Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999999998 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM135179)
  • known disease mutation at this position (HGMD CM994199)
  • known disease mutation: rs9285 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:55332094A>TN/A show variant in all transcripts   IGV
HGNC symbol GCH1
Ensembl transcript ID ENST00000536224
Genbank transcript ID NM_001024071
UniProt peptide P30793
alteration type single base exchange
alteration region CDS
DNA changes c.404T>A
cDNA.557T>A
g.37477T>A
AA changes I135K Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 135
frameshift no
known variant Reference ID: rs104894441
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs9285 (pathogenic for Dystonia 5) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM994199)

known disease mutation at this position, please check HGMD for details (HGMD ID CM994199)
known disease mutation at this position, please check HGMD for details (HGMD ID CM135179)

known disease mutation at this position, please check HGMD for details (HGMD ID CM994199)
known disease mutation at this position, please check HGMD for details (HGMD ID CM135179)
known disease mutation at this position, please check HGMD for details (HGMD ID CM994199)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1210.996
5.0541
(flanking)5.0541
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased37478wt: 0.9966 / mu: 0.9987 (marginal change - not scored)wt: GACATAGACATGTTT
mu: GACAAAGACATGTTT		 CATA|gaca
Donor increased37476wt: 0.65 / mu: 0.76wt: AGGACATAGACATGT
mu: AGGACAAAGACATGT		 GACA|taga
Donor gained374730.91mu: TGAAGGACAAAGACA AAGG|acaa
Donor gained374720.98mu: GTGAAGGACAAAGAC GAAG|gaca
distance from splice site 50
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      135EDHDEMVIVKDIDMFSMCEHHLVP
mutated  not conserved    135EDHDEMVIVKDKDMFSMCEHHLV
Ptroglodytes  all identical  ENSPTRG00000006365  135EDHDEMVIVKDIDMFSMCEHHLV
Mmulatta  all identical  ENSMMUG00000004084  135EDHDEMVIVKDIDMFSMCEHHLV
Fcatus  all identical  ENSFCAG00000008872  20EDHDEMVIVKDIDMFSMCEHHLV
Mmusculus  all identical  ENSMUSG00000037580  126IVKDIDMFSMCEHHLV
Ggallus  all identical  ENSGALG00000012200  121EDHDEMVIVKDIDMFSLCEHHLV
Trubripes  all identical  ENSTRUG00000015367  142EDHDEMVIVKDIDMFSMCEHHLV
Drerio  all identical  ENSDARG00000070453  136EDHDEMVIVKDIDMFSMCEHHLV
Dmelanogaster  all identical  FBgn0003162  208DHDEMVVVKDIEMFSMCEHHLV
Celegans  all identical  F32G8.6  107DHDEMVIVKDIEMFSLCEHHLV
Xtropicalis  all identical  ENSXETG00000012214  132MVIVKDIDMFSMCEHHLV
protein features
start (aa)end (aa)featuredetails 
130141STRANDlost
141141METALZinc.might get lost (downstream of altered splice site)
142144TURNmight get lost (downstream of altered splice site)
144144METALZinc.might get lost (downstream of altered splice site)
147156STRANDmight get lost (downstream of altered splice site)
165176HELIXmight get lost (downstream of altered splice site)
177180STRANDmight get lost (downstream of altered splice site)
182197HELIXmight get lost (downstream of altered splice site)
202210STRANDmight get lost (downstream of altered splice site)
206206CONFLICTV -> I (in Ref. 9; CAA78908).might get lost (downstream of altered splice site)
211214HELIXmight get lost (downstream of altered splice site)
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 642 / 642
position (AA) of stopcodon in wt / mu AA sequence 214 / 214
position of stopcodon in wt / mu cDNA 795 / 795
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 154 / 154
chromosome 14
strand -1
last intron/exon boundary 780
theoretical NMD boundary in CDS 576
length of CDS 642
coding sequence (CDS) position 404
cDNA position
(for ins/del: last normal base / first normal base)		 557
gDNA position
(for ins/del: last normal base / first normal base)		 37477
chromosomal position
(for ins/del: last normal base / first normal base)		 55332094
original gDNA sequence snippet GATGGTGATTGTGAAGGACATAGACATGTTTTCCATGTGTG
altered gDNA sequence snippet GATGGTGATTGTGAAGGACAAAGACATGTTTTCCATGTGTG
original cDNA sequence snippet GATGGTGATTGTGAAGGACATAGACATGTTTTCCATGTGTG
altered cDNA sequence snippet GATGGTGATTGTGAAGGACAAAGACATGTTTTCCATGTGTG
wildtype AA sequence MEKGPVRAPA EKPRGARCSN GFPERDPPRP GPSRPAEKPP RPEAKSAQPA DGWKGERPRS
EEDNELNLPN LAAAYSSILS SLGENPQRQG LLKTPWRAAS AMQFFTKGYQ ETISDVLNDA
IFDEDHDEMV IVKDIDMFSM CEHHLVPFVG KVHIGYLPNK QVLGLSKLAR IVEIYSRRLQ
VQERLTKQIA VAITEALRPA GVGVVVEATS AEP*
mutated AA sequence MEKGPVRAPA EKPRGARCSN GFPERDPPRP GPSRPAEKPP RPEAKSAQPA DGWKGERPRS
EEDNELNLPN LAAAYSSILS SLGENPQRQG LLKTPWRAAS AMQFFTKGYQ ETISDVLNDA
IFDEDHDEMV IVKDKDMFSM CEHHLVPFVG KVHIGYLPNK QVLGLSKLAR IVEIYSRRLQ
VQERLTKQIA VAITEALRPA GVGVVVEATS AEP*
speed 0.33 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