Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99999997396696 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM035677)
  • known disease mutation at this position (HGMD CM1212980)
  • known disease mutation: rs16145 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr7:44185217C>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.1129G>A
cDNA.1414G>A
g.52553G>A
AA changes A377T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 377
frameshift no
known variant Reference ID: rs104894016
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs16145 (pathogenic for Maturity-onset diabetes of the young, type 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM035677)

known disease mutation at this position, please check HGMD for details (HGMD ID CM035677)
known disease mutation at this position, please check HGMD for details (HGMD ID CM1212980)

known disease mutation at this position, please check HGMD for details (HGMD ID CM035677)
known disease mutation at this position, please check HGMD for details (HGMD ID CM1212980)
known disease mutation at this position, please check HGMD for details (HGMD ID CM035677)
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)5.8511
2.6220.999
(flanking)-0.1480.957
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 increased52558wt: 0.8010 / mu: 0.8547 (marginal change - not scored)wt: GCTGCGCACATGTGC
mu: ACTGCGCACATGTGC		 TGCG|caca
distance from splice site 113
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      377VRRACESVSTRAAHMCSAGLAGVI
mutated  not conserved    377VRRACESVSTRTAHMCSAGLAGV
Ptroglodytes  all identical  ENSPTRG00000019140  377VRRACESVSTRAAHMCSAGLAGV
Mmulatta  all identical  ENSMMUG00000002427  379VRRACESVSTRAAHMCSAGLAGV
Fcatus  all identical  ENSFCAG00000014361  363RAAHMCAAGLAGV
Mmusculus  all identical  ENSMUSG00000041798  378TRAAHMCSAGLAGV
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000068006  389STRAAHLCGAGLAGV
Dmelanogaster  all identical  FBgn0001186  458VRYICECVSKRAAHLVSAGIATL
Celegans  all identical  F14B4.2  407VAYVCSLISTRAAHLTAAGIAML
Xtropicalis  all identical  ENSXETG00000019003  378VSTRAAVMCSSGLAAI
protein features
start (aa)end (aa)featuredetails 
361396HELIXlost
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 1129
cDNA position
(for ins/del: last normal base / first normal base)		 1414
gDNA position
(for ins/del: last normal base / first normal base)		 52553
chromosomal position
(for ins/del: last normal base / first normal base)		 44185217
original gDNA sequence snippet GCGAGAGCGTGTCTACGCGCGCTGCGCACATGTGCTCGGCG
altered gDNA sequence snippet GCGAGAGCGTGTCTACGCGCACTGCGCACATGTGCTCGGCG
original cDNA sequence snippet GCGAGAGCGTGTCTACGCGCGCTGCGCACATGTGCTCGGCG
altered cDNA sequence snippet GCGAGAGCGTGTCTACGCGCACTGCGCACATGTGCTCGGCG
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 DSGELDEFLL EYDRLVDESS ANPGQQLYEK LIGGKYMGEL
VRLVLLRLVD ENLLFHGEAS EQLRTRGAFE TRFVSQVESD TGDRKQIYNI LSTLGLRPST
TDCDIVRRAC ESVSTRTAHM CSAGLAGVIN RMRESRSEDV MRITVGVDGS VYKLHPSFKE
RFHASVRRLT PSCEITFIES EEGSGRGAAL VSAVACKKAC MLGQ*
speed 0.22 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