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: ENST00000344255
Querying Taster for transcript #2: ENST00000320185
Querying Taster for transcript #3: ENST00000346714
Querying Taster for transcript #4: ENST00000347978
MT speed 0 s - this script 4.880449 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
FGF8disease_causing_automatic7.39880651184119e-10simple_aae0F40Lsingle base exchangers137852661show file
FGF8disease_causing_automatic8.17873989898618e-10simple_aae0F40Lsingle base exchangers137852661show file
FGF8disease_causing_automatic0.000446116846742042without_aae0single base exchangers137852661show file
FGF8disease_causing_automatic0.000446116846742042without_aae0single base exchangers137852661show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 7.39880651184119e-10 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM082673)
  • known disease mutation: rs9123 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:103534925A>GN/A show variant in all transcripts   IGV
HGNC symbol FGF8
Ensembl transcript ID ENST00000344255
Genbank transcript ID NM_033164
UniProt peptide P55075
alteration type single base exchange
alteration region CDS
DNA changes c.118T>C
cDNA.118T>C
g.903T>C
AA changes F40L Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 40
frameshift no
known variant Reference ID: rs137852661
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs9123 (pathogenic for Hypogonadotropic hypogonadism 6 with or without anosmia) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM082673)

known disease mutation at this position, please check HGMD for details (HGMD ID CM082673)
known disease mutation at this position, please check HGMD for details (HGMD ID CM082673)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.4390.025
-0.6150.039
(flanking)0.840.628
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 39
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      40GPALGRELASLFRAGREPQGVSQQ
mutated  not conserved    40GPALGRELASLLRAGREPQGVSQ
Ptroglodytes  all identical  ENSPTRG00000002874  40GPALGRELASLFRAGREPQGVSQ
Mmulatta  no alignment  ENSMMUG00000015771  n/a
Fcatus  not conserved  ENSFCAG00000007177  40GAALGRELASLCGAGRESQGVSQ
Mmusculus  not conserved  ENSMUSG00000025219  40GNPADTLGQGHEDRPFGQRSRAGKN
Ggallus  not conserved  ENSGALG00000007706  43PPNF------------------T
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000003399  40PPNF------------------T
Dmelanogaster  no alignment  FBgn0014135  n/a
Celegans  no alignment  C05D11.4  n/a
Xtropicalis  not conserved  ENSXETG00000014474  40GSPTERE--GIRRESEAPRGEVSTQVTVQSPPNFT
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 702 / 702
position (AA) of stopcodon in wt / mu AA sequence 234 / 234
position of stopcodon in wt / mu cDNA 702 / 702
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 10
strand -1
last intron/exon boundary 412
theoretical NMD boundary in CDS 361
length of CDS 702
coding sequence (CDS) position 118
cDNA position
(for ins/del: last normal base / first normal base)		 118
gDNA position
(for ins/del: last normal base / first normal base)		 903
chromosomal position
(for ins/del: last normal base / first normal base)		 103534925
original gDNA sequence snippet GCAGGGAGCTCGCTTCCCTGTTCCGGGCTGGCCGGGAGCCC
altered gDNA sequence snippet GCAGGGAGCTCGCTTCCCTGCTCCGGGCTGGCCGGGAGCCC
original cDNA sequence snippet GCAGGGAGCTCGCTTCCCTGTTCCGGGCTGGCCGGGAGCCC
altered cDNA sequence snippet GCAGGGAGCTCGCTTCCCTGCTCCGGGCTGGCCGGGAGCCC
wildtype AA sequence MGSPRSALSC LLLHLLVLCL QAQEGPGRGP ALGRELASLF RAGREPQGVS QQHVREQSLV
TDQLSRRLIR TYQLYSRTSG KHVQVLANKR INAMAEDGDP FAKLIVETDT FGSRVRVRGA
ETGLYICMNK KGKLIAKSNG KGKDCVFTEI VLENNYTALQ NAKYEGWYMA FTRKGRPRKG
SKTRQHQREV HFMKRLPRGH HTTEQSLRFE FLNYPPFTRS LRGSQRTWAP EPR*
mutated AA sequence MGSPRSALSC LLLHLLVLCL QAQEGPGRGP ALGRELASLL RAGREPQGVS QQHVREQSLV
TDQLSRRLIR TYQLYSRTSG KHVQVLANKR INAMAEDGDP FAKLIVETDT FGSRVRVRGA
ETGLYICMNK KGKLIAKSNG KGKDCVFTEI VLENNYTALQ NAKYEGWYMA FTRKGRPRKG
SKTRQHQREV HFMKRLPRGH HTTEQSLRFE FLNYPPFTRS LRGSQRTWAP EPR*
speed 1.39 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: 8.17873989898618e-10 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM082673)
  • known disease mutation: rs9123 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:103534925A>GN/A show variant in all transcripts   IGV
HGNC symbol FGF8
Ensembl transcript ID ENST00000320185
Genbank transcript ID NM_033163
UniProt peptide P55075
alteration type single base exchange
alteration region CDS
DNA changes c.118T>C
cDNA.177T>C
g.903T>C
AA changes F40L Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 40
frameshift no
known variant Reference ID: rs137852661
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs9123 (pathogenic for Hypogonadotropic hypogonadism 6 with or without anosmia) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM082673)

