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: ENST00000321897
Querying Taster for transcript #2: ENST00000541562
Querying Taster for transcript #3: ENST00000416670
Querying Taster for transcript #4: ENST00000542001
MT speed 6.19 s - this script 7.860529 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
VARS2polymorphism_automatic1.47970524722041e-11simple_aaeaffectedA995Tsingle base exchangers2252863show file
VARS2polymorphism_automatic1.47970524722041e-11simple_aaeaffectedA965Tsingle base exchangers2252863show file
VARS2polymorphism_automatic1.47970524722041e-11simple_aaeaffectedA965Tsingle base exchangers2252863show file
VARS2polymorphism_automatic1.47970524722041e-11simple_aaeaffectedA825Tsingle base exchangers2252863show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999985203 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:30893428G>AN/A show variant in all transcripts   IGV
HGNC symbol VARS2
Ensembl transcript ID ENST00000541562
Genbank transcript ID NM_001167734
UniProt peptide Q5ST30
alteration type single base exchange
alteration region CDS
DNA changes c.2983G>A
cDNA.3064G>A
g.17410G>A
AA changes A995T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS
995
frameshift no
known variant Reference ID: rs2252863
databasehomozygous (A/A)heterozygousallele carriers
1000G158801959
ExAC61072055326660
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-2.2940
-0.4970
(flanking)-0.0160
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased17402wt: 0.60 / mu: 0.76wt: GTTACCCCCAGGCGC
mu: GTTACCCCCAGGCAC
 TACC|ccca
Donor marginally increased17407wt: 0.8365 / mu: 0.8666 (marginal change - not scored)wt: CCCCAGGCGCAGCAG
mu: CCCCAGGCACAGCAG
 CCAG|gcgc
Donor increased17406wt: 0.56 / mu: 0.90wt: CCCCCAGGCGCAGCA
mu: CCCCCAGGCACAGCA
 CCCA|ggcg
Donor increased17412wt: 0.28 / mu: 0.66wt: GGCGCAGCAGCTCCC
mu: GGCACAGCAGCTCCC
 CGCA|gcag
distance from splice site 69
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      995YCGAVGLLPPGAAAPSGWAQAPLS
mutated  not conserved    995YCGAVGLLPPGTAAPSGWAQAPL
Ptroglodytes  all identical  ENSPTRG00000034497  974YCGAVGLLPPGAAAPSGWAQAPL
Mmulatta  all identical  ENSMMUG00000018609  966LLPPGAAAPSGWAQAPL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000038838  966FLSPGAAAPSGWALTPL
Ggallus  no homologue    
Trubripes  no alignment  ENSTRUG00000005264  n/a
Drerio  not conserved  ENSDARG00000056717  967CPPAKASAVGVVDHSL
Dmelanogaster  no alignment  FBgn0035942  n/a
Celegans  no alignment  ZC513.4  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 3282 / 3282
position (AA) of stopcodon in wt / mu AA sequence 1094 / 1094
