Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999991409285 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM012127)
  • known disease mutation: rs21078 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr7:44187322C>TN/A show variant in all transcripts   IGV
HGNC symbol GCK
Ensembl transcript ID ENST00000395796
Genbank transcript ID NM_033508
UniProt peptide P35557
alteration type single base exchange
alteration region CDS
DNA changes c.787G>A
cDNA.1072G>A
g.50448G>A
AA changes G263S Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 263
frameshift no
known variant Reference ID: rs193929373
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs21078 (pathogenic for Permanent neonatal diabetes mellitus) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM012127)

known disease mutation at this position, please check HGMD for details (HGMD ID CM012127)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012127)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
H2AZ, Histone, Histone 2A variant Z
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
Max, Transcription Factor, Max TF binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)5.9171
4.2410.999
(flanking)-5.1560
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased50448wt: 0.25 / mu: 0.45wt: ACTCCGGCGAGCTGG
mu: ACTCCAGCGAGCTGG		 TCCG|gcga
distance from splice site 74
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      263VNTEWGAFGDSGELDEFLLEYDRL
mutated  not conserved    263VNTEWGAFGDSSELDEFLLEYDR
Ptroglodytes  all identical  ENSPTRG00000019140  263VNTEWGAFGDSGELDEFLLEYDR
Mmulatta  all identical  ENSMMUG00000002427  265VNTEWGAFGDSGELDEFLLEYDR
Fcatus  all identical  ENSFCAG00000014361  249WGAFGDSGELDEFLLEYDR
Mmusculus  all identical  ENSMUSG00000041798  264EWGAFGNSGELDEFLLEYDR
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000068006  274EWGAFGDHSELEDFRLEYDR
Dmelanogaster  all identical  FBgn0001186  339INTEWGAFGDNGALDFVRTEFDR
Celegans  all identical  F14B4.2  282INTEWGAFGDDGALDFLRTEWDE
Xtropicalis  all identical  ENSXETG00000019003  264NTEWGAFGDTGELEDFRLEYDR
protein features
start (aa)end (aa)featuredetails 
260263TURNlost
267269HELIXmight get lost (downstream of altered splice site)
272280HELIXmight get lost (downstream of altered splice site)
281283STRANDmight get lost (downstream of altered splice site)
288291HELIXmight get lost (downstream of altered splice site)
290290BINDINGSubstrate.might get lost (downstream of altered splice site)
295296NP_BINDATP (By similarity).might get lost (downstream of altered splice site)
295311HELIXmight get lost (downstream of altered splice site)
316318HELIXmight get lost (downstream of altered splice site)
322325TURNmight get lost (downstream of altered splice site)
332336NP_BINDATP (By similarity).might get lost (downstream of altered splice site)
332339HELIXmight get lost (downstream of altered splice site)
340342STRANDmight get lost (downstream of altered splice site)
343345STRANDmight get lost (downstream of altered splice site)
346354HELIXmight get lost (downstream of altered splice site)
361396HELIXmight get lost (downstream of altered splice site)
400409STRANDmight get lost (downstream of altered splice site)
411415NP_BINDATP (By similarity).might get lost (downstream of altered splice site)
411415HELIXmight get lost (downstream of altered splice site)
414414MUTAGENK->A: Small change in activity.might get lost (downstream of altered splice site)
416418STRANDmight get lost (downstream of altered splice site)
419430HELIXmight get lost (downstream of altered splice site)
434440STRANDmight get lost (downstream of altered splice site)
444456HELIXmight get lost (downstream of altered splice site)
457459TURNmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1395 / 1395
position (AA) of stopcodon in wt / mu AA sequence 465 / 465
position of stopcodon in wt / mu cDNA 1680 / 1680
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 286 / 286
chromosome 7
strand -1
last intron/exon boundary 1536
theoretical NMD boundary in CDS 1200
length of CDS 1395
coding sequence (CDS) position 787
cDNA position
(for ins/del: last normal base / first normal base)		 1072
gDNA position
(for ins/del: last normal base / first normal base)		 50448
chromosomal position
(for ins/del: last normal base / first normal base)		 44187322
original gDNA sequence snippet GGGGCGCCTTCGGGGACTCCGGCGAGCTGGACGAGTTCCTG
altered gDNA sequence snippet GGGGCGCCTTCGGGGACTCCAGCGAGCTGGACGAGTTCCTG
original cDNA sequence snippet GGGGCGCCTTCGGGGACTCCGGCGAGCTGGACGAGTTCCTG
altered cDNA sequence snippet GGGGCGCCTTCGGGGACTCCAGCGAGCTGGACGAGTTCCTG
wildtype AA sequence MPRPRSQLPQ PNSQVEQILA EFQLQEEDLK KVMRRMQKEM DRGLRLETHE EASVKMLPTY
VRSTPEGSEV GDFLSLDLGG TNFRVMLVKV GEGEEGQWSV KTKHQMYSIP EDAMTGTAEM
LFDYISECIS DFLDKHQMKH KKLPLGFTFS FPVRHEDIDK GILLNWTKGF KASGAEGNNV
VGLLRDAIKR RGDFEMDVVA MVNDTVATMI SCYYEDHQCE VGMIVGTGCN ACYMEEMQNV
ELVEGDEGRM CVNTEWGAFG DSGELDEFLL EYDRLVDESS ANPGQQLYEK LIGGKYMGEL
VRLVLLRLVD ENLLFHGEAS EQLRTRGAFE TRFVSQVESD TGDRKQIYNI LSTLGLRPST
TDCDIVRRAC ESVSTRAAHM CSAGLAGVIN RMRESRSEDV MRITVGVDGS VYKLHPSFKE
RFHASVRRLT PSCEITFIES EEGSGRGAAL VSAVACKKAC MLGQ*
mutated AA sequence MPRPRSQLPQ PNSQVEQILA EFQLQEEDLK KVMRRMQKEM DRGLRLETHE EASVKMLPTY
VRSTPEGSEV GDFLSLDLGG TNFRVMLVKV GEGEEGQWSV KTKHQMYSIP EDAMTGTAEM
LFDYISECIS DFLDKHQMKH KKLPLGFTFS FPVRHEDIDK GILLNWTKGF KASGAEGNNV
VGLLRDAIKR RGDFEMDVVA MVNDTVATMI SCYYEDHQCE VGMIVGTGCN ACYMEEMQNV
ELVEGDEGRM CVNTEWGAFG DSSELDEFLL EYDRLVDESS ANPGQQLYEK LIGGKYMGEL
VRLVLLRLVD ENLLFHGEAS EQLRTRGAFE TRFVSQVESD TGDRKQIYNI LSTLGLRPST
TDCDIVRRAC ESVSTRAAHM CSAGLAGVIN RMRESRSEDV MRITVGVDGS VYKLHPSFKE
RFHASVRRLT PSCEITFIES EEGSGRGAAL VSAVACKKAC MLGQ*
speed 1.06 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