Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999529268 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM061668)
  • known disease mutation at this position (HGMD CM950197)
  • known disease mutation: rs17613 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:42703124G>AN/A show variant in all transcripts   IGV
HGNC symbol CAPN3
Ensembl transcript ID ENST00000397200
Genbank transcript ID NM_173088
UniProt peptide P20807
alteration type single base exchange
alteration region CDS
DNA changes c.770G>A
cDNA.939G>A
g.62824G>A
AA changes R257Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 257
frameshift no
known variant Reference ID: rs80338802
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC066

known disease mutation: rs17613 (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 CM950197)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061668)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950197)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.3911
6.0831
(flanking)0.0130.981
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased62828wt: 0.26 / mu: 0.67wt: CGGTACGCAGACAAA
mu: CAGTACGCAGACAAA		 GTAC|gcag
Donor gained628190.41mu: ATTACCATGCAGTAC TACC|atgc
distance from splice site 43
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      257LNNQLYDIITMRYADKHMNIDFDS
mutated  all conserved    257LNNQLYDIITMQYADKHMNIDFD
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000001534  769LNNQLYDIITMRYADKHMNIDFD
Fcatus  all identical  ENSFCAG00000018326  603LNSQLYDIITMRYADKHMNIDFD
Mmusculus  all identical  ENSMUSG00000079110  769LNSQLYDIITMRYADKHMNIDFD
Ggallus  all identical  ENSGALG00000009050  760LNNQLYDIITMRYADKNMNIDFD
Trubripes  all identical  ENSTRUG00000006900  706LNNQLYDIITMRYANENMNIDFD
Drerio  all identical  ENSDARG00000041864  673LNNQLYDIITMRYANESMNVDFE
Dmelanogaster  all identical  FBgn0025866  873LNALAHRYGSREGQIPFD
Celegans  no alignment  C06G4.2  n/a
Xtropicalis  all identical  ENSXETG00000012304  664LNNQLYDIITMRYANKRMDLDFD
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 930 / 930
position (AA) of stopcodon in wt / mu AA sequence 310 / 310
position of stopcodon in wt / mu cDNA 1099 / 1099
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 170 / 170
chromosome 15
strand 1
last intron/exon boundary 1073
theoretical NMD boundary in CDS 853
length of CDS 930
coding sequence (CDS) position 770
cDNA position
(for ins/del: last normal base / first normal base)		 939
gDNA position
(for ins/del: last normal base / first normal base)		 62824
chromosomal position
(for ins/del: last normal base / first normal base)		 42703124
original gDNA sequence snippet CTATGACATCATTACCATGCGGTACGCAGACAAACACATGA
altered gDNA sequence snippet CTATGACATCATTACCATGCAGTACGCAGACAAACACATGA
original cDNA sequence snippet CTATGACATCATTACCATGCGGTACGCAGACAAACACATGA
altered cDNA sequence snippet CTATGACATCATTACCATGCAGTACGCAGACAAACACATGA
wildtype AA sequence MHGNKQHLQK DFFLYNASKA RSKTYINMRE VSQRFRLPPS EYVIVPSTYE PHQEGEFILR
VFSEKRNLSE EVENTISVDR PVKKKKTKPI IFVSDRANSN KELGVDQESE EGKGKTSPDK
QKQSPQPQPG SSDQESEEQQ QFRNIFKQIA GDDMEICADE LKKVLNTVVN KHKDLKTHGF
TLESCRSMIA LMDTDGSGKL NLQEFHHLWN KIKAWQKIFK HYDTDQSGTI NSYEMRNAVN
DAGFHLNNQL YDIITMRYAD KHMNIDFDSF ICCFVRLEGM FRAFHAFDKD GDGIIKLNVL
EWLQLTMYA*
mutated AA sequence MHGNKQHLQK DFFLYNASKA RSKTYINMRE VSQRFRLPPS EYVIVPSTYE PHQEGEFILR
VFSEKRNLSE EVENTISVDR PVKKKKTKPI IFVSDRANSN KELGVDQESE EGKGKTSPDK
QKQSPQPQPG SSDQESEEQQ QFRNIFKQIA GDDMEICADE LKKVLNTVVN KHKDLKTHGF
TLESCRSMIA LMDTDGSGKL NLQEFHHLWN KIKAWQKIFK HYDTDQSGTI NSYEMRNAVN
DAGFHLNNQL YDIITMQYAD KHMNIDFDSF ICCFVRLEGM FRAFHAFDKD GDGIIKLNVL
EWLQLTMYA*
speed 0.58 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