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: ENST00000404460
Querying Taster for transcript #2: ENST00000303908
MT speed 0 s - this script 4.593653 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PLEKHB2	polymorphism_automatic	0.00119110081634899	simple_aae		affected		R220M	single base exchange	rs373666409		show file
PLEKHB2	polymorphism_automatic	0.00119110081634899	simple_aae		affected		R220M	single base exchange	rs373666409		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.998808899183651 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:132110828G>TN/A show variant in all transcripts IGV

HGNC symbol

PLEKHB2

Ensembl transcript ID

ENST00000404460

Genbank transcript ID

N/A

UniProt peptide

Q96CS7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.659G>T
cDNA.713G>T
g.248409G>T

AA changes

R220M Score: 91 explain score(s)

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

220

frameshift

known variant

Reference ID: rs373666409

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1424	917	2341
ExAC	1665	1600	3265

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.337	0.977
	-0.068	0.981
(flanking)	2.046	0.995

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	248412	wt: 0.32 / mu: 0.50	wt: GAGGGCGCCCAGCCT mu: GATGGCGCCCAGCCT	GGGC\|gccc

distance from splice site

236

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

220

mutated

not conserved

220

Ptroglodytes

all identical

ENSPTRG00000012461

219

Mmulatta

no alignment

ENSMMUG00000006158

n/a

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000026123

Ggallus

no alignment

ENSGALG00000002169

n/a

Trubripes

no alignment

ENSTRUG00000016204

n/a

Drerio

no alignment

ENSDARG00000013928

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000026788

n/a

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

930 / 930

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

310 / 310

position of stopcodon in wt / mu cDNA

984 / 984

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

55 / 55

chromosome

strand

last intron/exon boundary

478

theoretical NMD boundary in CDS

373

length of CDS

930

coding sequence (CDS) position

659

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

713

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

248409

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

132110828

original gDNA sequence snippet

AACATGGTTTGCAGGGAAGAGGGCGCCCAGCCTCCCCACAG

altered gDNA sequence snippet

AACATGGTTTGCAGGGAAGATGGCGCCCAGCCTCCCCACAG

original cDNA sequence snippet

AACATGGTTTGCAGGGAAGAGGGCGCCCAGCCTCCCCACAG

altered cDNA sequence snippet

AACATGGTTTGCAGGGAAGATGGCGCCCAGCCTCCCCACAG

wildtype AA sequence

MAFVKSGWLL RQSTILKRWK KNWFDLWSDG HLIYYDDQTR QNIEDKVHMP MDCINIRTGQ
ECRDTQPPDG KSKDCMLQIV CRDGKTISLC AESTDDCLAW KFTLQDSRTN TAYVGSAVMT
DETSVVSSPP PYTAYAAPAP EELHSKGPKI HTTTSAKTQA VLPTRCFFPS ESPIRRSVQI
SVLLPAVNIR RRIKLTFPQP ARPRAPRSLC LWQTWFAGKR APSLPTAATA PALPSCPSPP
APSQALPPSL AGWRSPSSAP LPPEQALAPR SFQLSKHQAR PRPHRPGTPP VPAWPGVPPP
PPARPPALR*

mutated AA sequence

MAFVKSGWLL RQSTILKRWK KNWFDLWSDG HLIYYDDQTR QNIEDKVHMP MDCINIRTGQ
ECRDTQPPDG KSKDCMLQIV CRDGKTISLC AESTDDCLAW KFTLQDSRTN TAYVGSAVMT
DETSVVSSPP PYTAYAAPAP EELHSKGPKI HTTTSAKTQA VLPTRCFFPS ESPIRRSVQI
SVLLPAVNIR RRIKLTFPQP ARPRAPRSLC LWQTWFAGKM APSLPTAATA PALPSCPSPP
APSQALPPSL AGWRSPSSAP LPPEQALAPR SFQLSKHQAR PRPHRPGTPP VPAWPGVPPP
PPARPPALR*

speed

1.32 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: 0.998808899183651 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:132110828G>TN/A show variant in all transcripts IGV

HGNC symbol

PLEKHB2

Ensembl transcript ID

ENST00000303908

Genbank transcript ID

N/A

UniProt peptide

Q96CS7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.659G>T
cDNA.659G>T
g.248409G>T

AA changes

R220M Score: 91 explain score(s)

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

220

frameshift

known variant

Reference ID: rs373666409

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1424	917	2341
ExAC	1665	1600	3265

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.337	0.977
	-0.068	0.981
(flanking)	2.046	0.995

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	248412	wt: 0.32 / mu: 0.50	wt: GAGGGCGCCCAGCCT mu: GATGGCGCCCAGCCT	GGGC\|gccc

distance from splice site

236

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

220

mutated

not conserved

220

Ptroglodytes

all identical

ENSPTRG00000012461

219

Mmulatta

no alignment

ENSMMUG00000006158

n/a

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000026123

Ggallus

no alignment

ENSGALG00000002169

n/a

Trubripes

no alignment

ENSTRUG00000016204

n/a

Drerio

no alignment

ENSDARG00000013928

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000026788

n/a

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

930 / 930

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

310 / 310

position of stopcodon in wt / mu cDNA

930 / 930

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

1 / 1

chromosome

strand

last intron/exon boundary

424

theoretical NMD boundary in CDS

373

length of CDS

930

coding sequence (CDS) position

659

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

659

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

248409

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

132110828

original gDNA sequence snippet

AACATGGTTTGCAGGGAAGAGGGCGCCCAGCCTCCCCACAG

altered gDNA sequence snippet

AACATGGTTTGCAGGGAAGATGGCGCCCAGCCTCCCCACAG

original cDNA sequence snippet

AACATGGTTTGCAGGGAAGAGGGCGCCCAGCCTCCCCACAG

altered cDNA sequence snippet

AACATGGTTTGCAGGGAAGATGGCGCCCAGCCTCCCCACAG

wildtype AA sequence

mutated AA sequence

MAFVKSGWLL RQSTILKRWK KNWFDLWSDG HLIYYDDQTR QNIEDKVHMP MDCINIRTGQ
ECRDTQPPDG KSKDCMLQIV CRDGKTISLC AESTDDCLAW KFTLQDSRTN TAYVGSAVMT
DETSVVSSPP PYTAYAAPAP EELHSKGPKI HTTTSAKTQA VLPTRCFFPS ESPIRRSVQI
SVLLPAVNIR RRIKLTFPQP ARPRAPRSLC LWQTWFAGKM APSLPTAATA PALPSCPSPP
APSQALPPSL AGWRSPSSAP LPPEQALAPR SFQLSKHQAR PRPHRPGTPP VPAWPGVPPP
PPARPPALR*

speed

1.32 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems