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: ENST00000273153
Querying Taster for transcript #2: ENST00000514182
MT speed 2.6 s - this script 5.995777 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CSRNP1polymorphism_automatic4.33100222352323e-11simple_aaeaffectedV453Isingle base exchangers1274958show file
CSRNP1polymorphism_automatic4.33100222352323e-11simple_aaeaffectedV453Isingle base exchangers1274958show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999999995669 (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) chr3:39184959C>TN/A show variant in all transcripts   IGV
HGNC symbol CSRNP1
Ensembl transcript ID ENST00000273153
Genbank transcript ID NM_033027
UniProt peptide Q96S65
alteration type single base exchange
alteration region CDS
DNA changes c.1357G>A
cDNA.1535G>A
g.11095G>A
AA changes V453I Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS
453
frameshift no
known variant Reference ID: rs1274958
databasehomozygous (T/T)heterozygousallele carriers
1000G15418472388
ExAC---
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9170.752
0.2210.169
(flanking)-0.520.077
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased11087wt: 0.40 / mu: 0.54wt: CTTCACATCAGGCGT
mu: CTTCACATCAGGCAT
 TCAC|atca
Donor marginally increased11100wt: 0.9155 / mu: 0.9756 (marginal change - not scored)wt: GTCCTGGATGAGAAT
mu: ATCCTGGATGAGAAT
 CCTG|gatg
Donor gained110910.51mu: ACATCAGGCATCCTG ATCA|ggca
distance from splice site 577
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      453HSYSGCSFTSGVLDENANLDASCF
mutated  all conserved    453HSYSGCSFTSGILDENANLDASC
Ptroglodytes  all conserved  ENSPTRG00000014768  451HSYSGCSFTSGILDENANLDASC
Mmulatta  all conserved  ENSMMUG00000020147  457HSYSGCSFTSGILDENANLDASC
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000032515  448HSQSGSSLASGILDENANLDASC
Ggallus  not conserved  ENSGALG00000006028  438PGPGASSHLSECLDENANQDSGG
Trubripes  all conserved  ENSTRUG00000017709  428HTDNRATAASELLDENANQANAL
Drerio  all conserved  ENSDARG00000038429  446QTDNSRTAMSELLDENAN
Dmelanogaster  all conserved  FBgn0261647  749SSSRLSQINDLLQHNRNTTAAL
Celegans  no alignment  C41D11.3  n/a
Xtropicalis  not conserved  ENSXETG00000004234  440SSFPKC------IDDN
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1770 / 1770
position (AA) of stopcodon in wt / mu AA sequence 590 / 590
position of stopcodon in wt / mu cDNA 1948 / 1948
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 179 / 179
chromosome 3
strand -1
last intron/exon boundary 959
theoretical NMD boundary in CDS 730
length of CDS 1770
coding sequence (CDS) position 1357
cDNA position
(for ins/del: last normal base / first normal base)
1535
gDNA position
(for ins/del: last normal base / first normal base)
11095
chromosomal position
(for ins/del: last normal base / first normal base)
39184959
original gDNA sequence snippet GCTGTAGCTTCACATCAGGCGTCCTGGATGAGAATGCCAAC
altered gDNA sequence snippet GCTGTAGCTTCACATCAGGCATCCTGGATGAGAATGCCAAC
original cDNA sequence snippet GCTGTAGCTTCACATCAGGCGTCCTGGATGAGAATGCCAAC
altered cDNA sequence snippet GCTGTAGCTTCACATCAGGCATCCTGGATGAGAATGCCAAC
wildtype AA sequence MTGLLKRKFD QLDEDNSSVS SSSSSSGCQS RSCSPSSSVS RAWDSEEEGP WDQMPLPDRD
FCGPRSFTPL SILKRARRER PGRVAFDGIT VFYFPRCQGF TSVPSRGGCT LGMALRHSAC
RRFSLAEFAQ EQARARHEKL RQRLKEEKLE MLQWKLSAAG VPQAEAGLPP VVDAIDDASV
EEDLAVAVAG GRLEEVSFLQ PYPARRRRAL LRASGVRRID REEKRELQAL RQSREDCGCH
CDRICDPETC SCSLAGIKCQ MDHTAFPCGC CREGCENPMG RVEFNQARVQ THFIHTLTRL
QLEQEAESFR ELEAPAQGSP PSPGEEALVP TFPLAKPPMN NELGDNSCSS DMTDSSTASS
SASGTSEAPD CPTHPGLPGP GFQPGVDDDS LARILSFSDS DFGGEEEEEE EGSVGNLDNL
SCFHPADIFG TSDPGGLASW THSYSGCSFT SGVLDENANL DASCFLNGGL EGSREGSLPG
TSVPPSMDAG RSSSVDLSLS SCDSFELLQA LPDYSLGPHY TSQKVSDSLD NIEAPHFPLP
GLSPPGDASS CFLESLMGFS EPAAEALDPF IDSQFEDTVP ASLMEPVPV*
mutated AA sequence MTGLLKRKFD QLDEDNSSVS SSSSSSGCQS RSCSPSSSVS RAWDSEEEGP WDQMPLPDRD
FCGPRSFTPL SILKRARRER PGRVAFDGIT VFYFPRCQGF TSVPSRGGCT LGMALRHSAC
RRFSLAEFAQ EQARARHEKL RQRLKEEKLE MLQWKLSAAG VPQAEAGLPP VVDAIDDASV
EEDLAVAVAG GRLEEVSFLQ PYPARRRRAL LRASGVRRID REEKRELQAL RQSREDCGCH
CDRICDPETC SCSLAGIKCQ MDHTAFPCGC CREGCENPMG RVEFNQARVQ THFIHTLTRL
QLEQEAESFR ELEAPAQGSP PSPGEEALVP TFPLAKPPMN NELGDNSCSS DMTDSSTASS
SASGTSEAPD CPTHPGLPGP GFQPGVDDDS LARILSFSDS DFGGEEEEEE EGSVGNLDNL
SCFHPADIFG TSDPGGLASW THSYSGCSFT SGILDENANL DASCFLNGGL EGSREGSLPG
TSVPPSMDAG RSSSVDLSLS SCDSFELLQA LPDYSLGPHY TSQKVSDSLD NIEAPHFPLP
GLSPPGDASS CFLESLMGFS EPAAEALDPF IDSQFEDTVP ASLMEPVPV*
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
Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999999995669 (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) chr3:39184959C>TN/A show variant in all transcripts   IGV
HGNC symbol CSRNP1
Ensembl transcript ID ENST00000514182
Genbank transcript ID N/A
UniProt peptide Q96S65
alteration type single base exchange
alteration region CDS
DNA changes c.1357G>A
cDNA.1463G>A
g.11095G>A
AA changes V453I Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS
453
frameshift no
known variant Reference ID: rs1274958
databasehomozygous (T/T)heterozygousallele carriers
1000G15418472388
ExAC---
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9170.752
0.2210.169
(flanking)-0.520.077
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased11087wt: 0.40 / mu: 0.54wt: CTTCACATCAGGCGT
mu: CTTCACATCAGGCAT
 TCAC|atca
Donor marginally increased11100wt: 0.9155 / mu: 0.9756 (marginal change - not scored)wt: GTCCTGGATGAGAAT
mu: ATCCTGGATGAGAAT
 CCTG|gatg
Donor gained110910.51mu: ACATCAGGCATCCTG ATCA|ggca
distance from splice site 577
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      453HSYSGCSFTSGVLDENANLDASCF
mutated  all conserved    453HSYSGCSFTSGILDENANLDASC
Ptroglodytes  all conserved  ENSPTRG00000014768  451HSYSGCSFTSGILDENANLDASC
Mmulatta  all conserved  ENSMMUG00000020147  457HSYSGCSFTSGILDENANLDASC
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000032515  448HSQSGSSLASGILDENANLDASC
Ggallus  not conserved  ENSGALG00000006028  438PGPGASSHLSECLDENANQDSGG
Trubripes  all conserved  ENSTRUG00000017709  428HTDNRATAASELLDENANQANAL
Drerio  all conserved  ENSDARG00000038429  446QTDNSRTAMSELLDENAN
Dmelanogaster  all conserved  FBgn0261647  749SSSRLSQINDLLQHNRNTTAAL
Celegans  no alignment  C41D11.3  n/a
Xtropicalis  not conserved  ENSXETG00000004234  440SSFPKC------IDDN
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1770 / 1770
position (AA) of stopcodon in wt / mu AA sequence 590 / 590
position of stopcodon in wt / mu cDNA 1876 / 1876
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 107 / 107
chromosome 3
strand -1
last intron/exon boundary 887
theoretical NMD boundary in CDS 730
length of CDS 1770
coding sequence (CDS) position 1357
cDNA position
(for ins/del: last normal base / first normal base)
1463
gDNA position
(for ins/del: last normal base / first normal base)
11095
chromosomal position
(for ins/del: last normal base / first normal base)
39184959
original gDNA sequence snippet GCTGTAGCTTCACATCAGGCGTCCTGGATGAGAATGCCAAC
altered gDNA sequence snippet GCTGTAGCTTCACATCAGGCATCCTGGATGAGAATGCCAAC
original cDNA sequence snippet GCTGTAGCTTCACATCAGGCGTCCTGGATGAGAATGCCAAC
altered cDNA sequence snippet GCTGTAGCTTCACATCAGGCATCCTGGATGAGAATGCCAAC
wildtype AA sequence MTGLLKRKFD QLDEDNSSVS SSSSSSGCQS RSCSPSSSVS RAWDSEEEGP WDQMPLPDRD
FCGPRSFTPL SILKRARRER PGRVAFDGIT VFYFPRCQGF TSVPSRGGCT LGMALRHSAC
RRFSLAEFAQ EQARARHEKL RQRLKEEKLE MLQWKLSAAG VPQAEAGLPP VVDAIDDASV
EEDLAVAVAG GRLEEVSFLQ PYPARRRRAL LRASGVRRID REEKRELQAL RQSREDCGCH
CDRICDPETC SCSLAGIKCQ MDHTAFPCGC CREGCENPMG RVEFNQARVQ THFIHTLTRL
QLEQEAESFR ELEAPAQGSP PSPGEEALVP TFPLAKPPMN NELGDNSCSS DMTDSSTASS
SASGTSEAPD CPTHPGLPGP GFQPGVDDDS LARILSFSDS DFGGEEEEEE EGSVGNLDNL
SCFHPADIFG TSDPGGLASW THSYSGCSFT SGVLDENANL DASCFLNGGL EGSREGSLPG
TSVPPSMDAG RSSSVDLSLS SCDSFELLQA LPDYSLGPHY TSQKVSDSLD NIEAPHFPLP
GLSPPGDASS CFLESLMGFS EPAAEALDPF IDSQFEDTVP ASLMEPVPV*
mutated AA sequence MTGLLKRKFD QLDEDNSSVS SSSSSSGCQS RSCSPSSSVS RAWDSEEEGP WDQMPLPDRD
FCGPRSFTPL SILKRARRER PGRVAFDGIT VFYFPRCQGF TSVPSRGGCT LGMALRHSAC
RRFSLAEFAQ EQARARHEKL RQRLKEEKLE MLQWKLSAAG VPQAEAGLPP VVDAIDDASV
EEDLAVAVAG GRLEEVSFLQ PYPARRRRAL LRASGVRRID REEKRELQAL RQSREDCGCH
CDRICDPETC SCSLAGIKCQ MDHTAFPCGC CREGCENPMG RVEFNQARVQ THFIHTLTRL
QLEQEAESFR ELEAPAQGSP PSPGEEALVP TFPLAKPPMN NELGDNSCSS DMTDSSTASS
SASGTSEAPD CPTHPGLPGP GFQPGVDDDS LARILSFSDS DFGGEEEEEE EGSVGNLDNL
SCFHPADIFG TSDPGGLASW THSYSGCSFT SGILDENANL DASCFLNGGL EGSREGSLPG
TSVPPSMDAG RSSSVDLSLS SCDSFELLQA LPDYSLGPHY TSQKVSDSLD NIEAPHFPLP
GLSPPGDASS CFLESLMGFS EPAAEALDPF IDSQFEDTVP ASLMEPVPV*
speed 1.12 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