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 2.827072 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AGXTdisease_causing0.999999999979722simple_aaeaffectedS187Fsingle base exchangers180177238show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999979722      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs140584 (probable pathogenic)
  • known disease mutation at this position (HGMD CI1511294)
  • known disease mutation at this position (HGMD CM1511275)
  • known disease mutation at this position (HGMD CM920012)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:241812431C>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.560C>T
cDNA.947C>T
g.4536C>T
AA changes S187F Score: 155 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 187
frameshift no
known variant Reference ID: rs180177238
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC011

known as potential disease variant: rs140584 (probable pathogenic for Primary hyperoxaluria, type I) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920012)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920012)
known disease mutation at this position, please check HGMD for details (HGMD ID CI1511294)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920012)
known disease mutation at this position, please check HGMD for details (HGMD ID CI1511294)
known disease mutation at this position, please check HGMD for details (HGMD ID CM1511275)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920012)
known disease mutation at this position, please check HGMD for details (HGMD ID CI1511294)
known disease mutation at this position, please check HGMD for details (HGMD ID CM1511275)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920012)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.5741
4.9021
(flanking)-0.3760.927
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased4541wt: 0.22 / mu: 0.33wt: TGGATTCGGTGGCATCCCTGGGCGGGACCCCCCTTTACATG
mu: TGGATTCGGTGGCATTCCTGGGCGGGACCCCCCTTTACATG		 ctgg|GCGG
distance from splice site 36
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      187YKCLLLVDSVASLGGTPLYMDRQG
mutated  not conserved    187LVDSVAFLGGTPLYMDRQ
Ptroglodytes  all identical  ENSPTRG00000013113  163LVDSVVSLGGTPLYMDQQ
Mmulatta  all identical  ENSMMUG00000023435  209LVDSVVSLGGTPLYMDQQ
Fcatus  all identical  ENSFCAG00000010448  187LVGSVASLCGTPLFMDQQ
Mmusculus  all identical  ENSMUSG00000026272  209LVDSVASLGGVPIYMDQQ
Ggallus  all identical  ENSGALG00000020943  210LVDAVASLGGAPILMDQQ
Trubripes  all identical  ENSTRUG00000007149  217HNCLFLVDTVASLGAAPIFMDKQ
Drerio  all identical  ENSDARG00000018478  217ASLGAAPLLMDQQ
Dmelanogaster  all identical  FBgn0014031  183SLGGTEFLMDEW
Celegans  all identical  T14D7.1  204HGALFLVDTVASLG
Xtropicalis  all identical  ENSXETG00000012149  210YNCLLLVDSVASLGGAPIYMDKQ
protein features
start (aa)end (aa)featuredetails 
185190TURNlost
195199TURNmight get lost (downstream of altered splice site)
201209STRANDmight get lost (downstream of altered splice site)
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 560
cDNA position
(for ins/del: last normal base / first normal base)		 947
gDNA position
(for ins/del: last normal base / first normal base)		 4536
chromosomal position
(for ins/del: last normal base / first normal base)		 241812431
original gDNA sequence snippet CCTGGTGGATTCGGTGGCATCCCTGGGCGGGACCCCCCTTT
altered gDNA sequence snippet CCTGGTGGATTCGGTGGCATTCCTGGGCGGGACCCCCCTTT
original cDNA sequence snippet CCTGGTGGATTCGGTGGCATCCCTGGGCGGGACCCCCCTTT
altered cDNA sequence snippet CCTGGTGGATTCGGTGGCATTCCTGGGCGGGACCCCCCTTT
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
LVDSVAFLGG TPLYMDRQGI DILYSGSQKA LNAPPGTSLI SFSDKAKKKM YSRKTKPFSF
YLDIKWLANF WGCDDQPRMY HHTIPVISLY SLRESLALIA EQGLENSWRQ HREAAAYLHG
RLQALGLQLF VKDPALRLPT VTTVAVPAGY DWRDIVSYVI DHFDIEIMGG LGPSTGKVLR
IGLLGCNATR ENVDRVTEAL RAALQHCPKK KL*
speed 0.59 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