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: ENST00000370656
Querying Taster for transcript #2: ENST00000370654
MT speed 0 s - this script 4.551319 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
RPF1	polymorphism_automatic	1.12689857445503e-11	simple_aae				S9G	single base exchange	rs2292191		show file
RPF1	polymorphism_automatic	1.12689857445503e-11	simple_aae				S9G	single base exchange	rs2292191		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999988731 (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)

chr1:84944989A>GN/A show variant in all transcripts IGV

HGNC symbol

RPF1

Ensembl transcript ID

ENST00000370656

Genbank transcript ID

N/A

UniProt peptide

Q9H9Y2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.25A>G
cDNA.48A>G
g.48A>G

AA changes

S9G Score: 56 explain score(s)

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

frameshift

known variant

Reference ID: rs2292191

database	homozygous (G/G)	heterozygous	allele carriers
1000G	706	1044	1750
ExAC	20187	-7607	12580

regulatory features

Cmyc, Transcription Factor, Cmyc TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
FAIRE, Open Chromatin, Formaldehyde-Assisted Isolation of Regulatory Elements
Gabp, Transcription Factor, Gabp TF binding
H2AZ, Histone, Histone 2A variant Z
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
H2BK20ac, Histone, Histone 2B Lysine 20 Acetylation
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36ac, Histone, Histone 3 Lysine 36 Acetylation
H3K4ac, Histone, Histone 3 Lysine 4 Acetylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Max, Transcription Factor, Max TF binding
Nanog, Transcription Factor, Nanog Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
Tr4, Transcription Factor, Tr4 Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.153	0.01
	0.728	0.027
(flanking)	1.231	0.053

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

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000000901

Mmulatta

all identical

ENSMMUG00000022181

Fcatus

not conserved

ENSFCAG00000008791

Mmusculus

not conserved

ENSMUSG00000028187

Ggallus

no alignment

ENSGALG00000008796

n/a

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000005738

n/a

Dmelanogaster

all conserved

FBgn0032408

Celegans

no alignment

F44G4.1

n/a

Xtropicalis

not conserved

ENSXETG00000008642

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

390 / 390

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

130 / 130

position of stopcodon in wt / mu cDNA

413 / 413

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

24 / 24

chromosome

strand

last intron/exon boundary

309

theoretical NMD boundary in CDS

235

length of CDS

390

coding sequence (CDS) position

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

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

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

84944989

original gDNA sequence snippet

CGAAAGCCGGGGATAAGAGCAGCAGCAGCGGGAAGAAAAGT

altered gDNA sequence snippet

CGAAAGCCGGGGATAAGAGCGGCAGCAGCGGGAAGAAAAGT

original cDNA sequence snippet

CGAAAGCCGGGGATAAGAGCAGCAGCAGCGGGAAGAAAAGT

altered cDNA sequence snippet

CGAAAGCCGGGGATAAGAGCGGCAGCAGCGGGAAGAAAAGT

wildtype AA sequence

MAKAGDKSSS SGKKSLKRKA AAEELQEAAG AGDGATENGV QPPKAAAFPP GFSISEIKNK
QRRHLMFTRW KQQQRKEKLA AKKKLKKERE ALGDKAPPKP VPKTIDNQRV YDETTVDPND
EEVMLEVLN*

mutated AA sequence

MAKAGDKSGS SGKKSLKRKA AAEELQEAAG AGDGATENGV QPPKAAAFPP GFSISEIKNK
QRRHLMFTRW KQQQRKEKLA AKKKLKKERE ALGDKAPPKP VPKTIDNQRV YDETTVDPND
EEVMLEVLN*

speed

1.33 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: 0.999999999988731 (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)

chr1:84944989A>GN/A show variant in all transcripts IGV

HGNC symbol

RPF1

Ensembl transcript ID

ENST00000370654

Genbank transcript ID

NM_025065

UniProt peptide

Q9H9Y2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.25A>G
cDNA.40A>G
g.48A>G

AA changes

S9G Score: 56 explain score(s)

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

frameshift

known variant

Reference ID: rs2292191

database	homozygous (G/G)	heterozygous	allele carriers
1000G	706	1044	1750
ExAC	20187	-7607	12580

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.153	0.01
	0.728	0.027
(flanking)	1.231	0.053

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

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000000901

Mmulatta

all identical

ENSMMUG00000022181

Fcatus

not conserved

ENSFCAG00000008791

Mmusculus

not conserved

ENSMUSG00000028187

Ggallus

no alignment

ENSGALG00000008796

n/a

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000005738

n/a

Dmelanogaster

all conserved

FBgn0032408

Celegans

no alignment

F44G4.1

n/a

Xtropicalis

not conserved

ENSXETG00000008642

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1050 / 1050

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

350 / 350

position of stopcodon in wt / mu cDNA

1065 / 1065

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

16 / 16

chromosome

strand

last intron/exon boundary

1024

theoretical NMD boundary in CDS

958

length of CDS

1050

coding sequence (CDS) position

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

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

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

84944989

original gDNA sequence snippet

CGAAAGCCGGGGATAAGAGCAGCAGCAGCGGGAAGAAAAGT

altered gDNA sequence snippet

CGAAAGCCGGGGATAAGAGCGGCAGCAGCGGGAAGAAAAGT

original cDNA sequence snippet

CGAAAGCCGGGGATAAGAGCAGCAGCAGCGGGAAGAAAAGT

altered cDNA sequence snippet

CGAAAGCCGGGGATAAGAGCGGCAGCAGCGGGAAGAAAAGT

wildtype AA sequence

MAKAGDKSSS SGKKSLKRKA AAEELQEAAG AGDGATENGV QPPKAAAFPP GFSISEIKNK
QRRHLMFTRW KQQQRKEKLA AKKKLKKERE ALGDKAPPKP VPKTIDNQRV YDETTVDPND
EEVAYDEATD EFASYFNKQT SPKILITTSD RPHGRTVRLC EQLSTVIPNS HVYYRRGLAL
KKIIPQCIAR DFTDLIVINE DRKTPNGLIL SHLPNGPTAH FKMSSVRLRK EIKRRGKDPT
EHIPEIILNN FTTRLGHSIG RMFASLFPHN PQFIGRQVAT FHNQRDYIFF RFHRYIFRSE
KKVGIQELGP RFTLKLRSLQ KGTFDSKYGE YEWVHKPREM DTSRRKFHL*

mutated AA sequence

MAKAGDKSGS SGKKSLKRKA AAEELQEAAG AGDGATENGV QPPKAAAFPP GFSISEIKNK
QRRHLMFTRW KQQQRKEKLA AKKKLKKERE ALGDKAPPKP VPKTIDNQRV YDETTVDPND
EEVAYDEATD EFASYFNKQT SPKILITTSD RPHGRTVRLC EQLSTVIPNS HVYYRRGLAL
KKIIPQCIAR DFTDLIVINE DRKTPNGLIL SHLPNGPTAH FKMSSVRLRK EIKRRGKDPT
EHIPEIILNN FTTRLGHSIG RMFASLFPHN PQFIGRQVAT FHNQRDYIFF RFHRYIFRSE
KKVGIQELGP RFTLKLRSLQ KGTFDSKYGE YEWVHKPREM DTSRRKFHL*

speed

1.32 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems