Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.998426614762133 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM910173)
  • known disease mutation: rs4301 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:155207932A>TN/A show variant in all transcripts   IGV
HGNC symbol GBA
Ensembl transcript ID ENST00000427500
Genbank transcript ID NM_001171812
UniProt peptide P04062
alteration type single base exchange
alteration region CDS
DNA changes c.607T>A
cDNA.770T>A
g.6722T>A
AA changes F203I Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 203
frameshift no
known variant Reference ID: rs381737
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs4301 (pathogenic for Gaucher's disease, type 1|Acute neuronopathic Gaucher's disease|Subacute neuronopathic Gaucher's disease|Gaucher disease|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM910173)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910173)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910173)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.5811
3.611
(flanking)2.6941
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 increased6724wt: 0.9951 / mu: 0.9959 (marginal change - not scored)wt: TACTTTGTGAAGTAA
mu: TACATTGTGAAGTAA		 CTTT|gtga
Donor increased6716wt: 0.66 / mu: 0.77wt: GGGCCAGATACTTTG
mu: GGGCCAGATACATTG		 GCCA|gata
distance from splice site 8
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      203GDIYHQTWARYFVKFLDAYAEHKL
mutated  not conserved    203GDIYHQTWARYIVKFLDAYAEHK
Ptroglodytes  all identical  ENSPTRG00000001416  252YHQTWARYFVKFLDAYAEHK
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000028048  232GDIFHQTWANYFVKFLDAYA
Ggallus  no homologue    
Trubripes  all conserved  ENSTRUG00000010884  238GGREHKTWAHYYIR
Drerio  all conserved  ENSDARG00000076058  234GGKEHKTWAQYYIRFLEEYRKYN
Dmelanogaster  not conserved  FBgn0051148  280---YYQTWADYHLRWLRLMKDNG
Celegans  all identical  Y4C6B.6  234NGKYYQTWAQYFVKFFEAYH
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
196206HELIXlost
212218STRANDmight get lost (downstream of altered splice site)
222224HELIXmight get lost (downstream of altered splice site)
225227STRANDmight get lost (downstream of altered splice site)
227227CONFLICTN -> R (in Ref. 5; BAA02546).might get lost (downstream of altered splice site)
229233STRANDmight get lost (downstream of altered splice site)
235238STRANDmight get lost (downstream of altered splice site)
243261HELIXmight get lost (downstream of altered splice site)
267271STRANDmight get lost (downstream of altered splice site)
274274ACT_SITEProton donor.might get lost (downstream of altered splice site)
275279HELIXmight get lost (downstream of altered splice site)
284286STRANDmight get lost (downstream of altered splice site)
292301HELIXmight get lost (downstream of altered splice site)
303308HELIXmight get lost (downstream of altered splice site)
309309CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
311314TURNmight get lost (downstream of altered splice site)
315323STRANDmight get lost (downstream of altered splice site)
324326HELIXmight get lost (downstream of altered splice site)
329335HELIXmight get lost (downstream of altered splice site)
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)
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 1464 / 1464
position (AA) of stopcodon in wt / mu AA sequence 488 / 488
position of stopcodon in wt / mu cDNA 1627 / 1627
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 164 / 164
chromosome 1
strand -1
last intron/exon boundary 1522
theoretical NMD boundary in CDS 1308
length of CDS 1464
coding sequence (CDS) position 607
cDNA position
(for ins/del: last normal base / first normal base)		 770
gDNA position
(for ins/del: last normal base / first normal base)		 6722
chromosomal position
(for ins/del: last normal base / first normal base)		 155207932
original gDNA sequence snippet ACCAGACCTGGGCCAGATACTTTGTGAAGTAAGGGATCAGC
altered gDNA sequence snippet ACCAGACCTGGGCCAGATACATTGTGAAGTAAGGGATCAGC
original cDNA sequence snippet ACCAGACCTGGGCCAGATACTTTGTGAAGTTCCTGGATGCC
altered cDNA sequence snippet ACCAGACCTGGGCCAGATACATTGTGAAGTTCCTGGATGCC
wildtype AA sequence MEFSSPSREE CPKPLSRVSI MAGSLTGLLL LQAVSWASGA RPCIPKSFGY SSVVCVCNAT
YCDSFDPPTF PALGTFSRYE STRSGRRMEL SMGPIQANHT GTGIGYNIIR VPMASCDFSI
RTYTYADTPD DFQLHNFSLP EEDTKLKIPL IHRALQLAQR PVSLLASPWT SPTWLKTNGA
VNGKGSLKGQ PGDIYHQTWA RYFVKFLDAY AEHKLQFWAV TAENEPSAGL LSGYPFQCLG
FTPEHQRDFI ARDLGPTLAN STHHNVRLLM LDDQRLLLPH WAKVVLTDPE AAKYVHGIAV
HWYLDFLAPA KATLGETHRL FPNTMLFASE ACVGSKFWEQ SVRLGSWDRG MQYSHSIITN
LLYHVVGWTD WNLALNPEGG PNWVRNFVDS PIIVDITKDT FYKQPMFYHL GHFSKFIPEG
SQRVGLVASQ KNDLDAVALM HPDGSAVVVV LNRSSKDVPL TIKDPAVGFL ETISPGYSIH
TYLWRRQ*
mutated AA sequence MEFSSPSREE CPKPLSRVSI MAGSLTGLLL LQAVSWASGA RPCIPKSFGY SSVVCVCNAT
YCDSFDPPTF PALGTFSRYE STRSGRRMEL SMGPIQANHT GTGIGYNIIR VPMASCDFSI
RTYTYADTPD DFQLHNFSLP EEDTKLKIPL IHRALQLAQR PVSLLASPWT SPTWLKTNGA
VNGKGSLKGQ PGDIYHQTWA RYIVKFLDAY AEHKLQFWAV TAENEPSAGL LSGYPFQCLG
FTPEHQRDFI ARDLGPTLAN STHHNVRLLM LDDQRLLLPH WAKVVLTDPE AAKYVHGIAV
HWYLDFLAPA KATLGETHRL FPNTMLFASE ACVGSKFWEQ SVRLGSWDRG MQYSHSIITN
LLYHVVGWTD WNLALNPEGG PNWVRNFVDS PIIVDITKDT FYKQPMFYHL GHFSKFIPEG
SQRVGLVASQ KNDLDAVALM HPDGSAVVVV LNRSSKDVPL TIKDPAVGFL ETISPGYSIH
TYLWRRQ*
speed 0.99 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