Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999935694678671 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM960704)
  • known disease mutation: rs2780 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:81695554A>TN/A show variant in all transcripts   IGV
HGNC symbol GBE1
Ensembl transcript ID ENST00000429644
Genbank transcript ID NM_000158
UniProt peptide Q04446
alteration type single base exchange
alteration region CDS
DNA changes c.771T>A
cDNA.1415T>A
g.115759T>A
AA changes F257L Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 257
frameshift no
known variant Reference ID: rs137852887
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs2780 (pathogenic for Glycogen storage disease, type IV|Glycogen storage disease IV, classic hepatic|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960704)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960704)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960704)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.6191
3.1211
(flanking)4.6561
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc decreased115770wt: 0.95 / mu: 0.81wt: AAGCTTCTTTGCAGCTTCCAGGTAAAATCAGAGACTCATTG
mu: AAGCTTCTTAGCAGCTTCCAGGTAAAATCAGAGACTCATTG		 ccag|GTAA
Donor gained1157590.38mu: TTCTTAGCAGCTTCC CTTA|gcag
distance from splice site 12
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      257YASFGYQITSFFAASSRYGTPEEL
mutated  not conserved    257YASFGYQITSFLAASSRYGTPEE
Ptroglodytes  all identical  ENSPTRG00000015119  257YASFGYQITSFFAASSRYGTPEE
Mmulatta  all identical  ENSMMUG00000015877  257YASFGYQITSFFAASSRYGTPEE
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000022707  257YASFGYQITSFFAASSRYGTPEE
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  all conserved  FBgn0053138  242FYAASSRYGNPEQ
Celegans  all identical  T04A8.7  238YASFGYQVSNFFAVSSRC
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
357357ACT_SITENucleophile (By similarity).might get lost (downstream of altered splice site)
412412ACT_SITEProton donor (By similarity).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2109 / 2109
position (AA) of stopcodon in wt / mu AA sequence 703 / 703
position of stopcodon in wt / mu cDNA 2753 / 2753
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 645 / 645
chromosome 3
strand -1
last intron/exon boundary 2697
theoretical NMD boundary in CDS 2002
length of CDS 2109
coding sequence (CDS) position 771
cDNA position
(for ins/del: last normal base / first normal base)		 1415
gDNA position
(for ins/del: last normal base / first normal base)		 115759
chromosomal position
(for ins/del: last normal base / first normal base)		 81695554
original gDNA sequence snippet TACCAAATCACAAGCTTCTTTGCAGCTTCCAGGTAAAATCA
altered gDNA sequence snippet TACCAAATCACAAGCTTCTTAGCAGCTTCCAGGTAAAATCA
original cDNA sequence snippet TACCAAATCACAAGCTTCTTTGCAGCTTCCAGCCGTTATGG
altered cDNA sequence snippet TACCAAATCACAAGCTTCTTAGCAGCTTCCAGCCGTTATGG
wildtype AA sequence MAAPMTPAAR PEDYEAALNA ALADVPELAR LLEIDPYLKP YAVDFQRRYK QFSQILKNIG
ENEGGIDKFS RGYESFGVHR CADGGLYCKE WAPGAEGVFL TGDFNGWNPF SYPYKKLDYG
KWELYIPPKQ NKSVLVPHGS KLKVVITSKS GEILYRISPW AKYVVREGDN VNYDWIHWDP
EHSYEFKHSR PKKPRSLRIY ESHVGISSHE GKVASYKHFT CNVLPRIKGL GYNCIQLMAI
MEHAYYASFG YQITSFFAAS SRYGTPEELQ ELVDTAHSMG IIVLLDVVHS HASKNSADGL
NMFDGTDSCY FHSGPRGTHD LWDSRLFAYS SWEILRFLLS NIRWWLEEYR FDGFRFDGVT
SMLYHHHGVG QGFSGDYSEY FGLQVDEDAL TYLMLANHLV HTLCPDSITI AEDVSGMPAL
CSPISQGGGG FDYRLAMAIP DKWIQLLKEF KDEDWNMGDI VYTLTNRRYL EKCIAYAESH
DQALVGDKSL AFWLMDAEMY TNMSVLTPFT PVIDRGIQLH KMIRLITHGL GGEGYLNFMG
NEFGHPEWLD FPRKGNNESY HYARRQFHLT DDDLLRYKFL NNFDRDMNRL EERYGWLAAP
QAYVSEKHEG NKIIAFERAG LLFIFNFHPS KSYTDYRVGT ALPGKFKIVL DSDAAEYGGH
QRLDHSTDFF SEAFEHNGRP YSLLVYIPSR VALILQNVDL PN*
mutated AA sequence MAAPMTPAAR PEDYEAALNA ALADVPELAR LLEIDPYLKP YAVDFQRRYK QFSQILKNIG
ENEGGIDKFS RGYESFGVHR CADGGLYCKE WAPGAEGVFL TGDFNGWNPF SYPYKKLDYG
KWELYIPPKQ NKSVLVPHGS KLKVVITSKS GEILYRISPW AKYVVREGDN VNYDWIHWDP
EHSYEFKHSR PKKPRSLRIY ESHVGISSHE GKVASYKHFT CNVLPRIKGL GYNCIQLMAI
MEHAYYASFG YQITSFLAAS SRYGTPEELQ ELVDTAHSMG IIVLLDVVHS HASKNSADGL
NMFDGTDSCY FHSGPRGTHD LWDSRLFAYS SWEILRFLLS NIRWWLEEYR FDGFRFDGVT
SMLYHHHGVG QGFSGDYSEY FGLQVDEDAL TYLMLANHLV HTLCPDSITI AEDVSGMPAL
CSPISQGGGG FDYRLAMAIP DKWIQLLKEF KDEDWNMGDI VYTLTNRRYL EKCIAYAESH
DQALVGDKSL AFWLMDAEMY TNMSVLTPFT PVIDRGIQLH KMIRLITHGL GGEGYLNFMG
NEFGHPEWLD FPRKGNNESY HYARRQFHLT DDDLLRYKFL NNFDRDMNRL EERYGWLAAP
QAYVSEKHEG NKIIAFERAG LLFIFNFHPS KSYTDYRVGT ALPGKFKIVL DSDAAEYGGH
QRLDHSTDFF SEAFEHNGRP YSLLVYIPSR VALILQNVDL PN*
speed 1.37 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