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 6 transcript(s)...
Querying Taster for transcript #1: ENST00000352397
Querying Taster for transcript #2: ENST00000407623
Querying Taster for transcript #3: ENST00000407332
Querying Taster for transcript #4: ENST00000402438
Querying Taster for transcript #5: ENST00000361740
Querying Taster for transcript #6: ENST00000396303
MT speed 0 s - this script 4.418804 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CYB5R3disease_causing_automatic0.999333003810338simple_aaeaffected0G292Dsingle base exchangers121965016show file
CYB5R3disease_causing_automatic0.999333003810338simple_aaeaffected0G269Dsingle base exchangers121965016show file
CYB5R3disease_causing_automatic0.999333003810338simple_aaeaffected0G269Dsingle base exchangers121965016show file
CYB5R3disease_causing_automatic0.999333003810338simple_aaeaffected0G269Dsingle base exchangers121965016show file
CYB5R3disease_causing_automatic0.999333003810338simple_aaeaffected0G325Dsingle base exchangers121965016show file
CYB5R3disease_causing_automatic0.999333003810338simple_aaeaffected0G269Dsingle base exchangers121965016show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999333003810338 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM024771)
  • known disease mutation: rs250 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr22:43015810C>TN/A show variant in all transcripts   IGV
HGNC symbol CYB5R3
Ensembl transcript ID ENST00000352397
Genbank transcript ID NM_000398
UniProt peptide P00387
alteration type single base exchange
alteration region CDS
DNA changes c.875G>A
cDNA.1128G>A
g.29765G>A
AA changes G292D Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 292
frameshift no
known variant Reference ID: rs121965016
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs250 (pathogenic for Methemoglobinemia, type I) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM024771)

known disease mutation at this position, please check HGMD for details (HGMD ID CM024771)
known disease mutation at this position, please check HGMD for details (HGMD ID CM024771)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.421
1.8121
(flanking)3.5281
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased29769wt: 0.46 / mu: 0.79wt: GGCCACCCCACGGAG
mu: GACCACCCCACGGAG		 CCAC|ccca
Donor gained297600.82mu: GACCACGTGGACCAC CCAC|gtgg
distance from splice site 142
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      292QYACLPNLDHVGHPTERCFVF*
mutated  not conserved    292QYACLPNLDHVDHPTERCFV
Ptroglodytes  all identical  ENSPTRG00000014461  292QYACLPNLDRVGHPKERCFA
Mmulatta  all identical  ENSMMUG00000010198  292QYACLPNLDRVGHPKERCFA
Fcatus  no homologue    
Mmusculus  no alignment  ENSMUSG00000018042  n/a
Ggallus  all identical  ENSGALG00000014122  292QYACIPNLDKLGYAKDMRFA
Trubripes  all identical  ENSTRUG00000013823  290QFACNPNLDKVGHAASRRFNF
Drerio  all identical  ENSDARG00000005891  289QFACNPSLDKVGHSNDRRFMF
Dmelanogaster  not conserved  FBgn0036211  307NFACNPALDKLGYHPDTR
Celegans  not conserved  T05H4.5  300NFACIPNLEKLEYDPANRLLF
Xtropicalis  not conserved  ENSXETG00000016513  294QYAINPSLDKLSYPQDRRFAY
protein features
start (aa)end (aa)featuredetails 
285291HELIXmight get lost (downstream of altered splice site)
295297HELIXmight get lost (downstream of altered splice site)
298300STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 906 / 906
position (AA) of stopcodon in wt / mu AA sequence 302 / 302
position of stopcodon in wt / mu cDNA 1159 / 1159
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 254 / 254
chromosome 22
strand -1
last intron/exon boundary 987
theoretical NMD boundary in CDS 683
length of CDS 906
coding sequence (CDS) position 875
cDNA position
(for ins/del: last normal base / first normal base)		 1128
gDNA position
(for ins/del: last normal base / first normal base)		 29765
chromosomal position
(for ins/del: last normal base / first normal base)		 43015810
original gDNA sequence snippet TCCCAACCTGGACCACGTGGGCCACCCCACGGAGCGCTGCT
altered gDNA sequence snippet TCCCAACCTGGACCACGTGGACCACCCCACGGAGCGCTGCT
original cDNA sequence snippet TCCCAACCTGGACCACGTGGGCCACCCCACGGAGCGCTGCT
altered cDNA sequence snippet TCCCAACCTGGACCACGTGGACCACCCCACGGAGCGCTGCT
wildtype AA sequence MGAQLSTLGH MVLFPVWFLY SLLMKLFQRS TPAITLESPD IKYPLRLIDR EIISHDTRRF
RFALPSPQHI LGLPVGQHIY LSARIDGNLV VRPYTPISSD DDKGFVDLVI KVYFKDTHPK
FPAGGKMSQY LESMQIGDTI EFRGPSGLLV YQGKGKFAIR PDKKSNPIIR TVKSVGMIAG
GTGITPMLQV IRAIMKDPDD HTVCHLLFAN QTEKDILLRP ELEELRNKHS ARFKLWYTLD
RAPEAWDYGQ GFVNEEMIRD HLPPPEEEPL VLMCGPPPMI QYACLPNLDH VGHPTERCFV
F*
mutated AA sequence MGAQLSTLGH MVLFPVWFLY SLLMKLFQRS TPAITLESPD IKYPLRLIDR EIISHDTRRF
RFALPSPQHI LGLPVGQHIY LSARIDGNLV VRPYTPISSD DDKGFVDLVI KVYFKDTHPK
FPAGGKMSQY LESMQIGDTI EFRGPSGLLV YQGKGKFAIR PDKKSNPIIR TVKSVGMIAG
GTGITPMLQV IRAIMKDPDD HTVCHLLFAN QTEKDILLRP ELEELRNKHS ARFKLWYTLD
RAPEAWDYGQ GFVNEEMIRD HLPPPEEEPL VLMCGPPPMI QYACLPNLDH VDHPTERCFV
F*
speed 0.73 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: 0.999333003810338 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM024771)
  • known disease mutation: rs250 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr22:43015810C>TN/A show variant in all transcripts   IGV
HGNC symbol CYB5R3
Ensembl transcript ID ENST00000407623
Genbank transcript ID N/A
UniProt peptide P00387
alteration type single base exchange
alteration region CDS
DNA changes c.806G>A
cDNA.1191G>A
g.29765G>A
AA changes G269D Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 269
frameshift no
known variant Reference ID: rs121965016
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs250 (pathogenic for Methemoglobinemia, type I) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM024771)

known disease mutation at this position, please check HGMD for details (HGMD ID CM024771)
known disease mutation at this position, please check HGMD for details (HGMD ID CM024771)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.421
1.8121
(flanking)3.5281
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased29769wt: 0.46 / mu: 0.79wt: GGCCACCCCACGGAG
mu: GACCACCCCACGGAG		 CCAC|ccca
Donor gained297600.82mu: GACCACGTGGACCAC CCAC|gtgg
distance from splice site 142
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      269QYACLPNLDHVGHPTERCFVF*
mutated  not conserved    269QYACLPNLDHVDHPTERCFVF
Ptroglodytes  all identical  ENSPTRG00000014461  292QYACLPNLDRVGHPKERCFAF
Mmulatta  all identical  ENSMMUG00000010198  292QYACLPNLDRVGHPKERCFAF
Fcatus  no homologue    
Mmusculus  no alignment  ENSMUSG00000018042  n/a
Ggallus  all identical  ENSGALG00000014122  292QYACIPNLDKLGYAKDMRFAF
Trubripes  all identical  ENSTRUG00000013823  290QFACNPNLDKVGHAASRRFNF
Drerio  all identical  ENSDARG00000005891  289QFACNPSLDKVGHSNDRRFMF
Dmelanogaster  not conserved  FBgn0036211  307NFACNPALDKLGYHPDTR
Celegans  not conserved  T05H4.5  300NFACIPNLEKLEYDPANRLLF
Xtropicalis  not conserved  ENSXETG00000016513  294QYAINPSLDKLSYPQDRRFAY
protein features
start (aa)end (aa)featuredetails 
270275STRANDmight get lost (downstream of altered splice site)
