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 3.588356 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AK1disease_causing_automatic0.999999940679113simple_aae0R128Wsingle base exchangers104894101show file
AK1disease_causing_automatic0.999999940679113simple_aae0R128Wsingle base exchangers104894101show file
AK1disease_causing_automatic0.999999940679113simple_aae0R144Wsingle base exchangers104894101show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999940679113 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM890004)
  • known disease mutation: rs18263 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:130630734G>AN/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.382C>T
cDNA.535C>T
g.9289C>T
AA changes R128W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 128
frameshift no
known variant Reference ID: rs104894101
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs18263 (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 CM890004)

known disease mutation at this position, please check HGMD for details (HGMD ID CM890004)
known disease mutation at this position, please check HGMD for details (HGMD ID CM890004)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.0841
0.3950.999
(flanking)0.7481
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 58
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      128YVDAGPETMTQRLLKRGETSGRVD
mutated  not conserved    128GPETMTQWLLKRGETSGRV
Ptroglodytes  all identical  ENSPTRG00000021402  128GPETMTQRLLKRGETSGRV
Mmulatta  all identical  ENSMMUG00000013998  144ETMTQRLLKRGETSGRV
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000026817  144ETMTQRLLKRGETSGRV
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000006830  145RGETMVKRLMKRGETSGRS
Drerio  all identical  ENSDARG00000001950  128KGETMVKRLMKRGETSGRA
Dmelanogaster  all identical  FBgn0022709  152YFECSEDTMVQRIMARAAASAVKRD
Celegans  all identical  F38B2.4  140FFDVAEETLVKRLLHRAQTSGRA
Xtropicalis  all identical  ENSXETG00000021999  495DTMVKRLLKRGETSGRA
protein features
start (aa)end (aa)featuredetails 
122133HELIXlost
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 382
cDNA position
(for ins/del: last normal base / first normal base)		 535
gDNA position
(for ins/del: last normal base / first normal base)		 9289
chromosomal position
(for ins/del: last normal base / first normal base)		 130630734
original gDNA sequence snippet GCCCTGAGACCATGACCCAGCGGCTCTTGAAACGTGGAGAG
altered gDNA sequence snippet GCCCTGAGACCATGACCCAGTGGCTCTTGAAACGTGGAGAG
original cDNA sequence snippet GCCCTGAGACCATGACCCAGCGGCTCTTGAAACGTGGAGAG
altered cDNA sequence snippet GCCCTGAGACCATGACCCAGTGGCTCTTGAAACGTGGAGAG
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 KYGYTHLSTG DLLRSEVSSG SARGKKLSEI
MEKGQLVPLE TVLDMLRDAM VAKVNTSKGF LIDGYPREVQ QGEEFERRIG QPTLLLYVDA
GPETMTQWLL KRGETSGRVD DNEETIKKRL ETYYKATEPV IAFYEKRGIV RKVNAEGSVD
SVFSQVCTHL DALK*
speed 0.93 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: 0.999999940679113 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM890004)
  • known disease mutation: rs18263 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:130630734G>AN/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.382C>T
cDNA.545C>T
g.9289C>T
AA changes R128W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 128
frameshift no
known variant Reference ID: rs104894101
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs18263 (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 CM890004)

known disease mutation at this position, please check HGMD for details (HGMD ID CM890004)
known disease mutation at this position, please check HGMD for details (HGMD ID CM890004)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.0841
0.3950.999
(flanking)0.7481
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 58
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      128YVDAGPETMTQRLLKRGETSGRVD
mutated  not conserved    128GPETMTQWLLKRGETSGRV
Ptroglodytes  all identical  ENSPTRG00000021402  128GPETMTQRLLKRGETSGRV
Mmulatta  all identical  ENSMMUG00000013998  144ETMTQRLLKRGETSGRV
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000026817  144ETMTQRLLKRGETSGRV
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000006830  145RGETMVKRLMKRGETSGRS
Drerio  all identical  ENSDARG00000001950  128KGETMVKRLMKRGETSGRA
Dmelanogaster  all identical  FBgn0022709  152YFECSEDTMVQRIMARAAASAVKRD
Celegans  all identical  F38B2.4  140FFDVAEETLVKRLLHRAQTSGRA
Xtropicalis  all identical  ENSXETG00000021999  495DTMVKRLLKRGETSGRA
protein features
start (aa)end (aa)featuredetails 
122133HELIXlost
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 382
cDNA position
(for ins/del: last normal base / first normal base)		 545
gDNA position
(for ins/del: last normal base / first normal base)		 9289
chromosomal position
(for ins/del: last normal base / first normal base)		 130630734
original gDNA sequence snippet GCCCTGAGACCATGACCCAGCGGCTCTTGAAACGTGGAGAG
altered gDNA sequence snippet GCCCTGAGACCATGACCCAGTGGCTCTTGAAACGTGGAGAG
original cDNA sequence snippet GCCCTGAGACCATGACCCAGCGGCTCTTGAAACGTGGAGAG
altered cDNA sequence snippet GCCCTGAGACCATGACCCAGTGGCTCTTGAAACGTGGAGAG
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 KYGYTHLSTG DLLRSEVSSG SARGKKLSEI
MEKGQLVPLE TVLDMLRDAM VAKVNTSKGF LIDGYPREVQ QGEEFERRIG QPTLLLYVDA
GPETMTQWLL KRGETSGRVD DNEETIKKRL ETYYKATEPV IAFYEKRGIV RKVNAEGSVD
SVFSQVCTHL DALK*
speed 0.97 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: 0.999999940679113 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM890004)
  • known disease mutation: rs18263 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:130630734G>AN/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.430C>T
cDNA.526C>T
g.9289C>T
AA changes R144W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 144
frameshift no
known variant Reference ID: rs104894101
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs18263 (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 CM890004)

known disease mutation at this position, please check HGMD for details (HGMD ID CM890004)
known disease mutation at this position, please check HGMD for details (HGMD ID CM890004)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.0841
0.3950.999
(flanking)0.7481
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 58
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      144YVDAGPETMTQRLLKRGETSGRVD
mutated  not conserved    144YVDAGPETMTQWLLKRGETSGRV
Ptroglodytes  all identical  ENSPTRG00000021402  128ETMTQRLLKRGETSGRV
Mmulatta  all identical  ENSMMUG00000013998  144YVDAGPETMTQRLLKRGETSGRV
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000026817  144YVDAGAETMTQRLLKRGETSGRV
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000006830  145ETMVKRLMKRGETSGRS
Drerio  all identical  ENSDARG00000001950  128ETMVKRLMKRGETSGRA
Dmelanogaster  all identical  FBgn0022709  152YFECSEDTMVQRIMARAAASAVKRD
Celegans  all identical  F38B2.4  140FFDVAEETLVKRLLHRAQTSGRA
Xtropicalis  all identical  ENSXETG00000021999  495DTMVKRLLKRGETSGRA
protein features
start (aa)end (aa)featuredetails 
143156HELIXlost
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 430
cDNA position
(for ins/del: last normal base / first normal base)		 526
gDNA position
(for ins/del: last normal base / first normal base)		 9289
chromosomal position
(for ins/del: last normal base / first normal base)		 130630734
original gDNA sequence snippet GCCCTGAGACCATGACCCAGCGGCTCTTGAAACGTGGAGAG
altered gDNA sequence snippet GCCCTGAGACCATGACCCAGTGGCTCTTGAAACGTGGAGAG
original cDNA sequence snippet GCCCTGAGACCATGACCCAGCGGCTCTTGAAACGTGGAGAG
altered cDNA sequence snippet GCCCTGAGACCATGACCCAGTGGCTCTTGAAACGTGGAGAG
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 THLSTGDLLR
SEVSSGSARG KKLSEIMEKG QLVPLETVLD MLRDAMVAKV NTSKGFLIDG YPREVQQGEE
FERRIGQPTL LLYVDAGPET MTQWLLKRGE TSGRVDDNEE TIKKRLETYY KATEPVIAFY
EKRGIVRKVN AEGSVDSVFS QVCTHLDALK *
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

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