Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999782324 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM960703)
  • known disease mutation: rs2778 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:81698027A>GN/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.671T>C
cDNA.1315T>C
g.113286T>C
AA changes L224P Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 224
frameshift no
known variant Reference ID: rs137852886
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs2778 (pathogenic for Glycogen storage disease, type IV|Glycogen storage disease IV, classic hepatic|Glycogen storage disease IV, nonprogressive hepatic|Adult polyglucosan body neuropathy) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960703)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960703)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960703)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.631
4.921
(flanking)4.3211
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 increased113291wt: 0.3619 / mu: 0.4466 (marginal change - not scored)wt: TACCAAGAATCAAAG
mu: CACCAAGAATCAAAG		 CCAA|gaat
distance from splice site 21
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      224VASYKHFTCNVLPRIKGLGYNCIQ
mutated  not conserved    224VASYKHFTCNVPPRIKGLGYNCI
Ptroglodytes  all identical  ENSPTRG00000015119  224VASYKHFTCNVLPRIKGLGYNCI
Mmulatta  all identical  ENSMMUG00000015877  224VASYKHFTCNVLPRIKDLGYNCI
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000022707  224IASYKHFTSNVLPRIKDLGYNCI
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  all conserved  FBgn0053138  209VGSYDEFADRIVPRIKRQGYNCI
Celegans  all identical  T04A8.7  205INTYREFADDVLPRIQKQGYNAI
Xtropicalis  no homologue    
protein features no protein features affected
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 671
cDNA position
(for ins/del: last normal base / first normal base)		 1315
gDNA position
(for ins/del: last normal base / first normal base)		 113286
chromosomal position
(for ins/del: last normal base / first normal base)		 81698027
original gDNA sequence snippet ACATTTTACATGCAATGTACTACCAAGAATCAAAGGCCTTG
altered gDNA sequence snippet ACATTTTACATGCAATGTACCACCAAGAATCAAAGGCCTTG
original cDNA sequence snippet ACATTTTACATGCAATGTACTACCAAGAATCAAAGGCCTTG
altered cDNA sequence snippet ACATTTTACATGCAATGTACCACCAAGAATCAAAGGCCTTG
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 CNVPPRIKGL 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*
speed 1.26 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