277282HELIXmight get lost (downstream of altered splice site)
280280CONFLICTI -> N (in Ref. 3; AAL87744).might get lost (downstream of altered splice site)
285291HELIXmight get lost (downstream of altered splice site)
295297HELIXmight get lost (downstream of altered splice site)
298300STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 837 / 837
position (AA) of stopcodon in wt / mu AA sequence 279 / 279
position of stopcodon in wt / mu cDNA 1222 / 1222
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 386 / 386
chromosome 22
strand -1
last intron/exon boundary 1050
theoretical NMD boundary in CDS 614
length of CDS 837
coding sequence (CDS) position 806
cDNA position
(for ins/del: last normal base / first normal base)		 1191
gDNA position
(for ins/del: last normal base / first normal base)		 29765
chromosomal position
(for ins/del: last normal base / first normal base)		 43015810
original gDNA sequence snippet TCCCAACCTGGACCACGTGGGCCACCCCACGGAGCGCTGCT
altered gDNA sequence snippet TCCCAACCTGGACCACGTGGACCACCCCACGGAGCGCTGCT
original cDNA sequence snippet TCCCAACCTGGACCACGTGGGCCACCCCACGGAGCGCTGCT
altered cDNA sequence snippet TCCCAACCTGGACCACGTGGACCACCCCACGGAGCGCTGCT
wildtype AA sequence MKLFQRSTPA ITLESPDIKY PLRLIDREII SHDTRRFRFA LPSPQHILGL PVGQHIYLSA
RIDGNLVVRP YTPISSDDDK GFVDLVIKVY FKDTHPKFPA GGKMSQYLES MQIGDTIEFR
GPSGLLVYQG KGKFAIRPDK KSNPIIRTVK SVGMIAGGTG ITPMLQVIRA IMKDPDDHTV
CHLLFANQTE KDILLRPELE ELRNKHSARF KLWYTLDRAP EAWDYGQGFV NEEMIRDHLP
PPEEEPLVLM CGPPPMIQYA CLPNLDHVGH PTERCFVF*
mutated AA sequence MKLFQRSTPA ITLESPDIKY PLRLIDREII SHDTRRFRFA LPSPQHILGL PVGQHIYLSA
RIDGNLVVRP YTPISSDDDK GFVDLVIKVY FKDTHPKFPA GGKMSQYLES MQIGDTIEFR
GPSGLLVYQG KGKFAIRPDK KSNPIIRTVK SVGMIAGGTG ITPMLQVIRA IMKDPDDHTV
CHLLFANQTE KDILLRPELE ELRNKHSARF KLWYTLDRAP EAWDYGQGFV NEEMIRDHLP
PPEEEPLVLM CGPPPMIQYA CLPNLDHVDH PTERCFVF*
speed 0.79 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: 0.999333003810338 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM024771)
  • known disease mutation: rs250 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr22:43015810C>TN/A show variant in all transcripts   IGV
HGNC symbol CYB5R3
Ensembl transcript ID ENST00000407332
Genbank transcript ID N/A
UniProt peptide P00387
alteration type single base exchange
alteration region CDS
DNA changes c.806G>A
cDNA.898G>A
g.29765G>A
AA changes G269D Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 269
frameshift no
known variant Reference ID: rs121965016
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs250 (pathogenic for Methemoglobinemia, type I) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM024771)

known disease mutation at this position, please check HGMD for details (HGMD ID CM024771)
known disease mutation at this position, please check HGMD for details (HGMD ID CM024771)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.421
1.8121
(flanking)3.5281
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased29769wt: 0.46 / mu: 0.79wt: GGCCACCCCACGGAG
mu: GACCACCCCACGGAG		 CCAC|ccca
Donor gained297600.82mu: GACCACGTGGACCAC CCAC|gtgg
distance from splice site 142
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      269QYACLPNLDHVGHPTERCFVF*
mutated  not conserved    269QYACLPNLDHVDHPTERCFVF
Ptroglodytes  all identical  ENSPTRG00000014461  292QYACLPNLDRVGHPKERCFAF
Mmulatta  all identical  ENSMMUG00000010198  292QYACLPNLDRVGHPKERCFAF
Fcatus  no homologue    
Mmusculus  no alignment  ENSMUSG00000018042  n/a
Ggallus  all identical  ENSGALG00000014122  292QYACIPNLDKLGYAKDMRFAF
