Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM011358)
  • known disease mutation: rs9281 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:55310826A>GN/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 intron
DNA changes g.58745T>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs104894434
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC044

known disease mutation: rs9281 (pathogenic for Intellectual disability|Autosomal recessive DOPA responsive dystonia) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM011358)

known disease mutation at this position, please check HGMD for details (HGMD ID CM011358)
known disease mutation at this position, please check HGMD for details (HGMD ID CM011358)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.4491
5.0241
(flanking)5.0241
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 increased58750wt: 0.9483 / mu: 0.9712 (marginal change - not scored)wt: TGAACAGCAAAACTG
mu: CGAACAGCAAAACTG		 AACA|gcaa
Donor marginally increased58739wt: 0.9869 / mu: 0.9874 (marginal change - not scored)wt: TGTACAGAAAATGAA
mu: TGTACAGAAAACGAA		 TACA|gaaa
Donor increased58740wt: 0.43 / mu: 0.61wt: GTACAGAAAATGAAC
mu: GTACAGAAAACGAAC		 ACAG|aaaa
Donor marginally increased58745wt: 0.9216 / mu: 0.9491 (marginal change - not scored)wt: GAAAATGAACAGCAA
mu: GAAAACGAACAGCAA		 AAAT|gaac
distance from splice site 1054
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
202210STRANDmight 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 N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 58745
chromosomal position
(for ins/del: last normal base / first normal base)		 55310826
original gDNA sequence snippet AATGCGAGGTGTACAGAAAATGAACAGCAAAACTGTGACCA
altered gDNA sequence snippet AATGCGAGGTGTACAGAAAACGAACAGCAAAACTGTGACCA
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
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 N/A
speed 0.97 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