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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 2.619131 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AGXTdisease_causing0.999999317907002simple_aaeaffectedE274Dsingle base exchangers146525143show file

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Prediction

disease causing

 Model: simple_aae, prob: 0.999999317907002      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM093806)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:241815397G>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.822G>C
cDNA.1209G>C
g.7502G>C
AA changes E274D Score: 45 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 274
frameshift no
known variant Reference ID: rs146525143
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC055

known disease mutation at this position, please check HGMD for details (HGMD ID CM093806)

known disease mutation at this position, please check HGMD for details (HGMD ID CM093806)
known disease mutation at this position, please check HGMD for details (HGMD ID CM093806)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.8891
3.0861
(flanking)0.6451
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased7503wt: 0.36 / mu: 0.79wt: GAGAGAGCCTGGCCC
mu: GAGACAGCCTGGCCC		 GAGA|gcct
Donor increased7497wt: 0.36 / mu: 0.69wt: GCCTGAGAGAGAGCC
mu: GCCTGAGAGACAGCC		 CTGA|gaga
Donor marginally increased7499wt: 0.6405 / mu: 0.6561 (marginal change - not scored)wt: CTGAGAGAGAGCCTG
mu: CTGAGAGACAGCCTG		 GAGA|gaga
distance from splice site 25
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      274TIPVISLYSLRESLALIAEQGLEN
mutated  all conserved    274TIPVISLYSLRDSLALIAEQGLE
Ptroglodytes  not conserved  ENSPTRG00000013113  236-----------------------
Mmulatta  all identical  ENSMMUG00000023435  296TIPVISLYSLRESLALIAEQGLE
Fcatus  all identical  ENSFCAG00000010448  274TTPVVSLYSLRESLALIAEQXXX
Mmusculus  all identical  ENSMUSG00000026272  296TTPVTSLYCLRESLALIAEQGLE
Ggallus  all identical  ENSGALG00000020943  297TVPISSIFCLREALAMLVELGLE
Trubripes  all identical  ENSTRUG00000007149  304TGPVSGFFALRESLAILAEKGLE
Drerio  all identical  ENSDARG00000018478  304TGPVSGFFALRESLAILAETGLE
Dmelanogaster  all identical  FBgn0014031  270TISSTLLYGLREALAHFCAVGLK
Celegans  not conserved  T14D7.1  291TAPISTVYALRAALSAIAKEGID
Xtropicalis  all identical  ENSXETG00000012149  297TGPVTNFFSLREGLAVLAEQGLE
protein features
start (aa)end (aa)featuredetails 
266282HELIXlost
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 822
cDNA position
(for ins/del: last normal base / first normal base)		 1209
gDNA position
(for ins/del: last normal base / first normal base)		 7502
chromosomal position
(for ins/del: last normal base / first normal base)		 241815397
original gDNA sequence snippet AGCCTGTACAGCCTGAGAGAGAGCCTGGCCCTCATTGCGGA
altered gDNA sequence snippet AGCCTGTACAGCCTGAGAGACAGCCTGGCCCTCATTGCGGA
original cDNA sequence snippet AGCCTGTACAGCCTGAGAGAGAGCCTGGCCCTCATTGCGGA
altered cDNA sequence snippet AGCCTGTACAGCCTGAGAGACAGCCTGGCCCTCATTGCGGA
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 GVLQPLDGFG ELCHRYKCLL
LVDSVASLGG TPLYMDRQGI DILYSGSQKA LNAPPGTSLI SFSDKAKKKM YSRKTKPFSF
YLDIKWLANF WGCDDQPRMY HHTIPVISLY SLRDSLALIA EQGLENSWRQ HREAAAYLHG
RLQALGLQLF VKDPALRLPT VTTVAVPAGY DWRDIVSYVI DHFDIEIMGG LGPSTGKVLR
IGLLGCNATR ENVDRVTEAL RAALQHCPKK KL*
speed 0.60 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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