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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: ENST00000269143
MT speed 1.65 s - this script 4.697336 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AFG3L2disease_causing_automatic0.999999991912604simple_aaeaffected0R702Qsingle base exchangers151344523show file

Taster files

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Prediction

disease causing

Model: simple_aae, prob: 0.999999991912604 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM088030)
  • known disease mutation: rs5473 (pathogenic)
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr18:12337410C>TN/A show variant in all transcripts   IGV
HGNC symbol AFG3L2
Ensembl transcript ID ENST00000269143
Genbank transcript ID NM_006796
UniProt peptide Q9Y4W6
alteration type single base exchange
alteration region CDS
DNA changes c.2105G>A
cDNA.2337G>A
g.39904G>A
AA changes R702Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS
702
frameshift no
known variant Reference ID: rs151344523
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs5473 (pathogenic for Spinocerebellar ataxia type 28|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM088030)

known disease mutation at this position, please check HGMD for details (HGMD ID CM088030)
known disease mutation at this position, please check HGMD for details (HGMD ID CM088030)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.0470.009
5.7250.994
(flanking)2.0810.991
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained399000.67mu: ATGAAGTACAAATAC GAAG|taca
Donor gained399040.49mu: AGTACAAATACTTAT TACA|aata
distance from splice site 71
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      702EATARLIDDEVRILINDAYKRTVA
mutated  all conserved    702EATARLIDDEVQILINDAYKRTV
Ptroglodytes  all identical  ENSPTRG00000009879  717ATARLIDDEVRILINDAYKRTV
Mmulatta  all identical  ENSMMUG00000021125  720EATARLIDDEVRILINDAYKRTV
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000024527  701EATARMIDDEVRILISDAYRRTV
Ggallus  all identical  ENSGALG00000013853  702EATARMIDEEVRSLINIAYDRTL
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000062272  697EATARLIDTEVRNLISTAYERT
Dmelanogaster  all identical  FBgn0036702  720EDTAQLIDNEVRSIIKCAHEATT
Celegans  all identical  Y47G6A.10  687EATAQLIDQEVRDLVMNALRRTR
Xtropicalis  all identical  ENSXETG00000032431  708EATARLIDDEVRVLINT
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2394 / 2394
position (AA) of stopcodon in wt / mu AA sequence 798 / 798
position of stopcodon in wt / mu cDNA 2626 / 2626
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 233 / 233
chromosome 18
strand -1
last intron/exon boundary 2408
theoretical NMD boundary in CDS 2125
length of CDS 2394
coding sequence (CDS) position 2105
cDNA position
(for ins/del: last normal base / first normal base)
2337
gDNA position
(for ins/del: last normal base / first normal base)
39904
chromosomal position
(for ins/del: last normal base / first normal base)
12337410
original gDNA sequence snippet ATTGATAGATGATGAAGTACGAATACTTATTAATGATGCTT
altered gDNA sequence snippet ATTGATAGATGATGAAGTACAAATACTTATTAATGATGCTT
original cDNA sequence snippet ATTGATAGATGATGAAGTACGAATACTTATTAATGATGCTT
altered cDNA sequence snippet ATTGATAGATGATGAAGTACAAATACTTATTAATGATGCTT
wildtype AA sequence MAHRCLRLWG RGGCWPRGLQ QLLVPGGVGP GEQPCLRTLY RFVTTQARAS RNSLLTDIIA
AYQRFCSRPP KGFEKYFPNG KNGKKASEPK EVMGEKKESK PAATTRSSGG GGGGGGKRGG
KKDDSHWWSR FQKGDIPWDD KDFRMFFLWT ALFWGGVMFY LLLKRSGREI TWKDFVNNYL
SKGVVDRLEV VNKRFVRVTF TPGKTPVDGQ YVWFNIGSVD TFERNLETLQ QELGIEGENR
VPVVYIAESD GSFLLSMLPT VLIIAFLLYT IRRGPAGIGR TGRGMGGLFS VGETTAKVLK
DEIDVKFKDV AGCEEAKLEI MEFVNFLKNP KQYQDLGAKI PKGAILTGPP GTGKTLLAKA
TAGEANVPFI TVSGSEFLEM FVGVGPARVR DLFALARKNA PCILFIDEID AVGRKRGRGN
FGGQSEQENT LNQLLVEMDG FNTTTNVVIL AGTNRPDILD PALLRPGRFD RQIFIGPPDI
KGRASIFKVH LRPLKLDSTL EKDKLARKLA SLTPGFSGAD VANVCNEAAL IAARHLSDSI
NQKHFEQAIE RVIGGLEKKT QVLQPEEKKT VAYHEAGHAV AGWYLEHADP LLKVSIIPRG
KGLGYAQYLP KEQYLYTKEQ LLDRMCMTLG GRVSEEIFFG RITTGAQDDL RKVTQSAYAQ
IVQFGMNEKV GQISFDLPRQ GDMVLEKPYS EATARLIDDE VRILINDAYK RTVALLTEKK
ADVEKVALLL LEKEVLDKND MVELLGPRPF AEKSTYEEFV EGTGSLDEDT SLPEGLKDWN
KEREKEKEEP PGEKVAN*
mutated AA sequence MAHRCLRLWG RGGCWPRGLQ QLLVPGGVGP GEQPCLRTLY RFVTTQARAS RNSLLTDIIA
AYQRFCSRPP KGFEKYFPNG KNGKKASEPK EVMGEKKESK PAATTRSSGG GGGGGGKRGG
KKDDSHWWSR FQKGDIPWDD KDFRMFFLWT ALFWGGVMFY LLLKRSGREI TWKDFVNNYL
SKGVVDRLEV VNKRFVRVTF TPGKTPVDGQ YVWFNIGSVD TFERNLETLQ QELGIEGENR
VPVVYIAESD GSFLLSMLPT VLIIAFLLYT IRRGPAGIGR TGRGMGGLFS VGETTAKVLK
DEIDVKFKDV AGCEEAKLEI MEFVNFLKNP KQYQDLGAKI PKGAILTGPP GTGKTLLAKA
TAGEANVPFI TVSGSEFLEM FVGVGPARVR DLFALARKNA PCILFIDEID AVGRKRGRGN
FGGQSEQENT LNQLLVEMDG FNTTTNVVIL AGTNRPDILD PALLRPGRFD RQIFIGPPDI
KGRASIFKVH LRPLKLDSTL EKDKLARKLA SLTPGFSGAD VANVCNEAAL IAARHLSDSI
NQKHFEQAIE RVIGGLEKKT QVLQPEEKKT VAYHEAGHAV AGWYLEHADP LLKVSIIPRG
KGLGYAQYLP KEQYLYTKEQ LLDRMCMTLG GRVSEEIFFG RITTGAQDDL RKVTQSAYAQ
IVQFGMNEKV GQISFDLPRQ GDMVLEKPYS EATARLIDDE VQILINDAYK RTVALLTEKK
ADVEKVALLL LEKEVLDKND MVELLGPRPF AEKSTYEEFV EGTGSLDEDT SLPEGLKDWN
KEREKEKEEP PGEKVAN*
speed 1.65 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