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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000295006
Querying Taster for transcript #2: ENST00000433674
MT speed 0 s - this script 3.331315 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CAPN2	polymorphism_automatic	0.999996133913102	simple_aae		affected		K568Q	single base exchange	rs17599		show file
CAPN2	polymorphism_automatic	0.999999146383587	simple_aae		affected		K490Q	single base exchange	rs17599		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 3.86608689769464e-06 (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

ENST00000295006

Genbank transcript ID

NM_001748

UniProt peptide

P17655

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1702A>C
cDNA.2011A>C
g.64786A>C

AA changes

K568Q Score: 53 explain score(s)

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

568

frameshift

known variant

Reference ID: rs17599

database	homozygous (C/C)	heterozygous	allele carriers
1000G	128	782	910
ExAC	3326	20973	24299

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.026	1
	3.116	1
(flanking)	3.482	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
Acc increased	64778	wt: 0.60 / mu: 0.71	wt: CTGATTTTGTCTTTTAGGCCAAGATATCAAGTCAGATGGCT mu: CTGATTTTGTCTTTTAGGCCAAGATATCCAGTCAGATGGCT	gcca\|AGAT
Acc increased	64779	wt: 0.34 / mu: 0.43	wt: TGATTTTGTCTTTTAGGCCAAGATATCAAGTCAGATGGCTT mu: TGATTTTGTCTTTTAGGCCAAGATATCCAGTCAGATGGCTT	ccaa\|GATA

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

568

mutated

all conserved

568

Ptroglodytes

all identical

ENSPTRG00000002016

568

Mmulatta

all identical

ENSMMUG00000011142

564

Fcatus

all identical

ENSFCAG00000010671

489

Mmusculus

all identical

ENSMUSG00000026509

568

Ggallus

all identical

ENSGALG00000009360

569

Trubripes

all identical

ENSTRUG00000007432

591

Drerio

all identical

ENSDARG00000090014

568

Dmelanogaster

not conserved

FBgn0025866

793

Celegans

no alignment

C06G4.2

n/a

Xtropicalis

all identical

ENSXETG00000018599

466

protein features

start (aa)	end (aa)	feature	details
530	700	REGION	Domain IV.	lost
561	564	TURN		might get lost (downstream of altered splice site)
572	605	DOMAIN	EF-hand 1.	might get lost (downstream of altered splice site)
574	582	HELIX		might get lost (downstream of altered splice site)
585	585	METAL	Calcium 6 (By similarity).	might get lost (downstream of altered splice site)
585	596	CA_BIND	1.	might get lost (downstream of altered splice site)
586	588	STRAND		might get lost (downstream of altered splice site)
587	587	METAL	Calcium 6 (By similarity).	might get lost (downstream of altered splice site)
589	589	METAL	Calcium 6; via carbonyl oxygen (By similarity).	might get lost (downstream of altered splice site)
590	592	STRAND		might get lost (downstream of altered splice site)
591	591	METAL	Calcium 6; via carbonyl oxygen (By similarity).	might get lost (downstream of altered splice site)
595	612	HELIX		might get lost (downstream of altered splice site)
596	596	METAL	Calcium 6 (By similarity).	might get lost (downstream of altered splice site)
602	637	DOMAIN	EF-hand 2.	might get lost (downstream of altered splice site)
615	615	METAL	Calcium 7 (By similarity).	might get lost (downstream of altered splice site)
615	626	CA_BIND	2.	might get lost (downstream of altered splice site)
617	617	METAL	Calcium 7 (By similarity).	might get lost (downstream of altered splice site)
619	619	METAL	Calcium 7; via carbonyl oxygen (By similarity).	might get lost (downstream of altered splice site)
621	621	METAL	Calcium 7; via carbonyl oxygen (By similarity).	might get lost (downstream of altered splice site)
622	624	STRAND		might get lost (downstream of altered splice site)
626	626	METAL	Calcium 7 (By similarity).	might get lost (downstream of altered splice site)
627	630	HELIX		might get lost (downstream of altered splice site)
631	635	TURN		might get lost (downstream of altered splice site)
640	650	HELIX		might get lost (downstream of altered splice site)
655	657	STRAND		might get lost (downstream of altered splice site)
658	658	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
659	679	HELIX		might get lost (downstream of altered splice site)
661	661	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
667	700	DOMAIN	EF-hand 3.	might get lost (downstream of altered splice site)
687	690	STRAND		might get lost (downstream of altered splice site)
691	698	HELIX		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2103 / 2103

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

701 / 701

position of stopcodon in wt / mu cDNA

2412 / 2412

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

310 / 310

chromosome

strand

last intron/exon boundary

2389

theoretical NMD boundary in CDS

2029

length of CDS

2103

coding sequence (CDS) position

1702

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

2011

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

MAGIAAKLAK DREAAEGLGS HDRAIKYLNQ DYEALRNECL EAGTLFQDPS FPAIPSALGF
KELGPYSSKT RGIEWKRPTE ICADPQFIIG GATRTDICQG ALGDCWLLAA IASLTLNEEI
LARVVPLNQS FQENYAGIFH FQFWQYGEWV EVVVDDRLPT KDGELLFVHS AEGSEFWSAL
LEKAYAKING CYEALSGGAT TEGFEDFTGG IAEWYELKKP PPNLFKIIQK ALQKGSLLGC
SIDITSAADS EAITFQKLVK GHAYSVTGAE EVESNGSLQK LIRIRNPWGE VEWTGRWNDN
CPSWNTIDPE ERERLTRRHE DGEFWMSFSD FLRHYSRLEI CNLTPDTLTS DTYKKWKLTK
MDGNWRRGST AGGCRNYPNT FWMNPQYLIK LEEEDEDEED GESGCTFLVG LIQKHRRRQR
KMGEDMHTIG FGIYEVPEEL SGQTNIHLSK NFFLTNRARE RSDTFINLRE VLNRFKLPPG
EYILVPSTFE PNKDGDFCIR VFSEKKADYQ AVDDEIEANL EEFDISEDDI DDGFRRLFAQ
LAGEDAEISA FELQTILRRV LAKRQDIKSD GFSIETCKIM VDMLDSDGSG KLGLKEFYIL
WTKIQKYQKI YREIDVDRSG TMNSYEMRKA LEEAGFKMPC QLHQVIVARF ADDQLIIDFD
NFVRCLVRLE TLFKIFKQLD PENTGTIELD LISWLCFSVL *

mutated AA sequence

MAGIAAKLAK DREAAEGLGS HDRAIKYLNQ DYEALRNECL EAGTLFQDPS FPAIPSALGF
KELGPYSSKT RGIEWKRPTE ICADPQFIIG GATRTDICQG ALGDCWLLAA IASLTLNEEI
LARVVPLNQS FQENYAGIFH FQFWQYGEWV EVVVDDRLPT KDGELLFVHS AEGSEFWSAL
LEKAYAKING CYEALSGGAT TEGFEDFTGG IAEWYELKKP PPNLFKIIQK ALQKGSLLGC
SIDITSAADS EAITFQKLVK GHAYSVTGAE EVESNGSLQK LIRIRNPWGE VEWTGRWNDN
CPSWNTIDPE ERERLTRRHE DGEFWMSFSD FLRHYSRLEI CNLTPDTLTS DTYKKWKLTK
MDGNWRRGST AGGCRNYPNT FWMNPQYLIK LEEEDEDEED GESGCTFLVG LIQKHRRRQR
KMGEDMHTIG FGIYEVPEEL SGQTNIHLSK NFFLTNRARE RSDTFINLRE VLNRFKLPPG
EYILVPSTFE PNKDGDFCIR VFSEKKADYQ AVDDEIEANL EEFDISEDDI DDGFRRLFAQ
LAGEDAEISA FELQTILRRV LAKRQDIQSD GFSIETCKIM VDMLDSDGSG KLGLKEFYIL
WTKIQKYQKI YREIDVDRSG TMNSYEMRKA LEEAGFKMPC QLHQVIVARF ADDQLIIDFD
NFVRCLVRLE TLFKIFKQLD PENTGTIELD LISWLCFSVL *

speed

0.62 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

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

known variant

Reference ID: rs17599

database	homozygous (C/C)	heterozygous	allele carriers
1000G	128	782	910
ExAC	3326	20973	24299

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.026	1
	3.116	1
(flanking)	3.482	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
Acc increased	64778	wt: 0.60 / mu: 0.71	wt: CTGATTTTGTCTTTTAGGCCAAGATATCAAGTCAGATGGCT mu: CTGATTTTGTCTTTTAGGCCAAGATATCCAGTCAGATGGCT	gcca\|AGAT
Acc increased	64779	wt: 0.34 / mu: 0.43	wt: TGATTTTGTCTTTTAGGCCAAGATATCAAGTCAGATGGCTT mu: TGATTTTGTCTTTTAGGCCAAGATATCCAGTCAGATGGCTT	ccaa\|GATA

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

490

mutated

all conserved

490

Ptroglodytes

all identical

ENSPTRG00000002016

568

Mmulatta

all identical

ENSMMUG00000011142

564

Fcatus

all identical

ENSFCAG00000010671

489

Mmusculus

all identical

ENSMUSG00000026509

568

Ggallus

all identical

ENSGALG00000009360

569

Trubripes

all identical

ENSTRUG00000007432

591

Drerio

all identical

ENSDARG00000090014

568

Dmelanogaster

not conserved

FBgn0025866

793

Celegans

no alignment

C06G4.2

n/a

Xtropicalis

all identical

ENSXETG00000018599

466

protein features

start (aa)	end (aa)	feature	details
345	514	REGION	Domain III.	lost
479	492	STRAND		lost
495	505	STRAND		might get lost (downstream of altered splice site)
507	509	STRAND		might get lost (downstream of altered splice site)
515	529	REGION	Linker.	might get lost (downstream of altered splice site)
527	530	STRAND		might get lost (downstream of altered splice site)
530	700	REGION	Domain IV.	might get lost (downstream of altered splice site)
533	541	HELIX		might get lost (downstream of altered splice site)
534	534	CONFLICT	F -> V (in Ref. 1; AAA35645 and 2; AAF99682).	might get lost (downstream of altered splice site)
542	542	METAL	Calcium 5; via carbonyl oxygen (By similarity).	might get lost (downstream of altered splice site)
542	546	STRAND		might get lost (downstream of altered splice site)
545	545	METAL	Calcium 5 (By similarity).	might get lost (downstream of altered splice site)
547	547	METAL	Calcium 5; via carbonyl oxygen (By similarity).	might get lost (downstream of altered splice site)
550	560	HELIX		might get lost (downstream of altered splice site)
552	552	METAL	Calcium 5 (By similarity).	might get lost (downstream of altered splice site)
561	564	TURN		might get lost (downstream of altered splice site)
572	605	DOMAIN	EF-hand 1.	might get lost (downstream of altered splice site)
574	582	HELIX		might get lost (downstream of altered splice site)
585	585	METAL	Calcium 6 (By similarity).	might get lost (downstream of altered splice site)
585	596	CA_BIND	1.	might get lost (downstream of altered splice site)
586	588	STRAND		might get lost (downstream of altered splice site)
587	587	METAL	Calcium 6 (By similarity).	might get lost (downstream of altered splice site)
589	589	METAL	Calcium 6; via carbonyl oxygen (By similarity).	might get lost (downstream of altered splice site)
590	592	STRAND		might get lost (downstream of altered splice site)
591	591	METAL	Calcium 6; via carbonyl oxygen (By similarity).	might get lost (downstream of altered splice site)
595	612	HELIX		might get lost (downstream of altered splice site)
596	596	METAL	Calcium 6 (By similarity).	might get lost (downstream of altered splice site)
602	637	DOMAIN	EF-hand 2.	might get lost (downstream of altered splice site)
615	615	METAL	Calcium 7 (By similarity).	might get lost (downstream of altered splice site)
615	626	CA_BIND	2.	might get lost (downstream of altered splice site)
617	617	METAL	Calcium 7 (By similarity).	might get lost (downstream of altered splice site)
619	619	METAL	Calcium 7; via carbonyl oxygen (By similarity).	might get lost (downstream of altered splice site)
621	621	METAL	Calcium 7; via carbonyl oxygen (By similarity).	might get lost (downstream of altered splice site)
622	624	STRAND		might get lost (downstream of altered splice site)
626	626	METAL	Calcium 7 (By similarity).	might get lost (downstream of altered splice site)
627	630	HELIX		might get lost (downstream of altered splice site)
631	635	TURN		might get lost (downstream of altered splice site)
640	650	HELIX		might get lost (downstream of altered splice site)
655	657	STRAND		might get lost (downstream of altered splice site)
658	658	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
659	679	HELIX		might get lost (downstream of altered splice site)
661	661	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
667	700	DOMAIN	EF-hand 3.	might get lost (downstream of altered splice site)
687	690	STRAND		might get lost (downstream of altered splice site)
691	698	HELIX		might 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

strand

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

0.64 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems