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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000417454
Querying Taster for transcript #2: ENST00000310373
Querying Taster for transcript #3: ENST00000333884
MT speed 0 s - this script 4.07746 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GP6	polymorphism_automatic	4.9960036108132e-15	simple_aae		affected		E237K	single base exchange	rs1654416		show file
GP6	polymorphism_automatic	4.9960036108132e-15	simple_aae		affected		E237K	single base exchange	rs1654416		show file
GP6	polymorphism_automatic	4.9960036108132e-15	simple_aae		affected		E219K	single base exchange	rs1654416		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
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:55530035C>TN/A show variant in all transcripts IGV

HGNC symbol

GP6

Ensembl transcript ID

ENST00000417454

Genbank transcript ID

NM_016363

UniProt peptide

Q9HCN6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.709G>A
cDNA.737G>A
g.19598G>A

AA changes

E237K Score: 56 explain score(s)

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

237

frameshift

known variant

Reference ID: rs1654416

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1408	908	2316
ExAC	-	-	-

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.549	0.001
	-0.901	0
(flanking)	-0.11	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	19595	wt: 0.40 / mu: 0.50	wt: AACTGACCGTCTCATTCACAAACGAAGTCTTCACAACTGGT mu: AACTGACCGTCTCATTCACAAACAAAGTCTTCACAACTGGT	acaa\|ACGA
Donor marginally increased	19595	wt: 0.9955 / mu: 0.9958 (marginal change - not scored)	wt: TCACAAACGAAGTCT mu: TCACAAACAAAGTCT	ACAA\|acga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

237

mutated

all conserved

237

Ptroglodytes

all conserved

ENSPTRG00000011482

237

Mmulatta

all conserved

ENSMMUG00000003117

238

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000078810

238

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000032533

n/a

protein features

start (aa)	end (aa)	feature	details
21	267	TOPO_DOM	Extracellular (Potential).	lost
268	288	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
289	339	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1020 / 1020

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

340 / 340

position of stopcodon in wt / mu cDNA

1048 / 1048

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

29 / 29

chromosome

strand

-1

last intron/exon boundary

804

theoretical NMD boundary in CDS

725

length of CDS

1020

coding sequence (CDS) position

709

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

737

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

19598

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

55530035

original gDNA sequence snippet

TGACCGTCTCATTCACAAACGAAGTCTTCACAACTGGTGAG

altered gDNA sequence snippet

TGACCGTCTCATTCACAAACAAAGTCTTCACAACTGGTGAG

original cDNA sequence snippet

TGACCGTCTCATTCACAAACGAAGTCTTCACAACTGAGACT

altered cDNA sequence snippet

TGACCGTCTCATTCACAAACAAAGTCTTCACAACTGAGACT

wildtype AA sequence

mutated AA sequence

speed

1.06 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
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:55530035C>TN/A show variant in all transcripts IGV

HGNC symbol

GP6

Ensembl transcript ID

ENST00000310373

Genbank transcript ID

NM_001083899

UniProt peptide

Q9HCN6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.709G>A
cDNA.737G>A
g.19598G>A

AA changes

E237K Score: 56 explain score(s)

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

237

frameshift

known variant

Reference ID: rs1654416

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1408	908	2316
ExAC	-	-	-

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.549	0.001
	-0.901	0
(flanking)	-0.11	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	19595	wt: 0.40 / mu: 0.50	wt: AACTGACCGTCTCATTCACAAACGAAGTCTTCACAACTGGT mu: AACTGACCGTCTCATTCACAAACAAAGTCTTCACAACTGGT	acaa\|ACGA
Donor marginally increased	19595	wt: 0.9955 / mu: 0.9958 (marginal change - not scored)	wt: TCACAAACGAAGTCT mu: TCACAAACAAAGTCT	ACAA\|acga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

237

mutated

all conserved

237

Ptroglodytes

all conserved

ENSPTRG00000011482

237

Mmulatta

all conserved

ENSMMUG00000003117

238

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000078810

238

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000032533

n/a

protein features

start (aa)	end (aa)	feature	details
21	267	TOPO_DOM	Extracellular (Potential).	lost
268	288	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
289	339	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1863 / 1863

