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: ENST00000403897
Querying Taster for transcript #2: ENST00000444918
MT speed 0 s - this script 3.656918 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CAPN14	polymorphism_automatic	6.07958128284736e-13	simple_aae		affected		D520N	single base exchange	rs7422120		show file
CAPN14	polymorphism_automatic	6.07958128284736e-13	simple_aae		affected		D520N	single base exchange	rs7422120		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999392 (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)

chr2:31410653C>TN/A show variant in all transcripts IGV

HGNC symbol

CAPN14

Ensembl transcript ID

ENST00000403897

Genbank transcript ID

NM_001145122

UniProt peptide

A8MX76

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1558G>A
cDNA.1700G>A
g.46072G>A

AA changes

D520N Score: 23 explain score(s)

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

520

frameshift

known variant

Reference ID: rs7422120

database	homozygous (T/T)	heterozygous	allele carriers
1000G	351	942	1293
ExAC	851	3920	4771

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.026	0.044
	-0.516	0.002
(flanking)	-0.079	0.001

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 increased	46072	wt: 0.42 / mu: 0.92	wt: GGCAGGATGAATTCT mu: GGCAGAATGAATTCT	CAGG\|atga
Donor gained	46067	0.88	mu: TGAAAGGCAGAATGA	AAAG\|gcag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

520

mutated

all conserved

520

Ptroglodytes

all conserved

ENSPTRG00000033895

519

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

not conserved

ENSGALG00000009069

503

FQKG

Trubripes

all identical

ENSTRUG00000002373

487

QDRGSGGFRVVLLDSGHG

Drerio

not conserved

ENSDARG00000008553

528

Dmelanogaster

all conserved

FBgn0260450

502

RCGGPKVKSVCQ

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000033183

592

protein features

start (aa)	end (aa)	feature	details
518	683	REGION	Domain IV.	lost
557	592	DOMAIN	EF-hand 1.	might get lost (downstream of altered splice site)
570	581	CA_BIND	Potential.	might get lost (downstream of altered splice site)
586	621	DOMAIN	EF-hand 2.	might get lost (downstream of altered splice site)
651	684	DOMAIN	EF-hand 3.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2055 / 2055

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

685 / 685

position of stopcodon in wt / mu cDNA

2197 / 2197

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

143 / 143

chromosome

strand

-1

last intron/exon boundary

2171

theoretical NMD boundary in CDS

1978

length of CDS

2055

coding sequence (CDS) position

1558

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

1700

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

46072

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

31410653

original gDNA sequence snippet

AAGACCAAAATGAAAGGCAGGATGAATTCTTCACCAAATTC

altered gDNA sequence snippet

AAGACCAAAATGAAAGGCAGAATGAATTCTTCACCAAATTC

original cDNA sequence snippet

AAGACCAAAATGAAAGGCAGGATGAATTCTTCACCAAATTC

altered cDNA sequence snippet

AAGACCAAAATGAAAGGCAGAATGAATTCTTCACCAAATTC

wildtype AA sequence

MSLWPPFRCR WKLAPRYSRR ASPQQPQQDF EALLAECLRN GCLFEDTSFP ATLSSIGSGS
LLQKLPPRLQ WKRPPELHSN PQFYFAKAKR LDLCQGIVGD CWFLAALQAL ALHQDILSRV
VPLNQSFTEK YAGIFRFWFW HYGNWVPVVI DDRLPVNEAG QLVFVSSTYK NLFWGALLEK
AYAKLSGSYE DLQSGQVSEA LVDFTGGVTM TINLAEAHGN LWDILIEATY NRTLIGCQTH
SGEKILENGL VEGHAYTLTG IRKVTCKHRP EYLVKLRNPW GKVEWKGDWS DSSSKWELLS
PKEKILLLRK DNDGEFWMTL QDFKTHFVLL VICKLTPGLL SQEAAQKWTY TMREGRWEKR
STAGGQRQLL QDTFWKNPQF LLSVWRPEEG RRSLRPCSVL VSLLQKPRHR CRKRKPLLAI
GFYLYRMNKY HDDQRRLPPE FFQRNTPLSQ PDRFLKEKEV SQELCLEPGT YLIVPCILEA
HQKSEFVLRV FSRKHIFYEI GSNSGVVFSK EIEDQNERQD EFFTKFFEKH PEINAVQLQN
LLNQMTWSSL GSRQPFFSLE ACQGILALLD LNASGTMSIQ EFRDLWKQLK LSQKVFHKQD
RGSGYLNWEQ LHAAMREAGI MLSDDVCQLM LIRYGGPRLQ MDFVSFIHLM LRVENMEDVF
QNLTQDGKGI YLQKPEWMMM ALYS*

mutated AA sequence

MSLWPPFRCR WKLAPRYSRR ASPQQPQQDF EALLAECLRN GCLFEDTSFP ATLSSIGSGS
LLQKLPPRLQ WKRPPELHSN PQFYFAKAKR LDLCQGIVGD CWFLAALQAL ALHQDILSRV
VPLNQSFTEK YAGIFRFWFW HYGNWVPVVI DDRLPVNEAG QLVFVSSTYK NLFWGALLEK
AYAKLSGSYE DLQSGQVSEA LVDFTGGVTM TINLAEAHGN LWDILIEATY NRTLIGCQTH
SGEKILENGL VEGHAYTLTG IRKVTCKHRP EYLVKLRNPW GKVEWKGDWS DSSSKWELLS
PKEKILLLRK DNDGEFWMTL QDFKTHFVLL VICKLTPGLL SQEAAQKWTY TMREGRWEKR
STAGGQRQLL QDTFWKNPQF LLSVWRPEEG RRSLRPCSVL VSLLQKPRHR CRKRKPLLAI
GFYLYRMNKY HDDQRRLPPE FFQRNTPLSQ PDRFLKEKEV SQELCLEPGT YLIVPCILEA
HQKSEFVLRV FSRKHIFYEI GSNSGVVFSK EIEDQNERQN EFFTKFFEKH PEINAVQLQN
LLNQMTWSSL GSRQPFFSLE ACQGILALLD LNASGTMSIQ EFRDLWKQLK LSQKVFHKQD
RGSGYLNWEQ LHAAMREAGI MLSDDVCQLM LIRYGGPRLQ MDFVSFIHLM LRVENMEDVF
QNLTQDGKGI YLQKPEWMMM ALYS*

speed

0.76 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: 0.999999999999392 (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)

chr2:31410653C>TN/A show variant in all transcripts IGV

HGNC symbol

CAPN14

Ensembl transcript ID

ENST00000444918

Genbank transcript ID

N/A

UniProt peptide

A8MX76

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1558G>A
cDNA.1700G>A
g.46072G>A

AA changes

D520N Score: 23 explain score(s)

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

520

frameshift

known variant

Reference ID: rs7422120

database	homozygous (T/T)	heterozygous	allele carriers
1000G	351	942	1293
ExAC	851	3920	4771

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.026	0.044
	-0.516	0.002
(flanking)	-0.079	0.001

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 increased	46072	wt: 0.42 / mu: 0.92	wt: GGCAGGATGAATTCT mu: GGCAGAATGAATTCT	CAGG\|atga
Donor gained	46067	0.88	mu: TGAAAGGCAGAATGA	AAAG\|gcag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

520

mutated

all conserved

520

Ptroglodytes

all conserved

ENSPTRG00000033895

519

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

not conserved

ENSGALG00000009069

503

FQKG

Trubripes

all identical

ENSTRUG00000002373

487

QDRGSGGFRVVLLDSGHG

Drerio

not conserved

ENSDARG00000008553

528

Dmelanogaster

all conserved

FBgn0260450

502

RCGGPKVKSVCQ

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000033183

592

protein features

start (aa)	end (aa)	feature	details
518	683	REGION	Domain IV.	lost
557	592	DOMAIN	EF-hand 1.	might get lost (downstream of altered splice site)
570	581	CA_BIND	Potential.	might get lost (downstream of altered splice site)
586	621	DOMAIN	EF-hand 2.	might get lost (downstream of altered splice site)
651	684	DOMAIN	EF-hand 3.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2055 / 2055

