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 4 transcript(s)...
Querying Taster for transcript #1: ENST00000377270
Querying Taster for transcript #2: ENST00000396366
Querying Taster for transcript #3: ENST00000498653
Querying Taster for transcript #4: ENST00000396364
MT speed 0 s - this script 5.191965 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
FXNdisease_causing0.999999682037825simple_aaeaffectedL182Fsingle base exchangers139616452show file
FXNdisease_causing0.999999682037825simple_aaeaffectedL107Fsingle base exchangers139616452show file
FXNdisease_causing1without_aaeaffectedsingle base exchangers139616452show file
FXNdisease_causing1without_aaeaffectedsingle base exchangers139616452show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999682037825      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM983507)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:71687589C>TN/A show variant in all transcripts   IGV
HGNC symbol FXN
Ensembl transcript ID ENST00000377270
Genbank transcript ID NM_000144
UniProt peptide Q16595
alteration type single base exchange
alteration region CDS
DNA changes c.544C>T
cDNA.1068C>T
g.37415C>T
AA changes L182F Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 182
frameshift no
known variant Reference ID: rs139616452
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation at this position, please check HGMD for details (HGMD ID CM983507)

known disease mutation at this position, please check HGMD for details (HGMD ID CM983507)
known disease mutation at this position, please check HGMD for details (HGMD ID CM983507)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2230.904
3.7681
(flanking)4.4721
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased37420wt: 0.53 / mu: 0.65wt: CACGACGGCGTGTCCCTCCATGAGCTGCTGGCCGCAGAGCT
mu: CACGACGGCGTGTCCTTCCATGAGCTGCTGGCCGCAGAGCT		 ccat|GAGC
Acc increased37418wt: 0.22 / mu: 0.43wt: CCCACGACGGCGTGTCCCTCCATGAGCTGCTGGCCGCAGAG
mu: CCCACGACGGCGTGTCCTTCCATGAGCTGCTGGCCGCAGAG		 ctcc|ATGA
Acc increased37419wt: 0.27 / mu: 0.50wt: CCACGACGGCGTGTCCCTCCATGAGCTGCTGGCCGCAGAGC
mu: CCACGACGGCGTGTCCTTCCATGAGCTGCTGGCCGCAGAGC		 tcca|TGAG
distance from splice site 62
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      182KNWVYSHDGVSLHELLAAELTKAL
mutated  not conserved    182SFHELLAAELTKA
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000000357  182SLHELLGAELTKA
Fcatus  all identical  ENSFCAG00000008813  180ESWVYAHDGVSLHQLLTTELTEA
Mmusculus  all identical  ENSMUSG00000059363  179SLHELLARELTKA
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000074356  176ERWVYTHDAVPLHSLLSKELSII
Dmelanogaster  all identical  FBgn0030092  160TVAAGRWIYKHSGQSLHELLQQEIPGI
Celegans  all identical  F59G1.7  112EGKWTYAHDGEQLDSLLNREFRKI
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
182194HELIXlost
202202CONFLICTS -> W (in Ref. 1; AAA98508/AAA98510).might get lost (downstream of altered splice site)
206208STRANDmight 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 1157 / 1157
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 525 / 525
chromosome 9
strand 1
last intron/exon boundary 1007
theoretical NMD boundary in CDS 432
length of CDS 633
coding sequence (CDS) position 544
cDNA position
(for ins/del: last normal base / first normal base)		 1068
gDNA position
(for ins/del: last normal base / first normal base)		 37415
chromosomal position
(for ins/del: last normal base / first normal base)		 71687589
original gDNA sequence snippet ACTCCCACGACGGCGTGTCCCTCCATGAGCTGCTGGCCGCA
altered gDNA sequence snippet ACTCCCACGACGGCGTGTCCTTCCATGAGCTGCTGGCCGCA
original cDNA sequence snippet ACTCCCACGACGGCGTGTCCCTCCATGAGCTGCTGGCCGCA
altered cDNA sequence snippet ACTCCCACGACGGCGTGTCCTTCCATGAGCTGCTGGCCGCA
wildtype AA sequence MWTLGRRAVA GLLASPSPAQ AQTLTRVPRP AELAPLCGRR GLRTDIDATC TPRRASSNQR
GLNQIWNVKK QSVYLMNLRK SGTLGHPGSL DETTYERLAE ETLDSLAEFF EDLADKPYTF
EDYDVSFGSG VLTVKLGGDL GTYVINKQTP NKQIWLSSPS SGPKRYDWTG KNWVYSHDGV
SLHELLAAEL TKALKTKLDL SSLAYSGKDA *
mutated AA sequence MWTLGRRAVA GLLASPSPAQ AQTLTRVPRP AELAPLCGRR GLRTDIDATC TPRRASSNQR
GLNQIWNVKK QSVYLMNLRK SGTLGHPGSL DETTYERLAE ETLDSLAEFF EDLADKPYTF
EDYDVSFGSG VLTVKLGGDL GTYVINKQTP NKQIWLSSPS SGPKRYDWTG KNWVYSHDGV
SFHELLAAEL TKALKTKLDL SSLAYSGKDA *
speed 1.15 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: 0.999999682037825      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM983507)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:71687589C>TN/A show variant in all transcripts   IGV
HGNC symbol FXN
Ensembl transcript ID ENST00000498653
Genbank transcript ID N/A
UniProt peptide Q16595
alteration type single base exchange
alteration region CDS
DNA changes c.319C>T
cDNA.424C>T
g.37415C>T
AA changes L107F Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 107
frameshift no
known variant Reference ID: rs139616452
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation at this position, please check HGMD for details (HGMD ID CM983507)

known disease mutation at this position, please check HGMD for details (HGMD ID CM983507)
known disease mutation at this position, please check HGMD for details (HGMD ID CM983507)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2230.904
3.7681
(flanking)4.4721
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased37420wt: 0.53 / mu: 0.65wt: CACGACGGCGTGTCCCTCCATGAGCTGCTGGCCGCAGAGCT
mu: CACGACGGCGTGTCCTTCCATGAGCTGCTGGCCGCAGAGCT		 ccat|GAGC
Acc increased37418wt: 0.22 / mu: 0.43wt: CCCACGACGGCGTGTCCCTCCATGAGCTGCTGGCCGCAGAG
mu: CCCACGACGGCGTGTCCTTCCATGAGCTGCTGGCCGCAGAG		 ctcc|ATGA
Acc increased37419wt: 0.27 / mu: 0.50wt: CCACGACGGCGTGTCCCTCCATGAGCTGCTGGCCGCAGAGC
mu: CCACGACGGCGTGTCCTTCCATGAGCTGCTGGCCGCAGAGC		 tcca|TGAG
distance from splice site 62
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      107KNWVYSHDGVSLHELLAAELTKAL
mutated  not conserved    107KNWVYSHDGVSFHELLAAELTKA
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000000357  182KNWVYSHDGVSLHELLGAELTKA
Fcatus  all identical  ENSFCAG00000008813  180ESWVYAHDGVSLHQLLTTELTEA
Mmusculus  all identical  ENSMUSG00000059363  179KNWVYSHDGVSLHELLARELTKA
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000074356  176ERWVYTHDAVPLHSLLSKELSII
Dmelanogaster  all identical  FBgn0030092  160TVAAGRWIYKHSGQSLHELLQQEIPGI
Celegans  all identical  F59G1.7  112EGKWTYAHDGEQLDSLLNREFRKI
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
92114HELIXlost
124128STRANDmight get lost (downstream of altered splice site)
131135STRANDmight get lost (downstream of altered splice site)
138140TURNmight get lost (downstream of altered splice site)
142148STRANDmight get lost (downstream of altered splice site)
149152TURNmight get lost (downstream of altered splice site)
153157STRANDmight get lost (downstream of altered splice site)
159161STRANDmight get lost (downstream of altered splice site)
164168STRANDmight get lost (downstream of altered splice site)
170175STRANDmight get lost (downstream of altered splice site)
175175CONFLICTY -> F (in Ref. 1; AAA98508/AAA98510).might get lost (downstream of altered splice site)
176178TURNmight get lost (downstream of altered splice site)
182194HELIXmight get lost (downstream of altered splice site)
202202CONFLICTS -> W (in Ref. 1; AAA98508/AAA98510).might get lost (downstream of altered splice site)
206208STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 408 / 408
position (AA) of stopcodon in wt / mu AA sequence 136 / 136
position of stopcodon in wt / mu cDNA 513 / 513
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 106 / 106
chromosome 9
strand 1
last intron/exon boundary 363
theoretical NMD boundary in CDS 207
length of CDS 408
coding sequence (CDS) position 319
cDNA position
(for ins/del: last normal base / first normal base)		 424
gDNA position
(for ins/del: last normal base / first normal base)		 37415
chromosomal position
(for ins/del: last normal base / first normal base)		 71687589
original gDNA sequence snippet ACTCCCACGACGGCGTGTCCCTCCATGAGCTGCTGGCCGCA
altered gDNA sequence snippet ACTCCCACGACGGCGTGTCCTTCCATGAGCTGCTGGCCGCA
original cDNA sequence snippet ACTCCCACGACGGCGTGTCCCTCCATGAGCTGCTGGCCGCA
altered cDNA sequence snippet ACTCCCACGACGGCGTGTCCTTCCATGAGCTGCTGGCCGCA
wildtype AA sequence MNLRKSGTLG HPGSLDETTY ERLAEETLDS LAEFFEDLAD KPYTFEDYDV SFGSGVLTVK
LGGDLGTYVI NKQTPNKQIW LSSPSSGPKR YDWTGKNWVY SHDGVSLHEL LAAELTKALK
TKLDLSSLAY SGKDA*
mutated AA sequence MNLRKSGTLG HPGSLDETTY ERLAEETLDS LAEFFEDLAD KPYTFEDYDV SFGSGVLTVK
LGGDLGTYVI NKQTPNKQIW LSSPSSGPKR YDWTGKNWVY SHDGVSFHEL LAAELTKALK
TKLDLSSLAY SGKDA*
speed 1.10 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: without_aae, prob: 1      (explain)
Summary
  • known disease mutation at this position (HGMD CM983507)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:71687589C>TN/A show variant in all transcripts   IGV
HGNC symbol FXN
Ensembl transcript ID ENST00000396366
Genbank transcript ID NM_181425
UniProt peptide Q16595
alteration type single base exchange
alteration region CDS
DNA changes c.552C>T
cDNA.573C>T
g.37415C>T
AA changes no AA changes
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift no
known variant Reference ID: rs139616452
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation at this position, please check HGMD for details (HGMD ID CM983507)

known disease mutation at this position, please check HGMD for details (HGMD ID CM983507)
known disease mutation at this position, please check HGMD for details (HGMD ID CM983507)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2230.904
3.7681
(flanking)4.4721
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased37420wt: 0.53 / mu: 0.65wt: CACGACGGCGTGTCCCTCCATGAGCTGCTGGCCGCAGAGCT
mu: CACGACGGCGTGTCCTTCCATGAGCTGCTGGCCGCAGAGCT		 ccat|GAGC
Acc increased37418wt: 0.22 / mu: 0.43wt: CCCACGACGGCGTGTCCCTCCATGAGCTGCTGGCCGCAGAG
mu: CCCACGACGGCGTGTCCTTCCATGAGCTGCTGGCCGCAGAG		 ctcc|ATGA
Acc increased37419wt: 0.27 / mu: 0.50wt: CCACGACGGCGTGTCCCTCCATGAGCTGCTGGCCGCAGAGC
mu: CCACGACGGCGTGTCCTTCCATGAGCTGCTGGCCGCAGAGC		 tcca|TGAG
distance from splice site 62
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
182194HELIXmight get lost (downstream of altered splice site)
202202CONFLICTS -> W (in Ref. 1; AAA98508/AAA98510).might get lost (downstream of altered splice site)
206208STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered no
position of stopcodon in wt / mu CDS 591 / 591
position (AA) of stopcodon in wt / mu AA sequence 197 / 197
position of stopcodon in wt / mu cDNA 612 / 612
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 22 / 22
chromosome 9
strand 1
last intron/exon boundary 512
theoretical NMD boundary in CDS 440
length of CDS 591
coding sequence (CDS) position 552
cDNA position
(for ins/del: last normal base / first normal base)		 573
gDNA position
(for ins/del: last normal base / first normal base)		 37415
chromosomal position
(for ins/del: last normal base / first normal base)		 71687589
