Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999998671094748      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs21077 (probable pathogenic)
  • known disease mutation at this position (HGMD CM057328)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr7:44185159C>AN/A show variant in all transcripts   IGV
HGNC symbol GCK
Ensembl transcript ID ENST00000345378
Genbank transcript ID NM_033507
UniProt peptide P35557
alteration type single base exchange
alteration region CDS
DNA changes c.1193G>T
cDNA.1355G>T
g.52611G>T
AA changes R398L Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 398
frameshift no
known variant Reference ID: rs193929375
Allele 'A' was neither found in ExAC nor 1000G.
known as potential disease variant: rs21077 (probable pathogenic for Permanent neonatal diabetes mellitus|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM057328)

known disease mutation at this position, please check HGMD for details (HGMD ID CM057328)
known disease mutation at this position, please check HGMD for details (HGMD ID CM057328)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H2AZ, Histone, Histone 2A variant Z
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)1.1060.998
4.3821
(flanking)3.1141
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 increased52613wt: 0.9656 / mu: 0.9853 (marginal change - not scored)wt: GCCGCAGCGAGGACG
mu: GCCTCAGCGAGGACG		 CGCA|gcga
Donor increased52616wt: 0.38 / mu: 0.73wt: GCAGCGAGGACGTAA
mu: TCAGCGAGGACGTAA		 AGCG|agga
distance from splice site 64
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      398LAGVINRMRESRSEDVMRITVGVD
mutated  not conserved    398LAGVINRMRESLSEDVMRITVGV
Ptroglodytes  all identical  ENSPTRG00000019140  396LAGVINRMRESRSEDVMRITVGV
Mmulatta  all identical  ENSMMUG00000002427  398LAGVINRMRESRSEDVMRITVGV
Fcatus  all identical  ENSFCAG00000014361  382LAGVINRMRESRSEDVMRITVGV
Mmusculus  all identical  ENSMUSG00000041798  397LAGVINRMRESRSEDVMRITVGV
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000068006  408LAGVINLMRERRCQEELKITVGV
Dmelanogaster  not conserved  FBgn0001186  477IATLINKM------DEPTVTVGV
Celegans  not conserved  F14B4.2  426IAMLLNRMNKK------HVTVGV
Xtropicalis  all identical  ENSXETG00000019003  397LAAILNRMHQSRRGELSRITVGV
protein features
start (aa)end (aa)featuredetails 
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 1401 / 1401
position (AA) of stopcodon in wt / mu AA sequence 467 / 467
position of stopcodon in wt / mu cDNA 1563 / 1563
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 163 / 163
chromosome 7
strand -1
last intron/exon boundary 1419
theoretical NMD boundary in CDS 1206
length of CDS 1401
coding sequence (CDS) position 1193
cDNA position
(for ins/del: last normal base / first normal base)		 1355
gDNA position
(for ins/del: last normal base / first normal base)		 52611
chromosomal position
(for ins/del: last normal base / first normal base)		 44185159
original gDNA sequence snippet CAACCGCATGCGCGAGAGCCGCAGCGAGGACGTAATGCGCA
altered gDNA sequence snippet CAACCGCATGCGCGAGAGCCTCAGCGAGGACGTAATGCGCA
original cDNA sequence snippet CAACCGCATGCGCGAGAGCCGCAGCGAGGACGTAATGCGCA
altered cDNA sequence snippet CAACCGCATGCGCGAGAGCCTCAGCGAGGACGTAATGCGCA
wildtype AA sequence MAMDVTRSQA QTALTLVEQI LAEFQLQEED LKKVMRRMQK EMDRGLRLET HEEASVKMLP
TYVRSTPEGS EVGDFLSLDL GGTNFRVMLV KVGEGEEGQW SVKTKHQMYS IPEDAMTGTA
EMLFDYISEC ISDFLDKHQM KHKKLPLGFT FSFPVRHEDI DKGILLNWTK GFKASGAEGN
NVVGLLRDAI KRRGDFEMDV VAMVNDTVAT MISCYYEDHQ CEVGMIVGTG CNACYMEEMQ
NVELVEGDEG RMCVNTEWGA FGDSGELDEF LLEYDRLVDE SSANPGQQLY EKLIGGKYMG
ELVRLVLLRL VDENLLFHGE ASEQLRTRGA FETRFVSQVE SDTGDRKQIY NILSTLGLRP
STTDCDIVRR ACESVSTRAA HMCSAGLAGV INRMRESRSE DVMRITVGVD GSVYKLHPSF
KERFHASVRR LTPSCEITFI ESEEGSGRGA ALVSAVACKK ACMLGQ*
mutated AA sequence MAMDVTRSQA QTALTLVEQI LAEFQLQEED LKKVMRRMQK EMDRGLRLET HEEASVKMLP
TYVRSTPEGS EVGDFLSLDL GGTNFRVMLV KVGEGEEGQW SVKTKHQMYS IPEDAMTGTA
EMLFDYISEC ISDFLDKHQM KHKKLPLGFT FSFPVRHEDI DKGILLNWTK GFKASGAEGN
NVVGLLRDAI KRRGDFEMDV VAMVNDTVAT MISCYYEDHQ CEVGMIVGTG CNACYMEEMQ
NVELVEGDEG RMCVNTEWGA FGDSGELDEF LLEYDRLVDE SSANPGQQLY EKLIGGKYMG
ELVRLVLLRL VDENLLFHGE ASEQLRTRGA FETRFVSQVE SDTGDRKQIY NILSTLGLRP
STTDCDIVRR ACESVSTRAA HMCSAGLAGV INRMRESLSE DVMRITVGVD GSVYKLHPSF
KERFHASVRR LTPSCEITFI ESEEGSGRGA ALVSAVACKK ACMLGQ*
speed 1.08 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