Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 8.53616413265772e-07 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:223954080A>CN/A show variant in all transcripts   IGV
HGNC symbol CAPN2
Ensembl transcript ID ENST00000433674
Genbank transcript ID NM_001146068
UniProt peptide P17655
alteration type single base exchange
alteration region CDS
DNA changes c.1468A>C
cDNA.1704A>C
g.64786A>C
AA changes K490Q Score: 53 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 490
frameshift no
known variant Reference ID: rs17599
databasehomozygous (C/C)heterozygousallele carriers
1000G128782910
ExAC33262097324299
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.0261
3.1161
(flanking)3.4821
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased64778wt: 0.60 / mu: 0.71wt: CTGATTTTGTCTTTTAGGCCAAGATATCAAGTCAGATGGCT
mu: CTGATTTTGTCTTTTAGGCCAAGATATCCAGTCAGATGGCT		 gcca|AGAT
Acc increased64779wt: 0.34 / mu: 0.43wt: TGATTTTGTCTTTTAGGCCAAGATATCAAGTCAGATGGCTT
mu: TGATTTTGTCTTTTAGGCCAAGATATCCAGTCAGATGGCTT		 ccaa|GATA
distance from splice site 12
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      490LRRVLAKRQDIKSDGFSIETCKIM
mutated  all conserved    490RVLAKRQDIQSDGFSIETCKI
Ptroglodytes  all identical  ENSPTRG00000002016  568VLAKRQDIKSDGFSIETCKI
Mmulatta  all identical  ENSMMUG00000011142  564VLAKRQDIKSDGFSIETCKI
Fcatus  all identical  ENSFCAG00000010671  489LRRVLAKRQDIKSDG
Mmusculus  all identical  ENSMUSG00000026509  568VLAKRQDIKSDGFSIETCKI
Ggallus  all identical  ENSGALG00000009360  569ILAKRQDIKSDGFSIETCKI
Trubripes  all identical  ENSTRUG00000007432  591VVTRRSDIKTDGFTLTTCRT
Drerio  all identical  ENSDARG00000090014  568VIAKRKEIKTDGFSLETCRN
Dmelanogaster  not conserved  FBgn0025866  793LDHSM-RDVMVGSDGFSKDAVRS
Celegans  no alignment  C06G4.2  n/a
Xtropicalis  all identical  ENSXETG00000018599  466LQKVISKREDIKSDGFSIETCRT
protein features
start (aa)end (aa)featuredetails 
345514REGIONDomain III.lost
479492STRANDlost
495505STRANDmight get lost (downstream of altered splice site)
507509STRANDmight get lost (downstream of altered splice site)
515529REGIONLinker.might get lost (downstream of altered splice site)
527530STRANDmight get lost (downstream of altered splice site)
530700REGIONDomain IV.might get lost (downstream of altered splice site)
533541HELIXmight get lost (downstream of altered splice site)
534534CONFLICTF -> V (in Ref. 1; AAA35645 and 2; AAF99682).might get lost (downstream of altered splice site)
542542METALCalcium 5; via carbonyl oxygen (By similarity).might get lost (downstream of altered splice site)
542546STRANDmight get lost (downstream of altered splice site)
545545METALCalcium 5 (By similarity).might get lost (downstream of altered splice site)
547547METALCalcium 5; via carbonyl oxygen (By similarity).might get lost (downstream of altered splice site)
550560HELIXmight get lost (downstream of altered splice site)
552552METALCalcium 5 (By similarity).might get lost (downstream of altered splice site)
561564TURNmight get lost (downstream of altered splice site)
572605DOMAINEF-hand 1.might get lost (downstream of altered splice site)
574582HELIXmight get lost (downstream of altered splice site)
585585METALCalcium 6 (By similarity).might get lost (downstream of altered splice site)
585596CA_BIND1.might get lost (downstream of altered splice site)
586588STRANDmight get lost (downstream of altered splice site)
587587METALCalcium 6 (By similarity).might get lost (downstream of altered splice site)
589589METALCalcium 6; via carbonyl oxygen (By similarity).might get lost (downstream of altered splice site)
590592STRANDmight get lost (downstream of altered splice site)
591591METALCalcium 6; via carbonyl oxygen (By similarity).might get lost (downstream of altered splice site)
595612HELIXmight get lost (downstream of altered splice site)
596596METALCalcium 6 (By similarity).might get lost (downstream of altered splice site)
602637DOMAINEF-hand 2.might get lost (downstream of altered splice site)
615615METALCalcium 7 (By similarity).might get lost (downstream of altered splice site)
615626CA_BIND2.might get lost (downstream of altered splice site)
617617METALCalcium 7 (By similarity).might get lost (downstream of altered splice site)
619619METALCalcium 7; via carbonyl oxygen (By similarity).might get lost (downstream of altered splice site)
621621METALCalcium 7; via carbonyl oxygen (By similarity).might get lost (downstream of altered splice site)
622624STRANDmight get lost (downstream of altered splice site)
626626METALCalcium 7 (By similarity).might get lost (downstream of altered splice site)
627630HELIXmight get lost (downstream of altered splice site)
631635TURNmight get lost (downstream of altered splice site)
640650HELIXmight get lost (downstream of altered splice site)
655657STRANDmight get lost (downstream of altered splice site)
658658METALCalcium 1 (By similarity).might get lost (downstream of altered splice site)
659679HELIXmight get lost (downstream of altered splice site)
661661METALCalcium 1 (By similarity).might get lost (downstream of altered splice site)
667700DOMAINEF-hand 3.might get lost (downstream of altered splice site)
687690STRANDmight get lost (downstream of altered splice site)
691698HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1869 / 1869
position (AA) of stopcodon in wt / mu AA sequence 623 / 623
position of stopcodon in wt / mu cDNA 2105 / 2105
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 237 / 237
chromosome 1
strand 1
last intron/exon boundary 2082
theoretical NMD boundary in CDS 1795
length of CDS 1869
coding sequence (CDS) position 1468
cDNA position
(for ins/del: last normal base / first normal base)		 1704
gDNA position
(for ins/del: last normal base / first normal base)		 64786
chromosomal position
(for ins/del: last normal base / first normal base)		 223954080
original gDNA sequence snippet GTCTTTTAGGCCAAGATATCAAGTCAGATGGCTTCAGCATC
altered gDNA sequence snippet GTCTTTTAGGCCAAGATATCCAGTCAGATGGCTTCAGCATC
original cDNA sequence snippet TAGCAAAGCGCCAAGATATCAAGTCAGATGGCTTCAGCATC
altered cDNA sequence snippet TAGCAAAGCGCCAAGATATCCAGTCAGATGGCTTCAGCATC
wildtype AA sequence MEICADPQFI IGGATRTDIC QGALGDCWLL AAIASLTLNE EILARVVPLN QSFQENYAGI
FHFQFWQYGE WVEVVVDDRL PTKDGELLFV HSAEGSEFWS ALLEKAYAKI NGCYEALSGG
ATTEGFEDFT GGIAEWYELK KPPPNLFKII QKALQKGSLL GCSIDITSAA DSEAITFQKL
VKGHAYSVTG AEEVESNGSL QKLIRIRNPW GEVEWTGRWN DNCPSWNTID PEERERLTRR
HEDGEFWMSF SDFLRHYSRL EICNLTPDTL TSDTYKKWKL TKMDGNWRRG STAGGCRNYP
NTFWMNPQYL IKLEEEDEDE EDGESGCTFL VGLIQKHRRR QRKMGEDMHT IGFGIYEVPE
ELSGQTNIHL SKNFFLTNRA RERSDTFINL REVLNRFKLP PGEYILVPST FEPNKDGDFC
IRVFSEKKAD YQAVDDEIEA NLEEFDISED DIDDGFRRLF AQLAGEDAEI SAFELQTILR
RVLAKRQDIK SDGFSIETCK IMVDMLDSDG SGKLGLKEFY ILWTKIQKYQ KIYREIDVDR
SGTMNSYEMR KALEEAGFKM PCQLHQVIVA RFADDQLIID FDNFVRCLVR LETLFKIFKQ
LDPENTGTIE LDLISWLCFS VL*
mutated AA sequence MEICADPQFI IGGATRTDIC QGALGDCWLL AAIASLTLNE EILARVVPLN QSFQENYAGI
FHFQFWQYGE WVEVVVDDRL PTKDGELLFV HSAEGSEFWS ALLEKAYAKI NGCYEALSGG
ATTEGFEDFT GGIAEWYELK KPPPNLFKII QKALQKGSLL GCSIDITSAA DSEAITFQKL
VKGHAYSVTG AEEVESNGSL QKLIRIRNPW GEVEWTGRWN DNCPSWNTID PEERERLTRR
HEDGEFWMSF SDFLRHYSRL EICNLTPDTL TSDTYKKWKL TKMDGNWRRG STAGGCRNYP
NTFWMNPQYL IKLEEEDEDE EDGESGCTFL VGLIQKHRRR QRKMGEDMHT IGFGIYEVPE
ELSGQTNIHL SKNFFLTNRA RERSDTFINL REVLNRFKLP PGEYILVPST FEPNKDGDFC
IRVFSEKKAD YQAVDDEIEA NLEEFDISED DIDDGFRRLF AQLAGEDAEI SAFELQTILR
RVLAKRQDIQ SDGFSIETCK IMVDMLDSDG SGKLGLKEFY ILWTKIQKYQ KIYREIDVDR
SGTMNSYEMR KALEEAGFKM PCQLHQVIVA RFADDQLIID FDNFVRCLVR LETLFKIFKQ
LDPENTGTIE LDLISWLCFS VL*
speed 0.65 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