Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999667199 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM053161)
  • known disease mutation at this position (HGMD CM950195)
  • known disease mutation: rs17614 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:42695170G>AN/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.1715G>A
cDNA.1936G>A
g.54870G>A
AA changes R572Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 572
frameshift no
known variant Reference ID: rs121434544
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs17614 (pathogenic for Limb-girdle muscular dystrophy, type 2A|Muscular dystrophy, limb-girdle, autosomal dominant 4|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950195)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950195)
known disease mutation at this position, please check HGMD for details (HGMD ID CM053161)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950195)
known disease mutation at this position, please check HGMD for details (HGMD ID CM053161)
known disease mutation at this position, please check HGMD for details (HGMD ID CM053161)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950195)
known disease mutation at this position, please check HGMD for details (HGMD ID CM053161)
known disease mutation at this position, please check HGMD for details (HGMD ID CM053161)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950195)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.5151
5.871
(flanking)-0.380.844
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased54880wt: 0.8628 / mu: 0.8787 (marginal change - not scored)wt: TTCATCCTCCGGGTCTTCTCTGAAAAGAGGAACCTCTCTGA
mu: TTCATCCTCCAGGTCTTCTCTGAAAAGAGGAACCTCTCTGA		 ctct|GAAA
Acc marginally increased54871wt: 0.4584 / mu: 0.4744 (marginal change - not scored)wt: GAGGGGGAATTCATCCTCCGGGTCTTCTCTGAAAAGAGGAA
mu: GAGGGGGAATTCATCCTCCAGGTCTTCTCTGAAAAGAGGAA		 ccgg|GTCT
Donor gained548660.80mu: TCATCCTCCAGGTCT ATCC|tcca
distance from splice site 31
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      572YEPHQEGEFILRVFSEKRNLSEEV
mutated  all conserved    572YEPHQEGEFILQVFSEKRNLSEE
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000001534  572YEPHQEGEFILRVFSEKRNLSEE
Fcatus  all identical  ENSFCAG00000018326  410YEPHQEGEFILRVFSENRNLSEE
Mmusculus  all identical  ENSMUSG00000079110  572YEPHQEGEFILRVFSEKRNLSEE
Ggallus  all identical  ENSGALG00000009050  567YEPHQEGEFILRVFSEKRSLSEE
Trubripes  all identical  ENSTRUG00000006900  528YEPHQEGEFILRVFSEKKNTSEE
Drerio  all identical  ENSDARG00000041864  508YEPHQEGEFILRVFSEKRNTSEE
Dmelanogaster  all identical  FBgn0025866  714FDPNEEGEFIIRVFSETRNNMEE
Celegans  all identical  C06G4.2  768FEPNEEAEFMLRVYTNGFIESEE
Xtropicalis  all identical  ENSXETG00000012304  465YEPHQEGEFILRVFSEKRN
protein features
start (aa)end (aa)featuredetails 
418586REGIONDomain III.lost
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 1715
cDNA position
(for ins/del: last normal base / first normal base)		 1936
gDNA position
(for ins/del: last normal base / first normal base)		 54870
chromosomal position
(for ins/del: last normal base / first normal base)		 42695170
original gDNA sequence snippet GGAGGGGGAATTCATCCTCCGGGTCTTCTCTGAAAAGAGGA
altered gDNA sequence snippet GGAGGGGGAATTCATCCTCCAGGTCTTCTCTGAAAAGAGGA
original cDNA sequence snippet GGAGGGGGAATTCATCCTCCGGGTCTTCTCTGAAAAGAGGA
altered cDNA sequence snippet GGAGGGGGAATTCATCCTCCAGGTCTTCTCTGAAAAGAGGA
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 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 LQVFSEKRNL 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 0.98 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