MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000279488
Querying Taster for transcript #2: ENST00000308385
MT speed 0 s - this script 3.737948 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
DUSP6	polymorphism_automatic	0.99999997025899	simple_aae				V114L	single base exchange	rs2279574		show file
DUSP6	polymorphism_automatic	0.999999992844012	simple_aae				V114L	single base exchange	rs2279574		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 2.97410102867992e-08 (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 CM168195)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:89745477C>AN/A show variant in all transcripts IGV

HGNC symbol

DUSP6

Ensembl transcript ID

ENST00000308385

Genbank transcript ID

NM_022652

UniProt peptide

Q16828

alteration type

single base exchange

alteration region

CDS

DNA changes

c.340G>T
cDNA.706G>T
g.1572G>T

AA changes

V114L Score: 32 explain score(s)

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

114

frameshift

known variant

Reference ID: rs2279574

database	homozygous (A/A)	heterozygous	allele carriers
1000G	587	1161	1748
ExAC	12719	7329	20048

known disease mutation at this position, please check HGMD for details (HGMD ID CM168195)

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
TAF1, Transcription Factor, TAF1 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.053	1
	4.066	1
(flanking)	0.359	0.999

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

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

114

mutated

all conserved

114

Ptroglodytes

all identical

ENSPTRG00000005282

114

Mmulatta

all identical

ENSMMUG00000006227

114

Fcatus

all identical

ENSFCAG00000006979

114

Mmusculus

all identical

ENSMUSG00000019960

114

Ggallus

all identical

ENSGALG00000011207

114

Trubripes

all identical

ENSTRUG00000017083

115

Drerio

all identical

ENSDARG00000070914

114

Dmelanogaster

all conserved

FBgn0036844

106

GAGSLAVAM

Celegans

no alignment

C05B10.1

n/a

Xtropicalis

all identical

ENSXETG00000021871

113

protein features

start (aa)	end (aa)	feature	details
30	148	DOMAIN	Rhodanese.	lost
114	124	HELIX		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

708 / 708

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

236 / 236

position of stopcodon in wt / mu cDNA

1074 / 1074

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

367 / 367

chromosome

strand

-1

last intron/exon boundary

767

theoretical NMD boundary in CDS

350

length of CDS

708

coding sequence (CDS) position

340

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

706

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

1572

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

89745477

original gDNA sequence snippet

AGAATACGGGCGGCGAGTCGGTGCTCGGGCTGCTGCTCAAG

altered gDNA sequence snippet

AGAATACGGGCGGCGAGTCGTTGCTCGGGCTGCTGCTCAAG

original cDNA sequence snippet

AGAATACGGGCGGCGAGTCGGTGCTCGGGCTGCTGCTCAAG

altered cDNA sequence snippet

AGAATACGGGCGGCGAGTCGTTGCTCGGGCTGCTGCTCAAG

wildtype AA sequence

MIDTLRPVPF ASEMAISKTV AWLNEQLELG NERLLLMDCR PQELYESSHI ESAINVAIPG
IMLRRLQKGN LPVRALFTRG EDRDRFTRRC GTDTVVLYDE SSSDWNENTG GESVLGLLLK
KLKDEGCRAF YLEDEARGKN CGVLVHCLAG ISRSVTVTVA YLMQKLNLSM NDAYDIVKMK
KSNISPNFNF MGQLLDFERT LGLSSPCDNR VPAQQLYFTT PSNQNVYQVD SLQST*

mutated AA sequence

MIDTLRPVPF ASEMAISKTV AWLNEQLELG NERLLLMDCR PQELYESSHI ESAINVAIPG
IMLRRLQKGN LPVRALFTRG EDRDRFTRRC GTDTVVLYDE SSSDWNENTG GESLLGLLLK
KLKDEGCRAF YLEDEARGKN CGVLVHCLAG ISRSVTVTVA YLMQKLNLSM NDAYDIVKMK
KSNISPNFNF MGQLLDFERT LGLSSPCDNR VPAQQLYFTT PSNQNVYQVD SLQST*

speed

1.02 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: 7.15598760880222e-09 (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 CM168195)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:89745477C>AN/A show variant in all transcripts IGV

HGNC symbol

DUSP6

Ensembl transcript ID

ENST00000279488

Genbank transcript ID

NM_001946

UniProt peptide

Q16828

alteration type

single base exchange

alteration region

CDS

DNA changes

c.340G>T
cDNA.1572G>T
g.1572G>T

AA changes

V114L Score: 32 explain score(s)

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

114

frameshift

known variant

Reference ID: rs2279574

database	homozygous (A/A)	heterozygous	allele carriers
1000G	587	1161	1748
ExAC	12719	7329	20048

known disease mutation at this position, please check HGMD for details (HGMD ID CM168195)

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.053	1
	4.066	1
(flanking)	0.359	0.999

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

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

114

mutated

all conserved

114

Ptroglodytes

all identical

ENSPTRG00000005282

114

Mmulatta

all identical

ENSMMUG00000006227

114

Fcatus

all identical

ENSFCAG00000006979

114

Mmusculus

all identical

ENSMUSG00000019960

114

Ggallus

all identical

ENSGALG00000011207

114

Trubripes

all identical

ENSTRUG00000017083

115

Drerio

all identical

ENSDARG00000070914

114

Dmelanogaster

all conserved

FBgn0036844

106

GAGSLAVAM

Celegans

all conserved

C05B10.1

107

Xtropicalis

all identical

ENSXETG00000021871

113

protein features

start (aa)	end (aa)	feature	details
30	148	DOMAIN	Rhodanese.	lost
114	124	HELIX		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1146 / 1146

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

382 / 382

position of stopcodon in wt / mu cDNA

2378 / 2378

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

1233 / 1233

chromosome

strand

-1

last intron/exon boundary

2071

theoretical NMD boundary in CDS

788

length of CDS

1146

coding sequence (CDS) position

340

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

1572

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

1572

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

89745477

original gDNA sequence snippet

AGAATACGGGCGGCGAGTCGGTGCTCGGGCTGCTGCTCAAG

altered gDNA sequence snippet

AGAATACGGGCGGCGAGTCGTTGCTCGGGCTGCTGCTCAAG

original cDNA sequence snippet

AGAATACGGGCGGCGAGTCGGTGCTCGGGCTGCTGCTCAAG

altered cDNA sequence snippet

AGAATACGGGCGGCGAGTCGTTGCTCGGGCTGCTGCTCAAG

wildtype AA sequence

MIDTLRPVPF ASEMAISKTV AWLNEQLELG NERLLLMDCR PQELYESSHI ESAINVAIPG
IMLRRLQKGN LPVRALFTRG EDRDRFTRRC GTDTVVLYDE SSSDWNENTG GESVLGLLLK
KLKDEGCRAF YLEGGFSKFQ AEFSLHCETN LDGSCSSSSP PLPVLGLGGL RISSDSSSDI
ESDLDRDPNS ATDSDGSPLS NSQPSFPVEI LPFLYLGCAK DSTNLDVLEE FGIKYILNVT
PNLPNLFENA GEFKYKQIPI SDHWSQNLSQ FFPEAISFID EARGKNCGVL VHCLAGISRS
VTVTVAYLMQ KLNLSMNDAY DIVKMKKSNI SPNFNFMGQL LDFERTLGLS SPCDNRVPAQ
QLYFTTPSNQ NVYQVDSLQS T*

mutated AA sequence

MIDTLRPVPF ASEMAISKTV AWLNEQLELG NERLLLMDCR PQELYESSHI ESAINVAIPG
IMLRRLQKGN LPVRALFTRG EDRDRFTRRC GTDTVVLYDE SSSDWNENTG GESLLGLLLK
KLKDEGCRAF YLEGGFSKFQ AEFSLHCETN LDGSCSSSSP PLPVLGLGGL RISSDSSSDI
ESDLDRDPNS ATDSDGSPLS NSQPSFPVEI LPFLYLGCAK DSTNLDVLEE FGIKYILNVT
PNLPNLFENA GEFKYKQIPI SDHWSQNLSQ FFPEAISFID EARGKNCGVL VHCLAGISRS
VTVTVAYLMQ KLNLSMNDAY DIVKMKKSNI SPNFNFMGQL LDFERTLGLS SPCDNRVPAQ
QLYFTTPSNQ NVYQVDSLQS T*

speed

0.76 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems