MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 5 transcript(s)...
Querying Taster for transcript #1: ENST00000357568
Querying Taster for transcript #2: ENST00000349748
Querying Taster for transcript #3: ENST00000397163
Querying Taster for transcript #4: ENST00000356316
Querying Taster for transcript #5: ENST00000318023
MT speed 0 s - this script 6.25281 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CAPN3	disease_causing_automatic	0.999999999249689	simple_aae		affected	0	P319L	single base exchange	rs121434547		show file
CAPN3	disease_causing_automatic	0.999999999249689	simple_aae		affected	0	P319L	single base exchange	rs121434547		show file
CAPN3	disease_causing_automatic	0.999999999249689	simple_aae		affected	0	P232L	single base exchange	rs121434547		show file
CAPN3	disease_causing_automatic	0.999999999249689	simple_aae		affected	0	P319L	single base exchange	rs121434547		show file
CAPN3	disease_causing_automatic	0.999999999990907	simple_aae		affected	0	P271L	single base exchange	rs121434547		show file

Taster files

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

ENST00000357568

Genbank transcript ID

NM_024344

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

known variant

Reference ID: rs121434547

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	5	5

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

	PhyloP	PhastCons
(flanking)	3.149	1
	3.214	0.996
(flanking)	-7.776	0

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
Acc increased	44553	wt: 0.53 / mu: 0.66	wt: ACAGACAATCATTCCGGTTCAGTATGAGACAAGAATGGCCT mu: ACAGACAATCATTCTGGTTCAGTATGAGACAAGAATGGCCT	ttca\|GTAT
Donor marginally increased	44548	wt: 0.9412 / mu: 0.9546 (marginal change - not scored)	wt: ATTCCGGTTCAGTAT mu: ATTCTGGTTCAGTAT	TCCG\|gttc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

319

mutated

not conserved

319

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000001534

319

Fcatus

all identical

ENSFCAG00000018326

192

Mmusculus

all identical

ENSMUSG00000079110

319

Ggallus

all identical

ENSGALG00000009050

312

Trubripes

all identical

ENSTRUG00000006900

292

Drerio

all identical

ENSDARG00000041864

269

Dmelanogaster

not conserved

FBgn0025866

488

Celegans

not conserved

C06G4.2

525

Xtropicalis

all identical

ENSXETG00000012304

215

protein features

start (aa)	end (aa)	feature	details
74	417	DOMAIN	Calpain catalytic.	lost
334	334	ACT_SITE	By similarity.	might get lost (downstream of altered splice site)
358	358	ACT_SITE	By similarity.	might get lost (downstream of altered splice site)
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

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

strand

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 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 ERPTRTIILV 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*

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
back to results table

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

ENST00000397163

Genbank transcript ID

NM_000070

UniProt peptide

P20807

alteration type

single base exchange

alteration region

CDS

DNA changes

c.956C>T
cDNA.1175C>T
g.44547C>T

AA changes

P319L Score: 98 explain score(s)

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

319

frameshift

known variant

Reference ID: rs121434547

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	5	5

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.149	1
	3.214	0.996
(flanking)	-7.776	0

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
Acc increased	44553	wt: 0.53 / mu: 0.66	wt: ACAGACAATCATTCCGGTTCAGTATGAGACAAGAATGGCCT mu: ACAGACAATCATTCTGGTTCAGTATGAGACAAGAATGGCCT	ttca\|GTAT
Donor marginally increased	44548	wt: 0.9412 / mu: 0.9546 (marginal change - not scored)	wt: ATTCCGGTTCAGTAT mu: ATTCTGGTTCAGTAT	TCCG\|gttc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

319

mutated

not conserved

319

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000001534

319

Fcatus

all identical

ENSFCAG00000018326

192

Mmusculus

all identical

ENSMUSG00000079110

319

Ggallus

all identical

ENSGALG00000009050

312

Trubripes

all identical

ENSTRUG00000006900

292

Drerio

all identical

ENSDARG00000041864

269

Dmelanogaster

not conserved

FBgn0025866

490

Celegans

not conserved

C06G4.2

525

Xtropicalis

all identical

ENSXETG00000012304

215

protein features

start (aa)	end (aa)	feature	details
74	417	DOMAIN	Calpain catalytic.	lost
334	334	ACT_SITE	By similarity.	might get lost (downstream of altered splice site)
358	358	ACT_SITE	By similarity.	might get lost (downstream of altered splice site)
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

