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: ENST00000301146
Querying Taster for transcript #2: ENST00000291764
MT speed 0 s - this script 3.507798 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CYP2A7	polymorphism_automatic	2.59792187762287e-14	simple_aae				T347A	single base exchange	rs2302987		show file
CYP2A7	polymorphism_automatic	2.59792187762287e-14	simple_aae				T296A	single base exchange	rs2302987		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999974 (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)

chr19:41383217T>CN/A show variant in all transcripts IGV

HGNC symbol

CYP2A7

Ensembl transcript ID

ENST00000301146

Genbank transcript ID

NM_000764

UniProt peptide

P20853

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1039A>G
cDNA.1581A>G
g.5441A>G

AA changes

T347A Score: 58 explain score(s)

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

347

frameshift

known variant

Reference ID: rs2302987

database	homozygous (C/C)	heterozygous	allele carriers
1000G	112	706	818
ExAC	3407	18796	22203

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.631	0.001
	-0.869	0
(flanking)	-1.338	0.001

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 marginally increased	5440	wt: 0.9294 / mu: 0.9969 (marginal change - not scored)	wt: GACCGGACCAAGATG mu: GACCGGGCCAAGATG	CCGG\|acca
Donor marginally increased	5433	wt: 0.2038 / mu: 0.2103 (marginal change - not scored)	wt: GTTTGAGGACCGGAC mu: GTTTGAGGACCGGGC	TTGA\|ggac

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

347

mutated

not conserved

347

Ptroglodytes

all identical

ENSPTRG00000033800

243

Mmulatta

not conserved

ENSMMUG00000021068

347

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000018696

349

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1485 / 1485

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

495 / 495

position of stopcodon in wt / mu cDNA

2027 / 2027

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

543 / 543

chromosome

strand

-1

last intron/exon boundary

1846

theoretical NMD boundary in CDS

1253

length of CDS

1485

coding sequence (CDS) position

1039

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

1581

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

5441

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

41383217

original gDNA sequence snippet

AGCCCAAGTTTGAGGACCGGACCAAGATGCCCTACATGGAG

altered gDNA sequence snippet

AGCCCAAGTTTGAGGACCGGGCCAAGATGCCCTACATGGAG

original cDNA sequence snippet

AGCCCAAGTTTGAGGACCGGACCAAGATGCCCTACATGGAG

altered cDNA sequence snippet

AGCCCAAGTTTGAGGACCGGGCCAAGATGCCCTACATGGAG

wildtype AA sequence

MLASGLLLVA LLACLTVMVL MSVWQQRKSR GKLPPGPTPL PFIGNYLQLN TEHICDSIMK
FSECYGPVFT IHLGPRRVVV LCGHDAVREA LVDQAEEFSG RGEQATFDWV FKGYGVAFSN
GERAKQLLRF AIATLRDFGV GKRGIEERIQ EESGFLIEAI RSTHGANIDP TFFLSRTVSN
VISSIVFGDR FDYEDKEFLS LLSMMLGIFQ FTSTSTGQLY EMFSSVMKHL PGPQQQAFKL
LQGLEDFIAK KVEHNQRTLD PNSPQDFIDS FLIHMQEEEK NPNTEFYLKN LMMSTLNLFI
AGTETVSTTL RYGFLLLMKH PEVEAKVHEE IDRVIGKNRQ PKFEDRTKMP YMEAVIHEIQ
RFGDVIPMSL ARRVKKDTKF RDFFLPKGTE VFPMLGSVLR DPSFFSNPQD FNPQHFLDDK
GQFKKSDAFV PFSIGKRNCF GEGLARMELF LFFTTVMQNF RLKSSQSPKD IDVSPKHVVF
ATIPRNYTMS FLPR*

mutated AA sequence

MLASGLLLVA LLACLTVMVL MSVWQQRKSR GKLPPGPTPL PFIGNYLQLN TEHICDSIMK
FSECYGPVFT IHLGPRRVVV LCGHDAVREA LVDQAEEFSG RGEQATFDWV FKGYGVAFSN
GERAKQLLRF AIATLRDFGV GKRGIEERIQ EESGFLIEAI RSTHGANIDP TFFLSRTVSN
VISSIVFGDR FDYEDKEFLS LLSMMLGIFQ FTSTSTGQLY EMFSSVMKHL PGPQQQAFKL
LQGLEDFIAK KVEHNQRTLD PNSPQDFIDS FLIHMQEEEK NPNTEFYLKN LMMSTLNLFI
AGTETVSTTL RYGFLLLMKH PEVEAKVHEE IDRVIGKNRQ PKFEDRAKMP YMEAVIHEIQ
RFGDVIPMSL ARRVKKDTKF RDFFLPKGTE VFPMLGSVLR DPSFFSNPQD FNPQHFLDDK
GQFKKSDAFV PFSIGKRNCF GEGLARMELF LFFTTVMQNF RLKSSQSPKD IDVSPKHVVF
ATIPRNYTMS FLPR*

speed

0.79 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: 0.999999999999974 (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)

chr19:41383217T>CN/A show variant in all transcripts IGV

HGNC symbol

CYP2A7

Ensembl transcript ID

ENST00000291764

Genbank transcript ID

NM_030589

UniProt peptide

P20853

alteration type

single base exchange

alteration region

CDS

DNA changes

c.886A>G
cDNA.1428A>G
g.5441A>G

AA changes

T296A Score: 58 explain score(s)

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

296

frameshift

known variant

Reference ID: rs2302987

database	homozygous (C/C)	heterozygous	allele carriers
1000G	112	706	818
ExAC	3407	18796	22203

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.631	0.001
	-0.869	0
(flanking)	-1.338	0.001

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 marginally increased	5440	wt: 0.9294 / mu: 0.9969 (marginal change - not scored)	wt: GACCGGACCAAGATG mu: GACCGGGCCAAGATG	CCGG\|acca
Donor marginally increased	5433	wt: 0.2038 / mu: 0.2103 (marginal change - not scored)	wt: GTTTGAGGACCGGAC mu: GTTTGAGGACCGGGC	TTGA\|ggac

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

296

mutated

not conserved

296

Ptroglodytes

all identical

ENSPTRG00000033800

243

Mmulatta

not conserved

ENSMMUG00000021068

347

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000018696

349

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1332 / 1332

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

444 / 444

position of stopcodon in wt / mu cDNA

1874 / 1874

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

543 / 543

chromosome

strand

-1

last intron/exon boundary

1693

theoretical NMD boundary in CDS

1100

length of CDS

1332

coding sequence (CDS) position

886

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

1428

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

5441

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

41383217

original gDNA sequence snippet

AGCCCAAGTTTGAGGACCGGACCAAGATGCCCTACATGGAG

altered gDNA sequence snippet

AGCCCAAGTTTGAGGACCGGGCCAAGATGCCCTACATGGAG

original cDNA sequence snippet

AGCCCAAGTTTGAGGACCGGACCAAGATGCCCTACATGGAG

altered cDNA sequence snippet

AGCCCAAGTTTGAGGACCGGGCCAAGATGCCCTACATGGAG

wildtype AA sequence

MLASGLLLVA LLACLTVMVL MSVWQQRKSR GKLPPGPTPL PFIGNYLQLN TEHICDSIMK
VSQGVAFSNG ERAKQLLRFA IATLRDFGVG KRGIEERIQE ESGFLIEAIR STHGANIDPT
FFLSRTVSNV ISSIVFGDRF DYEDKEFLSL LSMMLGIFQF TSTSTGQLYE MFSSVMKHLP
GPQQQAFKLL QGLEDFIAKK VEHNQRTLDP NSPQDFIDSF LIHMQEEEKN PNTEFYLKNL
MMSTLNLFIA GTETVSTTLR YGFLLLMKHP EVEAKVHEEI DRVIGKNRQP KFEDRTKMPY
MEAVIHEIQR FGDVIPMSLA RRVKKDTKFR DFFLPKGTEV FPMLGSVLRD PSFFSNPQDF
NPQHFLDDKG QFKKSDAFVP FSIGKRNCFG EGLARMELFL FFTTVMQNFR LKSSQSPKDI
DVSPKHVVFA TIPRNYTMSF LPR*

mutated AA sequence

MLASGLLLVA LLACLTVMVL MSVWQQRKSR GKLPPGPTPL PFIGNYLQLN TEHICDSIMK
VSQGVAFSNG ERAKQLLRFA IATLRDFGVG KRGIEERIQE ESGFLIEAIR STHGANIDPT
FFLSRTVSNV ISSIVFGDRF DYEDKEFLSL LSMMLGIFQF TSTSTGQLYE MFSSVMKHLP
GPQQQAFKLL QGLEDFIAKK VEHNQRTLDP NSPQDFIDSF LIHMQEEEKN PNTEFYLKNL
MMSTLNLFIA GTETVSTTLR YGFLLLMKHP EVEAKVHEEI DRVIGKNRQP KFEDRAKMPY
MEAVIHEIQR FGDVIPMSLA RRVKKDTKFR DFFLPKGTEV FPMLGSVLRD PSFFSNPQDF
NPQHFLDDKG QFKKSDAFVP FSIGKRNCFG EGLARMELFL FFTTVMQNFR LKSSQSPKDI
DVSPKHVVFA TIPRNYTMSF LPR*

speed

0.78 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems