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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 2.663811 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AGXTdisease_causing_automatic0.99999999903902simple_aaeaffected0D183Nsingle base exchangers180177236show file

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Prediction

disease causing

 Model: simple_aae, prob: 0.99999999903902 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM001055)
  • known disease mutation: rs204111 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:241812418G>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.547G>A
cDNA.934G>A
g.4523G>A
AA changes D183N Score: 23 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 183
frameshift no
known variant Reference ID: rs180177236
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs204111 (pathogenic for Primary hyperoxaluria, type I) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM001055)

known disease mutation at this position, please check HGMD for details (HGMD ID CM001055)
known disease mutation at this position, please check HGMD for details (HGMD ID CM001055)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1780.998
4.9021
(flanking)2.5880.996
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 increased4523wt: 0.5496 / mu: 0.5994 (marginal change - not scored)wt: ACAAGTGCCTGCTCCTGGTGGATTCGGTGGCATCCCTGGGC
mu: ACAAGTGCCTGCTCCTGGTGAATTCGGTGGCATCCCTGGGC		 gtgg|ATTC
Donor increased4528wt: 0.29 / mu: 0.51wt: GATTCGGTGGCATCC
mu: AATTCGGTGGCATCC		 TTCG|gtgg
Donor increased4519wt: 0.64 / mu: 0.97wt: CTCCTGGTGGATTCG
mu: CTCCTGGTGAATTCG		 CCTG|gtgg
Donor gained45180.32mu: GCTCCTGGTGAATTC TCCT|ggtg
distance from splice site 23
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      183LCHRYKCLLLVDSVASLGGTPLYM
mutated  all conserved    183LVNSVASLGGTPLY
Ptroglodytes  all identical  ENSPTRG00000013113  159LVDSVVSLGGTPLY
Mmulatta  all identical  ENSMMUG00000023435  205LVDSVVSLGGTPLY
Fcatus  not conserved  ENSFCAG00000010448  183LVGSVASLCGTPLF
Mmusculus  all identical  ENSMUSG00000026272  205LVDSVASLGGVPIY
Ggallus  all identical  ENSGALG00000020943  206LVDAVASLGGAPIL
Trubripes  all identical  ENSTRUG00000007149  213ICRKHNCLFLVDTVAS
Drerio  all identical  ENSDARG00000018478  213VCRKHNCLLLVDSV
Dmelanogaster  all identical  FBgn0014031  178LCRKYDCFLIVDTVA
Celegans  all identical  T14D7.1  200ACREHGALFLVDTVASLG
Xtropicalis  all identical  ENSXETG00000012149  206LCHRYNCLLLVDSVAS
protein features
start (aa)end (aa)featuredetails 
179183STRANDlost
185190TURNmight get lost (downstream of altered splice site)
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 547
cDNA position
(for ins/del: last normal base / first normal base)		 934
gDNA position
(for ins/del: last normal base / first normal base)		 4523
chromosomal position
(for ins/del: last normal base / first normal base)		 241812418
original gDNA sequence snippet ACAAGTGCCTGCTCCTGGTGGATTCGGTGGCATCCCTGGGC
altered gDNA sequence snippet ACAAGTGCCTGCTCCTGGTGAATTCGGTGGCATCCCTGGGC
original cDNA sequence snippet ACAAGTGCCTGCTCCTGGTGGATTCGGTGGCATCCCTGGGC
altered cDNA sequence snippet ACAAGTGCCTGCTCCTGGTGAATTCGGTGGCATCCCTGGGC
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
LVNSVASLGG TPLYMDRQGI DILYSGSQKA LNAPPGTSLI SFSDKAKKKM YSRKTKPFSF
YLDIKWLANF WGCDDQPRMY HHTIPVISLY SLRESLALIA EQGLENSWRQ HREAAAYLHG
RLQALGLQLF VKDPALRLPT VTTVAVPAGY DWRDIVSYVI DHFDIEIMGG LGPSTGKVLR
IGLLGCNATR ENVDRVTEAL RAALQHCPKK KL*
speed 0.64 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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