position of stopcodon in wt / mu cDNA 3363 / 3363
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 82 / 82
chromosome 6
strand 1
last intron/exon boundary 3262
theoretical NMD boundary in CDS 3130
length of CDS 3282
coding sequence (CDS) position 2983
cDNA position
(for ins/del: last normal base / first normal base)
3064
gDNA position
(for ins/del: last normal base / first normal base)
17410
chromosomal position
(for ins/del: last normal base / first normal base)
30893428
original gDNA sequence snippet TGGGCCTGTTACCCCCAGGCGCAGCAGCTCCCTCCGGCTGG
altered gDNA sequence snippet TGGGCCTGTTACCCCCAGGCACAGCAGCTCCCTCCGGCTGG
original cDNA sequence snippet TGGGCCTGTTACCCCCAGGCGCAGCAGCTCCCTCCGGCTGG
altered cDNA sequence snippet TGGGCCTGTTACCCCCAGGCACAGCAGCTCCCTCCGGCTGG
wildtype AA sequence MGGKAWPRRA VGTAGGPCAE QISAPFQTLL MPHLPLASFR PPFWGLRHSR GLPRFHSVST
QSEPHGSPIS RRNREAKQKR LREKQATLEA EIAGESKSPA ESIKAWRPKE LVLYEIPTKP
GEKKDVSGPL PPAYSPRYVE AAWYPWWVRE GFFKPEYQAR LPQATGETFS MCIPPPNVTG
SLHIGHALTV AIQDALVRWH RMRGDQVLWV PGSDHAGIAT QAVVEKQLWK ERGVRRHELS
REAFLREVWQ WKEAKGGEIC EQLRALGASL DWDRECFTMD VGSSVAVTEA FVRLYKAGLL
YRNHQLVNWS CALRSAISDI EVENRPLPGH TQLRLPGCPT PVSFGLLFSV AFPVDGEPDA
EVVVGTTRPE TLPGDVAVAV HPDDSRYTHL HGRQLRHPLM GQPLPLITDY AVQPHVGTGA
VKVTPAHSPA DAEMGARHGL SPLNVIAEDG TMTSLCGDWL QGLHRFVARE KIMSVLSEWG
LFRGLQNHPM VLPICSRSGD VIEYLLKNQW FVRCQEMGAR AAKAVESGAL ELSPSFHQKN
WQHWFSHIGD WCVSRQLWWG HQIPAYLVVE DHAQGEEDCW VVGRSEAEAR EVAAELTGRP
GAELTLERDP DVLDTWFSSA LFPFSALGWP QETPDLARFY PLSLLETGSD LLLFWVGRMV
MLGTQLTGQL PFSKVLLHPM VRDRQGRKMS KSLGNVLDPR DIISGVEMQV LQEKLRSGNL
DPAELAIVAA AQKKDFPHGI PECGTDALRF TLCSHGVQAG DLHLSVSEVQ SCRHFCNKIW
NALRFILNAL GEKFVPQPAE ELSPSSPMDA WILSRLALAA QECERGFLTR ELSLVTHALH
HFWLHNLCDV YLEAVKPVLW HSPRPLGPPQ VLFSCADLGL RLLAPLMPFL AEELWQRLPP
RPGCPPAPSI SVAPYPSACS LEHWRQPELE RRFSRVQEVV QVLRALRATY QLTKARPRVL
LQSSEPGDQG LFEAFLEPLG TLGYCGAVGL LPPGAAAPSG WAQAPLSDTA QVYMELQGLV
DPQIQLPLLA ARRYKLQKQL DSLTARTPSE GEAGTQRQQK LSSLQLELSK LDKAASHLRQ
LMDEPPAPGS PEL*
mutated AA sequence MGGKAWPRRA VGTAGGPCAE QISAPFQTLL MPHLPLASFR PPFWGLRHSR GLPRFHSVST
QSEPHGSPIS RRNREAKQKR LREKQATLEA EIAGESKSPA ESIKAWRPKE LVLYEIPTKP
GEKKDVSGPL PPAYSPRYVE AAWYPWWVRE GFFKPEYQAR LPQATGETFS MCIPPPNVTG
SLHIGHALTV AIQDALVRWH RMRGDQVLWV PGSDHAGIAT QAVVEKQLWK ERGVRRHELS
REAFLREVWQ WKEAKGGEIC EQLRALGASL DWDRECFTMD VGSSVAVTEA FVRLYKAGLL
YRNHQLVNWS CALRSAISDI EVENRPLPGH TQLRLPGCPT PVSFGLLFSV AFPVDGEPDA
EVVVGTTRPE TLPGDVAVAV HPDDSRYTHL HGRQLRHPLM GQPLPLITDY AVQPHVGTGA
VKVTPAHSPA DAEMGARHGL SPLNVIAEDG TMTSLCGDWL QGLHRFVARE KIMSVLSEWG
LFRGLQNHPM VLPICSRSGD VIEYLLKNQW FVRCQEMGAR AAKAVESGAL ELSPSFHQKN
WQHWFSHIGD WCVSRQLWWG HQIPAYLVVE DHAQGEEDCW VVGRSEAEAR EVAAELTGRP
GAELTLERDP DVLDTWFSSA LFPFSALGWP QETPDLARFY PLSLLETGSD LLLFWVGRMV
MLGTQLTGQL PFSKVLLHPM VRDRQGRKMS KSLGNVLDPR DIISGVEMQV LQEKLRSGNL
DPAELAIVAA AQKKDFPHGI PECGTDALRF TLCSHGVQAG DLHLSVSEVQ SCRHFCNKIW
NALRFILNAL GEKFVPQPAE ELSPSSPMDA WILSRLALAA QECERGFLTR ELSLVTHALH
HFWLHNLCDV YLEAVKPVLW HSPRPLGPPQ VLFSCADLGL RLLAPLMPFL AEELWQRLPP
RPGCPPAPSI SVAPYPSACS LEHWRQPELE RRFSRVQEVV QVLRALRATY QLTKARPRVL
LQSSEPGDQG LFEAFLEPLG TLGYCGAVGL LPPGTAAPSG WAQAPLSDTA QVYMELQGLV
DPQIQLPLLA ARRYKLQKQL DSLTARTPSE GEAGTQRQQK LSSLQLELSK LDKAASHLRQ
LMDEPPAPGS PEL*
speed 1.43 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: 0.999999999985203 (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) chr6:30893428G>AN/A show variant in all transcripts   IGV
HGNC symbol VARS2
Ensembl transcript ID ENST00000416670
Genbank transcript ID NM_020442
UniProt peptide Q5ST30
alteration type single base exchange
alteration region CDS
DNA changes c.2893G>A
cDNA.3060G>A
g.17410G>A
AA changes A965T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS
965
frameshift no
known variant Reference ID: rs2252863
databasehomozygous (A/A)heterozygousallele carriers
1000G158801959
ExAC61072055326660
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-2.2940
-0.4970
(flanking)-0.0160
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased17402wt: 0.60 / mu: 0.76wt: GTTACCCCCAGGCGC
mu: GTTACCCCCAGGCAC
 TACC|ccca
Donor marginally increased17407wt: 0.8365 / mu: 0.8666 (marginal change - not scored)wt: CCCCAGGCGCAGCAG
mu: CCCCAGGCACAGCAG
 CCAG|gcgc
Donor increased17406wt: 0.56 / mu: 0.90wt: CCCCCAGGCGCAGCA
mu: CCCCCAGGCACAGCA
 CCCA|ggcg
Donor increased17412wt: 0.28 / mu: 0.66wt: GGCGCAGCAGCTCCC
mu: GGCACAGCAGCTCCC
 CGCA|gcag
distance from splice site 69
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      965YCGAVGLLPPGAAAPSGWAQAPLS
mutated  not conserved    965LPPGTAAPSGWAQAPL
Ptroglodytes  all identical  ENSPTRG00000034497  974LPPGAAAPSGWAQAPL
Mmulatta  all identical  ENSMMUG00000018609  966LLPPGAAAPSGWAQAPL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000038838  966FLSPGAAAPSGWALTPL
Ggallus  no homologue    
Trubripes  no alignment  ENSTRUG00000005264  n/a
Drerio  not conserved  ENSDARG00000056717  967CPPAKASAVGVVDHSL
Dmelanogaster  no alignment  FBgn0035942  n/a
Celegans  no alignment  ZC513.4  n/a
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
985985CONFLICTE -> G (in Ref. 2; BAB15191).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3192 / 3192
position (AA) of stopcodon in wt / mu AA sequence 1064 / 1064
position of stopcodon in wt / mu cDNA 3359 / 3359
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 168 / 168
chromosome 6
strand 1
last intron/exon boundary 3258
theoretical NMD boundary in CDS 3040
length of CDS 3192
coding sequence (CDS) position 2893
cDNA position
(for ins/del: last normal base / first normal base)
3060
gDNA position
(for ins/del: last normal base / first normal base)
17410
chromosomal position
(for ins/del: last normal base / first normal base)
30893428
original gDNA sequence snippet TGGGCCTGTTACCCCCAGGCGCAGCAGCTCCCTCCGGCTGG
altered gDNA sequence snippet TGGGCCTGTTACCCCCAGGCACAGCAGCTCCCTCCGGCTGG
original cDNA sequence snippet TGGGCCTGTTACCCCCAGGCGCAGCAGCTCCCTCCGGCTGG
altered cDNA sequence snippet TGGGCCTGTTACCCCCAGGCACAGCAGCTCCCTCCGGCTGG
wildtype AA sequence MPHLPLASFR PPFWGLRHSR GLPRFHSVST QSEPHGSPIS RRNREAKQKR LREKQATLEA
EIAGESKSPA ESIKAWRPKE LVLYEIPTKP GEKKDVSGPL PPAYSPRYVE AAWYPWWVRE
GFFKPEYQAR LPQATGETFS MCIPPPNVTG SLHIGHALTV AIQDALVRWH RMRGDQVLWV
PGSDHAGIAT QAVVEKQLWK ERGVRRHELS REAFLREVWQ WKEAKGGEIC EQLRALGASL
DWDRECFTMD VGSSVAVTEA FVRLYKAGLL YRNHQLVNWS CALRSAISDI EVENRPLPGH
TQLRLPGCPT PVSFGLLFSV AFPVDGEPDA EVVVGTTRPE TLPGDVAVAV HPDDSRYTHL
HGRQLRHPLM GQPLPLITDY AVQPHVGTGA VKVTPAHSPA DAEMGARHGL SPLNVIAEDG
TMTSLCGDWL QGLHRFVARE KIMSVLSEWG LFRGLQNHPM VLPICSRSGD VIEYLLKNQW
FVRCQEMGAR AAKAVESGAL ELSPSFHQKN WQHWFSHIGD WCVSRQLWWG HQIPAYLVVE
DHAQGEEDCW VVGRSEAEAR EVAAELTGRP GAELTLERDP DVLDTWFSSA LFPFSALGWP
QETPDLARFY PLSLLETGSD LLLFWVGRMV MLGTQLTGQL PFSKVLLHPM VRDRQGRKMS
KSLGNVLDPR DIISGVEMQV LQEKLRSGNL DPAELAIVAA AQKKDFPHGI PECGTDALRF
TLCSHGVQAG DLHLSVSEVQ SCRHFCNKIW NALRFILNAL GEKFVPQPAE ELSPSSPMDA
WILSRLALAA QECERGFLTR ELSLVTHALH HFWLHNLCDV YLEAVKPVLW HSPRPLGPPQ
VLFSCADLGL RLLAPLMPFL AEELWQRLPP RPGCPPAPSI SVAPYPSACS LEHWRQPELE
RRFSRVQEVV QVLRALRATY QLTKARPRVL LQSSEPGDQG LFEAFLEPLG TLGYCGAVGL
LPPGAAAPSG WAQAPLSDTA QVYMELQGLV DPQIQLPLLA ARRYKLQKQL DSLTARTPSE
GEAGTQRQQK LSSLQLELSK LDKAASHLRQ LMDEPPAPGS PEL*
mutated AA sequence MPHLPLASFR PPFWGLRHSR GLPRFHSVST QSEPHGSPIS RRNREAKQKR LREKQATLEA
EIAGESKSPA ESIKAWRPKE LVLYEIPTKP GEKKDVSGPL PPAYSPRYVE AAWYPWWVRE
GFFKPEYQAR LPQATGETFS MCIPPPNVTG SLHIGHALTV AIQDALVRWH RMRGDQVLWV
PGSDHAGIAT QAVVEKQLWK ERGVRRHELS REAFLREVWQ WKEAKGGEIC EQLRALGASL
DWDRECFTMD VGSSVAVTEA FVRLYKAGLL YRNHQLVNWS CALRSAISDI EVENRPLPGH
TQLRLPGCPT PVSFGLLFSV AFPVDGEPDA EVVVGTTRPE TLPGDVAVAV HPDDSRYTHL
HGRQLRHPLM GQPLPLITDY AVQPHVGTGA VKVTPAHSPA DAEMGARHGL SPLNVIAEDG
TMTSLCGDWL QGLHRFVARE KIMSVLSEWG LFRGLQNHPM VLPICSRSGD VIEYLLKNQW
FVRCQEMGAR AAKAVESGAL ELSPSFHQKN WQHWFSHIGD WCVSRQLWWG HQIPAYLVVE
DHAQGEEDCW VVGRSEAEAR EVAAELTGRP GAELTLERDP DVLDTWFSSA LFPFSALGWP
QETPDLARFY PLSLLETGSD LLLFWVGRMV MLGTQLTGQL PFSKVLLHPM VRDRQGRKMS
KSLGNVLDPR DIISGVEMQV LQEKLRSGNL DPAELAIVAA AQKKDFPHGI PECGTDALRF
TLCSHGVQAG DLHLSVSEVQ SCRHFCNKIW NALRFILNAL GEKFVPQPAE ELSPSSPMDA
WILSRLALAA QECERGFLTR ELSLVTHALH HFWLHNLCDV YLEAVKPVLW HSPRPLGPPQ
VLFSCADLGL RLLAPLMPFL AEELWQRLPP RPGCPPAPSI SVAPYPSACS LEHWRQPELE
RRFSRVQEVV QVLRALRATY QLTKARPRVL LQSSEPGDQG LFEAFLEPLG TLGYCGAVGL
LPPGTAAPSG WAQAPLSDTA QVYMELQGLV DPQIQLPLLA ARRYKLQKQL DSLTARTPSE
GEAGTQRQQK LSSLQLELSK LDKAASHLRQ LMDEPPAPGS PEL*
speed 1.56 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: 0.999999999985203 (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) chr6:30893428G>AN/A show variant in all transcripts   IGV
HGNC symbol VARS2
Ensembl transcript ID ENST00000321897
Genbank transcript ID N/A
UniProt peptide Q5ST30
alteration type single base exchange
alteration region CDS
DNA changes c.2893G>A
cDNA.3525G>A
g.17410G>A
AA changes A965T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS
965
frameshift no
known variant Reference ID: rs2252863
databasehomozygous (A/A)heterozygousallele carriers
1000G158801959
ExAC61072055326660
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-2.2940
-0.4970
(flanking)-0.0160
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased17402wt: 0.60 / mu: 0.76wt: GTTACCCCCAGGCGC
mu: GTTACCCCCAGGCAC
 TACC|ccca
Donor marginally increased17407wt: 0.8365 / mu: 0.8666 (marginal change - not scored)wt: CCCCAGGCGCAGCAG
mu: CCCCAGGCACAGCAG
 CCAG|gcgc
Donor increased17406wt: 0.56 / mu: 0.90wt: CCCCCAGGCGCAGCA
mu: CCCCCAGGCACAGCA
 CCCA|ggcg
Donor increased17412wt: 0.28 / mu: 0.66wt: GGCGCAGCAGCTCCC
mu: GGCACAGCAGCTCCC
 CGCA|gcag
distance from splice site 69
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      965YCGAVGLLPPGAAAPSGWAQAPLS
mutated  not conserved    965LPPGTAAPSGWAQAPL
Ptroglodytes  all identical  ENSPTRG00000034497  974LPPGAAAPSGWAQAPL
Mmulatta  all identical  ENSMMUG00000018609  966LLPPGAAAPSGWAQAPL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000038838  966FLSPGAAAPSGWALTPL
Ggallus  no homologue    
Trubripes  no alignment  ENSTRUG00000005264  n/a
Drerio  not conserved  ENSDARG00000056717  967CPPAKASAVGVVDHSL
Dmelanogaster  no alignment  FBgn0035942  n/a
Celegans  no alignment  ZC513.4  n/a
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
985985CONFLICTE -> G (in Ref. 2; BAB15191).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3192 / 3192
position (AA) of stopcodon in wt / mu AA sequence 1064 / 1064
position of stopcodon in wt / mu cDNA 3824 / 3824
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 633 / 633
chromosome 6
strand 1
last intron/exon boundary 3723
theoretical NMD boundary in CDS 3040
