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: ENST00000261643
Querying Taster for transcript #2: ENST00000536205
Querying Taster for transcript #3: ENST00000537334
MT speed 0 s - this script 2.735808 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
COX10disease_causing_automatic0.999999981384433simple_aae0P225Lsingle base exchangers104894556show file
COX10disease_causing_automatic0.999999981384433simple_aae0P33Lsingle base exchangers104894556show file
COX10disease_causing_automatic0.999999981384433simple_aae0P8Lsingle base exchangers104894556show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999981384433 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM032559)
  • known disease mutation: rs7524 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:14063243C>TN/A show variant in all transcripts   IGV
HGNC symbol COX10
Ensembl transcript ID ENST00000261643
Genbank transcript ID NM_001303
UniProt peptide Q12887
alteration type single base exchange
alteration region CDS
DNA changes c.674C>T
cDNA.751C>T
g.90431C>T
AA changes P225L Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 225
frameshift no
known variant Reference ID: rs104894556
databasehomozygous (T/T)heterozygousallele carriers
1000G011
ExAC011

known disease mutation: rs7524 (pathogenic for Mitochondrial complex 4 deficiency, nuclear type 3) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM032559)

known disease mutation at this position, please check HGMD for details (HGMD ID CM032559)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032559)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)4.5811
4.5811
(flanking)-0.1130.993
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 22
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      225FDSNMNRTKNRPLVRGQISPLLAV
mutated  not conserved    225FDSNMNRTKNRLLVRGQISPLLA
Ptroglodytes  all identical  ENSPTRG00000008790  225FDSNMNRTKNRPLVRGQISPLLA
Mmulatta  all identical  ENSMMUG00000016157  225FDSNMNRTKNRPLVRGQISPLLA
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000042148  224FDSNMNRTKNRPLVRGQISPLLA
Ggallus  all identical  ENSGALG00000001375  217FDSNMNRTKNRPLVRGQISPLLA
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000034309  222FDSNMNRTKNRPLVRGQISPLHA
Dmelanogaster  not conserved  FBgn0032222  144FDSQMSRTKNRVLVTGQMTPLHA
Celegans  not conserved  Y46G5A.2  160QMRRTQTRVLVVHRFSPLHA
Xtropicalis  no homologue    
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1332 / 1332
position (AA) of stopcodon in wt / mu AA sequence 444 / 444
position of stopcodon in wt / mu cDNA 1409 / 1409
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 78 / 78
chromosome 17
strand 1
last intron/exon boundary 1006
theoretical NMD boundary in CDS 878
length of CDS 1332
coding sequence (CDS) position 674
cDNA position
(for ins/del: last normal base / first normal base)		 751
gDNA position
(for ins/del: last normal base / first normal base)		 90431
chromosomal position
(for ins/del: last normal base / first normal base)		 14063243
original gDNA sequence snippet GAATAGGACAAAGAACAGACCGCTGGTTCGTGGACAGATCA
altered gDNA sequence snippet GAATAGGACAAAGAACAGACTGCTGGTTCGTGGACAGATCA
original cDNA sequence snippet GAATAGGACAAAGAACAGACCGCTGGTTCGTGGACAGATCA
altered cDNA sequence snippet GAATAGGACAAAGAACAGACTGCTGGTTCGTGGACAGATCA
wildtype AA sequence MAASPHTLSS RLLTGCVGGS VWYLERRTIQ DSPHKFLHLL RNVNKQWITF QHFSFLKRMY
VTQLNRSHNQ QVRPKPEPVA SPFLEKTSSG QAKAEIYEMR PLSPPSLSLS RKPNEKELIE
LEPDSVIEDS IDVGKETKEE KRWKEMKLQV YDLPGILARL SKIKLTALVV STTAAGFALA
PGPFDWPCFL LTSVGTGLAS CAANSINQFF EVPFDSNMNR TKNRPLVRGQ ISPLLAVSFA
TCCAVPGVAI LTLGVNPLTG ALGLFNIFLY TCCYTPLKRI SIANTWVGAV VGAIPPVMGW
TAATGSLDAG AFLLGGILYS WQFPHFNALS WGLREDYSRG GYCMMSVTHP GLCRRVALRH
CLALLVLSAA APVLDITTWT FPIMALPINA YISYLGFRFY VDADRRSSRR LFFCSLWHLP
LLLLLMLTCK RPSGGGDAGP PPS*
mutated AA sequence MAASPHTLSS RLLTGCVGGS VWYLERRTIQ DSPHKFLHLL RNVNKQWITF QHFSFLKRMY
VTQLNRSHNQ QVRPKPEPVA SPFLEKTSSG QAKAEIYEMR PLSPPSLSLS RKPNEKELIE
LEPDSVIEDS IDVGKETKEE KRWKEMKLQV YDLPGILARL SKIKLTALVV STTAAGFALA
PGPFDWPCFL LTSVGTGLAS CAANSINQFF EVPFDSNMNR TKNRLLVRGQ ISPLLAVSFA
TCCAVPGVAI LTLGVNPLTG ALGLFNIFLY TCCYTPLKRI SIANTWVGAV VGAIPPVMGW
TAATGSLDAG AFLLGGILYS WQFPHFNALS WGLREDYSRG GYCMMSVTHP GLCRRVALRH
CLALLVLSAA APVLDITTWT FPIMALPINA YISYLGFRFY VDADRRSSRR LFFCSLWHLP
LLLLLMLTCK RPSGGGDAGP PPS*
speed 0.40 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: 0.999999981384433 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM032559)
  • known disease mutation: rs7524 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:14063243C>TN/A show variant in all transcripts   IGV
HGNC symbol COX10
Ensembl transcript ID ENST00000536205
Genbank transcript ID N/A
UniProt peptide Q12887
alteration type single base exchange
alteration region CDS
DNA changes c.98C>T
cDNA.551C>T
g.90431C>T
AA changes P33L Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 33
frameshift no
known variant Reference ID: rs104894556
databasehomozygous (T/T)heterozygousallele carriers
1000G011
ExAC011

known disease mutation: rs7524 (pathogenic for Mitochondrial complex 4 deficiency, nuclear type 3) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM032559)

known disease mutation at this position, please check HGMD for details (HGMD ID CM032559)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032559)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)4.5811
4.5811
(flanking)-0.1130.993
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 22
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      33FDSNMNRTKNRPLVRGQISPLLAV
mutated  not conserved    33FDSNMNRTKNRLLVRGQISPLLA
Ptroglodytes  all identical  ENSPTRG00000008790  225FDSNMNRTKNRPLVRGQISPLLA
Mmulatta  all identical  ENSMMUG00000016157  225FDSNMNRTKNRPLVRGQISPLLA
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000042148  224FDSNMNRTKNRPLVRGQISPLLA
Ggallus  all identical  ENSGALG00000001375  217FDSNMNRTKNRPLVRGQISPLLA
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000034309  222FDSNMNRTKNRPLVRGQISPLHA
Dmelanogaster  not conserved  FBgn0032222  144FDSQMSRTKNRVLVTGQMTPLHA
Celegans  not conserved  Y46G5A.2  160YDAQMRRTQTRVLVVHRFSPLHA
Xtropicalis  no homologue    
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 756 / 756
position (AA) of stopcodon in wt / mu AA sequence 252 / 252
position of stopcodon in wt / mu cDNA 1209 / 1209
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 454 / 454
chromosome 17
strand 1
last intron/exon boundary 806
theoretical NMD boundary in CDS 302
length of CDS 756
coding sequence (CDS) position 98
cDNA position
(for ins/del: last normal base / first normal base)		 551
gDNA position
(for ins/del: last normal base / first normal base)		 90431
chromosomal position
(for ins/del: last normal base / first normal base)		 14063243
original gDNA sequence snippet GAATAGGACAAAGAACAGACCGCTGGTTCGTGGACAGATCA
altered gDNA sequence snippet GAATAGGACAAAGAACAGACTGCTGGTTCGTGGACAGATCA
original cDNA sequence snippet GAATAGGACAAAGAACAGACCGCTGGTTCGTGGACAGATCA
altered cDNA sequence snippet GAATAGGACAAAGAACAGACTGCTGGTTCGTGGACAGATCA
wildtype AA sequence MICQEFWLDY PKSNSQFFEV PFDSNMNRTK NRPLVRGQIS PLLAVSFATC CAVPGVAILT
LGVNPLTGAL GLFNIFLYTC CYTPLKRISI ANTWVGAVVG AIPPVMGWTA ATGSLDAGAF
LLGGILYSWQ FPHFNALSWG LREDYSRGGY CMMSVTHPGL CRRVALRHCL ALLVLSAAAP
VLDITTWTFP IMALPINAYI SYLGFRFYVD ADRRSSRRLF FCSLWHLPLL LLLMLTCKRP
SGGGDAGPPP S*
mutated AA sequence MICQEFWLDY PKSNSQFFEV PFDSNMNRTK NRLLVRGQIS PLLAVSFATC CAVPGVAILT
LGVNPLTGAL GLFNIFLYTC CYTPLKRISI ANTWVGAVVG AIPPVMGWTA ATGSLDAGAF
LLGGILYSWQ FPHFNALSWG LREDYSRGGY CMMSVTHPGL CRRVALRHCL ALLVLSAAAP
VLDITTWTFP IMALPINAYI SYLGFRFYVD ADRRSSRRLF FCSLWHLPLL LLLMLTCKRP
SGGGDAGPPP S*
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
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999981384433 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM032559)
  • known disease mutation: rs7524 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:14063243C>TN/A show variant in all transcripts   IGV
HGNC symbol COX10
Ensembl transcript ID ENST00000537334
Genbank transcript ID N/A
UniProt peptide Q12887
alteration type single base exchange
alteration region CDS
DNA changes c.23C>T
cDNA.354C>T
g.90431C>T
AA changes P8L Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 8
frameshift no
known variant Reference ID: rs104894556
databasehomozygous (T/T)heterozygousallele carriers
1000G011
ExAC011