known disease mutation at this position, please check HGMD for details (HGMD ID CM082673)
known disease mutation at this position, please check HGMD for details (HGMD ID CM082673)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.4390.025
-0.6150.039
(flanking)0.840.628
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 39
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      40GPALGRELASLFRAGREPQGVSQQ
mutated  not conserved    40GPALGRELASLLRAGREPQGVSQ
Ptroglodytes  all identical  ENSPTRG00000002874  40GPALGRELASLFRAGREPQGVSQ
Mmulatta  no alignment  ENSMMUG00000015771  n/a
Fcatus  not conserved  ENSFCAG00000007177  40GAALGRELASLCGAGRESQGVSQ
Mmusculus  not conserved  ENSMUSG00000025219  40GNPADTLGQGHEDRPFGQRSRAGKN
Ggallus  not conserved  ENSGALG00000007706  43-----------------------
Trubripes  no homologue    
Drerio  no alignment  ENSDARG00000003399  n/a
Dmelanogaster  no alignment  FBgn0014135  n/a
Celegans  no alignment  C05D11.4  n/a
Xtropicalis  not conserved  ENSXETG00000014474  40GSPTERE--GIRRESEAPRGEVST
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 735 / 735
position (AA) of stopcodon in wt / mu AA sequence 245 / 245
position of stopcodon in wt / mu cDNA 794 / 794
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 60 / 60
chromosome 10
strand -1
last intron/exon boundary 504
theoretical NMD boundary in CDS 394
length of CDS 735
coding sequence (CDS) position 118
cDNA position
(for ins/del: last normal base / first normal base)		 177
gDNA position
(for ins/del: last normal base / first normal base)		 903
chromosomal position
(for ins/del: last normal base / first normal base)		 103534925
original gDNA sequence snippet GCAGGGAGCTCGCTTCCCTGTTCCGGGCTGGCCGGGAGCCC
altered gDNA sequence snippet GCAGGGAGCTCGCTTCCCTGCTCCGGGCTGGCCGGGAGCCC
original cDNA sequence snippet GCAGGGAGCTCGCTTCCCTGTTCCGGGCTGGCCGGGAGCCC
altered cDNA sequence snippet GCAGGGAGCTCGCTTCCCTGCTCCGGGCTGGCCGGGAGCCC
wildtype AA sequence MGSPRSALSC LLLHLLVLCL QAQEGPGRGP ALGRELASLF RAGREPQGVS QQVTVQSSPN
FTQHVREQSL VTDQLSRRLI RTYQLYSRTS GKHVQVLANK RINAMAEDGD PFAKLIVETD
TFGSRVRVRG AETGLYICMN KKGKLIAKSN GKGKDCVFTE IVLENNYTAL QNAKYEGWYM
AFTRKGRPRK GSKTRQHQRE VHFMKRLPRG HHTTEQSLRF EFLNYPPFTR SLRGSQRTWA
PEPR*
mutated AA sequence MGSPRSALSC LLLHLLVLCL QAQEGPGRGP ALGRELASLL RAGREPQGVS QQVTVQSSPN
FTQHVREQSL VTDQLSRRLI RTYQLYSRTS GKHVQVLANK RINAMAEDGD PFAKLIVETD
TFGSRVRVRG AETGLYICMN KKGKLIAKSN GKGKDCVFTE IVLENNYTAL QNAKYEGWYM
AFTRKGRPRK GSKTRQHQRE VHFMKRLPRG HHTTEQSLRF EFLNYPPFTR SLRGSQRTWA
PEPR*
speed 0.45 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: 0.000446116846742042 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM082673)
  • known disease mutation: rs9123 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:103534925A>GN/A show variant in all transcripts   IGV
HGNC symbol FGF8
Ensembl transcript ID ENST00000346714
Genbank transcript ID NM_033165
UniProt peptide N/A
alteration type single base exchange
alteration region intron
DNA changes g.903T>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs137852661
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs9123 (pathogenic for Hypogonadotropic hypogonadism 6 with or without anosmia) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM082673)

known disease mutation at this position, please check HGMD for details (HGMD ID CM082673)
known disease mutation at this position, please check HGMD for details (HGMD ID CM082673)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.4390.025
-0.6150.039
(flanking)0.840.628
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 289
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features N/A
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 75 / 75
chromosome 10
strand -1
last intron/exon boundary 399
theoretical NMD boundary in CDS 274
length of CDS 615
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)		 903
chromosomal position
(for ins/del: last normal base / first normal base)		 103534925
original gDNA sequence snippet GCAGGGAGCTCGCTTCCCTGTTCCGGGCTGGCCGGGAGCCC
altered gDNA sequence snippet GCAGGGAGCTCGCTTCCCTGCTCCGGGCTGGCCGGGAGCCC
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MGSPRSALSC LLLHLLVLCL QAQHVREQSL VTDQLSRRLI RTYQLYSRTS GKHVQVLANK
RINAMAEDGD PFAKLIVETD TFGSRVRVRG AETGLYICMN KKGKLIAKSN GKGKDCVFTE
IVLENNYTAL QNAKYEGWYM AFTRKGRPRK GSKTRQHQRE VHFMKRLPRG HHTTEQSLRF
EFLNYPPFTR SLRGSQRTWA PEPR*
mutated AA sequence N/A
speed 0.41 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: 0.000446116846742042 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM082673)
  • known disease mutation: rs9123 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:103534925A>GN/A show variant in all transcripts   IGV
HGNC symbol FGF8
Ensembl transcript ID ENST00000347978
Genbank transcript ID NM_006119
UniProt peptide N/A
alteration type single base exchange
alteration region intron
DNA changes g.903T>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs137852661
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs9123 (pathogenic for Hypogonadotropic hypogonadism 6 with or without anosmia) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM082673)

known disease mutation at this position, please check HGMD for details (HGMD ID CM082673)
known disease mutation at this position, please check HGMD for details (HGMD ID CM082673)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.4390.025
-0.6150.039
(flanking)0.840.628
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 256
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features N/A
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 171 / 171
chromosome 10
strand -1
last intron/exon boundary 528
theoretical NMD boundary in CDS 307
length of CDS 648
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)		 903
chromosomal position
(for ins/del: last normal base / first normal base)		 103534925
original gDNA sequence snippet GCAGGGAGCTCGCTTCCCTGTTCCGGGCTGGCCGGGAGCCC
altered gDNA sequence snippet GCAGGGAGCTCGCTTCCCTGCTCCGGGCTGGCCGGGAGCCC
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MGSPRSALSC LLLHLLVLCL QAQVTVQSSP NFTQHVREQS LVTDQLSRRL IRTYQLYSRT
SGKHVQVLAN KRINAMAEDG DPFAKLIVET DTFGSRVRVR GAETGLYICM NKKGKLIAKS
NGKGKDCVFT EIVLENNYTA LQNAKYEGWY MAFTRKGRPR KGSKTRQHQR EVHFMKRLPR
GHHTTEQSLR FEFLNYPPFT RSLRGSQRTW APEPR*
mutated AA sequence N/A
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

Problems