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

621 / 621

position of stopcodon in wt / mu cDNA

1891 / 1891

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

29 / 29

chromosome

strand

-1

last intron/exon boundary

808

theoretical NMD boundary in CDS

729

length of CDS

1863

coding sequence (CDS) position

709

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

737

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

19598

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

55530035

original gDNA sequence snippet

TGACCGTCTCATTCACAAACGAAGTCTTCACAACTGGTGAG

altered gDNA sequence snippet

TGACCGTCTCATTCACAAACAAAGTCTTCACAACTGGTGAG

original cDNA sequence snippet

TGACCGTCTCATTCACAAACGAAGTCTTCACAACTGAGACT

altered cDNA sequence snippet

TGACCGTCTCATTCACAAACAAAGTCTTCACAACTGAGACT

wildtype AA sequence

MSPSPTALFC LGLCLGRVPA QSGPLPKPSL QALPSSLVPL EKPVTLRCQG PPGVDLYRLE
KLSSSRYQDQ AVLFIPAMKR SLAGRYRCSY QNGSLWSLPS DQLELVATGV FAKPSLSAQP
GPAVSSGGDV TLQCQTRYGF DQFALYKEGD PAPYKNPERW YRASFPIITV TAAHSGTYRC
YSFSSRDPYL WSAPSDPLEL VVTGTSVTPS RLPTEPPSPV AEFSEATAEL TVSFTNEVFT
TETSRSITAS PKESDSPAGE SCPPVLHQGQ PGPDMPRGCD PNNPGGVSGR GLAQPEEAPA
AQGQGCAEAA SAPPAPPADP EIKRGSGWRP TGCSQPRVMF MTAEPQARSY PREGSWHGRR
LKDWRVWSVE AGGQRLQLWK RGHAASSWCS IREPFGQCLS VCLPLCLRAP SIWDGRNLWR
PHPPPCTLWM TWYPGWTTYW PLSSTSLIWA PDGSLRFPAL RVDSVPSSVQ NPPVLPFGPL
CSCLVFPRNS HPHSISHCGL TNLLSSLRTG LAGSLGMSFI FLSVKLARCP LPFTLENKIS
LCNMVKPHLY QQNKKTQKLA RCGGASLYSQ QLRGLRWENG LSLGGRGCSE LRSHHCTLAR
VTKPDFVSKN TGMNMSITLI *

mutated AA sequence

MSPSPTALFC LGLCLGRVPA QSGPLPKPSL QALPSSLVPL EKPVTLRCQG PPGVDLYRLE
KLSSSRYQDQ AVLFIPAMKR SLAGRYRCSY QNGSLWSLPS DQLELVATGV FAKPSLSAQP
GPAVSSGGDV TLQCQTRYGF DQFALYKEGD PAPYKNPERW YRASFPIITV TAAHSGTYRC
YSFSSRDPYL WSAPSDPLEL VVTGTSVTPS RLPTEPPSPV AEFSEATAEL TVSFTNKVFT
TETSRSITAS PKESDSPAGE SCPPVLHQGQ PGPDMPRGCD PNNPGGVSGR GLAQPEEAPA
AQGQGCAEAA SAPPAPPADP EIKRGSGWRP TGCSQPRVMF MTAEPQARSY PREGSWHGRR
LKDWRVWSVE AGGQRLQLWK RGHAASSWCS IREPFGQCLS VCLPLCLRAP SIWDGRNLWR
PHPPPCTLWM TWYPGWTTYW PLSSTSLIWA PDGSLRFPAL RVDSVPSSVQ NPPVLPFGPL
CSCLVFPRNS HPHSISHCGL TNLLSSLRTG LAGSLGMSFI FLSVKLARCP LPFTLENKIS
LCNMVKPHLY QQNKKTQKLA RCGGASLYSQ QLRGLRWENG LSLGGRGCSE LRSHHCTLAR
VTKPDFVSKN TGMNMSITLI *

speed

1.01 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
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:55530035C>TN/A show variant in all transcripts IGV

HGNC symbol

GP6

Ensembl transcript ID

ENST00000333884

Genbank transcript ID

NM_001256017

UniProt peptide

Q9HCN6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.655G>A
cDNA.683G>A
g.19598G>A

AA changes

E219K Score: 56 explain score(s)

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

219

frameshift

known variant

Reference ID: rs1654416

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1408	908	2316
ExAC	-	-	-

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.549	0.001
	-0.901	0
(flanking)	-0.11	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	19595	wt: 0.40 / mu: 0.50	wt: AACTGACCGTCTCATTCACAAACGAAGTCTTCACAACTGGT mu: AACTGACCGTCTCATTCACAAACAAAGTCTTCACAACTGGT	acaa\|ACGA
Donor marginally increased	19595	wt: 0.9955 / mu: 0.9958 (marginal change - not scored)	wt: TCACAAACGAAGTCT mu: TCACAAACAAAGTCT	ACAA\|acga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

219

mutated

all conserved

219

Ptroglodytes

all conserved

ENSPTRG00000011482

219

Mmulatta

all conserved

ENSMMUG00000003117

220

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000078810

220

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000032533

n/a

protein features

start (aa)	end (aa)	feature	details
21	267	TOPO_DOM	Extracellular (Potential).	lost
268	288	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
289	339	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

966 / 966

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

322 / 322

position of stopcodon in wt / mu cDNA

994 / 994

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

29 / 29

chromosome

strand

-1

last intron/exon boundary

750

theoretical NMD boundary in CDS

671

length of CDS

966

coding sequence (CDS) position

655

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

683

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

19598

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

55530035

original gDNA sequence snippet

TGACCGTCTCATTCACAAACGAAGTCTTCACAACTGGTGAG

altered gDNA sequence snippet

TGACCGTCTCATTCACAAACAAAGTCTTCACAACTGGTGAG

original cDNA sequence snippet

TGACCGTCTCATTCACAAACGAAGTCTTCACAACTGAGACT

altered cDNA sequence snippet

TGACCGTCTCATTCACAAACAAAGTCTTCACAACTGAGACT

wildtype AA sequence

mutated AA sequence

speed

0.85 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems