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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: ENST00000307503
MT speed 1.34 s - this script 3.986466 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AGXTdisease_causing_automatic0.999997485272579simple_aaeaffected0G47Rsingle base exchangers180177173show file

Taster files

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 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999997485272579 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM072843)
  • known disease mutation: rs204076 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:241808421G>AN/A show variant in all transcripts   IGV
HGNC symbol AGXT
Ensembl transcript ID ENST00000307503
Genbank transcript ID NM_000030
UniProt peptide P21549
alteration type single base exchange
alteration region CDS
DNA changes c.139G>A
cDNA.526G>A
g.526G>A
AA changes G47R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 47
frameshift no
known variant Reference ID: rs180177173
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs204076 (pathogenic for Primary hyperoxaluria, type I|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM072843)

known disease mutation at this position, please check HGMD for details (HGMD ID CM072843)
known disease mutation at this position, please check HGMD for details (HGMD ID CM072843)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.6580.013
1.3860.604
(flanking)4.4610.68
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased518wt: 0.41 / mu: 0.62wt: GCTGCAGATGATCGG
mu: GCTGCAGATGATCAG		 TGCA|gatg
Donor gained5220.85mu: CAGATGATCAGGTCC GATG|atca
distance from splice site 27
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      47RIMAAGGLQMIGSMSKDMYQIMDE
mutated  not conserved    47RIMAAGGLQMIRSMSKDMYQIMD
Ptroglodytes  all identical  ENSPTRG00000013113  47RIMAAGGLQMIGPMSKDMYQIMD
Mmulatta  all identical  ENSMMUG00000023435  69RIMSAGGMQIIGPMDKEMYQIMD
Fcatus  all identical  ENSFCAG00000010448  47RVLVAGGKQMIGHMHKEMFQIMD
Mmusculus  all identical  ENSMUSG00000026272  69RVLAAGSLRMIGHMQKEMLQIME
Ggallus  not conserved  ENSGALG00000020943  71RVRAAGGHQILCHMHPEVLQAMD
Trubripes  all identical  ENSTRUG00000007149  77RILAAGAKPIIGHMHSEMFEVMD
Drerio  all identical  ENSDARG00000018478  77RVLAAGGRPIIGHMHSEMFGIMN
Dmelanogaster  all identical  FBgn0014031  42RVLEAMSNPVLGHMHPECLQIMD
Celegans  all identical  T14D7.1  64SIAETQSRNLLGHLHPEFVQIMA
Xtropicalis  all identical  ENSXETG00000012149  70RIQAAGALQLIGHMHPEMFQIMD
protein features
start (aa)end (aa)featuredetails 
5168HELIXmight get lost (downstream of altered splice site)
7380STRANDmight get lost (downstream of altered splice site)
8293HELIXmight get lost (downstream of altered splice site)
100106STRANDmight get lost (downstream of altered splice site)
107118HELIXmight get lost (downstream of altered splice site)
123127STRANDmight get lost (downstream of altered splice site)
136146HELIXmight get lost (downstream of altered splice site)
149157STRANDmight get lost (downstream of altered splice site)
158161TURNmight get lost (downstream of altered splice site)
169175HELIXmight get lost (downstream of altered splice site)
179183STRANDmight get lost (downstream of altered splice site)
185190TURNmight get lost (downstream of altered splice site)
195199TURNmight get lost (downstream of altered splice site)
201209STRANDmight get lost (downstream of altered splice site)
209209MUTAGENK->R: Affects pyridoxal phosphate binding.might get lost (downstream of altered splice site)
209209MOD_RESN6-(pyridoxal phosphate)lysine.might get lost (downstream of altered splice site)
218222STRANDmight get lost (downstream of altered splice site)
224232HELIXmight get lost (downstream of altered splice site)
244250HELIXmight get lost (downstream of altered splice site)
254256STRANDmight get lost (downstream of altered splice site)
266282HELIXmight get lost (downstream of altered splice site)
284305HELIXmight get lost (downstream of altered splice site)
309311STRANDmight get lost (downstream of altered splice site)
314316HELIXmight get lost (downstream of altered splice site)
321325STRANDmight get lost (downstream of altered splice site)
332343HELIXmight get lost (downstream of altered splice site)
352354HELIXmight get lost (downstream of altered splice site)
355357TURNmight get lost (downstream of altered splice site)
358362STRANDmight get lost (downstream of altered splice site)
360360BINDINGSubstrate.might get lost (downstream of altered splice site)
365367HELIXmight get lost (downstream of altered splice site)
370386HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1179 / 1179
position (AA) of stopcodon in wt / mu AA sequence 393 / 393
position of stopcodon in wt / mu cDNA 1566 / 1566
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 388 / 388
chromosome 2
strand 1
last intron/exon boundary 1459
theoretical NMD boundary in CDS 1021
length of CDS 1179
coding sequence (CDS) position 139
cDNA position
(for ins/del: last normal base / first normal base)		 526
gDNA position
(for ins/del: last normal base / first normal base)		 526
chromosomal position
(for ins/del: last normal base / first normal base)		 241808421
original gDNA sequence snippet CCGGGGGGCTGCAGATGATCGGGTCCATGAGCAAGGATATG
altered gDNA sequence snippet CCGGGGGGCTGCAGATGATCAGGTCCATGAGCAAGGATATG
original cDNA sequence snippet CCGGGGGGCTGCAGATGATCGGGTCCATGAGCAAGGATATG
altered cDNA sequence snippet CCGGGGGGCTGCAGATGATCAGGTCCATGAGCAAGGATATG
wildtype AA sequence MASHKLLVTP PKALLKPLSI PNQLLLGPGP SNLPPRIMAA GGLQMIGSMS KDMYQIMDEI
KEGIQYVFQT RNPLTLVISG SGHCALEAAL VNVLEPGDSF LVGANGIWGQ RAVDIGERIG
ARVHPMTKDP GGHYTLQEVE EGLAQHKPVL LFLTHGESST GVLQPLDGFG ELCHRYKCLL
LVDSVASLGG TPLYMDRQGI DILYSGSQKA LNAPPGTSLI SFSDKAKKKM YSRKTKPFSF
YLDIKWLANF WGCDDQPRMY HHTIPVISLY SLRESLALIA EQGLENSWRQ HREAAAYLHG
RLQALGLQLF VKDPALRLPT VTTVAVPAGY DWRDIVSYVI DHFDIEIMGG LGPSTGKVLR
IGLLGCNATR ENVDRVTEAL RAALQHCPKK KL*
mutated AA sequence MASHKLLVTP PKALLKPLSI PNQLLLGPGP SNLPPRIMAA GGLQMIRSMS KDMYQIMDEI
KEGIQYVFQT RNPLTLVISG SGHCALEAAL VNVLEPGDSF LVGANGIWGQ RAVDIGERIG
ARVHPMTKDP GGHYTLQEVE EGLAQHKPVL LFLTHGESST GVLQPLDGFG ELCHRYKCLL
LVDSVASLGG TPLYMDRQGI DILYSGSQKA LNAPPGTSLI SFSDKAKKKM YSRKTKPFSF
YLDIKWLANF WGCDDQPRMY HHTIPVISLY SLRESLALIA EQGLENSWRQ HREAAAYLHG
RLQALGLQLF VKDPALRLPT VTTVAVPAGY DWRDIVSYVI DHFDIEIMGG LGPSTGKVLR
IGLLGCNATR ENVDRVTEAL RAALQHCPKK KL*
speed 1.34 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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