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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 0 s - this script 2.853123 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AGXTdisease_causing_automatic0.999999996453811simple_aaeaffected0L166Psingle base exchangers180177230show file

Taster files

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Prediction

disease causing

 Model: simple_aae, prob: 0.999999996453811 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM072847)
  • known disease mutation: rs204107 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:241810839T>CN/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.497T>C
cDNA.884T>C
g.2944T>C
AA changes L166P Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 166
frameshift no
known variant Reference ID: rs180177230
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs204107 (pathogenic for Primary hyperoxaluria, type I) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM072847)

known disease mutation at this position, please check HGMD for details (HGMD ID CM072847)
known disease mutation at this position, please check HGMD for details (HGMD ID CM072847)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0770.977
3.9350.99
(flanking)-0.2610.964
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased2943wt: 0.23 / mu: 0.40wt: AGCCCCTTGATGGCT
mu: AGCCCCCTGATGGCT		 CCCC|ttga
distance from splice site 28
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      166HGESSTGVLQPLDGFGELCHRYKC
mutated  not conserved    166HGESSTGVLQPPDGFGELCHRYK
Ptroglodytes  not conserved  ENSPTRG00000013113  166---------------------YK
Mmulatta  all identical  ENSMMUG00000023435  188HGESSTGVLQPLDGFGELCHRYK
Fcatus  all identical  ENSFCAG00000010448  166QGEFSCGVLQPLDGXXXXXXXYN
Mmusculus  all identical  ENSMUSG00000026272  188HGESSTGVVQPLDGFGELCHRYQ
Ggallus  all identical  ENSGALG00000020943  190HGESS-GVLQPLEGLGELCHRQG
Trubripes  all conserved  ENSTRUG00000007149  196HGESSAGLCHPVDGIGDICRKHN
Drerio  all conserved  ENSDARG00000018478  196HGESSAGLVHPMDGIGDVCRKHN
Dmelanogaster  all conserved  FBgn0014031  161QGDSSTGIIQQNIRELGELCRKYD
Celegans  all identical  T14D7.1  183QGDSSTGVAQPLETIGDACREHG
Xtropicalis  all identical  ENSXETG00000012149  189HGESSSGVVQPLDGLGDLCHRYN
protein features
start (aa)end (aa)featuredetails 
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 497
cDNA position
(for ins/del: last normal base / first normal base)		 884
gDNA position
(for ins/del: last normal base / first normal base)		 2944
chromosomal position
(for ins/del: last normal base / first normal base)		 241810839
original gDNA sequence snippet CACCGGCGTGCTGCAGCCCCTTGATGGCTTCGGGGAACTCT
altered gDNA sequence snippet CACCGGCGTGCTGCAGCCCCCTGATGGCTTCGGGGAACTCT
original cDNA sequence snippet CACCGGCGTGCTGCAGCCCCTTGATGGCTTCGGGGAACTCT
altered cDNA sequence snippet CACCGGCGTGCTGCAGCCCCCTGATGGCTTCGGGGAACTCT
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 GGLQMIGSMS KDMYQIMDEI
KEGIQYVFQT RNPLTLVISG SGHCALEAAL VNVLEPGDSF LVGANGIWGQ RAVDIGERIG
ARVHPMTKDP GGHYTLQEVE EGLAQHKPVL LFLTHGESST GVLQPPDGFG ELCHRYKCLL
LVDSVASLGG TPLYMDRQGI DILYSGSQKA LNAPPGTSLI SFSDKAKKKM YSRKTKPFSF
YLDIKWLANF WGCDDQPRMY HHTIPVISLY SLRESLALIA EQGLENSWRQ HREAAAYLHG
RLQALGLQLF VKDPALRLPT VTTVAVPAGY DWRDIVSYVI DHFDIEIMGG LGPSTGKVLR
IGLLGCNATR ENVDRVTEAL RAALQHCPKK KL*
speed 0.83 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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