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: ENST00000300215
Querying Taster for transcript #2: ENST00000540029
Querying Taster for transcript #3: ENST00000441366
MT speed 2.51 s - this script 3.688456 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
EPB42disease_causing_automatic0.992805264776931simple_aae0R310Qsingle base exchangers121917734show file
EPB42disease_causing_automatic0.992805264776931simple_aae0R202Qsingle base exchangers121917734show file
EPB42disease_causing_automatic0.992805264776931simple_aae0R280Qsingle base exchangers121917734show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.992805264776931 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM950361)
  • known disease mutation: rs13235 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:43500967C>TN/A show variant in all transcripts   IGV
HGNC symbol EPB42
Ensembl transcript ID ENST00000300215
Genbank transcript ID NM_000119
UniProt peptide P16452
alteration type single base exchange
alteration region CDS
DNA changes c.929G>A
cDNA.1387G>A
g.12515G>A
AA changes R310Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 310
frameshift no
known variant Reference ID: rs121917734
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs13235 (pathogenic for Spherocytosis type 5) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950361)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950361)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950361)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.7410.759
4.1730.989
(flanking)0.3660.988
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased12512wt: 0.9693 / mu: 0.9747 (marginal change - not scored)wt: AGTGCTGCGATGCCT
mu: AGTGCTGCAATGCCT		 TGCT|gcga
distance from splice site 7
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      310WVLAAVACTVLRCLGIPARVVTTF
mutated  all conserved    310LAAVACTVLQCLGIPARVVTT
Ptroglodytes  all identical  ENSPTRG00000006988  280WVLAAVACTVLRCLGIPARVVTT
Mmulatta  all identical  ENSMMUG00000022255  309LAAVACTVLRCLGIPARVVTT
Fcatus  all identical  ENSFCAG00000013219  307FAAVACTVLRCLGIPARVVTT
Mmusculus  all identical  ENSMUSG00000023216  280WVSAAVACTVLRCLGIPARVVTT
Ggallus  all identical  ENSGALG00000021230  286WVFAAVMCSVLRCLGIPTRVVT
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2166 / 2166
position (AA) of stopcodon in wt / mu AA sequence 722 / 722
position of stopcodon in wt / mu cDNA 2624 / 2624
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 459 / 459
chromosome 15
strand -1
last intron/exon boundary 2462
theoretical NMD boundary in CDS 1953
length of CDS 2166
coding sequence (CDS) position 929
cDNA position
(for ins/del: last normal base / first normal base)		 1387
gDNA position
(for ins/del: last normal base / first normal base)		 12515
chromosomal position
(for ins/del: last normal base / first normal base)		 43500967
original gDNA sequence snippet CCCTCTTCTCACAGTGCTGCGATGCCTGGGAATCCCTGCCC
altered gDNA sequence snippet CCCTCTTCTCACAGTGCTGCAATGCCTGGGAATCCCTGCCC
original cDNA sequence snippet TGTTGCTTGCACAGTGCTGCGATGCCTGGGAATCCCTGCCC
altered cDNA sequence snippet TGTTGCTTGCACAGTGCTGCAATGCCTGGGAATCCCTGCCC
wildtype AA sequence MGQGEPSQRS TGLAGLYAAP AASPVFIKGS GMDALGIKSC DFQAARNNEE HHTKALSSRR
LFVRRGQPFT IILYFRAPVR AFLPALKKVA LTAQTGEQPS KINRTQATFP ISSLGDRKWW
SAVVEERDAQ SWTISVTTPA DAVIGHYSLL LQVSGRKQLL LGQFTLLFNP WNREDAVFLK
NEAQRMEYLL NQNGLIYLGT ADCIQAESWD FGQFEGDVID LSLRLLSKDK QVEKWSQPVH
VARVLGALLH FLKEQRVLPT PQTQATQEGA LLNKRRGSVP ILRQWLTGRG RPVYDGQAWV
LAAVACTVLR CLGIPARVVT TFASAQGTGG RLLIDEYYNE EGLQNGEGQR GRIWIFQTST
ECWMTRPALP QGYDGWQILH PSAPNGGGVL GSCDLVPVRA VKEGTLGLTP AVSDLFAAIN
ASCVVWKCCE DGTLELTDSN TKYVGNNIST KGVGSDRCED ITQNYKYPEG SLQEKEVLER
VEKEKMEREK DNGIRPPSLE TASPLYLLLK APSSLPLRGD AQISVTLVNH SEQEKAVQLA
IGVQAVHYNG VLAAKLWRKK LHLTLSANLE KIITIGLFFS NFERNPPENT FLRLTAMATH
SESNLSCFAQ EDIAICRPHL AIKMPEKAEQ YQPLTASVSL QNSLDAPMED CVISILGRGL
IHRERSYRFR SVWPENTMCA KFQFTPTHVG LQRLTVEVDC NMFQNLTNYK SVTVVAPELS
A*
mutated AA sequence MGQGEPSQRS TGLAGLYAAP AASPVFIKGS GMDALGIKSC DFQAARNNEE HHTKALSSRR
LFVRRGQPFT IILYFRAPVR AFLPALKKVA LTAQTGEQPS KINRTQATFP ISSLGDRKWW
SAVVEERDAQ SWTISVTTPA DAVIGHYSLL LQVSGRKQLL LGQFTLLFNP WNREDAVFLK
NEAQRMEYLL NQNGLIYLGT ADCIQAESWD FGQFEGDVID LSLRLLSKDK QVEKWSQPVH
VARVLGALLH FLKEQRVLPT PQTQATQEGA LLNKRRGSVP ILRQWLTGRG RPVYDGQAWV
LAAVACTVLQ CLGIPARVVT TFASAQGTGG RLLIDEYYNE EGLQNGEGQR GRIWIFQTST
ECWMTRPALP QGYDGWQILH PSAPNGGGVL GSCDLVPVRA VKEGTLGLTP AVSDLFAAIN
ASCVVWKCCE DGTLELTDSN TKYVGNNIST KGVGSDRCED ITQNYKYPEG SLQEKEVLER
VEKEKMEREK DNGIRPPSLE TASPLYLLLK APSSLPLRGD AQISVTLVNH SEQEKAVQLA
IGVQAVHYNG VLAAKLWRKK LHLTLSANLE KIITIGLFFS NFERNPPENT FLRLTAMATH
SESNLSCFAQ EDIAICRPHL AIKMPEKAEQ YQPLTASVSL QNSLDAPMED CVISILGRGL
IHRERSYRFR SVWPENTMCA KFQFTPTHVG LQRLTVEVDC NMFQNLTNYK SVTVVAPELS
A*
speed 0.82 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

disease causing

 Model: simple_aae, prob: 0.992805264776931 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM950361)
  • known disease mutation: rs13235 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:43500967C>TN/A show variant in all transcripts   IGV
HGNC symbol EPB42
Ensembl transcript ID ENST00000540029
Genbank transcript ID N/A
UniProt peptide P16452
alteration type single base exchange
alteration region CDS
DNA changes c.605G>A
cDNA.789G>A
g.12515G>A
AA changes R202Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 202
frameshift no
known variant Reference ID: rs121917734
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs13235 (pathogenic for Spherocytosis type 5) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950361)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950361)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950361)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.7410.759
4.1730.989
(flanking)0.3660.988
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased12512wt: 0.9693 / mu: 0.9747 (marginal change - not scored)wt: AGTGCTGCGATGCCT
mu: AGTGCTGCAATGCCT		 TGCT|gcga
distance from splice site 7
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      202WVLAAVACTVLRCLGIPARVVTTF
mutated  all conserved    202WVLAAVACTVLQCLGIPARVVTT
Ptroglodytes  all identical  ENSPTRG00000006988  280WVLAAVACTVLRCLGIPARVVTT
Mmulatta  all identical  ENSMMUG00000022255  309WVLAAVACTVLRCLGIPARVVTT
Fcatus  all identical  ENSFCAG00000013219  307WVFAAVACTVLRCLGIPARVVTT
Mmusculus  all identical  ENSMUSG00000023216  280WVSAAVACTVLRCLGIPARVVTT
Ggallus  all identical  ENSGALG00000021230  286WVFAAVMCSVLRCLGIPTRVVTG
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1842 / 1842
position (AA) of stopcodon in wt / mu AA sequence 614 / 614
position of stopcodon in wt / mu cDNA 2026 / 2026
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 185 / 185
chromosome 15
strand -1
last intron/exon boundary 1864
theoretical NMD boundary in CDS 1629
length of CDS 1842
coding sequence (CDS) position 605
cDNA position
(for ins/del: last normal base / first normal base)		 789
gDNA position
(for ins/del: last normal base / first normal base)		 12515
chromosomal position
(for ins/del: last normal base / first normal base)		 43500967
original gDNA sequence snippet CCCTCTTCTCACAGTGCTGCGATGCCTGGGAATCCCTGCCC
altered gDNA sequence snippet CCCTCTTCTCACAGTGCTGCAATGCCTGGGAATCCCTGCCC
original cDNA sequence snippet TGTTGCTTGCACAGTGCTGCGATGCCTGGGAATCCCTGCCC
altered cDNA sequence snippet TGTTGCTTGCACAGTGCTGCAATGCCTGGGAATCCCTGCCC
wildtype AA sequence MGQALGIKSC DFQAARNNEE HHTKALSSRR LFVRRGQPFT IILYFRAPVR AFLPALKKVA
LTAQTEDAVF LKNEAQRMEY LLNQNGLIYL GTADCIQAES WDFGQFEGDV IDLSLRLLSK
DKQVEKWSQP VHVARVLGAL LHFLKEQRVL PTPQTQATQE GALLNKRRGS VPILRQWLTG
RGRPVYDGQA WVLAAVACTV LRCLGIPARV VTTFASAQGT GGRLLIDEYY NEEGLQNGEG
QRGRIWIFQT STECWMTRPA LPQGYDGWQI LHPSAPNGGG VLGSCDLVPV RAVKEGTLGL
TPAVSDLFAA INASCVVWKC CEDGTLELTD SNTKYVGNNI STKGVGSDRC EDITQNYKYP
EGSLQEKEVL ERVEKEKMER EKDNGIRPPS LETASPLYLL LKAPSSLPLR GDAQISVTLV
NHSEQEKAVQ LAIGVQAVHY NGVLAAKLWR KKLHLTLSAN LEKIITIGLF FSNFERNPPE
NTFLRLTAMA THSESNLSCF AQEDIAICRP HLAIKMPEKA EQYQPLTASV SLQNSLDAPM
EDCVISILGR GLIHRERSYR FRSVWPENTM CAKFQFTPTH VGLQRLTVEV DCNMFQNLTN
YKSVTVVAPE LSA*
mutated AA sequence MGQALGIKSC DFQAARNNEE HHTKALSSRR LFVRRGQPFT IILYFRAPVR AFLPALKKVA
LTAQTEDAVF LKNEAQRMEY LLNQNGLIYL GTADCIQAES WDFGQFEGDV IDLSLRLLSK
DKQVEKWSQP VHVARVLGAL LHFLKEQRVL PTPQTQATQE GALLNKRRGS VPILRQWLTG
RGRPVYDGQA WVLAAVACTV LQCLGIPARV VTTFASAQGT GGRLLIDEYY NEEGLQNGEG
QRGRIWIFQT STECWMTRPA LPQGYDGWQI LHPSAPNGGG VLGSCDLVPV RAVKEGTLGL
TPAVSDLFAA INASCVVWKC CEDGTLELTD SNTKYVGNNI STKGVGSDRC EDITQNYKYP
EGSLQEKEVL ERVEKEKMER EKDNGIRPPS LETASPLYLL LKAPSSLPLR GDAQISVTLV
NHSEQEKAVQ LAIGVQAVHY NGVLAAKLWR KKLHLTLSAN LEKIITIGLF FSNFERNPPE
NTFLRLTAMA THSESNLSCF AQEDIAICRP HLAIKMPEKA EQYQPLTASV SLQNSLDAPM
EDCVISILGR GLIHRERSYR FRSVWPENTM CAKFQFTPTH VGLQRLTVEV DCNMFQNLTN
YKSVTVVAPE LSA*
speed 0.89 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

disease causing

 Model: simple_aae, prob: 0.992805264776931 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM950361)
  • known disease mutation: rs13235 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:43500967C>TN/A show variant in all transcripts   IGV
HGNC symbol EPB42
Ensembl transcript ID ENST00000441366
Genbank transcript ID NM_001114134
UniProt peptide P16452
alteration type single base exchange
alteration region CDS
DNA changes c.839G>A
cDNA.1065G>A
g.12515G>A
AA changes R280Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 280
frameshift no
known variant Reference ID: rs121917734
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs13235 (pathogenic for Spherocytosis type 5) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950361)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950361)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950361)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.7410.759
4.1730.989
(flanking)0.3660.988
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased12512wt: 0.9693 / mu: 0.9747 (marginal change - not scored)wt: AGTGCTGCGATGCCT
mu: AGTGCTGCAATGCCT		 TGCT|gcga
distance from splice site 7
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      280WVLAAVACTVLRCLGIPARVVTTF
mutated  all conserved    280WVLAAVACTVLQCLGIPARVVTT
Ptroglodytes  all identical  ENSPTRG00000006988  280WVLAAVACTVLRCLGIPARVVTT
Mmulatta  all identical  ENSMMUG00000022255  309WVLAAVACTVLRCLGIPARVVTT
Fcatus  all identical  ENSFCAG00000013219  307WVFAAVACTVLRCLGIPARVVTT
Mmusculus  all identical  ENSMUSG00000023216  280WVSAAVACTVLRCLGIPARVVTT
Ggallus  all identical  ENSGALG00000021230  286WVFAAVMCSVLRCLGIPTRVVTG
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2076 / 2076
position (AA) of stopcodon in wt / mu AA sequence 692 / 692
position of stopcodon in wt / mu cDNA 2302 / 2302
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 227 / 227
chromosome 15
strand -1
last intron/exon boundary 2140
theoretical NMD boundary in CDS 1863
length of CDS 2076
coding sequence (CDS) position 839
cDNA position
(for ins/del: last normal base / first normal base)		 1065
gDNA position
(for ins/del: last normal base / first normal base)		 12515
chromosomal position
(for ins/del: last normal base / first normal base)		 43500967
original gDNA sequence snippet CCCTCTTCTCACAGTGCTGCGATGCCTGGGAATCCCTGCCC
altered gDNA sequence snippet CCCTCTTCTCACAGTGCTGCAATGCCTGGGAATCCCTGCCC
original cDNA sequence snippet TGTTGCTTGCACAGTGCTGCGATGCCTGGGAATCCCTGCCC
altered cDNA sequence snippet TGTTGCTTGCACAGTGCTGCAATGCCTGGGAATCCCTGCCC
wildtype AA sequence MGQALGIKSC DFQAARNNEE HHTKALSSRR LFVRRGQPFT IILYFRAPVR AFLPALKKVA
LTAQTGEQPS KINRTQATFP ISSLGDRKWW SAVVEERDAQ SWTISVTTPA DAVIGHYSLL
LQVSGRKQLL LGQFTLLFNP WNREDAVFLK NEAQRMEYLL NQNGLIYLGT ADCIQAESWD
FGQFEGDVID LSLRLLSKDK QVEKWSQPVH VARVLGALLH FLKEQRVLPT PQTQATQEGA
LLNKRRGSVP ILRQWLTGRG RPVYDGQAWV LAAVACTVLR CLGIPARVVT TFASAQGTGG
RLLIDEYYNE EGLQNGEGQR GRIWIFQTST ECWMTRPALP QGYDGWQILH PSAPNGGGVL
GSCDLVPVRA VKEGTLGLTP AVSDLFAAIN ASCVVWKCCE DGTLELTDSN TKYVGNNIST
KGVGSDRCED ITQNYKYPEG SLQEKEVLER VEKEKMEREK DNGIRPPSLE TASPLYLLLK
APSSLPLRGD AQISVTLVNH SEQEKAVQLA IGVQAVHYNG VLAAKLWRKK LHLTLSANLE
KIITIGLFFS NFERNPPENT FLRLTAMATH SESNLSCFAQ EDIAICRPHL AIKMPEKAEQ
YQPLTASVSL QNSLDAPMED CVISILGRGL IHRERSYRFR SVWPENTMCA KFQFTPTHVG
LQRLTVEVDC NMFQNLTNYK SVTVVAPELS A*
mutated AA sequence MGQALGIKSC DFQAARNNEE HHTKALSSRR LFVRRGQPFT IILYFRAPVR AFLPALKKVA
LTAQTGEQPS KINRTQATFP ISSLGDRKWW SAVVEERDAQ SWTISVTTPA DAVIGHYSLL
LQVSGRKQLL LGQFTLLFNP WNREDAVFLK NEAQRMEYLL NQNGLIYLGT ADCIQAESWD
FGQFEGDVID LSLRLLSKDK QVEKWSQPVH VARVLGALLH FLKEQRVLPT PQTQATQEGA
LLNKRRGSVP ILRQWLTGRG RPVYDGQAWV LAAVACTVLQ CLGIPARVVT TFASAQGTGG
RLLIDEYYNE EGLQNGEGQR GRIWIFQTST ECWMTRPALP QGYDGWQILH PSAPNGGGVL
GSCDLVPVRA VKEGTLGLTP AVSDLFAAIN ASCVVWKCCE DGTLELTDSN TKYVGNNIST
KGVGSDRCED ITQNYKYPEG SLQEKEVLER VEKEKMEREK DNGIRPPSLE TASPLYLLLK
APSSLPLRGD AQISVTLVNH SEQEKAVQLA IGVQAVHYNG VLAAKLWRKK LHLTLSANLE
KIITIGLFFS NFERNPPENT FLRLTAMATH SESNLSCFAQ EDIAICRPHL AIKMPEKAEQ
YQPLTASVSL QNSLDAPMED CVISILGRGL IHRERSYRFR SVWPENTMCA KFQFTPTHVG
LQRLTVEVDC NMFQNLTNYK SVTVVAPELS A*
speed 0.80 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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