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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: ENST00000287020
MT speed 1.23 s - this script 7.370619 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GDF6disease_causing_automatic5.19004653028441e-12simple_aaeaffected0A249Esingle base exchangers121909352show file

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Prediction

disease causing

Model: simple_aae, prob: 5.19004653028441e-12 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM082790)
  • known disease mutation: rs8371 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr8:97157413G>TN/A show variant in all transcripts   IGV
HGNC symbol GDF6
Ensembl transcript ID ENST00000287020
Genbank transcript ID NM_001001557
UniProt peptide Q6KF10
alteration type single base exchange
alteration region CDS
DNA changes c.746C>A
cDNA.846C>A
g.15608C>A
AA changes A249E Score: 107 explain score(s)
position(s) of altered AA
if AA alteration in CDS
249
frameshift no
known variant Reference ID: rs121909352
databasehomozygous (T/T)heterozygousallele carriers
1000G033
ExAC01010

known disease mutation: rs8371 (pathogenic for Klippel-Feil syndrome 1, autosomal dominant|Microphthalmia, isolated 4|Leber congenital amaurosis 17|Congenital anomalies of kidney and urinary tract|Klippel Feil syndrome|not specified|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM082790)

known disease mutation at this position, please check HGMD for details (HGMD ID CM082790)
known disease mutation at this position, please check HGMD for details (HGMD ID CM082790)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
Max, Transcription Factor, Max TF binding
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Rad21, Transcription Factor, Rad21 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0790
0.0840
(flanking)-0.6970
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased15608wt: 0.31 / mu: 0.79wt: GCGCGCGCGGGGACC
mu: GCGCGAGCGGGGACC
 GCGC|gcgg
distance from splice site 340
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      249GELDAGEAEARARGPQQPPPPDLR
mutated  not conserved    249DAGEAEARERGPQQPPPPDL
Ptroglodytes  not conserved  ENSPTRG00000020439  249XXGSAGG-------------
Mmulatta  all identical  ENSMMUG00000011267  249DAREAETHARGPQQPPPPDL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000051279  252GELDAGDTGARARGPQQPPPLDL
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000004399  245GKSDT--------------EVDL
Drerio  not conserved  ENSDARG00000053479  226GKSDT---------
Dmelanogaster  all conserved  FBgn0000490  424----------RSLKPAPHHHVRL
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
23330PROPEPPotential. /FTId=PRO_0000342206.lost
255255CONFLICTP -> L (in Ref. 2; AAH43222).might get lost (downstream of altered splice site)
255258COMPBIASPoly-Pro.might get lost (downstream of altered splice site)
331335COMPBIASPoly-Arg.might get lost (downstream of altered splice site)
354354DISULFIDBy similarity.might get lost (downstream of altered splice site)
383383DISULFIDBy similarity.might get lost (downstream of altered splice site)
387387DISULFIDBy similarity.might get lost (downstream of altered splice site)
419419DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
419419DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
420420DISULFIDBy similarity.might get lost (downstream of altered splice site)
452452DISULFIDBy similarity.might get lost (downstream of altered splice site)
454454DISULFIDBy similarity.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1368 / 1368
position (AA) of stopcodon in wt / mu AA sequence 456 / 456
position of stopcodon in wt / mu cDNA 1468 / 1468
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 101 / 101
chromosome 8
strand -1
last intron/exon boundary 507
theoretical NMD boundary in CDS 356
length of CDS 1368
coding sequence (CDS) position 746
cDNA position
(for ins/del: last normal base / first normal base)
846
gDNA position
(for ins/del: last normal base / first normal base)
15608
chromosomal position
(for ins/del: last normal base / first normal base)
97157413
original gDNA sequence snippet CGGGGAGGCCGAGGCGCGCGCGCGGGGACCCCAGCAACCGC
altered gDNA sequence snippet CGGGGAGGCCGAGGCGCGCGAGCGGGGACCCCAGCAACCGC
original cDNA sequence snippet CGGGGAGGCCGAGGCGCGCGCGCGGGGACCCCAGCAACCGC
altered cDNA sequence snippet CGGGGAGGCCGAGGCGCGCGAGCGGGGACCCCAGCAACCGC
wildtype AA sequence MDTPRVLLSA VFLISFLWDL PGFQQASISS SSSSAELGST KGMRSRKEGK MQRAPRDSDA
GREGQEPQPR PQDEPRAQQP RAQEPPGRGP RVVPHEYMLS IYRTYSIAEK LGINASFFQS
SKSANTITSF VDRGLDDLSH TPLRRQKYLF DVSMLSDKEE LVGAELRLFR QAPSAPWGPP
AGPLHVQLFP CLSPLLLDAR TLDPQGAPPA GWEVFDVWQG LRHQPWKQLC LELRAAWGEL
DAGEAEARAR GPQQPPPPDL RSLGFGRRVR PPQERALLVV FTRSQRKNLF AEMREQLGSA
EAAGPGAGAE GSWPPPSGAP DARPWLPSPG RRRRRTAFAS RHGKRHGKKS RLRCSKKPLH
VNFKELGWDD WIIAPLEYEA YHCEGVCDFP LRSHLEPTNH AIIQTLMNSM DPGSTPPSCC
VPTKLTPISI LYIDAGNNVV YKQYEDMVVE SCGCR*
mutated AA sequence MDTPRVLLSA VFLISFLWDL PGFQQASISS SSSSAELGST KGMRSRKEGK MQRAPRDSDA
GREGQEPQPR PQDEPRAQQP RAQEPPGRGP RVVPHEYMLS IYRTYSIAEK LGINASFFQS
SKSANTITSF VDRGLDDLSH TPLRRQKYLF DVSMLSDKEE LVGAELRLFR QAPSAPWGPP
AGPLHVQLFP CLSPLLLDAR TLDPQGAPPA GWEVFDVWQG LRHQPWKQLC LELRAAWGEL
DAGEAEARER GPQQPPPPDL RSLGFGRRVR PPQERALLVV FTRSQRKNLF AEMREQLGSA
EAAGPGAGAE GSWPPPSGAP DARPWLPSPG RRRRRTAFAS RHGKRHGKKS RLRCSKKPLH
VNFKELGWDD WIIAPLEYEA YHCEGVCDFP LRSHLEPTNH AIIQTLMNSM DPGSTPPSCC
VPTKLTPISI LYIDAGNNVV YKQYEDMVVE SCGCR*
speed 1.23 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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