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

685 / 685

position of stopcodon in wt / mu cDNA

2197 / 2197

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

143 / 143

chromosome

strand

-1

last intron/exon boundary

2171

theoretical NMD boundary in CDS

1978

length of CDS

2055

coding sequence (CDS) position

1558

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

1700

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

46072

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

31410653

original gDNA sequence snippet

AAGACCAAAATGAAAGGCAGGATGAATTCTTCACCAAATTC

altered gDNA sequence snippet

AAGACCAAAATGAAAGGCAGAATGAATTCTTCACCAAATTC

original cDNA sequence snippet

AAGACCAAAATGAAAGGCAGGATGAATTCTTCACCAAATTC

altered cDNA sequence snippet

AAGACCAAAATGAAAGGCAGAATGAATTCTTCACCAAATTC

wildtype AA sequence

MSLWPPFRCR WKLAPRYSRR ASPQQPQQDF EALLAECLRN GCLFEDTSFP ATLSSIGSGS
LLQKLPPRLQ WKRPPELHSN PQFYFAKAKR LDLCQGIVGD CWFLAALQAL ALHQDILSRV
VPLNQSFTEK YAGIFRFWFW HYGNWVPVVI DDRLPVNEAG QLVFVSSTYK NLFWGALLEK
AYAKLSGSYE DLQSGQVSEA LVDFTGGVTM TINLAEAHGN LWDILIEATY NRTLIGCQTH
SGEKILENGL VEGHAYTLTG IRKVTCKHRP EYLVKLRNPW GKVEWKGDWS DSSSKWELLS
PKEKILLLRK DNDGEFWMTL QDFKTHFVLL VICKLTPGLL SQEAAQKWTY TMREGRWEKR
STAGGQRQLL QDTFWKNPQF LLSVWRPEEG RRSLRPCSVL VSLLQKPRHR CRKRKPLLAI
GFYLYRVAKY HDDQRRLPPE FFQRNTPLSQ PDRFLKEKEV SQELCLEPGT YLIVPCILEA
HQKSEFVLRV FSRKHIFYEI GSNSGVVFSK EIEDQNERQD EFFTKFFEKH PEINAVQLQN
LLNQMTWSSL GSRQPFFSLE ACQGILALLD LNASGTMSIQ EFRDLWKQLK LSQKVFHKQD
RGSGYLNWEQ LHAAMREAGI MLSDDVCQLM LIRYGGPRLQ MDFVSFIHLM LRVENMEDVF
QNLTQDGKGI YLQKPEWMMM ALYS*

mutated AA sequence

MSLWPPFRCR WKLAPRYSRR ASPQQPQQDF EALLAECLRN GCLFEDTSFP ATLSSIGSGS
LLQKLPPRLQ WKRPPELHSN PQFYFAKAKR LDLCQGIVGD CWFLAALQAL ALHQDILSRV
VPLNQSFTEK YAGIFRFWFW HYGNWVPVVI DDRLPVNEAG QLVFVSSTYK NLFWGALLEK
AYAKLSGSYE DLQSGQVSEA LVDFTGGVTM TINLAEAHGN LWDILIEATY NRTLIGCQTH
SGEKILENGL VEGHAYTLTG IRKVTCKHRP EYLVKLRNPW GKVEWKGDWS DSSSKWELLS
PKEKILLLRK DNDGEFWMTL QDFKTHFVLL VICKLTPGLL SQEAAQKWTY TMREGRWEKR
STAGGQRQLL QDTFWKNPQF LLSVWRPEEG RRSLRPCSVL VSLLQKPRHR CRKRKPLLAI
GFYLYRVAKY HDDQRRLPPE FFQRNTPLSQ PDRFLKEKEV SQELCLEPGT YLIVPCILEA
HQKSEFVLRV FSRKHIFYEI GSNSGVVFSK EIEDQNERQN EFFTKFFEKH PEINAVQLQN
LLNQMTWSSL GSRQPFFSLE ACQGILALLD LNASGTMSIQ EFRDLWKQLK LSQKVFHKQD
RGSGYLNWEQ LHAAMREAGI MLSDDVCQLM LIRYGGPRLQ MDFVSFIHLM LRVENMEDVF
QNLTQDGKGI YLQKPEWMMM ALYS*

speed

0.90 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems