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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 2.248288 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AGXTpolymorphism0.000571200281513029simple_aaeaffectedS218Lsingle base exchangers180177253show file

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Prediction

polymorphism

 Model: simple_aae, prob: 0.999428799718487      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs188979 (probable pathogenic)
  • known disease mutation at this position (HGMD CM053748)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:241813452C>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.653C>T
cDNA.1040C>T
g.5557C>T
AA changes S218L Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 218
frameshift no
known variant Reference ID: rs180177253
Allele 'T' was neither found in ExAC nor 1000G.
known as potential disease variant: rs188979 (probable pathogenic for Primary hyperoxaluria, type I) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM053748)

known disease mutation at this position, please check HGMD for details (HGMD ID CM053748)
known disease mutation at this position, please check HGMD for details (HGMD ID CM053748)
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
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)0.2270.061
3.3950.102
(flanking)-2.7390.001
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased5565wt: 0.22 / mu: 0.37wt: CTCCAGGGACCTCGCTCATCTCCTTCAGTGACAAGGCCAAG
mu: CTCCAGGGACCTTGCTCATCTCCTTCAGTGACAAGGCCAAG		 atct|CCTT
Acc marginally increased5568wt: 0.2662 / mu: 0.3195 (marginal change - not scored)wt: CAGGGACCTCGCTCATCTCCTTCAGTGACAAGGCCAAGTGA
mu: CAGGGACCTTGCTCATCTCCTTCAGTGACAAGGCCAAGTGA		 tcct|TCAG
Acc marginally increased5550wt: 0.2713 / mu: 0.2917 (marginal change - not scored)wt: AGGCCCTGAACGCCCCTCCAGGGACCTCGCTCATCTCCTTC
mu: AGGCCCTGAACGCCCCTCCAGGGACCTTGCTCATCTCCTTC		 ccag|GGAC
Acc gained55670.33mu: CCAGGGACCTTGCTCATCTCCTTCAGTGACAAGGCCAAGTG ctcc|TTCA
distance from splice site 28
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      218SQKALNAPPGTSLISFSDKAKKKM
mutated  not conserved    218SQKALNAPPGTLLISFSDKAKKK
Ptroglodytes  all identical  ENSPTRG00000013113  194SQKALNAPPGTSLISFSDKA---
Mmulatta  all identical  ENSMMUG00000023435  240SQKVLNAPPGTSFISFSDKAKKK
Fcatus  all identical  ENSFCAG00000010448  218SQKVLNSPPGTSLISFSDKAXXX
Mmusculus  all identical  ENSMUSG00000026272  240SQKVLNAPPGISLISFNDKAKYK
Ggallus  all identical  ENSGALG00000020943  241SQKVLSAPPGSSPISFSERAREK
Trubripes  all conserved  ENSTRUG00000007149  248SQKALNAPPGTAPISFNDRACHK
Drerio  all conserved  ENSDARG00000018478  248SQKALNAPPGTAPISFNERACQK
Dmelanogaster  all conserved  FBgn0014031  214SQKSLGGPAGLTPISFSKRALTR
Celegans  all conserved  T14D7.1  235TQKVLNAPPGLAPISFSDRAMEK
Xtropicalis  all conserved  ENSXETG00000012149  241SQKVLNAPPGTAPISFSETASKK
protein features
start (aa)end (aa)featuredetails 
218222STRANDlost
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 653
cDNA position
(for ins/del: last normal base / first normal base)		 1040
gDNA position
(for ins/del: last normal base / first normal base)		 5557
chromosomal position
(for ins/del: last normal base / first normal base)		 241813452
original gDNA sequence snippet GAACGCCCCTCCAGGGACCTCGCTCATCTCCTTCAGTGACA
altered gDNA sequence snippet GAACGCCCCTCCAGGGACCTTGCTCATCTCCTTCAGTGACA
original cDNA sequence snippet GAACGCCCCTCCAGGGACCTCGCTCATCTCCTTCAGTGACA
altered cDNA sequence snippet GAACGCCCCTCCAGGGACCTTGCTCATCTCCTTCAGTGACA
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 LNAPPGTLLI SFSDKAKKKM YSRKTKPFSF
YLDIKWLANF WGCDDQPRMY HHTIPVISLY SLRESLALIA EQGLENSWRQ HREAAAYLHG
RLQALGLQLF VKDPALRLPT VTTVAVPAGY DWRDIVSYVI DHFDIEIMGG LGPSTGKVLR
IGLLGCNATR ENVDRVTEAL RAALQHCPKK KL*
speed 0.13 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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