Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999911634 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM980898)
  • known disease mutation: rs16140 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr7:44184770C>TN/A show variant in all transcripts   IGV
HGNC symbol GCK
Ensembl transcript ID ENST00000437084
Genbank transcript ID N/A
UniProt peptide P35557
alteration type single base exchange
alteration region CDS
DNA changes c.1312G>A
cDNA.1346G>A
g.53000G>A
AA changes V438M Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 438
frameshift no
known variant Reference ID: rs104894012
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs16140 (pathogenic for Hyperinsulinism due to glucokinase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980898)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980898)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980898)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Znf263, Transcription Factor, Znf263 TF binding
phyloP / phastCons
PhyloPPhastCons
(flanking)5.0551
6.1231
(flanking)-3.3040.002
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased53005wt: 0.21 / mu: 0.52wt: GTGGCCTGTAAGAAG
mu: ATGGCCTGTAAGAAG		 GGCC|tgta
Donor increased52996wt: 0.60 / mu: 0.99wt: GTCTCGGCGGTGGCC
mu: GTCTCGGCGATGGCC		 CTCG|gcgg
distance from splice site 40
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      438GSGRGAALVSAVACKKACMLGQ*
mutated  all conserved    438GSGRGAALVSAMACKKACMLGQ
Ptroglodytes  all identical  ENSPTRG00000019140  454GSGRGAALVSAVACKKACMLGQ
Mmulatta  all identical  ENSMMUG00000002427  456GSGRGAALVSAVACKKACMLGQ
Fcatus  all identical  ENSFCAG00000014361  440GNVRGAALVSAVACKKACMLGQ
Mmusculus  all identical  ENSMUSG00000041798  455GSGRGAALVSAVACKKACMLGQ
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000068006  466GSGRGAALISAVACKMAACML
Dmelanogaster  all identical  FBgn0001186  529GSGRGAALVAAVACREDILNGK
Celegans  all identical  F14B4.2  479GSGRGAALVAAVATR
Xtropicalis  all identical  ENSXETG00000019003  455GSGRGAALISAVAYKMAVLIG
protein features
start (aa)end (aa)featuredetails 
434440STRANDlost
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 1347 / 1347
position (AA) of stopcodon in wt / mu AA sequence 449 / 449
position of stopcodon in wt / mu cDNA 1381 / 1381
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 35 / 35
chromosome 7
strand -1
last intron/exon boundary 1237
theoretical NMD boundary in CDS 1152
length of CDS 1347
coding sequence (CDS) position 1312
cDNA position
(for ins/del: last normal base / first normal base)		 1346
gDNA position
(for ins/del: last normal base / first normal base)		 53000
chromosomal position
(for ins/del: last normal base / first normal base)		 44184770
original gDNA sequence snippet GCGCGGCCCTGGTCTCGGCGGTGGCCTGTAAGAAGGCCTGT
altered gDNA sequence snippet GCGCGGCCCTGGTCTCGGCGATGGCCTGTAAGAAGGCCTGT
original cDNA sequence snippet GCGCGGCCCTGGTCTCGGCGGTGGCCTGTAAGAAGGCCTGT
altered cDNA sequence snippet GCGCGGCCCTGGTCTCGGCGATGGCCTGTAAGAAGGCCTGT
wildtype AA sequence MLDDRARMEA AKKEKVEQIL AEFQLQEEDL KKVMRRMQKE MDRGLRLETH EEASVKMLPT
YVRSTPEGSE VGDFLSLDLG GTNFRVMLVK VGEGEEGQWS VKTKHQMYSI PEDAMTGTAE
MMKHKKLPLG FTFSFPVRHE DIDKGILLNW TKGFKASGAE GNNVVGLLRD AIKRRGDFEM
DVVAMVNDTV ATMISCYYED HQCEVGMIVG TGCNACYMEE MQNVELVEGD EGRMCVNTEW
GAFGDSGELD EFLLEYDRLV DESSANPGQQ LYEKLIGGKY MGELVRLVLL RLVDENLLFH
GEASEQLRTR GAFETRFVSQ VESDTGDRKQ IYNILSTLGL RPSTTDCDIV RRACESVSTR
AAHMCSAGLA GVINRMRESR SEDVMRITVG VDGSVYKLHP SFKERFHASV RRLTPSCEIT
FIESEEGSGR GAALVSAVAC KKACMLGQ*
mutated AA sequence MLDDRARMEA AKKEKVEQIL AEFQLQEEDL KKVMRRMQKE MDRGLRLETH EEASVKMLPT
YVRSTPEGSE VGDFLSLDLG GTNFRVMLVK VGEGEEGQWS VKTKHQMYSI PEDAMTGTAE
MMKHKKLPLG FTFSFPVRHE DIDKGILLNW TKGFKASGAE GNNVVGLLRD AIKRRGDFEM
DVVAMVNDTV ATMISCYYED HQCEVGMIVG TGCNACYMEE MQNVELVEGD EGRMCVNTEW
GAFGDSGELD EFLLEYDRLV DESSANPGQQ LYEKLIGGKY MGELVRLVLL RLVDENLLFH
GEASEQLRTR GAFETRFVSQ VESDTGDRKQ IYNILSTLGL RPSTTDCDIV RRACESVSTR
AAHMCSAGLA GVINRMRESR SEDVMRITVG VDGSVYKLHP SFKERFHASV RRLTPSCEIT
FIESEEGSGR GAALVSAMAC KKACMLGQ*
speed 0.84 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