original gDNA sequence snippet ACTCCCACGACGGCGTGTCCCTCCATGAGCTGCTGGCCGCA
altered gDNA sequence snippet ACTCCCACGACGGCGTGTCCTTCCATGAGCTGCTGGCCGCA
original cDNA sequence snippet ACTCCCACGACGGCGTGTCCCTCCATGAGCTGCTGGCCGCA
altered cDNA sequence snippet ACTCCCACGACGGCGTGTCCTTCCATGAGCTGCTGGCCGCA
wildtype AA sequence MWTLGRRAVA GLLASPSPAQ AQTLTRVPRP AELAPLCGRR GLRTDIDATC TPRRASSNQR
GLNQIWNVKK QSVYLMNLRK SGTLGHPGSL DETTYERLAE ETLDSLAEFF EDLADKPYTF
EDYDVSFGSG VLTVKLGGDL GTYVINKQTP NKQIWLSSPS RYVVDLSVMT GLGKTGCTPT
TACPSMSCWP QSSLKP*
mutated AA sequence MWTLGRRAVA GLLASPSPAQ AQTLTRVPRP AELAPLCGRR GLRTDIDATC TPRRASSNQR
GLNQIWNVKK QSVYLMNLRK SGTLGHPGSL DETTYERLAE ETLDSLAEFF EDLADKPYTF
EDYDVSFGSG VLTVKLGGDL GTYVINKQTP NKQIWLSSPS RYVVDLSVMT GLGKTGCTPT
TACPSMSCWP QSSLKP*
speed 0.59 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: without_aae, prob: 1      (explain)
Summary
  • known disease mutation at this position (HGMD CM983507)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:71687589C>TN/A show variant in all transcripts   IGV
HGNC symbol FXN
Ensembl transcript ID ENST00000396364
Genbank transcript ID NM_001161706
UniProt peptide Q16595
alteration type single base exchange
alteration region intron
DNA changes g.37415C>T
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs139616452
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation at this position, please check HGMD for details (HGMD ID CM983507)

known disease mutation at this position, please check HGMD for details (HGMD ID CM983507)
known disease mutation at this position, please check HGMD for details (HGMD ID CM983507)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2230.904
3.7681
(flanking)4.4721
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased37420wt: 0.53 / mu: 0.65wt: CACGACGGCGTGTCCCTCCATGAGCTGCTGGCCGCAGAGCT
mu: CACGACGGCGTGTCCTTCCATGAGCTGCTGGCCGCAGAGCT		 ccat|GAGC
Acc increased37418wt: 0.22 / mu: 0.43wt: CCCACGACGGCGTGTCCCTCCATGAGCTGCTGGCCGCAGAG
mu: CCCACGACGGCGTGTCCTTCCATGAGCTGCTGGCCGCAGAG		 ctcc|ATGA
Acc increased37419wt: 0.27 / mu: 0.50wt: CCACGACGGCGTGTCCCTCCATGAGCTGCTGGCCGCAGAGC
mu: CCACGACGGCGTGTCCTTCCATGAGCTGCTGGCCGCAGAGC		 tcca|TGAG
distance from splice site 7638
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
159161STRANDmight get lost (downstream of altered splice site)
164168STRANDmight get lost (downstream of altered splice site)
170175STRANDmight get lost (downstream of altered splice site)
175175CONFLICTY -> F (in Ref. 1; AAA98508/AAA98510).might get lost (downstream of altered splice site)
176178TURNmight get lost (downstream of altered splice site)
182194HELIXmight get lost (downstream of altered splice site)
202202CONFLICTS -> W (in Ref. 1; AAA98508/AAA98510).might get lost (downstream of altered splice site)
206208STRANDmight get lost (downstream of altered splice site)
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 221 / 221
chromosome 9
strand 1
last intron/exon boundary 703
theoretical NMD boundary in CDS 432
length of CDS 516
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 37415
chromosomal position
(for ins/del: last normal base / first normal base)		 71687589
original gDNA sequence snippet ACTCCCACGACGGCGTGTCCCTCCATGAGCTGCTGGCCGCA
altered gDNA sequence snippet ACTCCCACGACGGCGTGTCCTTCCATGAGCTGCTGGCCGCA
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MWTLGRRAVA GLLASPSPAQ AQTLTRVPRP AELAPLCGRR GLRTDIDATC TPRRASSNQR
GLNQIWNVKK QSVYLMNLRK SGTLGHPGSL DETTYERLAE ETLDSLAEFF EDLADKPYTF
EDYDVSFGSG VLTVKLGGDL GTYVINKQTP NKQIWLSSPS RLTWLLWLFH P*
mutated AA sequence N/A
speed 0.88 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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