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: ENST00000261623
Querying Taster for transcript #2: ENST00000567174
Querying Taster for transcript #3: ENST00000569359
MT speed 0 s - this script 4.067812 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CYBApolymorphism_automatic0.953762570847428simple_aaeaffectedY72Hsingle base exchangers4673show file
CYBApolymorphism_automatic0.953762570847428simple_aaeaffectedY72Hsingle base exchangers4673show file
CYBApolymorphism_automatic0.953762570847428simple_aaeaffectedY72Hsingle base exchangers4673show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.0462374291525724 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM983302)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:88713236A>GN/A show variant in all transcripts   IGV
HGNC symbol CYBA
Ensembl transcript ID ENST00000261623
Genbank transcript ID NM_000101
UniProt peptide P13498
alteration type single base exchange
alteration region CDS
DNA changes c.214T>C
cDNA.353T>C
g.4325T>C
AA changes Y72H Score: 83 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 72
frameshift no
known variant Reference ID: rs4673
databasehomozygous (G/G)heterozygousallele carriers
1000G115610152171
ExAC29452-261373315

known disease mutation at this position, please check HGMD for details (HGMD ID CM983302)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)2.1840.994
2.071
(flanking)1.6791
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased4322wt: 0.21 / mu: 0.25wt: GACAGAAGTACATGA
mu: GACAGAAGCACATGA		 CAGA|agta
Donor marginally increased4323wt: 0.2231 / mu: 0.2274 (marginal change - not scored)wt: ACAGAAGTACATGAC
mu: ACAGAAGCACATGAC		 AGAA|gtac
Donor gained43240.57mu: CAGAAGCACATGACC GAAG|caca
distance from splice site 11
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      72KGSTMERWGQKYMTAVVKLFGPFT
mutated  all conserved    72KGSTMERWGQKHMTAVVKLFGPF
Ptroglodytes  all identical  ENSPTRG00000008458  72KGSTMERWGQKYMTAVVKLFGPF
Mmulatta  all identical  ENSMMUG00000014325  71KGSTMERWGQKYMTSVVKLFGPL
Fcatus  all identical  ENSFCAG00000006655  72KGSTMERCGQKYLTKVVKVLGPL
Mmusculus  all identical  ENSMUSG00000006519  72KGSTMERCGQKYLTSVVKLFGPL
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000018180  72KGTSVERPGQRCFTVCVKAFGPV
Drerio  not conserved  ENSDARG00000018283  72KGTSIERSGQYCFTVCVKSFGPL
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000017431  72KGSTMERCGQKYLAAVVKLFGPL
protein features
start (aa)end (aa)featuredetails 
91127INTRAMEMmight get lost (downstream of altered splice site)
9494METALIron (heme axial ligand) (Potential).might get lost (downstream of altered splice site)
133189COMPBIASPro-rich.might get lost (downstream of altered splice site)
147147MOD_RESPhosphothreonine (By similarity).might get lost (downstream of altered splice site)
157157MUTAGENP->Q: Loss of interaction with NOXO1.might get lost (downstream of altered splice site)
161165HELIXmight get lost (downstream of altered splice site)
168168MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 588 / 588
position (AA) of stopcodon in wt / mu AA sequence 196 / 196
position of stopcodon in wt / mu cDNA 727 / 727
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 140 / 140
chromosome 16
strand -1
last intron/exon boundary 509
theoretical NMD boundary in CDS 319
length of CDS 588
coding sequence (CDS) position 214
cDNA position
(for ins/del: last normal base / first normal base)		 353
gDNA position
(for ins/del: last normal base / first normal base)		 4325
chromosomal position
(for ins/del: last normal base / first normal base)		 88713236
original gDNA sequence snippet CCTCCCCCAGGGGACAGAAGTACATGACCGCCGTGGTGAAG
altered gDNA sequence snippet CCTCCCCCAGGGGACAGAAGCACATGACCGCCGTGGTGAAG
original cDNA sequence snippet TGGAGCGCTGGGGACAGAAGTACATGACCGCCGTGGTGAAG
altered cDNA sequence snippet TGGAGCGCTGGGGACAGAAGCACATGACCGCCGTGGTGAAG
wildtype AA sequence MGQIEWAMWA NEQALASGLI LITGGIVATA GRFTQWYFGA YSIVAGVFVC LLEYPRGKRK
KGSTMERWGQ KYMTAVVKLF GPFTRNYYVR AVLHLLLSVP AGFLLATILG TACLAIASGI
YLLAAVRGEQ WTPIEPKPRE RPQIGGTIKQ PPSNPPPRPP AEARKKPSEE EAAVAAGGPP
GGPQVNPIPV TDEVV*
mutated AA sequence MGQIEWAMWA NEQALASGLI LITGGIVATA GRFTQWYFGA YSIVAGVFVC LLEYPRGKRK
KGSTMERWGQ KHMTAVVKLF GPFTRNYYVR AVLHLLLSVP AGFLLATILG TACLAIASGI
YLLAAVRGEQ WTPIEPKPRE RPQIGGTIKQ PPSNPPPRPP AEARKKPSEE EAAVAAGGPP
GGPQVNPIPV TDEVV*
speed 1.24 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: 0.0462374291525724 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM983302)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:88713236A>GN/A show variant in all transcripts   IGV
HGNC symbol CYBA
Ensembl transcript ID ENST00000567174
Genbank transcript ID N/A
UniProt peptide P13498
alteration type single base exchange
alteration region CDS
DNA changes c.214T>C
cDNA.242T>C
g.4325T>C
AA changes Y72H Score: 83 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 72
frameshift no
known variant Reference ID: rs4673
databasehomozygous (G/G)heterozygousallele carriers
1000G115610152171
ExAC29452-261373315

known disease mutation at this position, please check HGMD for details (HGMD ID CM983302)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)2.1840.994
2.071
(flanking)1.6791
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased4322wt: 0.21 / mu: 0.25wt: GACAGAAGTACATGA
mu: GACAGAAGCACATGA		 CAGA|agta
Donor marginally increased4323wt: 0.2231 / mu: 0.2274 (marginal change - not scored)wt: ACAGAAGTACATGAC
mu: ACAGAAGCACATGAC		 AGAA|gtac
Donor gained43240.57mu: CAGAAGCACATGACC GAAG|caca
distance from splice site 11
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      72KGSTMERWGQKYMTAVVKLFGPFT
mutated  all conserved    72KGSTMERWGQKHMTAVVKLFGPF
Ptroglodytes  all identical  ENSPTRG00000008458  72KGSTMERWGQKYMTAVVKLFGPF
Mmulatta  all identical  ENSMMUG00000014325  71KGSTMERWGQKYMTSVVKLFGPL
Fcatus  all identical  ENSFCAG00000006655  72KGSTMERCGQKYLTKVVKVLGPL
Mmusculus  all identical  ENSMUSG00000006519  72KGSTMERCGQKYLTSVVKLFGPL
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000018180  72KGTSVERPGQRCFTVCVKAFGPV
Drerio  not conserved  ENSDARG00000018283  72KGTSIERSGQYCFTVCVKSFGPL
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000017431  72KGSTMERCGQKYLAAVVKLFGPL
protein features
start (aa)end (aa)featuredetails 
91127INTRAMEMmight get lost (downstream of altered splice site)
9494METALIron (heme axial ligand) (Potential).might get lost (downstream of altered splice site)
133189COMPBIASPro-rich.might get lost (downstream of altered splice site)
147147MOD_RESPhosphothreonine (By similarity).might get lost (downstream of altered splice site)
157157MUTAGENP->Q: Loss of interaction with NOXO1.might get lost (downstream of altered splice site)
161165HELIXmight get lost (downstream of altered splice site)
168168MOD_RESPhosphoserine (By similarity).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 661 / 661
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 29 / 29
chromosome 16
strand -1
last intron/exon boundary 398
theoretical NMD boundary in CDS 319
length of CDS 633
coding sequence (CDS) position 214
cDNA position
(for ins/del: last normal base / first normal base)		 242
gDNA position
(for ins/del: last normal base / first normal base)		 4325
chromosomal position
(for ins/del: last normal base / first normal base)		 88713236
original gDNA sequence snippet CCTCCCCCAGGGGACAGAAGTACATGACCGCCGTGGTGAAG
altered gDNA sequence snippet CCTCCCCCAGGGGACAGAAGCACATGACCGCCGTGGTGAAG
original cDNA sequence snippet TGGAGCGCTGGGGACAGAAGTACATGACCGCCGTGGTGAAG
altered cDNA sequence snippet TGGAGCGCTGGGGACAGAAGCACATGACCGCCGTGGTGAAG
wildtype AA sequence MGQIEWAMWA NEQALASGLI LITGGIVATA GRFTQWYFGA YSIVAGVFVC LLEYPRGKRK
KGSTMERWGQ KYMTAVVKLF GPFTRNYYVR AVLHLLLSVP AGFLLATILG TACLAIASGI
YLLSQVPPAR RGNCPPLAVR LLVCVRGKGA ALSVYAFRVW KWSSVSSLTD LPPAELSFRT
PSCCQVLIWA VALFSGGHPH PPRLPAATHS *
mutated AA sequence MGQIEWAMWA NEQALASGLI LITGGIVATA GRFTQWYFGA YSIVAGVFVC LLEYPRGKRK
KGSTMERWGQ KHMTAVVKLF GPFTRNYYVR AVLHLLLSVP AGFLLATILG TACLAIASGI
YLLSQVPPAR RGNCPPLAVR LLVCVRGKGA ALSVYAFRVW KWSSVSSLTD LPPAELSFRT
PSCCQVLIWA VALFSGGHPH PPRLPAATHS *
speed 1.21 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: 0.0462374291525724 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM983302)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:88713236A>GN/A show variant in all transcripts   IGV
HGNC symbol CYBA
Ensembl transcript ID ENST00000569359
Genbank transcript ID N/A
UniProt peptide P13498
alteration type single base exchange
alteration region CDS
DNA changes c.214T>C
cDNA.231T>C
g.4325T>C
AA changes Y72H Score: 83 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 72
frameshift no
known variant Reference ID: rs4673
databasehomozygous (G/G)heterozygousallele carriers
1000G115610152171
ExAC29452-261373315

known disease mutation at this position, please check HGMD for details (HGMD ID CM983302)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)2.1840.994
2.071
(flanking)1.6791
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased4322wt: 0.21 / mu: 0.25wt: GACAGAAGTACATGA
mu: GACAGAAGCACATGA		 CAGA|agta
Donor marginally increased4323wt: 0.2231 / mu: 0.2274 (marginal change - not scored)wt: ACAGAAGTACATGAC
mu: ACAGAAGCACATGAC		 AGAA|gtac
Donor gained43240.57mu: CAGAAGCACATGACC GAAG|caca
distance from splice site 11
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      72KGSTMERWGQKYMTAVVKLFGPFT
mutated  all conserved    72KGSTMERWGQKHMTAVVKLFGPF
Ptroglodytes  all identical  ENSPTRG00000008458  72KGSTMERWGQKYMTAVVKLFGPF
Mmulatta  all identical  ENSMMUG00000014325  71KGSTMERWGQKYMTSVVKLFGPL
Fcatus  all identical  ENSFCAG00000006655  72KGSTMERCGQKYLTKVVKVLGPL
Mmusculus  all identical  ENSMUSG00000006519  72KGSTMERCGQKYLTSVVKLFGPL
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000018180  72KGTSVERPGQRCFTVCVKAFGPV
Drerio  not conserved  ENSDARG00000018283  72KGTSIERSGQYCFTVCVKSFGPL
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000017431  72KGSTMERCGQKYLAAVVKLFGPL
protein features
start (aa)end (aa)featuredetails 
91127INTRAMEMmight get lost (downstream of altered splice site)
9494METALIron (heme axial ligand) (Potential).might get lost (downstream of altered splice site)
133189COMPBIASPro-rich.might get lost (downstream of altered splice site)
147147MOD_RESPhosphothreonine (By similarity).might get lost (downstream of altered splice site)
157157MUTAGENP->Q: Loss of interaction with NOXO1.might get lost (downstream of altered splice site)
161165HELIXmight get lost (downstream of altered splice site)
168168MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 387 / 387
position (AA) of stopcodon in wt / mu AA sequence 129 / 129
position of stopcodon in wt / mu cDNA 404 / 404
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 18 / 18
chromosome 16
strand -1
last intron/exon boundary 305
theoretical NMD boundary in CDS 237
length of CDS 387
coding sequence (CDS) position 214
cDNA position
(for ins/del: last normal base / first normal base)		 231
gDNA position
(for ins/del: last normal base / first normal base)		 4325
chromosomal position
(for ins/del: last normal base / first normal base)		 88713236
original gDNA sequence snippet CCTCCCCCAGGGGACAGAAGTACATGACCGCCGTGGTGAAG
altered gDNA sequence snippet CCTCCCCCAGGGGACAGAAGCACATGACCGCCGTGGTGAAG
original cDNA sequence snippet TGGAGCGCTGGGGACAGAAGTACATGACCGCCGTGGTGAAG
altered cDNA sequence snippet TGGAGCGCTGGGGACAGAAGCACATGACCGCCGTGGTGAAG
wildtype AA sequence MGQIEWAMWA NEQALASGLI LITGGIVATA GRFTQWYFGA YSIVAGVFVC LLEYPRGKRK
KGSTMERWGQ KYMTAVVKLF GPFTRNYYVR AVLHLLLSVP AGFLLATILG TACLAIASGI
YLLVSGAL*
mutated AA sequence MGQIEWAMWA NEQALASGLI LITGGIVATA GRFTQWYFGA YSIVAGVFVC LLEYPRGKRK
KGSTMERWGQ KHMTAVVKLF GPFTRNYYVR AVLHLLLSVP AGFLLATILG TACLAIASGI
YLLVSGAL*
speed 0.42 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