000021089  29LSEVLAQLGVLDGWKFV
protein features
start (aa)end (aa)featuredetails 
1019HELIXlost
2431STRANDmight get lost (downstream of altered splice site)
3640HELIXmight get lost (downstream of altered splice site)
4654STRANDmight get lost (downstream of altered splice site)
5770HELIXmight get lost (downstream of altered splice site)
7174TURNmight get lost (downstream of altered splice site)
7373MUTAGENQ->R: No effect on enzymatic parameters.might get lost (downstream of altered splice site)
8688STRANDmight get lost (downstream of altered splice site)
9090MUTAGENC->S: Abolishes enzymatic activity.might get lost (downstream of altered splice site)
9090ACT_SITENucleophile.might get lost (downstream of altered splice site)
90100HELIXmight get lost (downstream of altered splice site)
9797MUTAGENH->Q,N: 2-fold increase in affinity for ubiquitin ethyl ester, slight reduction in enzymatic activity.might get lost (downstream of altered splice site)
101105TURNmight get lost (downstream of altered splice site)
113120HELIXmight get lost (downstream of altered splice site)
121123TURNmight get lost (downstream of altered splice site)
124124SITESusceptible to oxidation.might get lost (downstream of altered splice site)
126134HELIXmight get lost (downstream of altered splice site)
137147HELIXmight get lost (downstream of altered splice site)
160168STRANDmight get lost (downstream of altered splice site)
161161MUTAGENH->D: 10000-fold decrease in enzymatic activity; no change in affinity for ubiquitin ethyl ester.might get lost (downstream of altered splice site)
161161MUTAGENH->K,Q,N,Y: Abolishes enzymatic activity.might get lost (downstream of altered splice site)
161161ACT_SITEProton donor.might get lost (downstream of altered splice site)
171175STRANDmight get lost (downstream of altered splice site)
176176SITEImportant for enzyme activity.might get lost (downstream of altered splice site)
176176MUTAGEND->N: 6-fold decrease in affinity for ubiquitin ethyl ester; 97.5% decrease in enzymatic activity.might get lost (downstream of altered splice site)
179179SITESusceptible to oxidation.might get lost (downstream of altered splice site)
179181STRANDmight get lost (downstream of altered splice site)
183187STRANDmight get lost (downstream of altered splice site)
190192HELIXmight get lost (downstream of altered splice site)
193207HELIXmight get lost (downstream of altered splice site)
204204MUTAGENF->A: Almost complete loss of activity.might get lost (downstream of altered splice site)
211213HELIXmight get lost (downstream of altered splice site)
211216REGIONInteraction with ubiquitin.might get lost (downstream of altered splice site)
215221STRANDmight get lost (downstream of altered splice site)
220220SITESusceptible to oxidation.might get lost (downstream of altered splice site)
220220LIPIDS-farnesyl cysteine.might get lost (downstream of altered splice site)
221223PROPEPRemoved in mature form (Probable). /FTId=PRO_0000414311.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 726 / 726
position (AA) of stopcodon in wt / mu AA sequence 242 / 242
position of stopcodon in wt / mu cDNA 758 / 758
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 33 / 33
chromosome 4
strand 1
last intron/exon boundary 647
theoretical NMD boundary in CDS 564
length of CDS 726
coding sequence (CDS) position 53
cDNA position
(for ins/del: last normal base / first normal base)		 85
gDNA position
(for ins/del: last normal base / first normal base)		 1204
chromosomal position
(for ins/del: last normal base / first normal base)		 41259633
original gDNA sequence snippet CTCCTCTCCGCAGGTGCTGTCCCGGCTGGGGGTCGCCGGCC
altered gDNA sequence snippet CTCCTCTCCGCAGGTGCTGTACCGGCTGGGGGTCGCCGGCC
original cDNA sequence snippet GATGCTGAACAAAGTGCTGTCCCGGCTGGGGGTCGCCGGCC
altered cDNA sequence snippet GATGCTGAACAAAGTGCTGTACCGGCTGGGGGTCGCCGGCC
wildtype AA sequence MQLKPMEINP EMLNKVLSRL GVAGQWRFVD VLGLEEESLG SVPAPACALL LLFPLTAQHE
NFRKKQIEEL KGQEVSPKVY FMKQTIGNSC GTIGLIHAVA NNQDKLGFED GSVLKQFLSE
TEKMSPEDRA KCFEKNEAIQ AAHDAVAQEG QCRVDDKVNF HFILFNNVDG HLYELDGRMP
FPVNHGASSE DTLLKVIFGM HLFLMTLPRS AENSPSVSKE KSASLPWLSA RQPNALWEGL
C*
mutated AA sequence MQLKPMEINP EMLNKVLYRL GVAGQWRFVD VLGLEEESLG SVPAPACALL LLFPLTAQHE
NFRKKQIEEL KGQEVSPKVY FMKQTIGNSC GTIGLIHAVA NNQDKLGFED GSVLKQFLSE
TEKMSPEDRA KCFEKNEAIQ AAHDAVAQEG QCRVDDKVNF HFILFNNVDG HLYELDGRMP
FPVNHGASSE DTLLKVIFGM HLFLMTLPRS AENSPSVSKE KSASLPWLSA RQPNALWEGL
C*
speed 0.68 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
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Problems