Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999249689 (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 ENST00000318023
Genbank transcript ID N/A
UniProt peptide P20807
alteration type single base exchange
alteration region CDS
DNA changes c.956C>T
cDNA.1177C>T
g.44547C>T
AA changes P319L Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 319
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      319GSDERPTRTIIPVQYETRMACGLV
mutated  not conserved    319GSDERPTRTIILVQYETRMACGL
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000001534  319ASVERPTRTIVPVQYETRMACGL
Fcatus  all identical  ENSFCAG00000018326  192DSDDRPTRTIVPVQYETRMACGL
Mmusculus  all identical  ENSMUSG00000079110  319GSDDRPSRTIVPVQYETRMACGL
Ggallus  all identical  ENSGALG00000009050  312GTDERPAWTIMPMQYETRMSCGL
Trubripes  all identical  ENSTRUG00000006900  292------LQSLVPARFETRTATGL
Drerio  all identical  ENSDARG00000041864  269--------SLVPARFETRTATGL
Dmelanogaster  not conserved  FBgn0025866  488---------------------GL
Celegans  not conserved  C06G4.2  525-------------
Xtropicalis  all identical  ENSXETG00000012304  215GQPPKPVATLVPVQLETRMANGL
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 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 956
cDNA position
(for ins/del: last normal base / first normal base)		 1177
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 ACCGACCCGGACAATCATTCCGGTTCAGTATGAGACAAGAA
altered cDNA sequence snippet ACCGACCCGGACAATCATTCTGGTTCAGTATGAGACAAGAA
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 HQMHGNKQHL 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 PPDETSLFYS QKFPIQFVWK RPPEICENPR FIIDGANRTD
ICQGELGDCW FLAAIACLTL NQHLLFRVIP HDQSFIENYA GIFHFQFWRY GEWVDVVIDD
CLPTYNNQLV FTKSNHRNEF WSALLEKAYA KLHGSYEALK GGNTTEAMED FTGGVAEFFE
IRDAPSDMYK IMKKAIERGS LMGCSIDDGT NMTYGTSPSG LNMGELIARM VRNMDNSLLQ
DSDLDPRGSD ERPTRTIILV QYETRMACGL VRGHAYSVTG LDEVPFKGEK VKLVRLRNPW
GQVEWNGSWS DRWKDWSFVD KDEKARLQHQ VTEDGEFWMS YEDFIYHFTK LEICNLTADA
LQSDKLQTWT VSVNEGRWVR GCSAGGCRNF PDTFWTNPQY RLKLLEEDDD PDDSEVICSF
LVALMQKNRR KDRKLGASLF TIGFAIYEVP HQMHGNKQHL 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 0.74 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