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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 0.82 s - this script 2.943191 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AGXTdisease_causing_automatic0.999999975914119simple_aaeaffected0D243Hsingle base exchangers180177258show file

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 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999975914119 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM056520)
  • known disease mutation: rs204124 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:241814572G>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.727G>C
cDNA.1114G>C
g.6677G>C
AA changes D243H Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 243
frameshift no
known variant Reference ID: rs180177258
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs204124 (pathogenic for Primary hyperoxaluria, type I) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM056520)

known disease mutation at this position, please check HGMD for details (HGMD ID CM056520)
known disease mutation at this position, please check HGMD for details (HGMD ID CM056520)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.2260.999
4.5421
(flanking)3.7630.997
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased6681wt: 0.52 / mu: 0.78wt: CTTCTCCTTCTACCTGGACATCAAGTGGCTGGCCAACTTCT
mu: CTTCTCCTTCTACCTGCACATCAAGTGGCTGGCCAACTTCT		 acat|CAAG
Acc marginally increased6677wt: 0.9846 / mu: 0.9877 (marginal change - not scored)wt: AGCCCTTCTCCTTCTACCTGGACATCAAGTGGCTGGCCAAC
mu: AGCCCTTCTCCTTCTACCTGCACATCAAGTGGCTGGCCAAC		 ctgg|ACAT
Acc increased6684wt: 0.61 / mu: 0.89wt: CTCCTTCTACCTGGACATCAAGTGGCTGGCCAACTTCTGGG
mu: CTCCTTCTACCTGCACATCAAGTGGCTGGCCAACTTCTGGG		 tcaa|GTGG
Acc marginally increased6674wt: 0.7624 / mu: 0.8480 (marginal change - not scored)wt: CGAAGCCCTTCTCCTTCTACCTGGACATCAAGTGGCTGGCC
mu: CGAAGCCCTTCTCCTTCTACCTGCACATCAAGTGGCTGGCC		 tacc|TGGA
Acc marginally increased6675wt: 0.9694 / mu: 0.9711 (marginal change - not scored)wt: GAAGCCCTTCTCCTTCTACCTGGACATCAAGTGGCTGGCCA
mu: GAAGCCCTTCTCCTTCTACCTGCACATCAAGTGGCTGGCCA		 acct|GGAC
Acc gained66830.49mu: TCTCCTTCTACCTGCACATCAAGTGGCTGGCCAACTTCTGG atca|AGTG
Acc gained66790.97mu: CCCTTCTCCTTCTACCTGCACATCAAGTGGCTGGCCAACTT gcac|ATCA
distance from splice site 47
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      243SRKTKPFSFYLDIKWLANFWGCDD
mutated  not conserved    243YLHIKWLANFWGCD
Ptroglodytes  not conserved  ENSPTRG00000013113  205-----GLENSWRQH
Mmulatta  all identical  ENSMMUG00000023435  265YLDIKWLANFWGCD
Fcatus  not conserved  ENSFCAG00000010448  243XXXXXXXXXXXXXX
Mmusculus  all identical  ENSMUSG00000026272  265YTDITYLAKLWGCE
Ggallus  all identical  ENSGALG00000020943  266YLDMGCLASYWGCD
Trubripes  all identical  ENSTRUG00000007149  273NRKTKPLSYLFDMTYL
Drerio  all identical  ENSDARG00000018478  273NRKTKPVSYLLDMN
Dmelanogaster  all identical  FBgn0014031  239KRKTKPKVYYFDILL
Celegans  all identical  T14D7.1  260NRKQRVASFYFDAIELGN
Xtropicalis  all identical  ENSXETG00000012149  266SRKTKPPSLYVDLKWL
protein features
start (aa)end (aa)featuredetails 
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 727
cDNA position
(for ins/del: last normal base / first normal base)		 1114
gDNA position
(for ins/del: last normal base / first normal base)		 6677
chromosomal position
(for ins/del: last normal base / first normal base)		 241814572
original gDNA sequence snippet AGCCCTTCTCCTTCTACCTGGACATCAAGTGGCTGGCCAAC
altered gDNA sequence snippet AGCCCTTCTCCTTCTACCTGCACATCAAGTGGCTGGCCAAC
original cDNA sequence snippet AGCCCTTCTCCTTCTACCTGGACATCAAGTGGCTGGCCAAC
altered cDNA sequence snippet AGCCCTTCTCCTTCTACCTGCACATCAAGTGGCTGGCCAAC
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
YLHIKWLANF WGCDDQPRMY HHTIPVISLY SLRESLALIA EQGLENSWRQ HREAAAYLHG
RLQALGLQLF VKDPALRLPT VTTVAVPAGY DWRDIVSYVI DHFDIEIMGG LGPSTGKVLR
IGLLGCNATR ENVDRVTEAL RAALQHCPKK KL*
speed 0.82 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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