Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999997025629441 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM900106)
  • known disease mutation: rs4293 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:155205518C>GN/A show variant in all transcripts   IGV
HGNC symbol GBA
Ensembl transcript ID ENST00000536770
Genbank transcript ID N/A
UniProt peptide P04062
alteration type single base exchange
alteration region CDS
DNA changes c.1003G>C
cDNA.1117G>C
g.9136G>C
AA changes D335H Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 335
frameshift no
known variant Reference ID: rs1064651
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC01111

known disease mutation: rs4293 (pathogenic for Lewy body dementia|Parkinson disease, late-onset|Gaucher's disease, type 1|Acute neuronopathic Gaucher's disease|Subacute neuronopathic Gaucher's disease|Gaucher disease type 3C|Gaucher disease, perinatal lethal|Gaucher disease|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM900106)

known disease mutation at this position, please check HGMD for details (HGMD ID CM900106)
known disease mutation at this position, please check HGMD for details (HGMD ID CM900106)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.441
4.6781
(flanking)0.2440.999
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 increased9134wt: 0.2598 / mu: 0.2815 (marginal change - not scored)wt: CACCAAGGACACGTT
mu: CACCAAGCACACGTT		 CCAA|ggac
Donor marginally increased9133wt: 0.2131 / mu: 0.2183 (marginal change - not scored)wt: TCACCAAGGACACGT
mu: TCACCAAGCACACGT		 ACCA|agga
Donor increased9129wt: 0.64 / mu: 0.75wt: GACATCACCAAGGAC
mu: GACATCACCAAGCAC		 CATC|acca
distance from splice site 47
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      335VDSPIIVDITKDTFYKQPMFYHLG
mutated  not conserved    335VDSPIIVDITKHTFYKQPMFYHL
Ptroglodytes  all identical  ENSPTRG00000001416  448IVDITKDTFYKQPMFYHL
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000028048  427SPIIVDIPKDAFYKQPMFYHL
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000010884  434VDAQRDVFYKQPTFYSM
Drerio  all identical  ENSDARG00000076058  430VDPSKDIFYKQPTFYSM
Dmelanogaster  all conserved  FBgn0051148  475TFEEFYKQPMFYAI
Celegans  not conserved  Y4C6B.6  429VDSTIIVNATAQEY
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
329335HELIXlost
338341HELIXmight get lost (downstream of altered splice site)
346352STRANDmight get lost (downstream of altered splice site)
354356HELIXmight get lost (downstream of altered splice site)
359369HELIXmight get lost (downstream of altered splice site)
373381STRANDmight get lost (downstream of altered splice site)
379379MUTAGENE->G: Decreases activity 1000-fold.might get lost (downstream of altered splice site)
379379ACT_SITENucleophile.might get lost (downstream of altered splice site)
386388STRANDmight get lost (downstream of altered splice site)
396411HELIXmight get lost (downstream of altered splice site)
414424STRANDmight get lost (downstream of altered splice site)
426428STRANDmight get lost (downstream of altered splice site)
440444STRANDmight get lost (downstream of altered splice site)
445447HELIXmight get lost (downstream of altered splice site)
449452STRANDmight get lost (downstream of altered splice site)
454463HELIXmight get lost (downstream of altered splice site)
470470CONFLICTS -> I (in Ref. 15; AA sequence).might get lost (downstream of altered splice site)
471479STRANDmight get lost (downstream of altered splice site)
482489STRANDmight get lost (downstream of altered splice site)
495501STRANDmight get lost (downstream of altered splice site)
501501CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
503505STRANDmight get lost (downstream of altered splice site)
507513STRANDmight get lost (downstream of altered splice site)
514516TURNmight get lost (downstream of altered splice site)
517523STRANDmight get lost (downstream of altered splice site)
527533STRANDmight get lost (downstream of altered splice site)
534534CONFLICTR -> H (in Ref. 1; AAA35873).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1272 / 1272
position (AA) of stopcodon in wt / mu AA sequence 424 / 424
position of stopcodon in wt / mu cDNA 1386 / 1386
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 115 / 115
chromosome 1
strand -1
last intron/exon boundary 1281
theoretical NMD boundary in CDS 1116
length of CDS 1272
coding sequence (CDS) position 1003
cDNA position
(for ins/del: last normal base / first normal base)		 1117
gDNA position
(for ins/del: last normal base / first normal base)		 9136
chromosomal position
(for ins/del: last normal base / first normal base)		 155205518
original gDNA sequence snippet TCATTGTAGACATCACCAAGGACACGTTTTACAAACAGCCC
altered gDNA sequence snippet TCATTGTAGACATCACCAAGCACACGTTTTACAAACAGCCC
original cDNA sequence snippet TCATTGTAGACATCACCAAGGACACGTTTTACAAACAGCCC
altered cDNA sequence snippet TCATTGTAGACATCACCAAGCACACGTTTTACAAACAGCCC
wildtype AA sequence MEFSSPSREE CPKPLSRVSI MAGSLTGLLL LQAVSWASGI GYNIIRVPMA SCDFSIRTYT
YADTPDDFQL HNFSLPEEDT KLKIPLIHRA LQLAQRPVSL LASPWTSPTW LKTNGAVNGK
GSLKGQPGDI YHQTWARYFV KFLDAYAEHK LQFWAVTAEN EPSAGLLSGY PFQCLGFTPE
HQRDFIARDL GPTLANSTHH NVRLLMLDDQ RLLLPHWAKV VLTDPEAAKY VHGIAVHWYL
DFLAPAKATL GETHRLFPNT MLFASEACVG SKFWEQSVRL GSWDRGMQYS HSIITNLLYH
VVGWTDWNLA LNPEGGPNWV RNFVDSPIIV DITKDTFYKQ PMFYHLGHFS KFIPEGSQRV
GLVASQKNDL DAVALMHPDG SAVVVVLNRS SKDVPLTIKD PAVGFLETIS PGYSIHTYLW
RRQ*
mutated AA sequence MEFSSPSREE CPKPLSRVSI MAGSLTGLLL LQAVSWASGI GYNIIRVPMA SCDFSIRTYT
YADTPDDFQL HNFSLPEEDT KLKIPLIHRA LQLAQRPVSL LASPWTSPTW LKTNGAVNGK
GSLKGQPGDI YHQTWARYFV KFLDAYAEHK LQFWAVTAEN EPSAGLLSGY PFQCLGFTPE
HQRDFIARDL GPTLANSTHH NVRLLMLDDQ RLLLPHWAKV VLTDPEAAKY VHGIAVHWYL
DFLAPAKATL GETHRLFPNT MLFASEACVG SKFWEQSVRL GSWDRGMQYS HSIITNLLYH
VVGWTDWNLA LNPEGGPNWV RNFVDSPIIV DITKHTFYKQ PMFYHLGHFS KFIPEGSQRV
GLVASQKNDL DAVALMHPDG SAVVVVLNRS SKDVPLTIKD PAVGFLETIS PGYSIHTYLW
RRQ*
speed 1.08 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