Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999995125 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM920306)
  • known disease mutation: rs16135 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr7:44187331C>TN/A show variant in all transcripts   IGV
HGNC symbol GCK
Ensembl transcript ID ENST00000403799
Genbank transcript ID NM_000162
UniProt peptide P35557
alteration type single base exchange
alteration region CDS
DNA changes c.781G>A
cDNA.1251G>A
g.50439G>A
AA changes G261R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 261
frameshift no
known variant Reference ID: rs104894008
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs16135 (pathogenic for Maturity-onset diabetes of the young, type 2|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920306)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920306)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920306)
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
5.8641
(flanking)0.1980.998
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained504390.89mu: CCTTCAGGGACTCCG TTCA|ggga
distance from splice site 83
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      261RMCVNTEWGAFGDSGELDEFLLEY
mutated  not conserved    261RMCVNTEWGAFRDSGELDEFLLE
Ptroglodytes  all identical  ENSPTRG00000019140  260TEWGAFGDSGELDEFLLE
Mmulatta  all identical  ENSMMUG00000002427  262EWGAFGDSGELDEFLLE
Fcatus  all identical  ENSFCAG00000014361  246WGAFGDSGELDEFLLE
Mmusculus  all identical  ENSMUSG00000041798  261RMCVNTEWGAFGNSGELDEFLLE
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000068006  271EWGAFGDHSELEDFRLE
Dmelanogaster  all identical  FBgn0001186  336RKKHVLINTEWGAFGDNGALDFVRTE
Celegans  all identical  F14B4.2  282EMIINTEWGAFGDDGALDFLRTE
Xtropicalis  all identical  ENSXETG00000019003  261RMCVNTEWGAFGDTGELEDFRLE
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 1398 / 1398
position (AA) of stopcodon in wt / mu AA sequence 466 / 466
position of stopcodon in wt / mu cDNA 1868 / 1868
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 471 / 471
chromosome 7
strand -1
last intron/exon boundary 1724
theoretical NMD boundary in CDS 1203
length of CDS 1398
coding sequence (CDS) position 781
cDNA position
(for ins/del: last normal base / first normal base)		 1251
gDNA position
(for ins/del: last normal base / first normal base)		 50439
chromosomal position
(for ins/del: last normal base / first normal base)		 44187331
original gDNA sequence snippet ATACCGAGTGGGGCGCCTTCGGGGACTCCGGCGAGCTGGAC
altered gDNA sequence snippet ATACCGAGTGGGGCGCCTTCAGGGACTCCGGCGAGCTGGAC
original cDNA sequence snippet ATACCGAGTGGGGCGCCTTCGGGGACTCCGGCGAGCTGGAC
altered cDNA sequence snippet ATACCGAGTGGGGCGCCTTCAGGGACTCCGGCGAGCTGGAC
wildtype AA sequence MLDDRARMEA AKKEKVEQIL AEFQLQEEDL KKVMRRMQKE MDRGLRLETH EEASVKMLPT
YVRSTPEGSE VGDFLSLDLG GTNFRVMLVK VGEGEEGQWS VKTKHQMYSI PEDAMTGTAE
MLFDYISECI SDFLDKHQMK HKKLPLGFTF SFPVRHEDID KGILLNWTKG FKASGAEGNN
VVGLLRDAIK RRGDFEMDVV AMVNDTVATM ISCYYEDHQC EVGMIVGTGC NACYMEEMQN
VELVEGDEGR MCVNTEWGAF GDSGELDEFL LEYDRLVDES SANPGQQLYE KLIGGKYMGE
LVRLVLLRLV DENLLFHGEA SEQLRTRGAF ETRFVSQVES DTGDRKQIYN ILSTLGLRPS
TTDCDIVRRA CESVSTRAAH MCSAGLAGVI NRMRESRSED VMRITVGVDG SVYKLHPSFK
ERFHASVRRL TPSCEITFIE SEEGSGRGAA LVSAVACKKA CMLGQ*
mutated AA sequence MLDDRARMEA AKKEKVEQIL AEFQLQEEDL KKVMRRMQKE MDRGLRLETH EEASVKMLPT
YVRSTPEGSE VGDFLSLDLG GTNFRVMLVK VGEGEEGQWS VKTKHQMYSI PEDAMTGTAE
MLFDYISECI SDFLDKHQMK HKKLPLGFTF SFPVRHEDID KGILLNWTKG FKASGAEGNN
VVGLLRDAIK RRGDFEMDVV AMVNDTVATM ISCYYEDHQC EVGMIVGTGC NACYMEEMQN
VELVEGDEGR MCVNTEWGAF RDSGELDEFL LEYDRLVDES SANPGQQLYE KLIGGKYMGE
LVRLVLLRLV DENLLFHGEA SEQLRTRGAF ETRFVSQVES DTGDRKQIYN ILSTLGLRPS
TTDCDIVRRA CESVSTRAAH MCSAGLAGVI NRMRESRSED VMRITVGVDG SVYKLHPSFK
ERFHASVRRL TPSCEITFIE SEEGSGRGAA LVSAVACKKA CMLGQ*
speed 0.75 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