known disease mutation: rs7524 (pathogenic for Mitochondrial complex 4 deficiency, nuclear type 3) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM032559)

known disease mutation at this position, please check HGMD for details (HGMD ID CM032559)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032559)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)4.5811
4.5811
(flanking)-0.1130.993
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 22
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      8 MNRTKNRPLVRGQISPLLAV
mutated  not conserved    8 MNRTKNRLLVRGQISPLLAVSF
Ptroglodytes  all identical  ENSPTRG00000008790  225 MNRTKNRPLVRGQISPLLAVSF
Mmulatta  all identical  ENSMMUG00000016157  225 MNRTKNRPLVRGQISPLLAVAF
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000042148  224 MNRTKNRPLVRGQISPLLAVSF
Ggallus  all identical  ENSGALG00000001375  217 MNRTKNRPLVRGQISPLLAVCF
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000034309  222 MNRTKNRPLVRGQISPLHAVSF
Dmelanogaster  not conserved  FBgn0032222  144 MSRTKNRVLVTGQMTPLHAVTF
Celegans  not conserved  Y46G5A.2  160 MRRTQTRVLVVHRFSPLHAFTF
Xtropicalis  no homologue    
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 681 / 681
position (AA) of stopcodon in wt / mu AA sequence 227 / 227
position of stopcodon in wt / mu cDNA 1012 / 1012
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 332 / 332
chromosome 17
strand 1
last intron/exon boundary 609
theoretical NMD boundary in CDS 227
length of CDS 681
coding sequence (CDS) position 23
cDNA position
(for ins/del: last normal base / first normal base)		 354
gDNA position
(for ins/del: last normal base / first normal base)		 90431
chromosomal position
(for ins/del: last normal base / first normal base)		 14063243
original gDNA sequence snippet GAATAGGACAAAGAACAGACCGCTGGTTCGTGGACAGATCA
altered gDNA sequence snippet GAATAGGACAAAGAACAGACTGCTGGTTCGTGGACAGATCA
original cDNA sequence snippet GAATAGGACAAAGAACAGACCGCTGGTTCGTGGACAGATCA
altered cDNA sequence snippet GAATAGGACAAAGAACAGACTGCTGGTTCGTGGACAGATCA
wildtype AA sequence MNRTKNRPLV RGQISPLLAV SFATCCAVPG VAILTLGVNP LTGALGLFNI FLYTCCYTPL
KRISIANTWV GAVVGAIPPV MGWTAATGSL DAGAFLLGGI LYSWQFPHFN ALSWGLREDY
SRGGYCMMSV THPGLCRRVA LRHCLALLVL SAAAPVLDIT TWTFPIMALP INAYISYLGF
RFYVDADRRS SRRLFFCSLW HLPLLLLLML TCKRPSGGGD AGPPPS*
mutated AA sequence MNRTKNRLLV RGQISPLLAV SFATCCAVPG VAILTLGVNP LTGALGLFNI FLYTCCYTPL
KRISIANTWV GAVVGAIPPV MGWTAATGSL DAGAFLLGGI LYSWQFPHFN ALSWGLREDY
SRGGYCMMSV THPGLCRRVA LRHCLALLVL SAAAPVLDIT TWTFPIMALP INAYISYLGF
RFYVDADRRS SRRLFFCSLW HLPLLLLLML TCKRPSGGGD AGPPPS*
speed 0.34 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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