Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999731573646995 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM910174)
  • known disease mutation: rs4316 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:155206217G>AN/A show variant in all transcripts   IGV
HGNC symbol GBA
Ensembl transcript ID ENST00000368373
Genbank transcript ID NM_000157
UniProt peptide P04062
alteration type single base exchange
alteration region CDS
DNA changes c.1043C>T
cDNA.1165C>T
g.8437C>T
AA changes A348V Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 348
frameshift no
known variant Reference ID: rs78396650
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs4316 (pathogenic for Gaucher's disease, type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM910174)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910174)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910174)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0570.996
2.6631
(flanking)4.3460.999
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased8446wt: 0.37 / mu: 0.59wt: TCATGGCATTGCTGTACATTGGTACCTGGACTTTCTGGCTC
mu: TCATGGCATTGTTGTACATTGGTACCTGGACTTTCTGGCTC		 attg|GTAC
Acc increased8442wt: 0.31 / mu: 0.42wt: ATGTTCATGGCATTGCTGTACATTGGTACCTGGACTTTCTG
mu: ATGTTCATGGCATTGTTGTACATTGGTACCTGGACTTTCTG		 gtac|ATTG
distance from splice site 44
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      348DPEAAKYVHGIAVHWYLDFLAPAK
mutated  not conserved    348DPEAAKYVHGIVVHWYLDFLAPA
Ptroglodytes  all identical  ENSPTRG00000001416  348DPEAAKYVHGIAVHWYLDFLAPA
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000028048  327DPEAAKYVHGIAVHWYMDFLAPA
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000010884  334DVHAGRYVHGVAVHWYMDSLVPA
Drerio  not conserved  ENSDARG00000076058  330YVHGIGVHWYFDRLVPP
Dmelanogaster  all conserved  FBgn0051148  375SIDYLDGLSLHWYWDEIF-G
Celegans  all identical  Y4C6B.6  331DPTAAQYVHGIAIHWYEDFIDPA
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
346352STRANDlost
354356HELIXmight get lost (downstream of altered splice site)
359369HELIXmight get lost (downstream of altered splice site)
373381STRANDmight get lost (downstream of altered splice site)
379379ACT_SITENucleophile.might get lost (downstream of altered splice site)
379379MUTAGENE->G: Decreases activity 1000-fold.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 1611 / 1611
position (AA) of stopcodon in wt / mu AA sequence 537 / 537
position of stopcodon in wt / mu cDNA 1733 / 1733
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 123 / 123
chromosome 1
strand -1
last intron/exon boundary 1628
theoretical NMD boundary in CDS 1455
length of CDS 1611
coding sequence (CDS) position 1043
cDNA position
(for ins/del: last normal base / first normal base)		 1165
gDNA position
(for ins/del: last normal base / first normal base)		 8437
chromosomal position
(for ins/del: last normal base / first normal base)		 155206217
original gDNA sequence snippet TAAATATGTTCATGGCATTGCTGTACATTGGTACCTGGACT
altered gDNA sequence snippet TAAATATGTTCATGGCATTGTTGTACATTGGTACCTGGACT
original cDNA sequence snippet TAAATATGTTCATGGCATTGCTGTACATTGGTACCTGGACT
altered cDNA sequence snippet TAAATATGTTCATGGCATTGTTGTACATTGGTACCTGGACT
wildtype AA sequence MEFSSPSREE CPKPLSRVSI MAGSLTGLLL LQAVSWASGA RPCIPKSFGY SSVVCVCNAT
YCDSFDPPTF PALGTFSRYE STRSGRRMEL SMGPIQANHT GTGLLLTLQP EQKFQKVKGF
GGAMTDAAAL NILALSPPAQ NLLLKSYFSE EGIGYNIIRV PMASCDFSIR TYTYADTPDD
FQLHNFSLPE EDTKLKIPLI HRALQLAQRP VSLLASPWTS PTWLKTNGAV NGKGSLKGQP
GDIYHQTWAR YFVKFLDAYA EHKLQFWAVT AENEPSAGLL SGYPFQCLGF TPEHQRDFIA
RDLGPTLANS THHNVRLLML DDQRLLLPHW AKVVLTDPEA AKYVHGIAVH WYLDFLAPAK
ATLGETHRLF PNTMLFASEA CVGSKFWEQS VRLGSWDRGM QYSHSIITNL LYHVVGWTDW
NLALNPEGGP NWVRNFVDSP IIVDITKDTF YKQPMFYHLG HFSKFIPEGS QRVGLVASQK
NDLDAVALMH PDGSAVVVVL NRSSKDVPLT IKDPAVGFLE TISPGYSIHT YLWRRQ*
mutated AA sequence MEFSSPSREE CPKPLSRVSI MAGSLTGLLL LQAVSWASGA RPCIPKSFGY SSVVCVCNAT
YCDSFDPPTF PALGTFSRYE STRSGRRMEL SMGPIQANHT GTGLLLTLQP EQKFQKVKGF
GGAMTDAAAL NILALSPPAQ NLLLKSYFSE EGIGYNIIRV PMASCDFSIR TYTYADTPDD
FQLHNFSLPE EDTKLKIPLI HRALQLAQRP VSLLASPWTS PTWLKTNGAV NGKGSLKGQP
GDIYHQTWAR YFVKFLDAYA EHKLQFWAVT AENEPSAGLL SGYPFQCLGF TPEHQRDFIA
RDLGPTLANS THHNVRLLML DDQRLLLPHW AKVVLTDPEA AKYVHGIVVH WYLDFLAPAK
ATLGETHRLF PNTMLFASEA CVGSKFWEQS VRLGSWDRGM QYSHSIITNL LYHVVGWTDW
NLALNPEGGP NWVRNFVDSP IIVDITKDTF YKQPMFYHLG HFSKFIPEGS QRVGLVASQK
NDLDAVALMH PDGSAVVVVL NRSSKDVPLT IKDPAVGFLE TISPGYSIHT YLWRRQ*
speed 0.82 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