length of CDS 3192
coding sequence (CDS) position 2893
cDNA position
(for ins/del: last normal base / first normal base)
3525
gDNA position
(for ins/del: last normal base / first normal base)
17410
chromosomal position
(for ins/del: last normal base / first normal base)
30893428
original gDNA sequence snippet TGGGCCTGTTACCCCCAGGCGCAGCAGCTCCCTCCGGCTGG
altered gDNA sequence snippet TGGGCCTGTTACCCCCAGGCACAGCAGCTCCCTCCGGCTGG
original cDNA sequence snippet TGGGCCTGTTACCCCCAGGCGCAGCAGCTCCCTCCGGCTGG
altered cDNA sequence snippet TGGGCCTGTTACCCCCAGGCACAGCAGCTCCCTCCGGCTGG
wildtype AA sequence MPHLPLASFR PPFWGLRHSR GLPRFHSVST QSEPHGSPIS RRNREAKQKR LREKQATLEA
EIAGESKSPA ESIKAWRPKE LVLYEIPTKP GEKKDVSGPL PPAYSPRYVE AAWYPWWVRE
GFFKPEYQAR LPQATGETFS MCIPPPNVTG SLHIGHALTV AIQDALVRWH RMRGDQVLWV
PGSDHAGIAT QAVVEKQLWK ERGVRRHELS REAFLREVWQ WKEAKGGEIC EQLRALGASL
DWDRECFTMD VGSSVAVTEA FVRLYKAGLL YRNHQLVNWS CALRSAISDI EVENRPLPGH
TQLRLPGCPT PVSFGLLFSV AFPVDGEPDA EVVVGTTRPE TLPGDVAVAV HPDDSRYTHL
HGRQLRHPLM GQPLPLITDY AVQPHVGTGA VKVTPAHSPA DAEMGARHGL SPLNVIAEDG
TMTSLCGDWL QGLHRFVARE KIMSVLSEWG LFRGLQNHPM VLPICSRSGD VIEYLLKNQW
FVRCQEMGAR AAKAVESGAL ELSPSFHQKN WQHWFSHIGD WCVSRQLWWG HQIPAYLVVE
DHAQGEEDCW VVGRSEAEAR EVAAELTGRP GAELTLERDP DVLDTWFSSA LFPFSALGWP
QETPDLARFY PLSLLETGSD LLLFWVGRMV MLGTQLTGQL PFSKVLLHPM VRDRQGRKMS
KSLGNVLDPR DIISGVEMQV LQEKLRSGNL DPAELAIVAA AQKKDFPHGI PECGTDALRF
TLCSHGVQAG DLHLSVSEVQ SCRHFCNKIW NALRFILNAL GEKFVPQPAE ELSPSSPMDA
WILSRLALAA QECERGFLTR ELSLVTHALH HFWLHNLCDV YLEAVKPVLW HSPRPLGPPQ
VLFSCADLGL RLLAPLMPFL AEELWQRLPP RPGCPPAPSI SVAPYPSACS LEHWRQPELE
RRFSRVQEVV QVLRALRATY QLTKARPRVL LQSSEPGDQG LFEAFLEPLG TLGYCGAVGL
LPPGAAAPSG WAQAPLSDTA QVYMELQGLV DPQIQLPLLA ARRYKLQKQL DSLTARTPSE
GEAGTQRQQK LSSLQLELSK LDKAASHLRQ LMDEPPAPGS PEL*
mutated AA sequence MPHLPLASFR PPFWGLRHSR GLPRFHSVST QSEPHGSPIS RRNREAKQKR LREKQATLEA
EIAGESKSPA ESIKAWRPKE LVLYEIPTKP GEKKDVSGPL PPAYSPRYVE AAWYPWWVRE
GFFKPEYQAR LPQATGETFS MCIPPPNVTG SLHIGHALTV AIQDALVRWH RMRGDQVLWV
PGSDHAGIAT QAVVEKQLWK ERGVRRHELS REAFLREVWQ WKEAKGGEIC EQLRALGASL
DWDRECFTMD VGSSVAVTEA FVRLYKAGLL YRNHQLVNWS CALRSAISDI EVENRPLPGH
TQLRLPGCPT PVSFGLLFSV AFPVDGEPDA EVVVGTTRPE TLPGDVAVAV HPDDSRYTHL
HGRQLRHPLM GQPLPLITDY AVQPHVGTGA VKVTPAHSPA DAEMGARHGL SPLNVIAEDG
TMTSLCGDWL QGLHRFVARE KIMSVLSEWG LFRGLQNHPM VLPICSRSGD VIEYLLKNQW
FVRCQEMGAR AAKAVESGAL ELSPSFHQKN WQHWFSHIGD WCVSRQLWWG HQIPAYLVVE
DHAQGEEDCW VVGRSEAEAR EVAAELTGRP GAELTLERDP DVLDTWFSSA LFPFSALGWP
QETPDLARFY PLSLLETGSD LLLFWVGRMV MLGTQLTGQL PFSKVLLHPM VRDRQGRKMS
KSLGNVLDPR DIISGVEMQV LQEKLRSGNL DPAELAIVAA AQKKDFPHGI PECGTDALRF
TLCSHGVQAG DLHLSVSEVQ SCRHFCNKIW NALRFILNAL GEKFVPQPAE ELSPSSPMDA
WILSRLALAA QECERGFLTR ELSLVTHALH HFWLHNLCDV YLEAVKPVLW HSPRPLGPPQ
VLFSCADLGL RLLAPLMPFL AEELWQRLPP RPGCPPAPSI SVAPYPSACS LEHWRQPELE
RRFSRVQEVV QVLRALRATY QLTKARPRVL LQSSEPGDQG LFEAFLEPLG TLGYCGAVGL
LPPGTAAPSG WAQAPLSDTA QVYMELQGLV DPQIQLPLLA ARRYKLQKQL DSLTARTPSE
GEAGTQRQQK LSSLQLELSK LDKAASHLRQ LMDEPPAPGS PEL*
speed 1.59 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: 0.999999999985203 (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) chr6:30893428G>AN/A show variant in all transcripts   IGV
HGNC symbol VARS2
Ensembl transcript ID ENST00000542001
Genbank transcript ID NM_001167733
UniProt peptide Q5ST30
alteration type single base exchange
alteration region CDS
DNA changes c.2473G>A
cDNA.2832G>A
g.17410G>A
AA changes A825T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS
825
frameshift no
known variant Reference ID: rs2252863
databasehomozygous (A/A)heterozygousallele carriers
1000G158801959
ExAC61072055326660
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-2.2940
-0.4970
(flanking)-0.0160
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased17402wt: 0.60 / mu: 0.76wt: GTTACCCCCAGGCGC
mu: GTTACCCCCAGGCAC
 TACC|ccca
Donor marginally increased17407wt: 0.8365 / mu: 0.8666 (marginal change - not scored)wt: CCCCAGGCGCAGCAG
mu: CCCCAGGCACAGCAG
 CCAG|gcgc
Donor increased17406wt: 0.56 / mu: 0.90wt: CCCCCAGGCGCAGCA
mu: CCCCCAGGCACAGCA
 CCCA|ggcg
Donor increased17412wt: 0.28 / mu: 0.66wt: GGCGCAGCAGCTCCC
mu: GGCACAGCAGCTCCC
 CGCA|gcag
distance from splice site 69
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      825YCGAVGLLPPGAAAPSGWAQAPLS
mutated  not conserved    825YCGAVGLLPPGTAAPSGWAQAPL
Ptroglodytes  all identical  ENSPTRG00000034497  974YCGAVGLLPPGAAAPSGWAQAPL
Mmulatta  all identical  ENSMMUG00000018609  966HCGAVGLLPPGAAAPSGWAQAPL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000038838  966HCGAVGFLSPGAAAPSGWALTPL
Ggallus  no homologue    
Trubripes  no alignment  ENSTRUG00000005264  n/a
Drerio  not conserved  ENSDARG00000056717  965AGFSDCPPAKASAVGVVDHSL
Dmelanogaster  no alignment  FBgn0035942  n/a
Celegans  no alignment  ZC513.4  n/a
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
985985CONFLICTE -> G (in Ref. 2; BAB15191).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2772 / 2772
position (AA) of stopcodon in wt / mu AA sequence 924 / 924
position of stopcodon in wt / mu cDNA 3131 / 3131
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 360 / 360
chromosome 6
strand 1
last intron/exon boundary 3030
theoretical NMD boundary in CDS 2620
length of CDS 2772
coding sequence (CDS) position 2473
cDNA position
(for ins/del: last normal base / first normal base)
2832
gDNA position
(for ins/del: last normal base / first normal base)
17410
chromosomal position
(for ins/del: last normal base / first normal base)
30893428
original gDNA sequence snippet TGGGCCTGTTACCCCCAGGCGCAGCAGCTCCCTCCGGCTGG
altered gDNA sequence snippet TGGGCCTGTTACCCCCAGGCACAGCAGCTCCCTCCGGCTGG
original cDNA sequence snippet TGGGCCTGTTACCCCCAGGCGCAGCAGCTCCCTCCGGCTGG
altered cDNA sequence snippet TGGGCCTGTTACCCCCAGGCACAGCAGCTCCCTCCGGCTGG
wildtype AA sequence MCIPPPNVTG SLHIGHALTV AIQDALVRWH RMRGDQVLWV PGSDHAGIAT QAVVEKQLWK
ERGVRRHELS REAFLREVWQ WKEAKGGEIC EQLRALGASL DWDRECFTMD VGSSVAVTEA
FVRLYKAGLL YRNHQLVNWS CALRSAISDI EVENRPLPGH TQLRLPGCPT PVSFGLLFSV
AFPVDGEPDA EVVVGTTRPE TLPGDVAVAV HPDDSRYTHL HGRQLRHPLM GQPLPLITDY
AVQPHVGTGA VKVTPAHSPA DAEMGARHGL SPLNVIAEDG TMTSLCGDWL QGLHRFVARE
KIMSVLSEWG LFRGLQNHPM VLPICSRSGD VIEYLLKNQW FVRCQEMGAR AAKAVESGAL
ELSPSFHQKN WQHWFSHIGD WCVSRQLWWG HQIPAYLVVE DHAQGEEDCW VVGRSEAEAR
EVAAELTGRP GAELTLERDP DVLDTWFSSA LFPFSALGWP QETPDLARFY PLSLLETGSD
LLLFWVGRMV MLGTQLTGQL PFSKVLLHPM VRDRQGRKMS KSLGNVLDPR DIISGVEMQV
LQEKLRSGNL DPAELAIVAA AQKKDFPHGI PECGTDALRF TLCSHGVQAG DLHLSVSEVQ
SCRHFCNKIW NALRFILNAL GEKFVPQPAE ELSPSSPMDA WILSRLALAA QECERGFLTR
ELSLVTHALH HFWLHNLCDV YLEAVKPVLW HSPRPLGPPQ VLFSCADLGL RLLAPLMPFL
AEELWQRLPP RPGCPPAPSI SVAPYPSACS LEHWRQPELE RRFSRVQEVV QVLRALRATY
QLTKARPRVL LQSSEPGDQG LFEAFLEPLG TLGYCGAVGL LPPGAAAPSG WAQAPLSDTA
QVYMELQGLV DPQIQLPLLA ARRYKLQKQL DSLTARTPSE GEAGTQRQQK LSSLQLELSK
LDKAASHLRQ LMDEPPAPGS PEL*
mutated AA sequence MCIPPPNVTG SLHIGHALTV AIQDALVRWH RMRGDQVLWV PGSDHAGIAT QAVVEKQLWK
ERGVRRHELS REAFLREVWQ WKEAKGGEIC EQLRALGASL DWDRECFTMD VGSSVAVTEA
FVRLYKAGLL YRNHQLVNWS CALRSAISDI EVENRPLPGH TQLRLPGCPT PVSFGLLFSV
AFPVDGEPDA EVVVGTTRPE TLPGDVAVAV HPDDSRYTHL HGRQLRHPLM GQPLPLITDY
AVQPHVGTGA VKVTPAHSPA DAEMGARHGL SPLNVIAEDG TMTSLCGDWL QGLHRFVARE
KIMSVLSEWG LFRGLQNHPM VLPICSRSGD VIEYLLKNQW FVRCQEMGAR AAKAVESGAL
ELSPSFHQKN WQHWFSHIGD WCVSRQLWWG HQIPAYLVVE DHAQGEEDCW VVGRSEAEAR
EVAAELTGRP GAELTLERDP DVLDTWFSSA LFPFSALGWP QETPDLARFY PLSLLETGSD
LLLFWVGRMV MLGTQLTGQL PFSKVLLHPM VRDRQGRKMS KSLGNVLDPR DIISGVEMQV
LQEKLRSGNL DPAELAIVAA AQKKDFPHGI PECGTDALRF TLCSHGVQAG DLHLSVSEVQ
SCRHFCNKIW NALRFILNAL GEKFVPQPAE ELSPSSPMDA WILSRLALAA QECERGFLTR
ELSLVTHALH HFWLHNLCDV YLEAVKPVLW HSPRPLGPPQ VLFSCADLGL RLLAPLMPFL
AEELWQRLPP RPGCPPAPSI SVAPYPSACS LEHWRQPELE RRFSRVQEVV QVLRALRATY
QLTKARPRVL LQSSEPGDQG LFEAFLEPLG TLGYCGAVGL LPPGTAAPSG WAQAPLSDTA
QVYMELQGLV DPQIQLPLLA ARRYKLQKQL DSLTARTPSE GEAGTQRQQK LSSLQLELSK
LDKAASHLRQ LMDEPPAPGS PEL*
speed 1.61 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