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 0 s - this script 2.64394 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AGXTdisease_causing_automatic0.999999999995053simple_aaeaffected0D201Esingle base exchangers180177246show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999995053 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM056519)
  • known disease mutation: rs204115 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:241813402C>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.603C>A
cDNA.990C>A
g.5507C>A
AA changes D201E Score: 45 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 201
frameshift no
known variant Reference ID: rs180177246
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs204115 (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 CM056519)

known disease mutation at this position, please check HGMD for details (HGMD ID CM056519)
known disease mutation at this position, please check HGMD for details (HGMD ID CM056519)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
HNF4A, Transcription Factor, HNF4A Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)4.1861
-0.0690.952
(flanking)0.6410.961
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc decreased5499wt: 0.35 / mu: 0.24wt: GAGCAAACCACCCATCTACAGGCATCGACATCCTGTACTCG
mu: GAGCAAACCACCCATCTACAGGCATCGAAATCCTGTACTCG		 acag|GCAT
Donor increased5502wt: 0.44 / mu: 0.85wt: CAGGCATCGACATCC
mu: CAGGCATCGAAATCC		 GGCA|tcga
distance from splice site 8
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      201GTPLYMDRQGIDILYSGSQKALNA
mutated  all conserved    201GTPLYMDRQGIEILYSGSQKALN
Ptroglodytes  all identical  ENSPTRG00000013113  177GTPLYMDQQGIDILYSGSQKALN
Mmulatta  all identical  ENSMMUG00000023435  223GTPLYMDQQGIDILYSGSQKVLN
Fcatus  all identical  ENSFCAG00000010448  201GTPLFMDQQGIDVLYSGSQKVLN
Mmusculus  all identical  ENSMUSG00000026272  223GVPIYMDQQGIDIMYSSSQKVLN
Ggallus  all identical  ENSGALG00000020943  224GAPILMDQQGIDVLYTGSQKVLS
Trubripes  all identical  ENSTRUG00000007149  231AAPIFMDKQNIDILYTGSQKALN
Drerio  all identical  ENSDARG00000018478  231AAPLLMDQQKIDILYTGSQKALN
Dmelanogaster  all identical  FBgn0014031  197GTEFLMDEWKVDVAYTGSQKSLG
Celegans  all identical  T14D7.1  218GTPFAADDLKVDCVYSATQKVLN
Xtropicalis  all identical  ENSXETG00000012149  224GAPIYMDKQGIDILYSGSQKVLN
protein features
start (aa)end (aa)featuredetails 
195199TURNmight get lost (downstream of altered splice site)
201209STRANDlost
209209MOD_RESN6-(pyridoxal phosphate)lysine.might get lost (downstream of altered splice site)
209209MUTAGENK->R: Affects pyridoxal phosphate binding.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 603
cDNA position
(for ins/del: last normal base / first normal base)		 990
gDNA position
(for ins/del: last normal base / first normal base)		 5507
chromosomal position
(for ins/del: last normal base / first normal base)		 241813402
original gDNA sequence snippet CACCCATCTACAGGCATCGACATCCTGTACTCGGGCTCCCA
altered gDNA sequence snippet CACCCATCTACAGGCATCGAAATCCTGTACTCGGGCTCCCA
original cDNA sequence snippet ATGGACCGGCAAGGCATCGACATCCTGTACTCGGGCTCCCA
altered cDNA sequence snippet ATGGACCGGCAAGGCATCGAAATCCTGTACTCGGGCTCCCA
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 EILYSGSQKA LNAPPGTSLI SFSDKAKKKM YSRKTKPFSF
YLDIKWLANF WGCDDQPRMY HHTIPVISLY SLRESLALIA EQGLENSWRQ HREAAAYLHG
RLQALGLQLF VKDPALRLPT VTTVAVPAGY DWRDIVSYVI DHFDIEIMGG LGPSTGKVLR
IGLLGCNATR ENVDRVTEAL RAALQHCPKK KL*
speed 0.57 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