2466 / 2466

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

822 / 822

position of stopcodon in wt / mu cDNA

2685 / 2685

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

220 / 220

chromosome

strand

last intron/exon boundary

2659

theoretical NMD boundary in CDS

2389

length of CDS

2466

coding sequence (CDS) position

956

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

1175

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 KEMHGNKQHL QKDFFLYNAS KARSKTYINM
REVSQRFRLP PSEYVIVPST YEPHQEGEFI LRVFSEKRNL SEEVENTISV DRPVKKKKTK
PIIFVSDRAN SNKELGVDQE SEEGKGKTSP DKQKQSPQPQ PGSSDQESEE QQQFRNIFKQ
IAGDDMEICA DELKKVLNTV VNKHKDLKTH GFTLESCRSM IALMDTDGSG KLNLQEFHHL
WNKIKAWQKI FKHYDTDQSG TINSYEMRNA VNDAGFHLNN QLYDIITMRY ADKHMNIDFD
SFICCFVRLE GMFRAFHAFD KDGDGIIKLN VLEWLQLTMY A*

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 KEMHGNKQHL QKDFFLYNAS KARSKTYINM
REVSQRFRLP PSEYVIVPST YEPHQEGEFI LRVFSEKRNL SEEVENTISV DRPVKKKKTK
PIIFVSDRAN SNKELGVDQE SEEGKGKTSP DKQKQSPQPQ PGSSDQESEE QQQFRNIFKQ
IAGDDMEICA DELKKVLNTV VNKHKDLKTH GFTLESCRSM IALMDTDGSG KLNLQEFHHL
WNKIKAWQKI FKHYDTDQSG TINSYEMRNA VNDAGFHLNN QLYDIITMRY ADKHMNIDFD
SFICCFVRLE GMFRAFHAFD KDGDGIIKLN VLEWLQLTMY A*

speed

1.23 s

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

ENST00000356316

Genbank transcript ID

N/A

UniProt peptide

P20807

alteration type

single base exchange

alteration region

CDS

DNA changes

c.695C>T
cDNA.1187C>T
g.44547C>T

AA changes

P232L Score: 98 explain score(s)

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

232

frameshift

known variant

Reference ID: rs121434547

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	5	5

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.149	1
	3.214	0.996
(flanking)	-7.776	0

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
Acc increased	44553	wt: 0.53 / mu: 0.66	wt: ACAGACAATCATTCCGGTTCAGTATGAGACAAGAATGGCCT mu: ACAGACAATCATTCTGGTTCAGTATGAGACAAGAATGGCCT	ttca\|GTAT
Donor marginally increased	44548	wt: 0.9412 / mu: 0.9546 (marginal change - not scored)	wt: ATTCCGGTTCAGTAT mu: ATTCTGGTTCAGTAT	TCCG\|gttc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

232

mutated

not conserved

232

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000001534

319

Fcatus

all identical

ENSFCAG00000018326

192

Mmusculus

all identical

ENSMUSG00000079110

319

Ggallus

all identical

ENSGALG00000009050

313

Trubripes

all identical

ENSTRUG00000006900

294

Drerio

all identical

ENSDARG00000041864

294

Dmelanogaster

not conserved

FBgn0025866

500

Celegans

not conserved

C06G4.2

550

Xtropicalis

all identical

ENSXETG00000012304

215

protein features

start (aa)	end (aa)	feature	details
74	417	DOMAIN	Calpain catalytic.	lost
334	334	ACT_SITE	By similarity.	might get lost (downstream of altered splice site)
358	358	ACT_SITE	By similarity.	might get lost (downstream of altered splice site)
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

695

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

1187

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

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 ILVQYETRMA
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*

speed

1.29 s

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

known variant

Reference ID: rs121434547

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	5	5

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.149	1
	3.214	0.996
(flanking)	-7.776	0

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
Acc increased	44553	wt: 0.53 / mu: 0.66	wt: ACAGACAATCATTCCGGTTCAGTATGAGACAAGAATGGCCT mu: ACAGACAATCATTCTGGTTCAGTATGAGACAAGAATGGCCT	ttca\|GTAT
Donor marginally increased	44548	wt: 0.9412 / mu: 0.9546 (marginal change - not scored)	wt: ATTCCGGTTCAGTAT mu: ATTCTGGTTCAGTAT	TCCG\|gttc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

319

mutated

not conserved

319

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000001534

319

Fcatus

all identical

ENSFCAG00000018326

192

Mmusculus

all identical

ENSMUSG00000079110

319

Ggallus

all identical

ENSGALG00000009050

312

Trubripes

all identical

ENSTRUG00000006900

292

Drerio

all identical

ENSDARG00000041864

269

Dmelanogaster

not conserved

FBgn0025866

488

Celegans

not conserved

C06G4.2

525

Xtropicalis

all identical

ENSXETG00000012304

215

protein features

start (aa)	end (aa)	feature	details
74	417	DOMAIN	Calpain catalytic.	lost
334	334	ACT_SITE	By similarity.	might get lost (downstream of altered splice site)
358	358	ACT_SITE	By similarity.	might get lost (downstream of altered splice site)
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

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

strand

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

1.25 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999990907 (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

ENST00000349748

Genbank transcript ID

NM_173087

UniProt peptide

P20807

alteration type

single base exchange

alteration region

CDS

DNA changes

c.812C>T
cDNA.1033C>T
g.44547C>T

AA changes

P271L Score: 98 explain score(s)

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

271

frameshift

known variant

Reference ID: rs121434547

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	5	5

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.149	1
	3.214	0.996
(flanking)	-7.776	0

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
Acc increased	44553	wt: 0.53 / mu: 0.66	wt: ACAGACAATCATTCCGGTTCAGTATGAGACAAGAATGGCCT mu: ACAGACAATCATTCTGGTTCAGTATGAGACAAGAATGGCCT	ttca\|GTAT
Donor marginally increased	44548	wt: 0.9412 / mu: 0.9546 (marginal change - not scored)	wt: ATTCCGGTTCAGTAT mu: ATTCTGGTTCAGTAT	TCCG\|gttc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

271

mutated

not conserved

271

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000001534

304

DSDLDPRASVERPTR

Fcatus

all identical

ENSFCAG00000018326

184

DSDDRPTR

Mmusculus

all identical

ENSMUSG00000079110

304

DSDLDPRGSDDRPSR

Ggallus

all identical

ENSGALG00000009050

298

STVDYQGTDERPAW

Trubripes

all identical

ENSTRUG00000006900

273

Drerio

all identical

ENSDARG00000041864

252

Dmelanogaster

all identical

FBgn0025866

456

Celegans

all identical

C06G4.2

513

Xtropicalis

all identical

ENSXETG00000012304

184

DAIMKMIESVGDTRPDTNGRGQPPKPVA

protein features

start (aa)	end (aa)	feature	details
74	417	DOMAIN	Calpain catalytic.	lost
334	334	ACT_SITE	By similarity.	might get lost (downstream of altered splice site)
358	358	ACT_SITE	By similarity.	might get lost (downstream of altered splice site)
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

2190 / 2190

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

730 / 730

position of stopcodon in wt / mu cDNA

2411 / 2411

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

strand

last intron/exon boundary

2385

theoretical NMD boundary in CDS

2113

length of CDS

2190

coding sequence (CDS) position

812

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

1033

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

CTCCATTGATACAATCATTCCGGTTCAGTATGAGACAAGAA

altered cDNA sequence snippet

CTCCATTGATACAATCATTCTGGTTCAGTATGAGACAAGAA

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 LMGCSIDTII PVQYETRMAC GLVRGHAYSV TGLDEVPFKG
EKVKLVRLRN PWGQVEWNGS WSDRWKDWSF VDKDEKARLQ HQVTEDGEFW MSYEDFIYHF
TKLEICNLTA DALQSDKLQT WTVSVNEGRW VRGCSAGGCR NFPDTFWTNP QYRLKLLEED
DDPDDSEVIC SFLVALMQKN RRKDRKLGAS LFTIGFAIYE VPKEMHGNKQ HLQKDFFLYN
ASKARSKTYI NMREVSQRFR LPPSEYVIVP STYEPHQEGE FILRVFSEKR NLSEEVENTI
SVDRPVPQPG SSDQESEEQQ QFRNIFKQIA GDDMEICADE LKKVLNTVVN KHKDLKTHGF
TLESCRSMIA LMDTDGSGKL NLQEFHHLWN KIKAWQKIFK HYDTDQSGTI NSYEMRNAVN
DAGFHLNNQL YDIITMRYAD KHMNIDFDSF ICCFVRLEGM FRAFHAFDKD GDGIIKLNVL
EWLQLTMYA*

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 LMGCSIDTII LVQYETRMAC GLVRGHAYSV TGLDEVPFKG
EKVKLVRLRN PWGQVEWNGS WSDRWKDWSF VDKDEKARLQ HQVTEDGEFW MSYEDFIYHF
TKLEICNLTA DALQSDKLQT WTVSVNEGRW VRGCSAGGCR NFPDTFWTNP QYRLKLLEED
DDPDDSEVIC SFLVALMQKN RRKDRKLGAS LFTIGFAIYE VPKEMHGNKQ HLQKDFFLYN
ASKARSKTYI NMREVSQRFR LPPSEYVIVP STYEPHQEGE FILRVFSEKR NLSEEVENTI
SVDRPVPQPG SSDQESEEQQ QFRNIFKQIA GDDMEICADE LKKVLNTVVN KHKDLKTHGF
TLESCRSMIA LMDTDGSGKL NLQEFHHLWN KIKAWQKIFK HYDTDQSGTI NSYEMRNAVN
DAGFHLNNQL YDIITMRYAD KHMNIDFDSF ICCFVRLEGM FRAFHAFDKD GDGIIKLNVL
EWLQLTMYA*

speed

1.34 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems