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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 0 s - this script 2.870881 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GDF6disease_causing_automatic0.99996083741328simple_aaeaffected0G42Vsingle base exchangers121909354show file

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Prediction

disease causing

 Model: simple_aae, prob: 0.99996083741328 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • heterozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM0910801)
  • known disease mutation: rs8374 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr8:97172796C>AN/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.125G>T
cDNA.225G>T
g.225G>T
AA changes G42V Score: 109 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 42
frameshift no
known variant Reference ID: rs121909354
databasehomozygous (A/A)heterozygousallele carriers
1000G077
ExAC03232

known disease mutation: rs8374 (pathogenic for Klippel-Feil syndrome 1, autosomal dominant) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM0910801)

known disease mutation at this position, please check HGMD for details (HGMD ID CM0910801)
known disease mutation at this position, please check HGMD for details (HGMD ID CM0910801)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H2AZ, Histone, Histone 2A variant Z
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
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)1.0080.983
0.1360.986
(flanking)2.3010.998
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased218wt: 0.79 / mu: 0.96wt: GTTCCACCAAGGGCA
mu: GTTCCACCAAGGTCA		 TCCA|ccaa
Donor marginally increased228wt: 0.9957 / mu: 0.9978 (marginal change - not scored)wt: GGGCATGCGAAGCCG
mu: GGTCATGCGAAGCCG		 GCAT|gcga
Donor marginally increased223wt: 0.9697 / mu: 0.9909 (marginal change - not scored)wt: ACCAAGGGCATGCGA
mu: ACCAAGGTCATGCGA		 CAAG|ggca
Acc gained2300.34mu: TGGGTTCCACCAAGGTCATGCGAAGCCGCAAGGAAGGCAAG atgc|GAAG
distance from splice site 225
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      42SSSSAELGSTKGMRSRKEGKMQRA
mutated  not conserved    42SSSSAELGSTKVMRSRKEGKMQR
Ptroglodytes  all identical  ENSPTRG00000020439  42SSSSAELGSTKGMRSRKEGKMQR
Mmulatta  all identical  ENSMMUG00000011267  42SSSSAELGSTKGMRSRKEGKMQR
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000051279  42SSSSSTELDSTKDVGNRKEGKMQR
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004399  42PSAPRR---HKGARSSHQ-----
Drerio  all identical  ENSDARG00000053479  41QKRS------KGARSAFDGQRSH
Dmelanogaster  no alignment  FBgn0000490  n/a
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
23330PROPEPPotential. /FTId=PRO_0000342206.lost
114114CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
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 125
cDNA position
(for ins/del: last normal base / first normal base)		 225
gDNA position
(for ins/del: last normal base / first normal base)		 225
chromosomal position
(for ins/del: last normal base / first normal base)		 97172796
original gDNA sequence snippet CGAGCTGGGTTCCACCAAGGGCATGCGAAGCCGCAAGGAAG
altered gDNA sequence snippet CGAGCTGGGTTCCACCAAGGTCATGCGAAGCCGCAAGGAAG
original cDNA sequence snippet CGAGCTGGGTTCCACCAAGGGCATGCGAAGCCGCAAGGAAG
altered cDNA sequence snippet CGAGCTGGGTTCCACCAAGGTCATGCGAAGCCGCAAGGAAG
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 KVMRSRKEGK 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*
speed 0.81 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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