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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: ENST00000389266
MT speed 0.79 s - this script 4.929413 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GARS1disease_causing_automatic0.999999999999852simple_aae0P298Lsingle base exchangers137852648show file

Taster files

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Prediction

disease causing

Model: simple_aae, prob: 0.999999999999852 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM093238)
  • known disease mutation: rs9209 (pathogenic)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr7:30651723C>TN/A show variant in all transcripts   IGV
HGNC symbol GARS1
Ensembl transcript ID ENST00000389266
Genbank transcript ID NM_002047
UniProt peptide P41250
alteration type single base exchange
alteration region CDS
DNA changes c.893C>T
cDNA.1134C>T
g.17427C>T
AA changes P298L Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS
298
frameshift no
known variant Reference ID: rs137852648
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs9209 (pathogenic for Charcot-Marie-Tooth disease type 2D) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM093238)

known disease mutation at this position, please check HGMD for details (HGMD ID CM093238)
known disease mutation at this position, please check HGMD for details (HGMD ID CM093238)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.6741
4.0521
(flanking)0.1520.998
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased17423wt: 0.9750 / mu: 0.9941 (marginal change - not scored)wt: ACTTGAGACCAGAAA
mu: ACTTGAGACTAGAAA
 TTGA|gacc
distance from splice site 12
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      298GPGGNMPGYLRPETAQGIFLNFKR
mutated  not conserved    298GPGGNMPGYLRLET
Ptroglodytes  all identical  ENSPTRG00000019042  298GPGGNMPGYLRPET
Mmulatta  no homologue    
Fcatus  all identical  ENSFCAG00000011415  224GPGGNMPGYLRPETAQGIFLNFK
Mmusculus  all identical  ENSMUSG00000029777  288GPGGNMPGYLRPET
Ggallus  all identical  ENSGALG00000005694  306GPGGNMPGYLRPETAQGIFLNFK
Trubripes  all identical  ENSTRUG00000017557  329GPGGNMPGYLRPET
Drerio  all identical  ENSDARG00000059070  323GYLRPETAQGIFLNFK
Dmelanogaster  all identical  FBgn0027088  330GPTGLVKGFLRPETAQGIFVNFK
Celegans  all identical  T10F2.1  308GPTGDFKAFLRPET
Xtropicalis  all identical  ENSXETG00000018474  305PGYLRPETAQGIFLNFK
protein features
start (aa)end (aa)featuredetails 
298300STRANDlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2220 / 2220
position (AA) of stopcodon in wt / mu AA sequence 740 / 740
position of stopcodon in wt / mu cDNA 2461 / 2461
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 242 / 242
chromosome 7
strand 1
last intron/exon boundary 2336
theoretical NMD boundary in CDS 2044
length of CDS 2220
coding sequence (CDS) position 893
cDNA position
(for ins/del: last normal base / first normal base)
1134
gDNA position
(for ins/del: last normal base / first normal base)
17427
chromosomal position
(for ins/del: last normal base / first normal base)
30651723
original gDNA sequence snippet AATTTATAGGTACTTGAGACCAGAAACTGCACAGGGGATTT
altered gDNA sequence snippet AATTTATAGGTACTTGAGACTAGAAACTGCACAGGGGATTT
original cDNA sequence snippet CATGCCTGGGTACTTGAGACCAGAAACTGCACAGGGGATTT
altered cDNA sequence snippet CATGCCTGGGTACTTGAGACTAGAAACTGCACAGGGGATTT
wildtype AA sequence MPSPRPVLLR GARAALLLLL PPRLLARPSL LLRRSLSAAS CPPISLPAAA SRSSMDGAGA
EEVLAPLRLA VRQQGDLVRK LKEDKAPQVD VDKAVAELKA RKRVLEAKEL ALQPKDDIVD
RAKMEDTLKR RFFYDQAFAI YGGVSGLYDF GPVGCALKNN IIQTWRQHFI QEEQILEIDC
TMLTPEPVLK TSGHVDKFAD FMVKDVKNGE CFRADHLLKA HLQKLMSDKK CSVEKKSEME
SVLAQLDNYG QQELADLFVN YNVKSPITGN DLSPPVSFNL MFKTFIGPGG NMPGYLRPET
AQGIFLNFKR LLEFNQGKLP FAAAQIGNSF RNEISPRSGL IRVREFTMAE IEHFVDPSEK
DHPKFQNVAD LHLYLYSAKA QVSGQSARKM RLGDAVEQGV INNTVLGYFI GRIYLYLTKV
GISPDKLRFR QHMENEMAHY ACDCWDAESK TSYGWIEIVG CADRSCYDLS CHARATKVPL
VAEKPLKEPK TVNVVQFEPS KGAIGKAYKK DAKLVMEYLA ICDECYITEM EMLLNEKGEF
TIETEGKTFQ LTKDMINVKR FQKTLYVEEV VPNVIEPSFG LGRIMYTVFE HTFHVREGDE
QRTFFSFPAV VAPFKCSVLP LSQNQEFMPF VKELSEALTR HGVSHKVDDS SGSIGRRYAR
TDEIGVAFGV TIDFDTVNKT PHTATLRDRD SMRQIRAEIS ELPSIVQDLA NGNITWADVE
ARYPLFEGQE TGKKETIEE*
mutated AA sequence MPSPRPVLLR GARAALLLLL PPRLLARPSL LLRRSLSAAS CPPISLPAAA SRSSMDGAGA
EEVLAPLRLA VRQQGDLVRK LKEDKAPQVD VDKAVAELKA RKRVLEAKEL ALQPKDDIVD
RAKMEDTLKR RFFYDQAFAI YGGVSGLYDF GPVGCALKNN IIQTWRQHFI QEEQILEIDC
TMLTPEPVLK TSGHVDKFAD FMVKDVKNGE CFRADHLLKA HLQKLMSDKK CSVEKKSEME
SVLAQLDNYG QQELADLFVN YNVKSPITGN DLSPPVSFNL MFKTFIGPGG NMPGYLRLET
AQGIFLNFKR LLEFNQGKLP FAAAQIGNSF RNEISPRSGL IRVREFTMAE IEHFVDPSEK
DHPKFQNVAD LHLYLYSAKA QVSGQSARKM RLGDAVEQGV INNTVLGYFI GRIYLYLTKV
GISPDKLRFR QHMENEMAHY ACDCWDAESK TSYGWIEIVG CADRSCYDLS CHARATKVPL
VAEKPLKEPK TVNVVQFEPS KGAIGKAYKK DAKLVMEYLA ICDECYITEM EMLLNEKGEF
TIETEGKTFQ LTKDMINVKR FQKTLYVEEV VPNVIEPSFG LGRIMYTVFE HTFHVREGDE
QRTFFSFPAV VAPFKCSVLP LSQNQEFMPF VKELSEALTR HGVSHKVDDS SGSIGRRYAR
TDEIGVAFGV TIDFDTVNKT PHTATLRDRD SMRQIRAEIS ELPSIVQDLA NGNITWADVE
ARYPLFEGQE TGKKETIEE*
speed 0.79 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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