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: ENST00000264093
Querying Taster for transcript #2: ENST00000348222
Querying Taster for transcript #3: ENST00000356837
MT speed 0 s - this script 3.484187 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
DGUOKdisease_causing_automatic0.999999972188246simple_aae0R120Ksingle base exchangers104893631show file
DGUOKdisease_causing_automatic0.999999999286166simple_aae0R142Ksingle base exchangers104893631show file
DGUOKdisease_causing_automatic0.999999999928903simple_aae0R142Ksingle base exchangers104893631show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999972188246 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM024768)
  • known disease mutation: rs8157 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:74174015G>AN/A show variant in all transcripts   IGV
HGNC symbol DGUOK
Ensembl transcript ID ENST00000356837
Genbank transcript ID N/A
UniProt peptide Q16854
alteration type single base exchange
alteration region CDS
DNA changes c.359G>A
cDNA.362G>A
g.20063G>A
AA changes R120K Score: 26 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 120
frameshift no
known variant Reference ID: rs104893631
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs8157 (pathogenic for Mitochondrial DNA-depletion syndrome 3, hepatocerebral) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM024768)

known disease mutation at this position, please check HGMD for details (HGMD ID CM024768)
known disease mutation at this position, please check HGMD for details (HGMD ID CM024768)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.4721
5.9091
(flanking)-0.1350.974
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 increased20058wt: 0.9850 / mu: 0.9962 (marginal change - not scored)wt: ATCTTTGAGAGGTCT
mu: ATCTTTGAGAAGTCT		 CTTT|gaga
distance from splice site 19
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      120LQARKPVQIFERSVYSDRYIFAKN
mutated  all conserved    120LQARKPVQIFEKSVYSDRYIFAK
Ptroglodytes  all identical  ENSPTRG00000012074  142LQARKPVQIFERSVYSDRYIFAK
Mmulatta  all identical  ENSMMUG00000017830  142LQARKPVQIFERSVYSDRYIFAK
Fcatus  no alignment  ENSFCAG00000012099  n/a
Mmusculus  all identical  ENSMUSG00000014554  142LQAEKSVRVFERSVYSDRYIFAK
Ggallus  no alignment  ENSGALG00000022134  n/a
Trubripes  all identical  ENSTRUG00000012499  130LTSVGTAVQVYERSVYSDRY
Drerio  all identical  ENSDARG00000075395  133LRSRGGAVRVYERSVYSDRYIFAL
Dmelanogaster  all identical  FBgn0022338  112-------KIMERSIFSARYCFVE
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000019642  126LHQQEPVQIFERSVYSDRYIF
protein features
start (aa)end (aa)featuredetails 
103123HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 768 / 768
position (AA) of stopcodon in wt / mu AA sequence 256 / 256
position of stopcodon in wt / mu cDNA 771 / 771
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 4 / 4
chromosome 2
strand 1
last intron/exon boundary 745
theoretical NMD boundary in CDS 691
length of CDS 768
coding sequence (CDS) position 359
cDNA position
(for ins/del: last normal base / first normal base)		 362
gDNA position
(for ins/del: last normal base / first normal base)		 20063
chromosomal position
(for ins/del: last normal base / first normal base)		 74174015
original gDNA sequence snippet GCCAGTACAGATCTTTGAGAGGTCTGTGTACAGTGACAGGT
altered gDNA sequence snippet GCCAGTACAGATCTTTGAGAAGTCTGTGTACAGTGACAGGT
original cDNA sequence snippet GCCAGTACAGATCTTTGAGAGGTCTGTGTACAGTGACAGGT
altered cDNA sequence snippet GCCAGTACAGATCTTTGAGAAGTCTGTGTACAGTGACAGGT
wildtype AA sequence MAAGRLFLSR LRAPFSSMAK SPLEGVSSSR GLHAGRGPRR LSIEGNIGNI LKQIRMRAPI
QETACTAQSL GNLLDMMYRE PARWSYTFQT FSFLSRLKVQ LEPFPEKLLQ ARKPVQIFER
SVYSDRYIFA KNLFENGSLS DIEWHIYQDW HSFLLWEFAS RITLHGFIYL QASPQVCLKR
LYQRAREEEK GIELAYLEQL HGQHEAWLIH KTTKLHFEAL MNIPVLVLDV NDDFSEEVTK
QEDLMREVNT FVKNL*
mutated AA sequence MAAGRLFLSR LRAPFSSMAK SPLEGVSSSR GLHAGRGPRR LSIEGNIGNI LKQIRMRAPI
QETACTAQSL GNLLDMMYRE PARWSYTFQT FSFLSRLKVQ LEPFPEKLLQ ARKPVQIFEK
SVYSDRYIFA KNLFENGSLS DIEWHIYQDW HSFLLWEFAS RITLHGFIYL QASPQVCLKR
LYQRAREEEK GIELAYLEQL HGQHEAWLIH KTTKLHFEAL MNIPVLVLDV NDDFSEEVTK
QEDLMREVNT FVKNL*
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
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999286166 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM024768)
  • known disease mutation: rs8157 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:74174015G>AN/A show variant in all transcripts   IGV
HGNC symbol DGUOK
Ensembl transcript ID ENST00000264093
Genbank transcript ID NM_080916
UniProt peptide Q16854
alteration type single base exchange
alteration region CDS
DNA changes c.425G>A
cDNA.510G>A
g.20063G>A
AA changes R142K Score: 26 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 142
frameshift no
known variant Reference ID: rs104893631
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs8157 (pathogenic for Mitochondrial DNA-depletion syndrome 3, hepatocerebral) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM024768)

known disease mutation at this position, please check HGMD for details (HGMD ID CM024768)
known disease mutation at this position, please check HGMD for details (HGMD ID CM024768)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.4721
5.9091
(flanking)-0.1350.974
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 increased20058wt: 0.9850 / mu: 0.9962 (marginal change - not scored)wt: ATCTTTGAGAGGTCT
mu: ATCTTTGAGAAGTCT		 CTTT|gaga
distance from splice site 19
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      142LQARKPVQIFERSVYSDRYIFAKN
mutated  all conserved    142LQARKPVQIFEKSVYSDRYIFAK
Ptroglodytes  all identical  ENSPTRG00000012074  142LQARKPVQIFERSVYSDRYIFAK
Mmulatta  all identical  ENSMMUG00000017830  142LQARKPVQIFERSVYSDRYIFAK
Fcatus  no alignment  ENSFCAG00000012099  n/a
Mmusculus  all identical  ENSMUSG00000014554  142LQAEKSVRVFERSVYSDRYIFAK
Ggallus  no alignment  ENSGALG00000022134  n/a
Trubripes  all identical  ENSTRUG00000012499  130LTSVGTAVQVYERSVYSDRYIFAL
Drerio  all identical  ENSDARG00000075395  133LRSRGGAVRVYERSVYSDRYIFAL
Dmelanogaster  all identical  FBgn0022338  112-------KIMERSIFSARYCFVE
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000019642  126LHQQEPVQIFERSVYSDRYIFAK
protein features
start (aa)end (aa)featuredetails 
137142STRANDlost
142142BINDINGSubstrate.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 834 / 834
position (AA) of stopcodon in wt / mu AA sequence 278 / 278
position of stopcodon in wt / mu cDNA 919 / 919
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 86 / 86
chromosome 2
strand 1
last intron/exon boundary 893
theoretical NMD boundary in CDS 757
length of CDS 834
coding sequence (CDS) position 425
cDNA position
(for ins/del: last normal base / first normal base)		 510
gDNA position
(for ins/del: last normal base / first normal base)		 20063
chromosomal position
(for ins/del: last normal base / first normal base)		 74174015
original gDNA sequence snippet GCCAGTACAGATCTTTGAGAGGTCTGTGTACAGTGACAGGT
altered gDNA sequence snippet GCCAGTACAGATCTTTGAGAAGTCTGTGTACAGTGACAGGT
original cDNA sequence snippet GCCAGTACAGATCTTTGAGAGGTCTGTGTACAGTGACAGGT
altered cDNA sequence snippet GCCAGTACAGATCTTTGAGAAGTCTGTGTACAGTGACAGGT
wildtype AA sequence MAAGRLFLSR LRAPFSSMAK SPLEGVSSSR GLHAGRGPRR LSIEGNIAVG KSTFVKLLTK
TYPEWHVATE PVATWQNIQA AGTQKACTAQ SLGNLLDMMY REPARWSYTF QTFSFLSRLK
VQLEPFPEKL LQARKPVQIF ERSVYSDRYI FAKNLFENGS LSDIEWHIYQ DWHSFLLWEF
ASRITLHGFI YLQASPQVCL KRLYQRAREE EKGIELAYLE QLHGQHEAWL IHKTTKLHFE
ALMNIPVLVL DVNDDFSEEV TKQEDLMREV NTFVKNL*
mutated AA sequence MAAGRLFLSR LRAPFSSMAK SPLEGVSSSR GLHAGRGPRR LSIEGNIAVG KSTFVKLLTK
TYPEWHVATE PVATWQNIQA AGTQKACTAQ SLGNLLDMMY REPARWSYTF QTFSFLSRLK
VQLEPFPEKL LQARKPVQIF EKSVYSDRYI FAKNLFENGS LSDIEWHIYQ DWHSFLLWEF
ASRITLHGFI YLQASPQVCL KRLYQRAREE EKGIELAYLE QLHGQHEAWL IHKTTKLHFE
ALMNIPVLVL DVNDDFSEEV TKQEDLMREV NTFVKNL*
speed 0.72 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: 0.999999999928903 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM024768)
  • known disease mutation: rs8157 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:74174015G>AN/A show variant in all transcripts   IGV
HGNC symbol DGUOK
Ensembl transcript ID ENST00000348222
Genbank transcript ID NM_080918
UniProt peptide Q16854
alteration type single base exchange
alteration region CDS
DNA changes c.425G>A
cDNA.510G>A
g.20063G>A
AA changes R142K Score: 26 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 142
frameshift no
known variant Reference ID: rs104893631
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs8157 (pathogenic for Mitochondrial DNA-depletion syndrome 3, hepatocerebral) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM024768)

known disease mutation at this position, please check HGMD for details (HGMD ID CM024768)
known disease mutation at this position, please check HGMD for details (HGMD ID CM024768)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.4721
5.9091
(flanking)-0.1350.974
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 increased20058wt: 0.9850 / mu: 0.9962 (marginal change - not scored)wt: ATCTTTGAGAGGTCT
mu: ATCTTTGAGAAGTCT		 CTTT|gaga
distance from splice site 19
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      142LQARKPVQIFERSVYSDRLHFEAL
mutated  all conserved    142LQARKPVQIFEKSVYSDRLHFEA
Ptroglodytes  all identical  ENSPTRG00000012074  142LQARKPVQIFERSVYSDRYIF
Mmulatta  all identical  ENSMMUG00000017830  142LQARKPVQIFERSVYSDRYIF
Fcatus  no alignment  ENSFCAG00000012099  n/a
Mmusculus  all identical  ENSMUSG00000014554  142LQAEKSVRVFERSVYSDRYIF
Ggallus  all identical  ENSGALG00000022134  86LHAQHERWLLERSA---EVHFAE
Trubripes  all identical  ENSTRUG00000012499  130LTSVGTAVQVYERSVYSDRYIF
Drerio  all identical  ENSDARG00000075395  133LRSRGGAVRVYERSVYSDRYIF
Dmelanogaster  all identical  FBgn0022338  112-------KIMERSIFSARYCF
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000019642  126LHQQEPVQIFERSVYSDRYIF
protein features
start (aa)end (aa)featuredetails 
137142STRANDlost
142142BINDINGSubstrate.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 570 / 570
position (AA) of stopcodon in wt / mu AA sequence 190 / 190
position of stopcodon in wt / mu cDNA 655 / 655
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 86 / 86
chromosome 2
strand 1
last intron/exon boundary 629
theoretical NMD boundary in CDS 493
length of CDS 570
coding sequence (CDS) position 425
cDNA position
(for ins/del: last normal base / first normal base)		 510
gDNA position
(for ins/del: last normal base / first normal base)		 20063
chromosomal position
(for ins/del: last normal base / first normal base)		 74174015
original gDNA sequence snippet GCCAGTACAGATCTTTGAGAGGTCTGTGTACAGTGACAGGT
altered gDNA sequence snippet GCCAGTACAGATCTTTGAGAAGTCTGTGTACAGTGACAGGT
original cDNA sequence snippet GCCAGTACAGATCTTTGAGAGGTCTGTGTACAGTGACAGGC
altered cDNA sequence snippet GCCAGTACAGATCTTTGAGAAGTCTGTGTACAGTGACAGGC
wildtype AA sequence MAAGRLFLSR LRAPFSSMAK SPLEGVSSSR GLHAGRGPRR LSIEGNIAVG KSTFVKLLTK
TYPEWHVATE PVATWQNIQA AGTQKACTAQ SLGNLLDMMY REPARWSYTF QTFSFLSRLK
VQLEPFPEKL LQARKPVQIF ERSVYSDRLH FEALMNIPVL VLDVNDDFSE EVTKQEDLMR
EVNTFVKNL*
mutated AA sequence MAAGRLFLSR LRAPFSSMAK SPLEGVSSSR GLHAGRGPRR LSIEGNIAVG KSTFVKLLTK
TYPEWHVATE PVATWQNIQA AGTQKACTAQ SLGNLLDMMY REPARWSYTF QTFSFLSRLK
VQLEPFPEKL LQARKPVQIF EKSVYSDRLH FEALMNIPVL VLDVNDDFSE EVTKQEDLMR
EVNTFVKNL*
speed 0.78 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