Trubripes  all identical  ENSTRUG00000013823  290QFACNPNLDKVGHAASRRFNF
Drerio  all identical  ENSDARG00000005891  289QFACNPSLDKVGHSNDRRFMF
Dmelanogaster  not conserved  FBgn0036211  307NFACNPALDKLGYHPDTR
Celegans  not conserved  T05H4.5  300NFACIPNLEKLEYDPANRLLF
Xtropicalis  not conserved  ENSXETG00000016513  294QYAINPSLDKLSYPQDRRFAY
protein features
start (aa)end (aa)featuredetails 
270275STRANDmight get lost (downstream of altered splice site)
277282HELIXmight get lost (downstream of altered splice site)
280280CONFLICTI -> N (in Ref. 3; AAL87744).might get lost (downstream of altered splice site)
285291HELIXmight get lost (downstream of altered splice site)
295297HELIXmight get lost (downstream of altered splice site)
298300STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 837 / 837
position (AA) of stopcodon in wt / mu AA sequence 279 / 279
position of stopcodon in wt / mu cDNA 929 / 929
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 93 / 93
chromosome 22
strand -1
last intron/exon boundary 757
theoretical NMD boundary in CDS 614
length of CDS 837
coding sequence (CDS) position 806
cDNA position
(for ins/del: last normal base / first normal base)		 898
gDNA position
(for ins/del: last normal base / first normal base)		 29765
chromosomal position
(for ins/del: last normal base / first normal base)		 43015810
original gDNA sequence snippet TCCCAACCTGGACCACGTGGGCCACCCCACGGAGCGCTGCT
altered gDNA sequence snippet TCCCAACCTGGACCACGTGGACCACCCCACGGAGCGCTGCT
original cDNA sequence snippet TCCCAACCTGGACCACGTGGGCCACCCCACGGAGCGCTGCT
altered cDNA sequence snippet TCCCAACCTGGACCACGTGGACCACCCCACGGAGCGCTGCT
wildtype AA sequence MKLFQRSTPA ITLESPDIKY PLRLIDREII SHDTRRFRFA LPSPQHILGL PVGQHIYLSA
RIDGNLVVRP YTPISSDDDK GFVDLVIKVY FKDTHPKFPA GGKMSQYLES MQIGDTIEFR
GPSGLLVYQG KGKFAIRPDK KSNPIIRTVK SVGMIAGGTG ITPMLQVIRA IMKDPDDHTV
CHLLFANQTE KDILLRPELE ELRNKHSARF KLWYTLDRAP EAWDYGQGFV NEEMIRDHLP
PPEEEPLVLM CGPPPMIQYA CLPNLDHVGH PTERCFVF*
mutated AA sequence MKLFQRSTPA ITLESPDIKY PLRLIDREII SHDTRRFRFA LPSPQHILGL PVGQHIYLSA
RIDGNLVVRP YTPISSDDDK GFVDLVIKVY FKDTHPKFPA GGKMSQYLES MQIGDTIEFR
GPSGLLVYQG KGKFAIRPDK KSNPIIRTVK SVGMIAGGTG ITPMLQVIRA IMKDPDDHTV
CHLLFANQTE KDILLRPELE ELRNKHSARF KLWYTLDRAP EAWDYGQGFV NEEMIRDHLP
PPEEEPLVLM CGPPPMIQYA CLPNLDHVDH PTERCFVF*
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
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999333003810338 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM024771)
  • known disease mutation: rs250 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr22:43015810C>TN/A show variant in all transcripts   IGV
HGNC symbol CYB5R3
Ensembl transcript ID ENST00000402438
Genbank transcript ID N/A
UniProt peptide P00387
alteration type single base exchange
alteration region CDS
DNA changes c.806G>A
cDNA.990G>A
g.29765G>A
AA changes G269D Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 269
frameshift no
known variant Reference ID: rs121965016
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs250 (pathogenic for Methemoglobinemia, type I) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM024771)

known disease mutation at this position, please check HGMD for details (HGMD ID CM024771)
known disease mutation at this position, please check HGMD for details (HGMD ID CM024771)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.421
1.8121
(flanking)3.5281
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased29769wt: 0.46 / mu: 0.79wt: GGCCACCCCACGGAG
mu: GACCACCCCACGGAG		 CCAC|ccca
Donor gained297600.82mu: GACCACGTGGACCAC CCAC|gtgg
distance from splice site 61
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      269QYACLPNLDHVGHPTERCFVF*
mutated  not conserved    269QYACLPNLDHVDHPTERCFVF
Ptroglodytes  all identical  ENSPTRG00000014461  292QYACLPNLDRVGHPKERCFAF
Mmulatta  all identical  ENSMMUG00000010198  292QYACLPNLDRVGHPKERCFAF
Fcatus  no homologue    
Mmusculus  no alignment  ENSMUSG00000018042  n/a
Ggallus  all identical  ENSGALG00000014122  292QYACIPNLDKLGYAKDMRFAF
Trubripes  all identical  ENSTRUG00000013823  290QFACNPNLDKVGHAASRRFNF
Drerio  all identical  ENSDARG00000005891  289QFACNPSLDKVGHSNDRRFMF
Dmelanogaster  not conserved  FBgn0036211  307NFACNPALDKLGYHPDTR
Celegans  not conserved  T05H4.5  300NFACIPNLEKLEYDPANRLLF
Xtropicalis  not conserved  ENSXETG00000016513  294QYAINPSLDKLSYPQDRRFAY
protein features
start (aa)end (aa)featuredetails 
270275STRANDmight get lost (downstream of altered splice site)
277282HELIXmight get lost (downstream of altered splice site)
280280CONFLICTI -> N (in Ref. 3; AAL87744).might get lost (downstream of altered splice site)
285291HELIXmight get lost (downstream of altered splice site)
295297HELIXmight get lost (downstream of altered splice site)
298300STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 837 / 837
position (AA) of stopcodon in wt / mu AA sequence 279 / 279
position of stopcodon in wt / mu cDNA 1021 / 1021
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 22
strand -1
last intron/exon boundary 849
theoretical NMD boundary in CDS 614
length of CDS 837
coding sequence (CDS) position 806
cDNA position
(for ins/del: last normal base / first normal base)		 990
gDNA position
(for ins/del: last normal base / first normal base)		 29765
chromosomal position
(for ins/del: last normal base / first normal base)		 43015810
original gDNA sequence snippet TCCCAACCTGGACCACGTGGGCCACCCCACGGAGCGCTGCT
altered gDNA sequence snippet TCCCAACCTGGACCACGTGGACCACCCCACGGAGCGCTGCT
original cDNA sequence snippet TCCCAACCTGGACCACGTGGGCCACCCCACGGAGCGCTGCT
altered cDNA sequence snippet TCCCAACCTGGACCACGTGGACCACCCCACGGAGCGCTGCT
wildtype AA sequence MKLFQRSTPA ITLESPDIKY PLRLIDREII SHDTRRFRFA LPSPQHILGL PVGQHIYLSA
RIDGNLVVRP YTPISSDDDK GFVDLVIKVY FKDTHPKFPA GGKMSQYLES MQIGDTIEFR
GPSGLLVYQG KGKFAIRPDK KSNPIIRTVK SVGMIAGGTG ITPMLQVIRA IMKDPDDHTV
CHLLFANQTE KDILLRPELE ELRNKHSARF KLWYTLDRAP EAWDYGQGFV NEEMIRDHLP
PPEEEPLVLM CGPPPMIQYA CLPNLDHVGH PTERCFVF*
mutated AA sequence MKLFQRSTPA ITLESPDIKY PLRLIDREII SHDTRRFRFA LPSPQHILGL PVGQHIYLSA
RIDGNLVVRP YTPISSDDDK GFVDLVIKVY FKDTHPKFPA GGKMSQYLES MQIGDTIEFR
GPSGLLVYQG KGKFAIRPDK KSNPIIRTVK SVGMIAGGTG ITPMLQVIRA IMKDPDDHTV
CHLLFANQTE KDILLRPELE ELRNKHSARF KLWYTLDRAP EAWDYGQGFV NEEMIRDHLP
PPEEEPLVLM CGPPPMIQYA CLPNLDHVDH PTERCFVF*
speed 0.61 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: 0.999333003810338 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM024771)
  • known disease mutation: rs250 (pathogenic)
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr22:43015810C>TN/A show variant in all transcripts   IGV
HGNC symbol CYB5R3
Ensembl transcript ID ENST00000361740
Genbank transcript ID NM_001171660
UniProt peptide P00387
alteration type single base exchange
alteration region CDS
DNA changes c.974G>A
cDNA.974G>A
g.29765G>A
AA changes G325D Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 325
frameshift no
known variant Reference ID: rs121965016
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs250 (pathogenic for Methemoglobinemia, type I) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM024771)

known disease mutation at this position, please check HGMD for details (HGMD ID CM024771)
known disease mutation at this position, please check HGMD for details (HGMD ID CM024771)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.421
1.8121
(flanking)3.5281
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased29769wt: 0.46 / mu: 0.79wt: GGCCACCCCACGGAG
mu: GACCACCCCACGGAG		 CCAC|ccca
Donor gained297600.82mu: GACCACGTGGACCAC CCAC|gtgg
distance from splice site 142
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      325QYACLPNLDHVGHPTERCFVF*
mutated  not conserved    325QYACLPNLDHVDHPTERCFVF
Ptroglodytes  all identical  ENSPTRG00000014461  292QYACLPNLDRVGHPKERCFAF
Mmulatta  all identical  ENSMMUG00000010198  292QYACLPNLDRVGHPKERCFAF
Fcatus  no homologue    
Mmusculus  no alignment  ENSMUSG00000018042  n/a
Ggallus  all identical  ENSGALG00000014122  292QYACIPNLDKLGYAKDMRFAF
Trubripes  all identical  ENSTRUG00000013823  290QFACNPNLDKVGHAASRRFNF
Drerio  all identical  ENSDARG00000005891  289QFACNPSLDKVGHSNDRRFMF
Dmelanogaster  not conserved  FBgn0036211  307NFACNPALDKLGYHPDTR
Celegans  not conserved  T05H4.5  300NFACIPNLEKLEYDPANRLLF
Xtropicalis  not conserved  ENSXETG00000016513  294QYAINPSLDKLSYPQDRRFAY
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1005 / 1005
position (AA) of stopcodon in wt / mu AA sequence 335 / 335
position of stopcodon in wt / mu cDNA 1005 / 1005
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 1 / 1
chromosome 22
strand -1
last intron/exon boundary 833
theoretical NMD boundary in CDS 782
length of CDS 1005
coding sequence (CDS) position 974
cDNA position
(for ins/del: last normal base / first normal base)		 974
gDNA position
(for ins/del: last normal base / first normal base)		 29765
chromosomal position
(for ins/del: last normal base / first normal base)		 43015810
original gDNA sequence snippet TCCCAACCTGGACCACGTGGGCCACCCCACGGAGCGCTGCT
altered gDNA sequence snippet TCCCAACCTGGACCACGTGGACCACCCCACGGAGCGCTGCT
original cDNA sequence snippet TCCCAACCTGGACCACGTGGGCCACCCCACGGAGCGCTGCT
altered cDNA sequence snippet TCCCAACCTGGACCACGTGGACCACCCCACGGAGCGCTGCT
wildtype AA sequence MNRSLLVGCM QSKDIWGREE SICERLKQDG LDVERAESWE LGHMVLFPVW FLYSLLMKLF
QRSTPAITLE SPDIKYPLRL IDREIISHDT RRFRFALPSP QHILGLPVGQ HIYLSARIDG
NLVVRPYTPI SSDDDKGFVD LVIKVYFKDT HPKFPAGGKM SQYLESMQIG DTIEFRGPSG
LLVYQGKGKF AIRPDKKSNP IIRTVKSVGM IAGGTGITPM LQVIRAIMKD PDDHTVCHLL
FANQTEKDIL LRPELEELRN KHSARFKLWY TLDRAPEAWD YGQGFVNEEM IRDHLPPPEE
EPLVLMCGPP PMIQYACLPN LDHVGHPTER CFVF*
mutated AA sequence MNRSLLVGCM QSKDIWGREE SICERLKQDG LDVERAESWE LGHMVLFPVW FLYSLLMKLF
QRSTPAITLE SPDIKYPLRL IDREIISHDT RRFRFALPSP QHILGLPVGQ HIYLSARIDG
NLVVRPYTPI SSDDDKGFVD LVIKVYFKDT HPKFPAGGKM SQYLESMQIG DTIEFRGPSG
LLVYQGKGKF AIRPDKKSNP IIRTVKSVGM IAGGTGITPM LQVIRAIMKD PDDHTVCHLL
FANQTEKDIL LRPELEELRN KHSARFKLWY TLDRAPEAWD YGQGFVNEEM IRDHLPPPEE
EPLVLMCGPP PMIQYACLPN LDHVDHPTER CFVF*
speed 0.83 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
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Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999333003810338 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM024771)
  • known disease mutation: rs250 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr22:43015810C>TN/A show variant in all transcripts   IGV
HGNC symbol CYB5R3
Ensembl transcript ID ENST00000396303
Genbank transcript ID NM_001129819
UniProt peptide P00387
alteration type single base exchange
alteration region CDS
DNA changes c.806G>A
cDNA.958G>A
g.29765G>A
AA changes G269D Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 269
frameshift no
known variant Reference ID: rs121965016
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs250 (pathogenic for Methemoglobinemia, type I) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM024771)

known disease mutation at this position, please check HGMD for details (HGMD ID CM024771)
known disease mutation at this position, please check HGMD for details (HGMD ID CM024771)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.421
1.8121
(flanking)3.5281
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased29769wt: 0.46 / mu: 0.79wt: GGCCACCCCACGGAG
mu: GACCACCCCACGGAG		 CCAC|ccca
Donor gained297600.82mu: GACCACGTGGACCAC CCAC|gtgg
distance from splice site 142
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      269QYACLPNLDHVGHPTERCFVF*
mutated  not conserved    269QYACLPNLDHVDHPTERCFVF
Ptroglodytes  all identical  ENSPTRG00000014461  292QYACLPNLDRVGHPKERCFAF
Mmulatta  all identical  ENSMMUG00000010198  292QYACLPNLDRVGHPKERCFAF
Fcatus  no homologue    
Mmusculus  no alignment  ENSMUSG00000018042  n/a
Ggallus  all identical  ENSGALG00000014122  292QYACIPNLDKLGYAKDMRFAF
Trubripes  all identical  ENSTRUG00000013823  290QFACNPNLDKVGHAASRRFNF
Drerio  all identical  ENSDARG00000005891  289QFACNPSLDKVGHSNDRRFMF
Dmelanogaster  not conserved  FBgn0036211  307NFACNPALDKLGYHPDTR
Celegans  not conserved  T05H4.5  300NFACIPNLEKLEYDPANRLLF
Xtropicalis  not conserved  ENSXETG00000016513  294QYAINPSLDKLSYPQDRRFAY
protein features
start (aa)end (aa)featuredetails 
270275STRANDmight get lost (downstream of altered splice site)
277282HELIXmight get lost (downstream of altered splice site)
280280CONFLICTI -> N (in Ref. 3; AAL87744).might get lost (downstream of altered splice site)
285291HELIXmight get lost (downstream of altered splice site)
295297HELIXmight get lost (downstream of altered splice site)
298300STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 837 / 837
position (AA) of stopcodon in wt / mu AA sequence 279 / 279
position of stopcodon in wt / mu cDNA 989 / 989
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 153 / 153
chromosome 22
strand -1
last intron/exon boundary 817
theoretical NMD boundary in CDS 614
length of CDS 837
coding sequence (CDS) position 806
cDNA position
(for ins/del: last normal base / first normal base)		 958
gDNA position
(for ins/del: last normal base / first normal base)		 29765
chromosomal position
(for ins/del: last normal base / first normal base)		 43015810
original gDNA sequence snippet TCCCAACCTGGACCACGTGGGCCACCCCACGGAGCGCTGCT
altered gDNA sequence snippet TCCCAACCTGGACCACGTGGACCACCCCACGGAGCGCTGCT
original cDNA sequence snippet TCCCAACCTGGACCACGTGGGCCACCCCACGGAGCGCTGCT
altered cDNA sequence snippet TCCCAACCTGGACCACGTGGACCACCCCACGGAGCGCTGCT
wildtype AA sequence MKLFQRSTPA ITLESPDIKY PLRLIDREII SHDTRRFRFA LPSPQHILGL PVGQHIYLSA
RIDGNLVVRP YTPISSDDDK GFVDLVIKVY FKDTHPKFPA GGKMSQYLES MQIGDTIEFR
GPSGLLVYQG KGKFAIRPDK KSNPIIRTVK SVGMIAGGTG ITPMLQVIRA IMKDPDDHTV
CHLLFANQTE KDILLRPELE ELRNKHSARF KLWYTLDRAP EAWDYGQGFV NEEMIRDHLP
PPEEEPLVLM CGPPPMIQYA CLPNLDHVGH PTERCFVF*
mutated AA sequence MKLFQRSTPA ITLESPDIKY PLRLIDREII SHDTRRFRFA LPSPQHILGL PVGQHIYLSA
RIDGNLVVRP YTPISSDDDK GFVDLVIKVY FKDTHPKFPA GGKMSQYLES MQIGDTIEFR
GPSGLLVYQG KGKFAIRPDK KSNPIIRTVK SVGMIAGGTG ITPMLQVIRA IMKDPDDHTV
CHLLFANQTE KDILLRPELE ELRNKHSARF KLWYTLDRAP EAWDYGQGFV NEEMIRDHLP
PPEEEPLVLM CGPPPMIQYA CLPNLDHVDH PTERCFVF*
speed 0.39 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
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Problems