Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999702729 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM960706)
  • known disease mutation: rs2779 (pathogenic)
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:81627151G>AN/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.1543C>T
cDNA.2187C>T
g.184162C>T
AA changes R515C Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 515
frameshift no
known variant Reference ID: rs80338672
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC066

known disease mutation: rs2779 (pathogenic for Glycogen storage disease, type IV|Inborn genetic diseases|Glycogen storage disease IV, classic hepatic) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960706)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960706)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960706)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.8011
5.8011
(flanking)1.7221
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased184162wt: 0.2071 / mu: 0.2161 (marginal change - not scored)wt: CTTTTACTCCAGTTATTGATCGTGGAATACAGCTTCATAAA
mu: CTTTTACTCCAGTTATTGATTGTGGAATACAGCTTCATAAA		 gatc|GTGG
Acc increased184152wt: 0.64 / mu: 0.76wt: GTCCTGACTCCTTTTACTCCAGTTATTGATCGTGGAATACA
mu: GTCCTGACTCCTTTTACTCCAGTTATTGATTGTGGAATACA		 tcca|GTTA
Acc increased184166wt: 0.34 / mu: 0.56wt: TACTCCAGTTATTGATCGTGGAATACAGCTTCATAAAATGA
mu: TACTCCAGTTATTGATTGTGGAATACAGCTTCATAAAATGA		 gtgg|AATA
distance from splice site 76
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      515SVLTPFTPVIDRGIQLHKMIRLIT
mutated  not conserved    515SVLTPFTPVIDCGIQLHKMIRLI
Ptroglodytes  all identical  ENSPTRG00000015119  515SVLTPFTPVIDRGIQLHKMIRLI
Mmulatta  all identical  ENSMMUG00000015877  515SVLSPFTPVIDRGIQLHKMIRLI
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000022707  515SVLAPFTPVIDRGIQLHKMIRLI
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  all identical  FBgn0053138  500STLSDSSVIIDRGLALHKMIRLI
Celegans  all identical  T04A8.7  496STDSPLTPIIDRGLSLHKLIRLI
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 1543
cDNA position
(for ins/del: last normal base / first normal base)		 2187
gDNA position
(for ins/del: last normal base / first normal base)		 184162
chromosomal position
(for ins/del: last normal base / first normal base)		 81627151
original gDNA sequence snippet CTTTTACTCCAGTTATTGATCGTGGAATACAGCTTCATAAA
altered gDNA sequence snippet CTTTTACTCCAGTTATTGATTGTGGAATACAGCTTCATAAA
original cDNA sequence snippet CTTTTACTCCAGTTATTGATCGTGGAATACAGCTTCATAAA
altered cDNA sequence snippet CTTTTACTCCAGTTATTGATTGTGGAATACAGCTTCATAAA
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 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 PVIDCGIQLH KMIRLITHGL GGEGYLNFMG
NEFGHPEWLD FPRKGNNESY HYARRQFHLT DDDLLRYKFL NNFDRDMNRL EERYGWLAAP
QAYVSEKHEG NKIIAFERAG LLFIFNFHPS KSYTDYRVGT ALPGKFKIVL DSDAAEYGGH
QRLDHSTDFF SEAFEHNGRP YSLLVYIPSR VALILQNVDL PN*
speed 2.25 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