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 ENST00000427500
Genbank transcript ID NM_001171812
UniProt peptide P04062
alteration type single base exchange
alteration region CDS
DNA changes c.1195G>C
cDNA.1358G>C
g.9136G>C
AA changes D399H Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 399
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      399VDSPIIVDITKDTFYKQPMFYHLG
mutated  not conserved    399VDSPIIVDITKHTFYKQPMFYHL
Ptroglodytes  all identical  ENSPTRG00000001416  448VDSPIIVDITKDTFYKQPMFYHL
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000028048  427IIVDIPKDAFYKQPMFYHL
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000010884  434VDSTVIVDAQRDVFYKQPTFYSM
Drerio  all identical  ENSDARG00000076058  430VDSPIIVDPSKDIFYKQPTFYSM
Dmelanogaster  all conserved  FBgn0051148  475TFEEFYKQPMFYAI
Celegans  not conserved  Y4C6B.6  429TIIVNATAQEYYKQPIWHVM
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
396411HELIXlost
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 1195
cDNA position
(for ins/del: last normal base / first normal base)		 1358
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 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 RYFVKFLDAY AEHKLQFWAV TAENEPSAGL LSGYPFQCLG
FTPEHQRDFI ARDLGPTLAN STHHNVRLLM LDDQRLLLPH WAKVVLTDPE AAKYVHGIAV
HWYLDFLAPA KATLGETHRL FPNTMLFASE ACVGSKFWEQ SVRLGSWDRG MQYSHSIITN
LLYHVVGWTD WNLALNPEGG PNWVRNFVDS PIIVDITKHT FYKQPMFYHL GHFSKFIPEG
SQRVGLVASQ KNDLDAVALM HPDGSAVVVV LNRSSKDVPL TIKDPAVGFL ETISPGYSIH
TYLWRRQ*
speed 1.05 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