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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 3.268142 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AGXTdisease_causing_automatic0.999999999995106simple_aaeaffected0G216Rsingle base exchangers180177252show file

Taster files

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 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999995106 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM065967)
  • known disease mutation: rs204121 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:241813445G>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.646G>A
cDNA.1033G>A
g.5550G>A
AA changes G216R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 216
frameshift no
known variant Reference ID: rs180177252
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs204121 (pathogenic for Primary hyperoxaluria, type I) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM065967)

known disease mutation at this position, please check HGMD for details (HGMD ID CM065967)
known disease mutation at this position, please check HGMD for details (HGMD ID CM065967)
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
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.2910.432
5.0531
(flanking)5.0531
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased5550wt: 0.2713 / mu: 0.3095 (marginal change - not scored)wt: AGGCCCTGAACGCCCCTCCAGGGACCTCGCTCATCTCCTTC
mu: AGGCCCTGAACGCCCCTCCAAGGACCTCGCTCATCTCCTTC		 ccag|GGAC
Donor gained55450.94mu: CGCCCCTCCAAGGAC CCCC|tcca
distance from splice site 35
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      216SGSQKALNAPPGTSLISFSDKAKK
mutated  not conserved    216SGSQKALNAPPRTSLISFSDKAK
Ptroglodytes  all identical  ENSPTRG00000013113  192SGSQKALNAPPGTSLISFSDKA-
Mmulatta  all identical  ENSMMUG00000023435  238SGSQKVLNAPPGTSFISFSDKAK
Fcatus  all identical  ENSFCAG00000010448  216SGSQKVLNSPPGTSLISFSDKAX
Mmusculus  all identical  ENSMUSG00000026272  238SSSQKVLNAPPGISLISFNDKAK
Ggallus  all identical  ENSGALG00000020943  239TGSQKVLSAPPGSSPISFSERAR
Trubripes  all identical  ENSTRUG00000007149  246TGSQKALNAPPGTAPISFNDRAC
Drerio  all identical  ENSDARG00000018478  246TGSQKALNAPPGTAPISFNERAC
Dmelanogaster  all identical  FBgn0014031  212TGSQKSLGGPAGLTPISFSKRAL
Celegans  all identical  T14D7.1  233SATQKVLNAPPGLAPISFSDRAM
Xtropicalis  all identical  ENSXETG00000012149  239SGSQKVLNAPPGTAPISFSETAS
protein features
start (aa)end (aa)featuredetails 
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 646
cDNA position
(for ins/del: last normal base / first normal base)		 1033
gDNA position
(for ins/del: last normal base / first normal base)		 5550
chromosomal position
(for ins/del: last normal base / first normal base)		 241813445
original gDNA sequence snippet AGGCCCTGAACGCCCCTCCAGGGACCTCGCTCATCTCCTTC
altered gDNA sequence snippet AGGCCCTGAACGCCCCTCCAAGGACCTCGCTCATCTCCTTC
original cDNA sequence snippet AGGCCCTGAACGCCCCTCCAGGGACCTCGCTCATCTCCTTC
altered cDNA sequence snippet AGGCCCTGAACGCCCCTCCAAGGACCTCGCTCATCTCCTTC
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 LNAPPRTSLI SFSDKAKKKM YSRKTKPFSF
YLDIKWLANF WGCDDQPRMY HHTIPVISLY SLRESLALIA EQGLENSWRQ HREAAAYLHG
RLQALGLQLF VKDPALRLPT VTTVAVPAGY DWRDIVSYVI DHFDIEIMGG LGPSTGKVLR
IGLLGCNATR ENVDRVTEAL RAALQHCPKK KL*
speed 1.19 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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