Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999999183 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM950570)
  • known disease mutation: rs9287 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:55310855C>TN/A show variant in all transcripts   IGV
HGNC symbol GCH1
Ensembl transcript ID ENST00000491895
Genbank transcript ID NM_000161
UniProt peptide P30793
alteration type single base exchange
alteration region CDS
DNA changes c.633G>A
cDNA.822G>A
g.58716G>A
AA changes M211I Score: 10 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 211
frameshift no
known variant Reference ID: rs104894443
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs9287 (pathogenic for GTP cyclohydrolase I deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950570)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950570)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950570)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.9641
6.0071
(flanking)4.9641
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 increased58713wt: 0.2995 / mu: 0.3339 (marginal change - not scored)wt: GTTGCCTTATTTTGTAGACACATGTGTATGGTAATGCGAGG
mu: GTTGCCTTATTTTGTAGACACATATGTATGGTAATGCGAGG		 acac|ATGT
Acc marginally increased58707wt: 0.7965 / mu: 0.8437 (marginal change - not scored)wt: ACCTGTGTTGCCTTATTTTGTAGACACATGTGTATGGTAAT
mu: ACCTGTGTTGCCTTATTTTGTAGACACATATGTATGGTAAT		 ttgt|AGAC
Donor increased58712wt: 0.81 / mu: 0.97wt: TAGACACATGTGTAT
mu: TAGACACATATGTAT		 GACA|catg
Donor increased58708wt: 0.67 / mu: 0.86wt: TTTGTAGACACATGT
mu: TTTGTAGACACATAT		 TGTA|gaca
Donor increased58721wt: 0.23 / mu: 0.42wt: GTGTATGGTAATGCG
mu: ATGTATGGTAATGCG		 GTAT|ggta
distance from splice site 7
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      211AGVGVVVEATHMCMVMRGVQKMNS
mutated  all conserved    211AGVGVVVEATHICMVMRGVQKMN
Ptroglodytes  all identical  ENSPTRG00000006365  211AGVGVVVEATHMCMVMRGVQKMN
Mmulatta  all identical  ENSMMUG00000004084  211AGVGVVVEATHMCMVMRGVQKMN
Fcatus  all identical  ENSFCAG00000008872  96AGVGVVVEATHMCMVMRGVQKMN
Mmusculus  all identical  ENSMUSG00000037580  202AGVGVVIEATHMCMVMRGVQKMN
Ggallus  all identical  ENSGALG00000012200  197AGVGVVIEATHMCMVMRGVQKMN
Trubripes  all identical  ENSTRUG00000015367  218ATHMCMVMRGVQKMN
Drerio  all identical  ENSDARG00000070453  212AGVGVVVEATHMCMVMRGVQKMN
Dmelanogaster  all identical  FBgn0003162  284AGVAVVVEGVHMCMVMRGVQKIN
Celegans  all identical  F32G8.6  183SGVAVVIEASHMCMVMRGVQKIN
Xtropicalis  all identical  ENSXETG00000012214  208SGVGVVVEATHMCMVMRGVQKMN
protein features
start (aa)end (aa)featuredetails 
202210STRANDmight get lost (downstream of altered splice site)
211214HELIXlost
212212METALZinc.might get lost (downstream of altered splice site)
215217TURNmight get lost (downstream of altered splice site)
224230STRANDmight get lost (downstream of altered splice site)
233236HELIXmight get lost (downstream of altered splice site)
238248HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 753 / 753
position (AA) of stopcodon in wt / mu AA sequence 251 / 251
position of stopcodon in wt / mu cDNA 942 / 942
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 190 / 190
chromosome 14
strand -1
last intron/exon boundary 816
theoretical NMD boundary in CDS 576
length of CDS 753
coding sequence (CDS) position 633
cDNA position
(for ins/del: last normal base / first normal base)		 822
gDNA position
(for ins/del: last normal base / first normal base)		 58716
chromosomal position
(for ins/del: last normal base / first normal base)		 55310855
original gDNA sequence snippet GCCTTATTTTGTAGACACATGTGTATGGTAATGCGAGGTGT
altered gDNA sequence snippet GCCTTATTTTGTAGACACATATGTATGGTAATGCGAGGTGT
original cDNA sequence snippet GTGGTTGAAGCAACACACATGTGTATGGTAATGCGAGGTGT
altered cDNA sequence snippet GTGGTTGAAGCAACACACATATGTATGGTAATGCGAGGTGT
wildtype AA sequence MEKGPVRAPA EKPRGARCSN GFPERDPPRP GPSRPAEKPP RPEAKSAQPA DGWKGERPRS
EEDNELNLPN LAAAYSSILS SLGENPQRQG LLKTPWRAAS AMQFFTKGYQ ETISDVLNDA
IFDEDHDEMV IVKDIDMFSM CEHHLVPFVG KVHIGYLPNK QVLGLSKLAR IVEIYSRRLQ
VQERLTKQIA VAITEALRPA GVGVVVEATH MCMVMRGVQK MNSKTVTSTM LGVFREDPKT
REEFLTLIRS *
mutated AA sequence MEKGPVRAPA EKPRGARCSN GFPERDPPRP GPSRPAEKPP RPEAKSAQPA DGWKGERPRS
EEDNELNLPN LAAAYSSILS SLGENPQRQG LLKTPWRAAS AMQFFTKGYQ ETISDVLNDA
IFDEDHDEMV IVKDIDMFSM CEHHLVPFVG KVHIGYLPNK QVLGLSKLAR IVEIYSRRLQ
VQERLTKQIA VAITEALRPA GVGVVVEATH ICMVMRGVQK MNSKTVTSTM LGVFREDPKT
REEFLTLIRS *
speed 0.66 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