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: ENST00000373176
Querying Taster for transcript #2: ENST00000373156
Querying Taster for transcript #3: ENST00000223836
MT speed 0 s - this script 3.823858 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AK1disease_causing_automatic0.99999999999301simple_aaeaffected0G40Rsingle base exchangers137853204show file
AK1disease_causing_automatic0.99999999999301simple_aaeaffected0G40Rsingle base exchangers137853204show file
AK1disease_causing_automatic0.99999999999301simple_aaeaffected0G56Rsingle base exchangers137853204show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99999999999301 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM031607)
  • known disease mutation: rs18266 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:130635058C>TN/A show variant in all transcripts   IGV
HGNC symbol AK1
Ensembl transcript ID ENST00000373156
Genbank transcript ID N/A
UniProt peptide P00568
alteration type single base exchange
alteration region CDS
DNA changes c.118G>A
cDNA.281G>A
g.4965G>A
AA changes G40R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 40
frameshift no
known variant Reference ID: rs137853204
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs18266 (pathogenic for Adenylate kinase deficiency, hemolytic anemia due to) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM031607)

known disease mutation at this position, please check HGMD for details (HGMD ID CM031607)
known disease mutation at this position, please check HGMD for details (HGMD ID CM031607)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.5411
5.5411
(flanking)-0.6230.815
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 increased4965wt: 0.9755 / mu: 0.9818 (marginal change - not scored)wt: GCTACACCCACCTCTCCACCGGGGACCTCCTGCGGTCCGAG
mu: GCTACACCCACCTCTCCACCAGGGACCTCCTGCGGTCCGAG		 accg|GGGA
Donor marginally increased4962wt: 0.5436 / mu: 0.5829 (marginal change - not scored)wt: TCTCCACCGGGGACC
mu: TCTCCACCAGGGACC		 TCCA|ccgg
Donor increased4965wt: 0.71 / mu: 0.97wt: CCACCGGGGACCTCC
mu: CCACCAGGGACCTCC		 ACCG|ggga
Donor gained49610.30mu: CTCTCCACCAGGGAC CTCC|acca
distance from splice site 75
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      40VQKYGYTHLSTGDLLRSEVSSGSA
mutated  not conserved    40VQKYGYTHLSTRDLLRSEVSSGS
Ptroglodytes  all identical  ENSPTRG00000021402  40VQKYGYTHLSTGDLLRSEVSSGS
Mmulatta  all identical  ENSMMUG00000013998  56VQKYGYTHLSTGDLLRAEVSSGS
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000026817  56VQKYGYTHLSTGDLLRAEVSSGS
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000006830  57VAKYGYTHLSSGDLLRAEVASGS
Drerio  all identical  ENSDARG00000001950  40VAKYGYTHLSSGDLLRAEVASGS
Dmelanogaster  all identical  FBgn0022709  53VEKYGFTHLSSGDLLRNEVASG
Celegans  all identical  F38B2.4  52VAKYGLTHLSSGDLLRDEVKSGS
Xtropicalis  all identical  ENSXETG00000021999  407VHQYGYTHLSTGDLLRAEVSSGS
protein features
start (aa)end (aa)featuredetails 
3939BINDINGAMP.might get lost (downstream of altered splice site)
3948HELIXlost
5262HELIXmight get lost (downstream of altered splice site)
6983HELIXmight get lost (downstream of altered splice site)
8486TURNmight get lost (downstream of altered splice site)
9094STRANDmight get lost (downstream of altered splice site)
94101NP_BINDAMP (By similarity).might get lost (downstream of altered splice site)
99108HELIXmight get lost (downstream of altered splice site)
113119STRANDmight get lost (downstream of altered splice site)
122133HELIXmight get lost (downstream of altered splice site)
127127CONFLICTQ -> R (in Ref. 1; AA sequence).might get lost (downstream of altered splice site)
135137STRANDmight get lost (downstream of altered splice site)
139141HELIXmight get lost (downstream of altered splice site)
