Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999990907 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM970213)
  • known disease mutation: rs17617 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:42684847C>TN/A show variant in all transcripts   IGV
HGNC symbol CAPN3
Ensembl transcript ID ENST00000349748
Genbank transcript ID NM_173087
UniProt peptide P20807
alteration type single base exchange
alteration region CDS
DNA changes c.812C>T
cDNA.1033C>T
g.44547C>T
AA changes P271L Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 271
frameshift no
known variant Reference ID: rs121434547
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC055

known disease mutation: rs17617 (pathogenic for Limb-girdle muscular dystrophy, type 2A|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970213)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970213)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970213)
regulatory features Cmyc, Transcription Factor, Cmyc TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
HNF4A, Transcription Factor, HNF4A Transcription Factor Binding
HNF4G, Transcription Factor, HNF4G Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
RXRA, Transcription Factor, RXRA Transcription Factor Binding
SP1, Transcription Factor, SP1 Transcription Factor Binding
USF1, Transcription Factor, USF1 Transcription Factor Binding
p300, Transcription Factor, p300 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)3.1491
3.2140.996
(flanking)-7.7760
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased44553wt: 0.53 / mu: 0.66wt: ACAGACAATCATTCCGGTTCAGTATGAGACAAGAATGGCCT
mu: ACAGACAATCATTCTGGTTCAGTATGAGACAAGAATGGCCT		 ttca|GTAT
Donor marginally increased44548wt: 0.9412 / mu: 0.9546 (marginal change - not scored)wt: ATTCCGGTTCAGTAT
mu: ATTCTGGTTCAGTAT		 TCCG|gttc
distance from splice site 11
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      271SLMGCSIDTIIPVQYETRMACGLV
mutated  not conserved    271SLMGCSIDTIILVQYETRMACGL
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000001534  304DSDLDPRASVERPTRTIVPVQYETRMACGL
Fcatus  all identical  ENSFCAG00000018326  184DSDDRPTRTIVPVQYETRMACGL
Mmusculus  all identical  ENSMUSG00000079110  304DSDLDPRGSDDRPSRTIVPVQYETRMACGL
Ggallus  all identical  ENSGALG00000009050  298STVDYQGTDERPAWTIMPMQYETRMSCGL
Trubripes  all identical  ENSTRUG00000006900  273LQSLVPARFETRTATGL
Drerio  all identical  ENSDARG00000041864  252SLMGCSIDSLVPARFETRTATGL
Dmelanogaster  all identical  FBgn0025866  456SMMGCSLEP-DPHVLEAETPQGL
Celegans  all identical  C06G4.2  513SLFGCSIEA-DPNVWEAKMSNGL
Xtropicalis  all identical  ENSXETG00000012304  184DAIMKMIESVGDTRPDTNGRGQPPKPVATLVPVQLETRMANGL
protein features
start (aa)end (aa)featuredetails 
74417DOMAINCalpain catalytic.lost
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 2190 / 2190
position (AA) of stopcodon in wt / mu AA sequence 730 / 730
position of stopcodon in wt / mu cDNA 2411 / 2411
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 2385
theoretical NMD boundary in CDS 2113
length of CDS 2190
coding sequence (CDS) position 812
cDNA position
(for ins/del: last normal base / first normal base)		 1033
gDNA position
(for ins/del: last normal base / first normal base)		 44547
chromosomal position
(for ins/del: last normal base / first normal base)		 42684847
original gDNA sequence snippet TGCTCTACAGACAATCATTCCGGTTCAGTATGAGACAAGAA
altered gDNA sequence snippet TGCTCTACAGACAATCATTCTGGTTCAGTATGAGACAAGAA
original cDNA sequence snippet CTCCATTGATACAATCATTCCGGTTCAGTATGAGACAAGAA
altered cDNA sequence snippet CTCCATTGATACAATCATTCTGGTTCAGTATGAGACAAGAA
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 LMGCSIDTII PVQYETRMAC GLVRGHAYSV TGLDEVPFKG
EKVKLVRLRN PWGQVEWNGS WSDRWKDWSF VDKDEKARLQ HQVTEDGEFW MSYEDFIYHF
TKLEICNLTA DALQSDKLQT WTVSVNEGRW VRGCSAGGCR NFPDTFWTNP QYRLKLLEED
DDPDDSEVIC SFLVALMQKN RRKDRKLGAS LFTIGFAIYE VPKEMHGNKQ HLQKDFFLYN
ASKARSKTYI NMREVSQRFR LPPSEYVIVP STYEPHQEGE FILRVFSEKR NLSEEVENTI
SVDRPVPQPG SSDQESEEQQ QFRNIFKQIA GDDMEICADE LKKVLNTVVN KHKDLKTHGF
TLESCRSMIA LMDTDGSGKL NLQEFHHLWN KIKAWQKIFK HYDTDQSGTI NSYEMRNAVN
DAGFHLNNQL YDIITMRYAD KHMNIDFDSF ICCFVRLEGM FRAFHAFDKD GDGIIKLNVL
EWLQLTMYA*
mutated 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 LMGCSIDTII LVQYETRMAC GLVRGHAYSV TGLDEVPFKG
EKVKLVRLRN PWGQVEWNGS WSDRWKDWSF VDKDEKARLQ HQVTEDGEFW MSYEDFIYHF
TKLEICNLTA DALQSDKLQT WTVSVNEGRW VRGCSAGGCR NFPDTFWTNP QYRLKLLEED
DDPDDSEVIC SFLVALMQKN RRKDRKLGAS LFTIGFAIYE VPKEMHGNKQ HLQKDFFLYN
ASKARSKTYI NMREVSQRFR LPPSEYVIVP STYEPHQEGE FILRVFSEKR NLSEEVENTI
SVDRPVPQPG SSDQESEEQQ QFRNIFKQIA GDDMEICADE LKKVLNTVVN KHKDLKTHGF
TLESCRSMIA LMDTDGSGKL NLQEFHHLWN KIKAWQKIFK HYDTDQSGTI NSYEMRNAVN
DAGFHLNNQL YDIITMRYAD KHMNIDFDSF ICCFVRLEGM FRAFHAFDKD GDGIIKLNVL
EWLQLTMYA*
speed 0.67 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