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 3.34252 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AGXTdisease_causing_automatic0.999999999979155simple_aaeaffected0L284Psingle base exchangers180177287show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999979155 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM093810)
  • known disease mutation: rs204133 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:241816958T>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.851T>C
cDNA.1238T>C
g.9063T>C
AA changes L284P Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 284
frameshift no
known variant Reference ID: rs180177287
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs204133 (pathogenic for Primary hyperoxaluria, type I) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM093810)

known disease mutation at this position, please check HGMD for details (HGMD ID CM093810)
known disease mutation at this position, please check HGMD for details (HGMD ID CM093810)
regulatory features H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)2.3071
3.1491
(flanking)1.4161
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased9054wt: 0.33 / mu: 0.38wt: CCCACCAGCGCCATCTCCCACACAGGGCCTGGAGAACAGCT
mu: CCCACCAGCGCCATCTCCCACACAGGGCCCGGAGAACAGCT		 ccac|ACAG
Acc marginally increased9056wt: 0.8739 / mu: 0.8856 (marginal change - not scored)wt: CACCAGCGCCATCTCCCACACAGGGCCTGGAGAACAGCTGG
mu: CACCAGCGCCATCTCCCACACAGGGCCCGGAGAACAGCTGG		 acac|AGGG
Donor increased9064wt: 0.58 / mu: 0.86wt: GGCCTGGAGAACAGC
mu: GGCCCGGAGAACAGC		 CCTG|gaga
distance from splice site 5
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      284RESLALIAEQGLENSWRQHREAAA
mutated  not conserved    284RESLALIAEQGPENSWRQHREAA
Ptroglodytes  not conserved  ENSPTRG00000013113  246-----------------------
Mmulatta  all identical  ENSMMUG00000023435  306RESLALIAEQGLENSWRQHRETT
Fcatus  not conserved  ENSFCAG00000010448  284RESLALIAEQXXXXXXXXXXXXX
Mmusculus  all identical  ENSMUSG00000026272  306RESLALIAEQGLENCWRRHREAT
Ggallus  all identical  ENSGALG00000020943  307REALAMLVELGLESSWKQHRAAC
Trubripes  all identical  ENSTRUG00000007149  314RESLAILAEKGLEESWRKHKEIA
Drerio  all identical  ENSDARG00000018478  314RESLAILAETGLENSWRHHTEVA
Dmelanogaster  all identical  FBgn0014031  280REALAHFCAVGLKAVVRRHQECS
Celegans  all conserved  T14D7.1  301RAALSAIAKEGIDESIQRHKDNA
Xtropicalis  all identical  ENSXETG00000012149  307REGLAVLAEQGLERSWAVHQENA
protein features
start (aa)end (aa)featuredetails 
266282HELIXmight get lost (downstream of altered splice site)
284305HELIXlost
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 851
cDNA position
(for ins/del: last normal base / first normal base)		 1238
gDNA position
(for ins/del: last normal base / first normal base)		 9063
chromosomal position
(for ins/del: last normal base / first normal base)		 241816958
original gDNA sequence snippet GCCATCTCCCACACAGGGCCTGGAGAACAGCTGGCGCCAGC
altered gDNA sequence snippet GCCATCTCCCACACAGGGCCCGGAGAACAGCTGGCGCCAGC
original cDNA sequence snippet CCTCATTGCGGAACAGGGCCTGGAGAACAGCTGGCGCCAGC
altered cDNA sequence snippet CCTCATTGCGGAACAGGGCCCGGAGAACAGCTGGCGCCAGC
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 SLRESLALIA EQGPENSWRQ HREAAAYLHG
RLQALGLQLF VKDPALRLPT VTTVAVPAGY DWRDIVSYVI DHFDIEIMGG LGPSTGKVLR
IGLLGCNATR ENVDRVTEAL RAALQHCPKK KL*
speed 1.33 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