Yum, tasty mutations...

MutationTaster - study a chromosomal position

MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
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 1.83 s - this script 7.297222 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AGXTdisease_causing_automatic0.999810593376168simple_aaeaffected0E141Dsingle base exchangers180177217show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999810593376168 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM072848)
  • known disease mutation: rs204100 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:241810125G>TN/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.423G>T
cDNA.810G>T
g.2230G>T
AA changes E141D Score: 45 explain score(s)
position(s) of altered AA
if AA alteration in CDS
141
frameshift no
known variant Reference ID: rs180177217
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs204100 (pathogenic for Primary hyperoxaluria, type I) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM072848)

known disease mutation at this position, please check HGMD for details (HGMD ID CM072848)
known disease mutation at this position, please check HGMD for details (HGMD ID CM072848)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.0341
2.1511
(flanking)3.6451
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost2229sequence motif lost- wt: GGAG|gtag
 mu: GGAT.gtag
Donor lost22290.35wt: GGAGGAGGTAGGGGA AGGA|ggta
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      141PGGHYTLQEVEEGLAQHKPVLLFL
mutated  all conserved    141PGGHYTLQEVEDGLAQHKPVLLF
Ptroglodytes  all identical  ENSPTRG00000013113  141PGGHYTLQEVEEGLAQHKPVLL-
Mmulatta  all identical  ENSMMUG00000023435  163PGGHYTLQEVEEGLAQHKPVLLF
Fcatus  all identical  ENSFCAG00000010448  141PGNHYTLQELEEGLVQHKPVLLF
Mmusculus  all identical  ENSMUSG00000026272  163PGEHYTLQEVEEGLAQHKPVLLF
Ggallus  all identical  ENSGALG00000020943  165PGEYFTLRDIQEGLAQHKPSLLF
Trubripes  all conserved  ENSTRUG00000007149  171PGGYFSNKEIEQAMQKHKPVLFF
Drerio  all conserved  ENSDARG00000018478  171PGGHFTNAEIEQALAKHKPVLFF
Dmelanogaster  not conserved  FBgn0014031  136FGRALSHEEITFAFEAHRPKVFF
Celegans  all conserved  T14D7.1  158QGQAVPVEDIRKAIADYKPNLVF
Xtropicalis  all conserved  ENSXETG00000012149  164VGEGFTLKEVEKALVEHKPSLFF
protein features
start (aa)end (aa)featuredetails 
136146HELIXlost
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 423
cDNA position
(for ins/del: last normal base / first normal base)
810
gDNA position
(for ins/del: last normal base / first normal base)
2230
chromosomal position
(for ins/del: last normal base / first normal base)
241810125
original gDNA sequence snippet ACACTGCAGGAGGTGGAGGAGGTAGGGGACCCGGGGTGGGG
altered gDNA sequence snippet ACACTGCAGGAGGTGGAGGATGTAGGGGACCCGGGGTGGGG
original cDNA sequence snippet ACACTGCAGGAGGTGGAGGAGGGCCTGGCCCAGCACAAGCC
altered cDNA sequence snippet ACACTGCAGGAGGTGGAGGATGGCCTGGCCCAGCACAAGCC
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 DGLAQHKPVL 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 1.83 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
back to results table

Problems