Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM970211)
  • known disease mutation: rs17616 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:42652260C>TN/A show variant in all transcripts   IGV
HGNC symbol CAPN3
Ensembl transcript ID ENST00000356316
Genbank transcript ID N/A
UniProt peptide P20807
alteration type single base exchange
alteration region intron
DNA changes g.11960C>T
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs121434546
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs17616 (pathogenic for Limb-girdle muscular dystrophy, type 2A) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970211)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970211)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970211)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.4281
5.351
(flanking)-0.3280.965
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased11969wt: 0.52 / mu: 0.77wt: GGATGAGACCTCTCTCTTTTATAGCCAGAAGTTCCCCATCC
mu: GGATGAGACCTTTCTCTTTTATAGCCAGAAGTTCCCCATCC		 ttta|TAGC
Acc marginally increased11967wt: 0.2034 / mu: 0.2280 (marginal change - not scored)wt: CCGGATGAGACCTCTCTCTTTTATAGCCAGAAGTTCCCCAT
mu: CCGGATGAGACCTTTCTCTTTTATAGCCAGAAGTTCCCCAT		 cttt|TATA
Acc marginally increased11968wt: 0.8776 / mu: 0.9417 (marginal change - not scored)wt: CGGATGAGACCTCTCTCTTTTATAGCCAGAAGTTCCCCATC
mu: CGGATGAGACCTTTCTCTTTTATAGCCAGAAGTTCCCCATC		 tttt|ATAG
Acc marginally increased11971wt: 0.7319 / mu: 0.7759 (marginal change - not scored)wt: ATGAGACCTCTCTCTTTTATAGCCAGAAGTTCCCCATCCAG
mu: ATGAGACCTTTCTCTTTTATAGCCAGAAGTTCCCCATCCAG		 tata|GCCA
Acc increased11970wt: 0.82 / mu: 0.91wt: GATGAGACCTCTCTCTTTTATAGCCAGAAGTTCCCCATCCA
mu: GATGAGACCTTTCTCTTTTATAGCCAGAAGTTCCCCATCCA		 ttat|AGCC
distance from splice site 5609
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
74417DOMAINCalpain catalytic.might get lost (downstream of altered splice site)
129129MUTAGENC->S: Loss of activity. No effect on CMYA5-binding.might get lost (downstream of altered splice site)
129129ACT_SITEBy similarity.might get lost (downstream of altered splice site)
334334ACT_SITEBy similarity.might get lost (downstream of altered splice site)
358358ACT_SITEBy similarity.might get lost (downstream of altered splice site)
418586REGIONDomain III.might get lost (downstream of altered splice site)
587649REGIONLinker.might get lost (downstream of altered splice site)
649683DOMAINEF-hand 1.might get lost (downstream of altered splice site)
650821REGIONDomain IV.might get lost (downstream of altered splice site)
692725DOMAINEF-hand 2.might get lost (downstream of altered splice site)
705716CA_BIND1 (Probable).might get lost (downstream of altered splice site)
722757DOMAINEF-hand 3.might get lost (downstream of altered splice site)
735746CA_BIND2 (Probable).might get lost (downstream of altered splice site)
787821DOMAINEF-hand 4.might get lost (downstream of altered splice site)
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 493 / 493
chromosome 15
strand 1
last intron/exon boundary 2653
theoretical NMD boundary in CDS 2110
length of CDS 2187
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 11960
chromosomal position
(for ins/del: last normal base / first normal base)		 42652260
original gDNA sequence snippet GTTCCCACCGGATGAGACCTCTCTCTTTTATAGCCAGAAGT
altered gDNA sequence snippet GTTCCCACCGGATGAGACCTTTCTCTTTTATAGCCAGAAGT
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MSWQISLKTQ TTQQKNEICE NPRFIIDGAN RTDICQGELG DCWFLAAIAC LTLNQHLLFR
VIPHDQSFIE NYAGIFHFQF WRYGEWVDVV IDDCLPTYNN QLVFTKSNHR NEFWSALLEK
AYAKLHGSYE ALKGGNTTEA MEDFTGGVAE FFEIRDAPSD MYKIMKKAIE RGSLMGCSID
DGTNMTYGTS PSGLNMGELI ARMVRNMDNS LLQDSDLDPR GSDERPTRTI IPVQYETRMA
CGLVRGHAYS VTGLDEVPFK GEKVKLVRLR NPWGQVEWNG SWSDRWKDWS FVDKDEKARL
QHQVTEDGEF WMSYEDFIYH FTKLEICNLT ADALQSDKLQ TWTVSVNEGR WVRGCSAGGC
RNFPDTFWTN PQYRLKLLEE DDDPDDSEVI CSFLVALMQK NRRKDRKLGA SLFTIGFAIY
EVPKEMHGNK QHLQKDFFLY NASKARSKTY INMREVSQRF RLPPSEYVIV PSTYEPHQEG
EFILRVFSEK RNLSEEVENT ISVDRPVPII FVSDRANSNK ELGVDQESEE GKGKTSPDKQ
KQSPQPQPGS SDQESEEQQQ FRNIFKQIAG DDMEICADEL KKVLNTVVNK HKDLKTHGFT
LESCRSMIAL MDTDGSGKLN LQEFHHLWNK IKAWQKIFKH YDTDQSGTIN SYEMRNAVND
AGFHLNNQLY DIITMRYADK HMNIDFDSFI CCFVRLEGMF RAFHAFDKDG DGIIKLNVLE
WLQLTMYA*
mutated AA sequence N/A
speed 0.96 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