143156HELIXmight get lost (downstream of altered splice site)
158167HELIXmight get lost (downstream of altered splice site)
170174STRANDmight get lost (downstream of altered splice site)
179193HELIXmight get lost (downstream of altered splice site)
181181CONFLICTS -> E (in Ref. 1; AA sequence).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 585 / 585
position (AA) of stopcodon in wt / mu AA sequence 195 / 195
position of stopcodon in wt / mu cDNA 748 / 748
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 164 / 164
chromosome 9
strand -1
last intron/exon boundary 680
theoretical NMD boundary in CDS 466
length of CDS 585
coding sequence (CDS) position 118
cDNA position
(for ins/del: last normal base / first normal base)		 281
gDNA position
(for ins/del: last normal base / first normal base)		 4965
chromosomal position
(for ins/del: last normal base / first normal base)		 130635058
original gDNA sequence snippet GCTACACCCACCTCTCCACCGGGGACCTCCTGCGGTCCGAG
altered gDNA sequence snippet GCTACACCCACCTCTCCACCAGGGACCTCCTGCGGTCCGAG
original cDNA sequence snippet GCTACACCCACCTCTCCACCGGGGACCTCCTGCGGTCCGAG
altered cDNA sequence snippet GCTACACCCACCTCTCCACCAGGGACCTCCTGCGGTCCGAG
wildtype AA sequence MEEKLKKTKI IFVVGGPGSG KGTQCEKIVQ KYGYTHLSTG DLLRSEVSSG SARGKKLSEI
MEKGQLVPLE TVLDMLRDAM VAKVNTSKGF LIDGYPREVQ QGEEFERRIG QPTLLLYVDA
GPETMTQRLL KRGETSGRVD DNEETIKKRL ETYYKATEPV IAFYEKRGIV RKVNAEGSVD
SVFSQVCTHL DALK*
mutated AA sequence MEEKLKKTKI IFVVGGPGSG KGTQCEKIVQ KYGYTHLSTR DLLRSEVSSG SARGKKLSEI
MEKGQLVPLE TVLDMLRDAM VAKVNTSKGF LIDGYPREVQ QGEEFERRIG QPTLLLYVDA
GPETMTQRLL KRGETSGRVD DNEETIKKRL ETYYKATEPV IAFYEKRGIV RKVNAEGSVD
SVFSQVCTHL DALK*
speed 0.58 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: 0.99999999999301 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM031607)
  • known disease mutation: rs18266 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:130635058C>TN/A show variant in all transcripts   IGV
HGNC symbol AK1
Ensembl transcript ID ENST00000373176
Genbank transcript ID NM_000476
UniProt peptide P00568
alteration type single base exchange
alteration region CDS
DNA changes c.118G>A
cDNA.271G>A
g.4965G>A
AA changes G40R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 40
frameshift no
known variant Reference ID: rs137853204
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs18266 (pathogenic for Adenylate kinase deficiency, hemolytic anemia due to) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM031607)

known disease mutation at this position, please check HGMD for details (HGMD ID CM031607)
known disease mutation at this position, please check HGMD for details (HGMD ID CM031607)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.5411
5.5411
(flanking)-0.6230.815
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 increased4965wt: 0.9755 / mu: 0.9818 (marginal change - not scored)wt: GCTACACCCACCTCTCCACCGGGGACCTCCTGCGGTCCGAG
mu: GCTACACCCACCTCTCCACCAGGGACCTCCTGCGGTCCGAG		 accg|GGGA
Donor marginally increased4962wt: 0.5436 / mu: 0.5829 (marginal change - not scored)wt: TCTCCACCGGGGACC
mu: TCTCCACCAGGGACC		 TCCA|ccgg
Donor increased4965wt: 0.71 / mu: 0.97wt: CCACCGGGGACCTCC
mu: CCACCAGGGACCTCC		 ACCG|ggga
Donor gained49610.30mu: CTCTCCACCAGGGAC CTCC|acca
distance from splice site 75
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      40VQKYGYTHLSTGDLLRSEVSSGSA
mutated  not conserved    40VQKYGYTHLSTRDLLRSEVSSGS
Ptroglodytes  all identical  ENSPTRG00000021402  40VQKYGYTHLSTGDLLRSEVSSGS
Mmulatta  all identical  ENSMMUG00000013998  56VQKYGYTHLSTGDLLRAEVSSGS
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000026817  56VQKYGYTHLSTGDLLRAEVSSGS
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000006830  57VAKYGYTHLSSGDLLRAEVASGS
Drerio  all identical  ENSDARG00000001950  40VAKYGYTHLSSGDLLRAEVASGS
Dmelanogaster  all identical  FBgn0022709  53VEKYGFTHLSSGDLLRNEVASG
Celegans  all identical  F38B2.4  52VAKYGLTHLSSGDLLRDEVKSGS
Xtropicalis  all identical  ENSXETG00000021999  407VHQYGYTHLSTGDLLRAEVSSGS
protein features
start (aa)end (aa)featuredetails 
3939BINDINGAMP.might get lost (downstream of altered splice site)
3948HELIXlost
5262HELIXmight get lost (downstream of altered splice site)
6983HELIXmight get lost (downstream of altered splice site)
8486TURNmight get lost (downstream of altered splice site)
9094STRANDmight get lost (downstream of altered splice site)
94101NP_BINDAMP (By similarity).might get lost (downstream of altered splice site)
99108HELIXmight get lost (downstream of altered splice site)
113119STRANDmight get lost (downstream of altered splice site)
122133HELIXmight get lost (downstream of altered splice site)
127127CONFLICTQ -> R (in Ref. 1; AA sequence).might get lost (downstream of altered splice site)
135137STRANDmight get lost (downstream of altered splice site)
139141HELIXmight get lost (downstream of altered splice site)
143156HELIXmight get lost (downstream of altered splice site)
158167HELIXmight get lost (downstream of altered splice site)
170174STRANDmight get lost (downstream of altered splice site)
179193HELIXmight get lost (downstream of altered splice site)
181181CONFLICTS -> E (in Ref. 1; AA sequence).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 585 / 585
position (AA) of stopcodon in wt / mu AA sequence 195 / 195
position of stopcodon in wt / mu cDNA 738 / 738
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 154 / 154
chromosome 9
strand -1
last intron/exon boundary 670
theoretical NMD boundary in CDS 466
length of CDS 585
coding sequence (CDS) position 118
cDNA position
(for ins/del: last normal base / first normal base)		 271
gDNA position
(for ins/del: last normal base / first normal base)		 4965
chromosomal position
(for ins/del: last normal base / first normal base)		 130635058
original gDNA sequence snippet GCTACACCCACCTCTCCACCGGGGACCTCCTGCGGTCCGAG
altered gDNA sequence snippet GCTACACCCACCTCTCCACCAGGGACCTCCTGCGGTCCGAG
original cDNA sequence snippet GCTACACCCACCTCTCCACCGGGGACCTCCTGCGGTCCGAG
altered cDNA sequence snippet GCTACACCCACCTCTCCACCAGGGACCTCCTGCGGTCCGAG
wildtype AA sequence MEEKLKKTKI IFVVGGPGSG KGTQCEKIVQ KYGYTHLSTG DLLRSEVSSG SARGKKLSEI
MEKGQLVPLE TVLDMLRDAM VAKVNTSKGF LIDGYPREVQ QGEEFERRIG QPTLLLYVDA
GPETMTQRLL KRGETSGRVD DNEETIKKRL ETYYKATEPV IAFYEKRGIV RKVNAEGSVD
SVFSQVCTHL DALK*
mutated AA sequence MEEKLKKTKI IFVVGGPGSG KGTQCEKIVQ KYGYTHLSTR DLLRSEVSSG SARGKKLSEI
MEKGQLVPLE TVLDMLRDAM VAKVNTSKGF LIDGYPREVQ QGEEFERRIG QPTLLLYVDA
GPETMTQRLL KRGETSGRVD DNEETIKKRL ETYYKATEPV IAFYEKRGIV RKVNAEGSVD
SVFSQVCTHL DALK*
speed 0.86 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: 0.99999999999301 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM031607)
  • known disease mutation: rs18266 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:130635058C>TN/A show variant in all transcripts   IGV
HGNC symbol AK1
Ensembl transcript ID ENST00000223836
Genbank transcript ID N/A
UniProt peptide P00568
alteration type single base exchange
alteration region CDS
DNA changes c.166G>A
cDNA.262G>A
g.4965G>A
AA changes G56R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 56
frameshift no
known variant Reference ID: rs137853204
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs18266 (pathogenic for Adenylate kinase deficiency, hemolytic anemia due to) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM031607)

known disease mutation at this position, please check HGMD for details (HGMD ID CM031607)
known disease mutation at this position, please check HGMD for details (HGMD ID CM031607)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.5411
5.5411
(flanking)-0.6230.815
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 increased4965wt: 0.9755 / mu: 0.9818 (marginal change - not scored)wt: GCTACACCCACCTCTCCACCGGGGACCTCCTGCGGTCCGAG
mu: GCTACACCCACCTCTCCACCAGGGACCTCCTGCGGTCCGAG		 accg|GGGA
Donor marginally increased4962wt: 0.5436 / mu: 0.5829 (marginal change - not scored)wt: TCTCCACCGGGGACC
mu: TCTCCACCAGGGACC		 TCCA|ccgg
Donor increased4965wt: 0.71 / mu: 0.97wt: CCACCGGGGACCTCC
mu: CCACCAGGGACCTCC		 ACCG|ggga
Donor gained49610.30mu: CTCTCCACCAGGGAC CTCC|acca
distance from splice site 75
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      56VQKYGYTHLSTGDLLRSEVSSGSA
mutated  not conserved    56VQKYGYTHLSTRDLLR
Ptroglodytes  all identical  ENSPTRG00000021402  40VQKYGYTHLSTGDLLRSEVSSGS
Mmulatta  all identical  ENSMMUG00000013998  56VQKYGYTHLSTGDLLR
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000026817  56VQKYGYTHLSTGDLLR
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000006830  57VAKYGYTHLSSGDLLRAEVASGS
Drerio  all identical  ENSDARG00000001950  40VAKYGYTHLSSGDLLRAEVASGS
Dmelanogaster  all identical  FBgn0022709  64VEKYGFTHLSSGDLLRNEVASGS
Celegans  all identical  F38B2.4  52VAKYGLTHLSSGDLLRDEVKSGS
Xtropicalis  all identical  ENSXETG00000021999  407VHQYGYTHLSTGDLLRAEVSSGS
protein features
start (aa)end (aa)featuredetails 
5262HELIXlost
6983HELIXmight get lost (downstream of altered splice site)
8486TURNmight get lost (downstream of altered splice site)
9094STRANDmight get lost (downstream of altered splice site)
94101NP_BINDAMP (By similarity).might get lost (downstream of altered splice site)
99108HELIXmight get lost (downstream of altered splice site)
113119STRANDmight get lost (downstream of altered splice site)
122133HELIXmight get lost (downstream of altered splice site)
127127CONFLICTQ -> R (in Ref. 1; AA sequence).might get lost (downstream of altered splice site)
135137STRANDmight get lost (downstream of altered splice site)
139141HELIXmight get lost (downstream of altered splice site)
143156HELIXmight get lost (downstream of altered splice site)
158167HELIXmight get lost (downstream of altered splice site)
170174STRANDmight get lost (downstream of altered splice site)
179193HELIXmight get lost (downstream of altered splice site)
181181CONFLICTS -> E (in Ref. 1; AA sequence).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 633 / 633
position (AA) of stopcodon in wt / mu AA sequence 211 / 211
position of stopcodon in wt / mu cDNA 729 / 729
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 97 / 97
chromosome 9
strand -1
last intron/exon boundary 661
theoretical NMD boundary in CDS 514
length of CDS 633
coding sequence (CDS) position 166
cDNA position
(for ins/del: last normal base / first normal base)		 262
gDNA position
(for ins/del: last normal base / first normal base)		 4965
chromosomal position
(for ins/del: last normal base / first normal base)		 130635058
original gDNA sequence snippet GCTACACCCACCTCTCCACCGGGGACCTCCTGCGGTCCGAG
altered gDNA sequence snippet GCTACACCCACCTCTCCACCAGGGACCTCCTGCGGTCCGAG
original cDNA sequence snippet GCTACACCCACCTCTCCACCGGGGACCTCCTGCGGTCCGAG
altered cDNA sequence snippet GCTACACCCACCTCTCCACCAGGGACCTCCTGCGGTCCGAG
wildtype AA sequence MGCCSSSDPR REDDLRAREK LKKTKIIFVV GGPGSGKGTQ CEKIVQKYGY THLSTGDLLR
SEVSSGSARG KKLSEIMEKG QLVPLETVLD MLRDAMVAKV NTSKGFLIDG YPREVQQGEE
FERRIGQPTL LLYVDAGPET MTQRLLKRGE TSGRVDDNEE TIKKRLETYY KATEPVIAFY
EKRGIVRKVN AEGSVDSVFS QVCTHLDALK *
mutated AA sequence MGCCSSSDPR REDDLRAREK LKKTKIIFVV GGPGSGKGTQ CEKIVQKYGY THLSTRDLLR
SEVSSGSARG KKLSEIMEKG QLVPLETVLD MLRDAMVAKV NTSKGFLIDG YPREVQQGEE
FERRIGQPTL LLYVDAGPET MTQRLLKRGE TSGRVDDNEE TIKKRLETYY KATEPVIAFY
EKRGIVRKVN AEGSVDSVFS QVCTHLDALK *
speed 0.85 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