MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 4 transcript(s)...
Querying Taster for transcript #1: ENST00000396505
Querying Taster for transcript #2: ENST00000326932
Querying Taster for transcript #3: ENST00000525493
Querying Taster for transcript #4: ENST00000450094
MT speed 0 s - this script 4.337571 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
DKK3	polymorphism_automatic	4.9960036108132e-15	simple_aae		affected		R335G	single base exchange	rs3206824		show file
DKK3	polymorphism_automatic	4.9960036108132e-15	simple_aae		affected		R349G	single base exchange	rs3206824		show file
DKK3	polymorphism_automatic	4.9960036108132e-15	simple_aae		affected		R335G	single base exchange	rs3206824		show file
DKK3	polymorphism_automatic	4.9960036108132e-15	simple_aae		affected		R307G	single base exchange	rs3206824		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999995 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM063956)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:11986061T>CN/A show variant in all transcripts IGV

HGNC symbol

DKK3

Ensembl transcript ID

ENST00000326932

Genbank transcript ID

NM_013253

UniProt peptide

Q9UBP4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1003A>G
cDNA.1228A>G
g.45256A>G

AA changes

R335G Score: 125 explain score(s)

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

335

frameshift

known variant

Reference ID: rs3206824

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1655	757	2412
ExAC	-	-	-

known disease mutation at this position, please check HGMD for details (HGMD ID CM063956)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.042	0.042
	-0.82	0
(flanking)	-0.691	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
Donor increased	45255	wt: 0.45 / mu: 0.70	wt: GCGCTGAGGGAGCCT mu: GCGCTGGGGGAGCCT	GCTG\|aggg

distance from splice site

173

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

335

mutated

not conserved

335

Ptroglodytes

not conserved

ENSPTRG00000003368

335

Mmulatta

not conserved

ENSMMUG00000022862

335

Fcatus

not conserved

ENSFCAG00000000925

269

Mmusculus

not conserved

ENSMUSG00000030772

335

Ggallus

all conserved

ENSGALG00000005551

335

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000077630

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
338	343	COMPBIAS	Poly-Ala.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1053 / 1053

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

351 / 351

position of stopcodon in wt / mu cDNA

1278 / 1278

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

226 / 226

chromosome

strand

-1

last intron/exon boundary

1056

theoretical NMD boundary in CDS

780

length of CDS

1053

coding sequence (CDS) position

1003

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

1228

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

45256

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

11986061

original gDNA sequence snippet

TGACTGAAGAGATGGCGCTGAGGGAGCCTGCGGCTGCCGCC

altered gDNA sequence snippet

TGACTGAAGAGATGGCGCTGGGGGAGCCTGCGGCTGCCGCC

original cDNA sequence snippet

TGACTGAAGAGATGGCGCTGAGGGAGCCTGCGGCTGCCGCC

altered cDNA sequence snippet

TGACTGAAGAGATGGCGCTGGGGGAGCCTGCGGCTGCCGCC

wildtype AA sequence

MQRLGATLLC LLLAAAVPTA PAPAPTATSA PVKPGPALSY PQEEATLNEM FREVEELMED
TQHKLRSAVE EMEAEEAAAK ASSEVNLANL PPSYHNETNT DTKVGNNTIH VHREIHKITN
NQTGQMVFSE TVITSVGDEE GRRSHECIID EDCGPSMYCQ FASFQYTCQP CRGQRMLCTR
DSECCGDQLC VWGHCTKMAT RGSNGTICDN QRDCQPGLCC AFQRGLLFPV CTPLPVEGEL
CHDPASRLLD LITWELEPDG ALDRCPCASG LLCQPHSHSL VYVCKPTFVG SRDQDGEILL
PREVPDEYEV GSFMEEVRQE LEDLERSLTE EMALREPAAA AAALLGGEEI *

mutated AA sequence

speed

0.63 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: 0.999999999999995 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM063956)
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:11986061T>CN/A show variant in all transcripts IGV

HGNC symbol

DKK3

Ensembl transcript ID

ENST00000525493

Genbank transcript ID

N/A

UniProt peptide

Q9UBP4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1045A>G
cDNA.1203A>G
g.45256A>G

AA changes

R349G Score: 125 explain score(s)

