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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 2.858868 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GDF6disease_causing0.99355246206398simple_aaeK424Rsingle base exchangers121909353show file

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Prediction

disease causing

 Model: simple_aae, prob: 0.99355246206398      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM0910797)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr8:97156888T>CN/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.1271A>G
cDNA.1371A>G
g.16133A>G
AA changes K424R Score: 26 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 424
frameshift no
known variant Reference ID: rs121909353
databasehomozygous (C/C)heterozygousallele carriers
1000G044
ExAC02525

known disease mutation at this position, please check HGMD for details (HGMD ID CM0910797)

known disease mutation at this position, please check HGMD for details (HGMD ID CM0910797)
known disease mutation at this position, please check HGMD for details (HGMD ID CM0910797)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)0.6431
2.1981
(flanking)3.081
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 865
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      424GSTPPSCCVPTKLTPISILYIDAG
mutated  all conserved    424VPTRLTPISILYIDA
Ptroglodytes  all identical  ENSPTRG00000020439  402VPTKLTPISILYIDA
Mmulatta  all identical  ENSMMUG00000011267  424VPTKLTPISILYIDA
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000051279  423SCCVPTKLTPISILYIDA
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004399  398NSTPPSCCVPTKLSPISILYIDS
Drerio  all identical  ENSDARG00000053479  373NSTPPSCCVPTKLSPISI
Dmelanogaster  all conserved  FBgn0000490  557GKVPKACCVPTQLDSVAMLYLND
Celegans  no homologue    
Xtropicalis  no homologue    
protein features no protein features affected
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 1271
cDNA position
(for ins/del: last normal base / first normal base)		 1371
gDNA position
(for ins/del: last normal base / first normal base)		 16133
chromosomal position
(for ins/del: last normal base / first normal base)		 97156888
original gDNA sequence snippet CAGCTGCTGCGTGCCCACCAAATTGACTCCCATCAGCATTC
altered gDNA sequence snippet CAGCTGCTGCGTGCCCACCAGATTGACTCCCATCAGCATTC
original cDNA sequence snippet CAGCTGCTGCGTGCCCACCAAATTGACTCCCATCAGCATTC
altered cDNA sequence snippet CAGCTGCTGCGTGCCCACCAGATTGACTCCCATCAGCATTC
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
DAGEAEARAR GPQQPPPPDL RSLGFGRRVR PPQERALLVV FTRSQRKNLF AEMREQLGSA
EAAGPGAGAE GSWPPPSGAP DARPWLPSPG RRRRRTAFAS RHGKRHGKKS RLRCSKKPLH
VNFKELGWDD WIIAPLEYEA YHCEGVCDFP LRSHLEPTNH AIIQTLMNSM DPGSTPPSCC
VPTRLTPISI LYIDAGNNVV YKQYEDMVVE SCGCR*
speed 0.84 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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Problems