Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999612022 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • 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 ENST00000357568
Genbank transcript ID NM_024344
UniProt peptide P20807
alteration type single base exchange
alteration region CDS
DNA changes c.257C>T
cDNA.478C>T
g.11960C>T
AA changes S86F Score: 155 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 86
frameshift no
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 53
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      86YVDPEFPPDETSLFYSQKFPIQFV
mutated  not conserved    86YVDPEFPPDETFLFYSQKFPIQF
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000001534  86YVDPEFPPDETSLFYSQKFPIQF
Fcatus  no alignment  ENSFCAG00000018326  n/a
Mmusculus  all identical  ENSMUSG00000079110  86YLDPEFPPDETSLFYSQKFPIQF
Ggallus  all identical  ENSGALG00000009050  80YEDPDFPPNETSLFYSQKVPIKF
Trubripes  all identical  ENSTRUG00000006900  62FEDDTFPATVESLGYKELGHKSNKVKNI
Drerio  all identical  ENSDARG00000041864  62FEDETFPATVDSLGYKELGHKSNKVKNI
Dmelanogaster  all identical  FBgn0025866  271FEDPDFPATNASLMYSRRPDRYY
Celegans  all identical  C06G4.2  328PQFLANDSSLFFSKRPPKRV
Xtropicalis  no alignment  ENSXETG00000012304  n/a
protein features
start (aa)end (aa)featuredetails 
74417DOMAINCalpain catalytic.lost
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 normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2448 / 2448
position (AA) of stopcodon in wt / mu AA sequence 816 / 816
position of stopcodon in wt / mu cDNA 2669 / 2669
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 222 / 222
chromosome 15
strand 1
last intron/exon boundary 2643
theoretical NMD boundary in CDS 2371
length of CDS 2448
coding sequence (CDS) position 257
cDNA position
(for ins/del: last normal base / first normal base)		 478
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 GTTCCCACCGGATGAGACCTCTCTCTTTTATAGCCAGAAGT
altered cDNA sequence snippet GTTCCCACCGGATGAGACCTTTCTCTTTTATAGCCAGAAGT
wildtype AA sequence MPTVISASVA PRTAAEPRSP GPVPHPAQSK ATEAGGGNPS GIYSAIISRN FPIIGVKEKT
FEQLHKKCLE KKVLYVDPEF PPDETSLFYS QKFPIQFVWK RPPEICENPR FIIDGANRTD
ICQGELGDCW FLAAIACLTL NQHLLFRVIP HDQSFIENYA GIFHFQFWRY GEWVDVVIDD
CLPTYNNQLV FTKSNHRNEF WSALLEKAYA KLHGSYEALK GGNTTEAMED FTGGVAEFFE
IRDAPSDMYK IMKKAIERGS LMGCSIDDGT NMTYGTSPSG LNMGELIARM VRNMDNSLLQ
DSDLDPRGSD ERPTRTIIPV QYETRMACGL VRGHAYSVTG LDEVPFKGEK VKLVRLRNPW
GQVEWNGSWS DRWKDWSFVD KDEKARLQHQ VTEDGEFWMS YEDFIYHFTK LEICNLTADA
LQSDKLQTWT VSVNEGRWVR GCSAGGCRNF PDTFWTNPQY RLKLLEEDDD PDDSEVICSF
LVALMQKNRR KDRKLGASLF TIGFAIYEVP KEMHGNKQHL QKDFFLYNAS KARSKTYINM
REVSQRFRLP PSEYVIVPST YEPHQEGEFI LRVFSEKRNL SEEVENTISV DRPVPIIFVS
DRANSNKELG VDQESEEGKG KTSPDKQKQS PQPQPGSSDQ ESEEQQQFRN IFKQIAGDDM
EICADELKKV LNTVVNKHKD LKTHGFTLES CRSMIALMDT DGSGKLNLQE FHHLWNKIKA
WQKIFKHYDT DQSGTINSYE MRNAVNDAGF HLNNQLYDII TMRYADKHMN IDFDSFICCF
VRLEGMFRAF HAFDKDGDGI IKLNVLEWLQ LTMYA*
mutated AA sequence MPTVISASVA PRTAAEPRSP GPVPHPAQSK ATEAGGGNPS GIYSAIISRN FPIIGVKEKT
FEQLHKKCLE KKVLYVDPEF PPDETFLFYS QKFPIQFVWK RPPEICENPR FIIDGANRTD
ICQGELGDCW FLAAIACLTL NQHLLFRVIP HDQSFIENYA GIFHFQFWRY GEWVDVVIDD
CLPTYNNQLV FTKSNHRNEF WSALLEKAYA KLHGSYEALK GGNTTEAMED FTGGVAEFFE
IRDAPSDMYK IMKKAIERGS LMGCSIDDGT NMTYGTSPSG LNMGELIARM VRNMDNSLLQ
DSDLDPRGSD ERPTRTIIPV QYETRMACGL VRGHAYSVTG LDEVPFKGEK VKLVRLRNPW
GQVEWNGSWS DRWKDWSFVD KDEKARLQHQ VTEDGEFWMS YEDFIYHFTK LEICNLTADA
LQSDKLQTWT VSVNEGRWVR GCSAGGCRNF PDTFWTNPQY RLKLLEEDDD PDDSEVICSF
LVALMQKNRR KDRKLGASLF TIGFAIYEVP KEMHGNKQHL QKDFFLYNAS KARSKTYINM
REVSQRFRLP PSEYVIVPST YEPHQEGEFI LRVFSEKRNL SEEVENTISV DRPVPIIFVS
DRANSNKELG VDQESEEGKG KTSPDKQKQS PQPQPGSSDQ ESEEQQQFRN IFKQIAGDDM
EICADELKKV LNTVVNKHKD LKTHGFTLES CRSMIALMDT DGSGKLNLQE FHHLWNKIKA
WQKIFKHYDT DQSGTINSYE MRNAVNDAGF HLNNQLYDII TMRYADKHMN IDFDSFICCF
VRLEGMFRAF HAFDKDGDGI IKLNVLEWLQ LTMYA*
speed 0.73 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