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

349

frameshift

known variant

Reference ID: rs3206824

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1655	757	2412
ExAC	-	-	-

known disease mutation at this position, please check HGMD for details (HGMD ID CM063956)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.042	0.042
	-0.82	0
(flanking)	-0.691	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
Donor increased	45255	wt: 0.45 / mu: 0.70	wt: GCGCTGAGGGAGCCT mu: GCGCTGGGGGAGCCT	GCTG\|aggg

distance from splice site

124

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

349

mutated

not conserved

349

Ptroglodytes

not conserved

ENSPTRG00000003368

335

Mmulatta

not conserved

ENSMMUG00000022862

335

Fcatus

not conserved

ENSFCAG00000000925

269

Mmusculus

not conserved

ENSMUSG00000030772

335

Ggallus

all conserved

ENSGALG00000005551

339

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000077630

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1095 / 1095

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

365 / 365

position of stopcodon in wt / mu cDNA

1253 / 1253

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

159 / 159

chromosome

strand

-1

last intron/exon boundary

989

theoretical NMD boundary in CDS

780

length of CDS

1095

coding sequence (CDS) position

1045

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

1203

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

45256

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

11986061

original gDNA sequence snippet

TGACTGAAGAGATGGCGCTGAGGGAGCCTGCGGCTGCCGCC

altered gDNA sequence snippet

TGACTGAAGAGATGGCGCTGGGGGAGCCTGCGGCTGCCGCC

original cDNA sequence snippet

TGACTGAAGAGATGGCGCTGAGGGAGCCTGCGGCTGCCGCC

altered cDNA sequence snippet

TGACTGAAGAGATGGCGCTGGGGGAGCCTGCGGCTGCCGCC

wildtype AA sequence

MQRLGATLLC LLLAAAVPTA PAPAPTATSA PVKPGPALSY PQEEATLNEM FREVEELMED
TQHKLRSAVE EMEAEEAAAK ASSEVNLANL PPSYHNETNT DTKVGNNTIH VHREIHKITN
NQTGQMVFSE TVITSVGDEE GRRSHECIID EDCGPSMYCQ FASFQYTCQP CRGQRMLCTR
DSECCGDQLC VWGHCTKMAT RGSNGTICDN QRDCQPGLCC AFQRGLLFPV CTPLPVEGEL
CHDPASRLLD LITWELEPDG ALDRCPCASG LLCQPHRLPR LEPGFVPSLP SHSLVYVCKP
TFVGSRDQDG EILLPREVPD EYEVGSFMEE VRQELEDLER SLTEEMALRE PAAAAAALLG
GEEI*

mutated AA sequence

MQRLGATLLC LLLAAAVPTA PAPAPTATSA PVKPGPALSY PQEEATLNEM FREVEELMED
TQHKLRSAVE EMEAEEAAAK ASSEVNLANL PPSYHNETNT DTKVGNNTIH VHREIHKITN
NQTGQMVFSE TVITSVGDEE GRRSHECIID EDCGPSMYCQ FASFQYTCQP CRGQRMLCTR
DSECCGDQLC VWGHCTKMAT RGSNGTICDN QRDCQPGLCC AFQRGLLFPV CTPLPVEGEL
CHDPASRLLD LITWELEPDG ALDRCPCASG LLCQPHRLPR LEPGFVPSLP SHSLVYVCKP
TFVGSRDQDG EILLPREVPD EYEVGSFMEE VRQELEDLER SLTEEMALGE PAAAAAALLG
GEEI*

speed

0.89 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999995 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM063956)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:11986061T>CN/A show variant in all transcripts IGV

HGNC symbol

DKK3

Ensembl transcript ID

ENST00000396505

Genbank transcript ID

NM_001018057

UniProt peptide

Q9UBP4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1003A>G
cDNA.1242A>G
g.45256A>G

AA changes

R335G Score: 125 explain score(s)

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

335

frameshift

known variant

Reference ID: rs3206824

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1655	757	2412
ExAC	-	-	-

known disease mutation at this position, please check HGMD for details (HGMD ID CM063956)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.042	0.042
	-0.82	0
(flanking)	-0.691	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
Donor increased	45255	wt: 0.45 / mu: 0.70	wt: GCGCTGAGGGAGCCT mu: GCGCTGGGGGAGCCT	GCTG\|aggg

distance from splice site

173

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

335

mutated

not conserved

335

Ptroglodytes

not conserved

ENSPTRG00000003368

335

Mmulatta

not conserved

ENSMMUG00000022862

335

Fcatus

not conserved

ENSFCAG00000000925

269

Mmusculus

not conserved

ENSMUSG00000030772

335

Ggallus

all conserved

ENSGALG00000005551

335

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000077630

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
338	343	COMPBIAS	Poly-Ala.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1053 / 1053

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

351 / 351

position of stopcodon in wt / mu cDNA

1292 / 1292

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

240 / 240

chromosome

strand

-1

last intron/exon boundary

1070

theoretical NMD boundary in CDS

780

length of CDS

1053

coding sequence (CDS) position

1003

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

1242

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

45256

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

11986061

original gDNA sequence snippet

TGACTGAAGAGATGGCGCTGAGGGAGCCTGCGGCTGCCGCC

altered gDNA sequence snippet

TGACTGAAGAGATGGCGCTGGGGGAGCCTGCGGCTGCCGCC

original cDNA sequence snippet

TGACTGAAGAGATGGCGCTGAGGGAGCCTGCGGCTGCCGCC

altered cDNA sequence snippet

TGACTGAAGAGATGGCGCTGGGGGAGCCTGCGGCTGCCGCC

wildtype AA sequence

mutated AA sequence

speed

0.65 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999995 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM063956)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:11986061T>CN/A show variant in all transcripts IGV

HGNC symbol

DKK3

Ensembl transcript ID

ENST00000450094

Genbank transcript ID

N/A

UniProt peptide

Q9UBP4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.919A>G
cDNA.920A>G
g.45256A>G

AA changes

R307G Score: 125 explain score(s)

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

307

frameshift

known variant

Reference ID: rs3206824

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1655	757	2412
ExAC	-	-	-

known disease mutation at this position, please check HGMD for details (HGMD ID CM063956)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.042	0.042
	-0.82	0
(flanking)	-0.691	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
Donor increased	45255	wt: 0.45 / mu: 0.70	wt: GCGCTGAGGGAGCCT mu: GCGCTGGGGGAGCCT	GCTG\|aggg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

307

mutated

not conserved

307

Ptroglodytes

not conserved

ENSPTRG00000003368

335

Mmulatta

not conserved

ENSMMUG00000022862

335

Fcatus

not conserved

ENSFCAG00000000925

269

Mmusculus

not conserved

ENSMUSG00000030772

335

Ggallus

all conserved

ENSGALG00000005551

335

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000077630

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
338	343	COMPBIAS	Poly-Ala.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

969 / 969

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

323 / 323

position of stopcodon in wt / mu cDNA

970 / 970

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

2 / 2

chromosome

strand

-1

last intron/exon boundary

748

theoretical NMD boundary in CDS

696

length of CDS

969

coding sequence (CDS) position

919

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

920

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

45256

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

11986061

original gDNA sequence snippet

TGACTGAAGAGATGGCGCTGAGGGAGCCTGCGGCTGCCGCC

altered gDNA sequence snippet

TGACTGAAGAGATGGCGCTGGGGGAGCCTGCGGCTGCCGCC

original cDNA sequence snippet

TGACTGAAGAGATGGCGCTGAGGGAGCCTGCGGCTGCCGCC

altered cDNA sequence snippet

TGACTGAAGAGATGGCGCTGGGGGAGCCTGCGGCTGCCGCC

wildtype AA sequence

MQRLGATLLC LLLAAAVPTA PAPAPTATSA PVKPGPALSY PQEEATLNEM FREVEELMED
TQHKLRSAVE EMEAEEAAAK ASSEVNLANL PPSYHNETNT DTKVGNNTIH VHREIHKECI
IDEDCGPSMY CQFASFQYTC QPCRGQRMLC TRDSECCGDQ LCVWGHCTKM ATRGSNGTIC
DNQRDCQPGL CCAFQRGLLF PVCTPLPVEG ELCHDPASRL LDLITWELEP DGALDRCPCA
SGLLCQPHSH SLVYVCKPTF VGSRDQDGEI LLPREVPDEY EVGSFMEEVR QELEDLERSL
TEEMALREPA AAAAALLGGE EI*

mutated AA sequence

speed

0.70 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems