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: ENST00000355468
Querying Taster for transcript #2: ENST00000393928
MT speed 0 s - this script 3.702307 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
P3H4	polymorphism_automatic	2.93397887239921e-05	simple_aae				Q186R	single base exchange	rs13412		show file
P3H4	polymorphism_automatic	2.93397887239921e-05	simple_aae				Q186R	single base exchange	rs13412		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999970660211276 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:39967442T>CN/A show variant in all transcripts IGV

HGNC symbol

P3H4

Ensembl transcript ID

ENST00000355468

Genbank transcript ID

N/A

UniProt peptide

Q92791

alteration type

single base exchange

alteration region

CDS

DNA changes

c.557A>G
cDNA.1024A>G
g.1415A>G

AA changes

Q186R Score: 43 explain score(s)

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

186

frameshift

known variant

Reference ID: rs13412

database	homozygous (C/C)	heterozygous	allele carriers
1000G	380	1089	1469
ExAC	8970	14827	23797

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
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
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.868	0.989
	0.819	0.986
(flanking)	0.016	0.978

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

186

mutated

all conserved

186

Ptroglodytes

no homologue

Mmulatta

no homologue

Fcatus

all conserved

ENSFCAG00000002135

Mmusculus

all conserved

ENSMUSG00000006931

192

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000016036

180

Drerio

all conserved

ENSDARG00000057946

184

Dmelanogaster

no homologue

Celegans

not conserved

Y73F8A.26

165

Xtropicalis

all conserved

ENSXETG00000002284

189

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1314 / 1314

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

438 / 438

position of stopcodon in wt / mu cDNA

1781 / 1781

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

468 / 468

chromosome

strand

-1

last intron/exon boundary

1759

theoretical NMD boundary in CDS

1241

length of CDS

1314

coding sequence (CDS) position

557

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

1024

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

1415

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

39967442

original gDNA sequence snippet

CAAGTATCTCAACTACTATCAGGGGATGCTGGACGTCGCCG

altered gDNA sequence snippet

CAAGTATCTCAACTACTATCGGGGGATGCTGGACGTCGCCG

original cDNA sequence snippet

CAAGTATCTCAACTACTATCAGGGGATGCTGGACGTCGCCG

altered cDNA sequence snippet

CAAGTATCTCAACTACTATCGGGGGATGCTGGACGTCGCCG

wildtype AA sequence

MARVAWGLLW LLLGSAGAQY EKYSFRGFPP EDLMPLAAAY GHALEQYEGE SWRESARYLE
AALRLHRLLR DSEAFCHANC SGPAPAAKPD PDGGRADEWA CELRLFGRVL ERAACLRRCK
RTLPAFQVPY PPRQLLRDFQ SRLPYQYLHY ALFKANRLEK AVAAAYTFLQ RNPKHELTAK
YLNYYQGMLD VADESLTDLE AQPYEAVFLR AVKLYNSGDF RSSTEDMERA LSEYLAVFAR
CLAGCEGAHE QVDFKDFYPA IADLFAESLQ CKVDCEANLT PNVGGYFVDK FVATMYHYLQ
FAYYKLNDVR QAARSAASYM LFDPKDSVMQ QNLVYYRFHR ARWGLEEEDF QPREEAMLYH
NQTAELRELL EFTHMYLQSD DEMELEETEP PLEPEDALSD AEFEGEGDYE EGMYADWWQE
PDAKGDEAEA EPEPELA*

mutated AA sequence

MARVAWGLLW LLLGSAGAQY EKYSFRGFPP EDLMPLAAAY GHALEQYEGE SWRESARYLE
AALRLHRLLR DSEAFCHANC SGPAPAAKPD PDGGRADEWA CELRLFGRVL ERAACLRRCK
RTLPAFQVPY PPRQLLRDFQ SRLPYQYLHY ALFKANRLEK AVAAAYTFLQ RNPKHELTAK
YLNYYRGMLD VADESLTDLE AQPYEAVFLR AVKLYNSGDF RSSTEDMERA LSEYLAVFAR
CLAGCEGAHE QVDFKDFYPA IADLFAESLQ CKVDCEANLT PNVGGYFVDK FVATMYHYLQ
FAYYKLNDVR QAARSAASYM LFDPKDSVMQ QNLVYYRFHR ARWGLEEEDF QPREEAMLYH
NQTAELRELL EFTHMYLQSD DEMELEETEP PLEPEDALSD AEFEGEGDYE EGMYADWWQE
PDAKGDEAEA EPEPELA*

speed

0.43 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: 0.999970660211276 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:39967442T>CN/A show variant in all transcripts IGV

HGNC symbol

P3H4

Ensembl transcript ID

ENST00000393928

Genbank transcript ID

NM_006455

UniProt peptide

Q92791

alteration type

single base exchange

alteration region

CDS

DNA changes

c.557A>G
cDNA.841A>G
g.1415A>G

AA changes

Q186R Score: 43 explain score(s)

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

186

frameshift

known variant

Reference ID: rs13412

database	homozygous (C/C)	heterozygous	allele carriers
1000G	380	1089	1469
ExAC	8970	14827	23797

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.868	0.989
	0.819	0.986
(flanking)	0.016	0.978

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

186

mutated

all conserved

186

Ptroglodytes

no homologue

Mmulatta

no homologue

Fcatus

all conserved

ENSFCAG00000002135

Mmusculus

all conserved

ENSMUSG00000006931

192

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000016036

180

Drerio

all conserved

ENSDARG00000057946

184

Dmelanogaster

no homologue

Celegans

not conserved

Y73F8A.26

165

Xtropicalis

all conserved

ENSXETG00000002284

189

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1314 / 1314

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

438 / 438

position of stopcodon in wt / mu cDNA

1598 / 1598

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

285 / 285

chromosome

strand

-1

last intron/exon boundary

1576

theoretical NMD boundary in CDS

1241

length of CDS

1314

coding sequence (CDS) position

557

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

841

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

1415

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

39967442

original gDNA sequence snippet

CAAGTATCTCAACTACTATCAGGGGATGCTGGACGTCGCCG

altered gDNA sequence snippet

CAAGTATCTCAACTACTATCGGGGGATGCTGGACGTCGCCG

original cDNA sequence snippet

CAAGTATCTCAACTACTATCAGGGGATGCTGGACGTCGCCG

altered cDNA sequence snippet

CAAGTATCTCAACTACTATCGGGGGATGCTGGACGTCGCCG

wildtype AA sequence

mutated AA sequence

MARVAWGLLW LLLGSAGAQY EKYSFRGFPP EDLMPLAAAY GHALEQYEGE SWRESARYLE
AALRLHRLLR DSEAFCHANC SGPAPAAKPD PDGGRADEWA CELRLFGRVL ERAACLRRCK
RTLPAFQVPY PPRQLLRDFQ SRLPYQYLHY ALFKANRLEK AVAAAYTFLQ RNPKHELTAK
YLNYYRGMLD VADESLTDLE AQPYEAVFLR AVKLYNSGDF RSSTEDMERA LSEYLAVFAR
CLAGCEGAHE QVDFKDFYPA IADLFAESLQ CKVDCEANLT PNVGGYFVDK FVATMYHYLQ
FAYYKLNDVR QAARSAASYM LFDPKDSVMQ QNLVYYRFHR ARWGLEEEDF QPREEAMLYH
NQTAELRELL EFTHMYLQSD DEMELEETEP PLEPEDALSD AEFEGEGDYE EGMYADWWQE
PDAKGDEAEA EPEPELA*

speed

1.31 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems