mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999999341944 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM970217)
known disease mutation: rs17622 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr15:42693953G>AN/A show variant in all transcripts IGV

HGNC symbol

CAPN3

Ensembl transcript ID

ENST00000356316

Genbank transcript ID

N/A

UniProt peptide

P20807

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1208G>A
cDNA.1700G>A
g.53653G>A

AA changes

R403Q Score: 43 explain score(s)

position(s) of altered AA
if AA alteration in CDS

403

frameshift

known variant

Reference ID: rs121434548

database	homozygous (A/A)	heterozygous	allele carriers
1000G	0	1	1
ExAC	0	7	7

known disease mutation: rs17622 (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 CM970217)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970217)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970217)

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gabp, Transcription Factor, Gabp TF binding
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.181	0.996
	5.734	1
(flanking)	0.594	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Donor marginally increased	53651	wt: 0.9683 / mu: 0.9814 (marginal change - not scored)	wt: AACCGGCGGAAGGAC mu: AACCGGCAGAAGGAC	CCGG\|cgga
Donor increased	53650	wt: 0.32 / mu: 0.37	wt: GAACCGGCGGAAGGA mu: GAACCGGCAGAAGGA	ACCG\|gcgg
Donor gained	53649	0.40	mu: AGAACCGGCAGAAGG	AACC\|ggca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

403

mutated

all conserved

403

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000001534

490

Fcatus

all identical

ENSFCAG00000018326

363

Mmusculus

all identical

ENSMUSG00000079110

490

Ggallus

all identical

ENSGALG00000009050

483

Trubripes

all identical

ENSTRUG00000006900

446

Drerio

all identical

ENSDARG00000041864

426

Dmelanogaster

all identical

FBgn0025866

635

Celegans

all identical

C06G4.2

692

Xtropicalis

all identical

ENSXETG00000012304

383

protein features

start (aa)	end (aa)	feature	details
74	417	DOMAIN	Calpain catalytic.	lost
418	586	REGION	Domain III.	might get lost (downstream of altered splice site)
587	649	REGION	Linker.	might get lost (downstream of altered splice site)
649	683	DOMAIN	EF-hand 1.	might get lost (downstream of altered splice site)
650	821	REGION	Domain IV.	might get lost (downstream of altered splice site)
692	725	DOMAIN	EF-hand 2.	might get lost (downstream of altered splice site)
705	716	CA_BIND	1 (Probable).	might get lost (downstream of altered splice site)
722	757	DOMAIN	EF-hand 3.	might get lost (downstream of altered splice site)
735	746	CA_BIND	2 (Probable).	might get lost (downstream of altered splice site)
787	821	DOMAIN	EF-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

2187 / 2187

position (AA) of stopcodon in wt / mu AA sequence

729 / 729

position of stopcodon in wt / mu cDNA

2679 / 2679

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

493 / 493

chromosome

strand

last intron/exon boundary

2653

theoretical NMD boundary in CDS

2110

length of CDS

2187

coding sequence (CDS) position

1208

cDNA position
(for ins/del: last normal base / first normal base)

1700

gDNA position
(for ins/del: last normal base / first normal base)

53653

chromosomal position
(for ins/del: last normal base / first normal base)

42693953

original gDNA sequence snippet

CCTGATGCAGAAGAACCGGCGGAAGGACCGGAAGCTAGGGG

altered gDNA sequence snippet

CCTGATGCAGAAGAACCGGCAGAAGGACCGGAAGCTAGGGG

original cDNA sequence snippet

CCTGATGCAGAAGAACCGGCGGAAGGACCGGAAGCTAGGGG

altered cDNA sequence snippet

CCTGATGCAGAAGAACCGGCAGAAGGACCGGAAGCTAGGGG

wildtype AA sequence

MSWQISLKTQ TTQQKNEICE NPRFIIDGAN RTDICQGELG DCWFLAAIAC LTLNQHLLFR
VIPHDQSFIE NYAGIFHFQF WRYGEWVDVV IDDCLPTYNN QLVFTKSNHR NEFWSALLEK
AYAKLHGSYE ALKGGNTTEA MEDFTGGVAE FFEIRDAPSD MYKIMKKAIE RGSLMGCSID
DGTNMTYGTS PSGLNMGELI ARMVRNMDNS LLQDSDLDPR GSDERPTRTI IPVQYETRMA
CGLVRGHAYS VTGLDEVPFK GEKVKLVRLR NPWGQVEWNG SWSDRWKDWS FVDKDEKARL
QHQVTEDGEF WMSYEDFIYH FTKLEICNLT ADALQSDKLQ TWTVSVNEGR WVRGCSAGGC
RNFPDTFWTN PQYRLKLLEE DDDPDDSEVI CSFLVALMQK NRRKDRKLGA SLFTIGFAIY
EVPKEMHGNK QHLQKDFFLY NASKARSKTY INMREVSQRF RLPPSEYVIV PSTYEPHQEG
EFILRVFSEK RNLSEEVENT ISVDRPVPII FVSDRANSNK ELGVDQESEE GKGKTSPDKQ
KQSPQPQPGS SDQESEEQQQ FRNIFKQIAG DDMEICADEL KKVLNTVVNK HKDLKTHGFT
LESCRSMIAL MDTDGSGKLN LQEFHHLWNK IKAWQKIFKH YDTDQSGTIN SYEMRNAVND
AGFHLNNQLY DIITMRYADK HMNIDFDSFI CCFVRLEGMF RAFHAFDKDG DGIIKLNVLE
WLQLTMYA*

mutated AA sequence

MSWQISLKTQ TTQQKNEICE NPRFIIDGAN RTDICQGELG DCWFLAAIAC LTLNQHLLFR
VIPHDQSFIE NYAGIFHFQF WRYGEWVDVV IDDCLPTYNN QLVFTKSNHR NEFWSALLEK
AYAKLHGSYE ALKGGNTTEA MEDFTGGVAE FFEIRDAPSD MYKIMKKAIE RGSLMGCSID
DGTNMTYGTS PSGLNMGELI ARMVRNMDNS LLQDSDLDPR GSDERPTRTI IPVQYETRMA
CGLVRGHAYS VTGLDEVPFK GEKVKLVRLR NPWGQVEWNG SWSDRWKDWS FVDKDEKARL
QHQVTEDGEF WMSYEDFIYH FTKLEICNLT ADALQSDKLQ TWTVSVNEGR WVRGCSAGGC
RNFPDTFWTN PQYRLKLLEE DDDPDDSEVI CSFLVALMQK NRQKDRKLGA SLFTIGFAIY
EVPKEMHGNK QHLQKDFFLY NASKARSKTY INMREVSQRF RLPPSEYVIV PSTYEPHQEG
EFILRVFSEK RNLSEEVENT ISVDRPVPII FVSDRANSNK ELGVDQESEE GKGKTSPDKQ
KQSPQPQPGS SDQESEEQQQ FRNIFKQIAG DDMEICADEL KKVLNTVVNK HKDLKTHGFT
LESCRSMIAL MDTDGSGKLN LQEFHHLWNK IKAWQKIFKH YDTDQSGTIN SYEMRNAVND
AGFHLNNQLY DIITMRYADK HMNIDFDSFI CCFVRLEGMF RAFHAFDKDG DGIIKLNVLE
WLQLTMYA*

speed

1.28 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