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MutationTaster - study a chromosomal position

 MTQE documentation
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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000330315
MT speed 0 s - this script 2.413563 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
FOXL2disease_causing0.999999857237763simple_aaeaffectedG187Dsingle base exchangers121908359show file

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Prediction

disease causing

 Model: simple_aae, prob: 0.999999857237763      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs4871 (probable pathogenic)
  • known disease mutation at this position (HGMD CM093924)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:138665005C>TN/A show variant in all transcripts   IGV
HGNC symbol FOXL2
Ensembl transcript ID ENST00000330315
Genbank transcript ID NM_023067
UniProt peptide P58012
alteration type single base exchange
alteration region CDS
DNA changes c.560G>A
cDNA.978G>A
g.978G>A
AA changes G187D Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 187
frameshift no
known variant Reference ID: rs121908359
Allele 'T' was neither found in ExAC nor 1000G.
known as potential disease variant: rs4871 (probable pathogenic for Blepharophimosis, ptosis, and epicanthus inversus|Premature ovarian failure 3) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM093924)

known disease mutation at this position, please check HGMD for details (HGMD ID CM093924)
known disease mutation at this position, please check HGMD for details (HGMD ID CM093924)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
Max, Transcription Factor, Max TF binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)1.0771
4.8631
(flanking)2.391
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased984wt: 0.22 / mu: 0.29wt: GGCCGACGGCTACGGCTACCTGGCGCCCCCCAAGTACCTGC
mu: GGCCGACGGCTACGACTACCTGGCGCCCCCCAAGTACCTGC		 acct|GGCG
Donor increased982wt: 0.23 / mu: 0.25wt: GGCTACCTGGCGCCC
mu: GACTACCTGGCGCCC		 CTAC|ctgg
Donor marginally increased971wt: 0.9362 / mu: 0.9421 (marginal change - not scored)wt: CCGACGGCTACGGCT
mu: CCGACGGCTACGACT		 GACG|gcta
distance from splice site 978
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      187CGVAGAGADGYGYLAPPKYLQSGF
mutated  not conserved    187AGADGYDYLAPPKYLQSG
Ptroglodytes  all identical  ENSPTRG00000015453  187AAADGYGYLAPPKYLQSG
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000050397  183AGADGYGYLAPPKYLQSG
Ggallus  all identical  ENSGALG00000021009  167-GPDGYGYLSPPKYLQST
Trubripes  all identical  ENSTRUG00000007925  167-GGDGYGYLSPPKYLQSS
Drerio  all identical  ENSDARG00000042180  166-GGEGYGYLSPPKYLQSG
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000008253  167-SSDTYGYLSPPKYLQST
protein features
start (aa)end (aa)featuredetails 
221234COMPBIASPoly-Ala.might get lost (downstream of altered splice site)
284292COMPBIASPoly-Pro.might get lost (downstream of altered splice site)
301304COMPBIASPoly-Ala.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1131 / 1131
position (AA) of stopcodon in wt / mu AA sequence 377 / 377
position of stopcodon in wt / mu cDNA 1549 / 1549
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 419 / 419
chromosome 3
strand -1
last intron/exon boundary 1
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 1131
coding sequence (CDS) position 560
cDNA position
(for ins/del: last normal base / first normal base)		 978
gDNA position
(for ins/del: last normal base / first normal base)		 978
chromosomal position
(for ins/del: last normal base / first normal base)		 138665005
original gDNA sequence snippet CGCCGGGGCCGACGGCTACGGCTACCTGGCGCCCCCCAAGT
altered gDNA sequence snippet CGCCGGGGCCGACGGCTACGACTACCTGGCGCCCCCCAAGT
original cDNA sequence snippet CGCCGGGGCCGACGGCTACGGCTACCTGGCGCCCCCCAAGT
altered cDNA sequence snippet CGCCGGGGCCGACGGCTACGACTACCTGGCGCCCCCCAAGT
wildtype AA sequence MMASYPEPED AAGALLAPET GRTVKEPEGP PPSPGKGGGG GGGTAPEKPD PAQKPPYSYV
ALIAMAIRES AEKRLTLSGI YQYIIAKFPF YEKNKKGWQN SIRHNLSLNE CFIKVPREGG
GERKGNYWTL DPACEDMFEK GNYRRRRRMK RPFRPPPAHF QPGKGLFGAG GAAGGCGVAG
AGADGYGYLA PPKYLQSGFL NNSWPLPQPP SPMPYASCQM AAAAAAAAAA AAAAGPGSPG
AAAVVKGLAG PAASYGPYTR VQSMALPPGV VNSYNGLGGP PAAPPPPPHP HPHPHAHHLH
AAAAPPPAPP HHGAAAPPPG QLSPASPATA APPAPAPTSA PGLQFACARQ PELAMMHCSY
WDHDSKTGAL HSRLDL*
mutated AA sequence MMASYPEPED AAGALLAPET GRTVKEPEGP PPSPGKGGGG GGGTAPEKPD PAQKPPYSYV
ALIAMAIRES AEKRLTLSGI YQYIIAKFPF YEKNKKGWQN SIRHNLSLNE CFIKVPREGG
GERKGNYWTL DPACEDMFEK GNYRRRRRMK RPFRPPPAHF QPGKGLFGAG GAAGGCGVAG
AGADGYDYLA PPKYLQSGFL NNSWPLPQPP SPMPYASCQM AAAAAAAAAA AAAAGPGSPG
AAAVVKGLAG PAASYGPYTR VQSMALPPGV VNSYNGLGGP PAAPPPPPHP HPHPHAHHLH
AAAAPPPAPP HHGAAAPPPG QLSPASPATA APPAPAPTSA PGLQFACARQ PELAMMHCSY
WDHDSKTGAL HSRLDL*
speed 0.35 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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