Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999988767 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM024596)
  • known disease mutation: rs16143 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr7:44184766G>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.1370C>T
cDNA.1532C>T
g.53004C>T
AA changes A457V Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 457
frameshift no
known variant Reference ID: rs104894014
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs16143 (pathogenic for Hyperinsulinism due to glucokinase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM024596)

known disease mutation at this position, please check HGMD for details (HGMD ID CM024596)
known disease mutation at this position, please check HGMD for details (HGMD ID CM024596)
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)1.1041
6.1231
(flanking)6.1231
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased53010wt: 0.41 / mu: 0.50wt: GGTCTCGGCGGTGGCCTGTAAGAAGGCCTGTATGCTGGGCC
mu: GGTCTCGGCGGTGGTCTGTAAGAAGGCCTGTATGCTGGGCC		 gtaa|GAAG
Donor marginally increased53008wt: 0.7452 / mu: 0.7561 (marginal change - not scored)wt: GCCTGTAAGAAGGCC
mu: GTCTGTAAGAAGGCC		 CTGT|aaga
distance from splice site 114
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      457SGRGAALVSAVACKKACMLGQ*
mutated  not conserved    457SGRGAALVSAVVCKKACMLGQ
Ptroglodytes  all identical  ENSPTRG00000019140  455SGRGAALVSAVACKKACMLGQ
Mmulatta  all identical  ENSMMUG00000002427  457SGRGAALVSAVACKKACMLGQ
Fcatus  all identical  ENSFCAG00000014361  441NVRGAALVSAVACKKACMLGQ
Mmusculus  all identical  ENSMUSG00000041798  456SGRGAALVSAVACKKACMLGQ
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000068006  467SGRGAALISAVACKMAACML
Dmelanogaster  all identical  FBgn0001186  530SGRGAALVAAVACREDILNGK
Celegans  all identical  F14B4.2  480SGRGAALVAAVATR
Xtropicalis  all identical  ENSXETG00000019003  456SGRGAALISAVAYKMAVLIG
protein features
start (aa)end (aa)featuredetails 
457459TURNlost
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 1370
cDNA position
(for ins/del: last normal base / first normal base)		 1532
gDNA position
(for ins/del: last normal base / first normal base)		 53004
chromosomal position
(for ins/del: last normal base / first normal base)		 44184766
original gDNA sequence snippet GGCCCTGGTCTCGGCGGTGGCCTGTAAGAAGGCCTGTATGC
altered gDNA sequence snippet GGCCCTGGTCTCGGCGGTGGTCTGTAAGAAGGCCTGTATGC
original cDNA sequence snippet GGCCCTGGTCTCGGCGGTGGCCTGTAAGAAGGCCTGTATGC
altered cDNA sequence snippet GGCCCTGGTCTCGGCGGTGGTCTGTAAGAAGGCCTGTATGC
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 INRMRESRSE DVMRITVGVD GSVYKLHPSF
KERFHASVRR LTPSCEITFI ESEEGSGRGA ALVSAVVCKK ACMLGQ*
speed 1.17 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