MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000395097
Querying Taster for transcript #2: ENST00000338488
Querying Taster for transcript #3: ENST00000330847
MT speed 0 s - this script 2.393968 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
NR4A3	polymorphism_automatic	0.00665102416865504	simple_aae				S240G	single base exchange	rs12344570		show file
NR4A3	polymorphism_automatic	0.00665102416865504	simple_aae				S240G	single base exchange	rs12344570		show file
NR4A3	polymorphism_automatic	0.00665102416865504	simple_aae				S251G	single base exchange	rs12344570		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.993348975831345 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:102591042A>GN/A show variant in all transcripts IGV

HGNC symbol

NR4A3

Ensembl transcript ID

ENST00000395097

Genbank transcript ID

NM_006981

UniProt peptide

Q92570

alteration type

single base exchange

alteration region

CDS

DNA changes

c.718A>G
cDNA.1447A>G
g.6906A>G

AA changes

S240G Score: 56 explain score(s)

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

240

frameshift

known variant

Reference ID: rs12344570

database	homozygous (G/G)	heterozygous	allele carriers
1000G	385	1099	1484
ExAC	313	1257	1570

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.928	1
	0.678	1
(flanking)	2.201	1

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

234

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

240

mutated

not conserved

240

Ptroglodytes

not conserved

ENSPTRG00000021186

251

Mmulatta

not conserved

ENSMMUG00000011410

251

Fcatus

no alignment

ENSFCAG00000008621

n/a

Mmusculus

not conserved

ENSMUSG00000028341

271

Ggallus

all identical

ENSGALG00000013568

216

Trubripes

not conserved

ENSTRUG00000011235

204

SVSLH

Drerio

all identical

ENSDARG00000055854

209

Dmelanogaster

all identical

FBgn0014859

669

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
240	240	CONFLICT	S -> G (in Ref. 1 and 2).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1881 / 1881

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

627 / 627

position of stopcodon in wt / mu cDNA

2610 / 2610

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

730 / 730

chromosome

strand

last intron/exon boundary

2363

theoretical NMD boundary in CDS

1583

length of CDS

1881

coding sequence (CDS) position

718

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

1447

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

6906

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

102591042

original gDNA sequence snippet

GCCAGGCCGCCGCGCTTGAGAGCCACCCGTACGGGCTGCCG

altered gDNA sequence snippet

GCCAGGCCGCCGCGCTTGAGGGCCACCCGTACGGGCTGCCG

original cDNA sequence snippet

GCCAGGCCGCCGCGCTTGAGAGCCACCCGTACGGGCTGCCG

altered cDNA sequence snippet

GCCAGGCCGCCGCGCTTGAGGGCCACCCGTACGGGCTGCCG

wildtype AA sequence

MPCVQAQYSP SPPGSSYAAQ TYSSEYTTEI MNPDYTKLTM DLGSTEITAT ATTSLPSIST
FVEGYSSNYE LKPSCVYQMQ RPLIKVEEGR APSYHHHHHH HHHHHHHHQQ QHQQPSIPPA
SSPEDEVLPS TSMYFKQSPP STPTTPAFPP QAGALWDEAL PSAPGCIAPG PLLDPPMKAV
PTVAGARFPL FHFKPSPPHP PAPSPAGGHH LGYDPTAAAA LSLPLGAAAA AGSQAAALES
HPYGLPLAKR AAPLAFPPLG LTPSPTASSL LGESPSLPSP PSRSSSSGEG TCAVCGDNAA
CQHYGVRTCE GCKGFFKRTV QKNAKYVCLA NKNCPVDKRR RNRCQYCRFQ KCLSVGMVKE
VVRTDSLKGR RGRLPSKPKS PLQQEPSQPS PPSPPICMMN ALVRALTDST PRDLDYSRYC
PTDQAAAGTD AEHVQQFYNL LTASIDVSRS WAEKIPGFTD LPKEDQTLLI ESAFLELFVL
RLSIRSNTAE DKFVFCNGLV LHRLQCLRGF GEWLDSIKDF SLNLQSLNLD IQALACLSAL
SMITERHGLK EPKRVEELCN KITSSLKDHQ SKGQALEPTE SKVLGALVEL RKICTLGLQR
IFYLKLEDLV SPPSIIDKLF LDTLPF*

mutated AA sequence

MPCVQAQYSP SPPGSSYAAQ TYSSEYTTEI MNPDYTKLTM DLGSTEITAT ATTSLPSIST
FVEGYSSNYE LKPSCVYQMQ RPLIKVEEGR APSYHHHHHH HHHHHHHHQQ QHQQPSIPPA
SSPEDEVLPS TSMYFKQSPP STPTTPAFPP QAGALWDEAL PSAPGCIAPG PLLDPPMKAV
PTVAGARFPL FHFKPSPPHP PAPSPAGGHH LGYDPTAAAA LSLPLGAAAA AGSQAAALEG
HPYGLPLAKR AAPLAFPPLG LTPSPTASSL LGESPSLPSP PSRSSSSGEG TCAVCGDNAA
CQHYGVRTCE GCKGFFKRTV QKNAKYVCLA NKNCPVDKRR RNRCQYCRFQ KCLSVGMVKE
VVRTDSLKGR RGRLPSKPKS PLQQEPSQPS PPSPPICMMN ALVRALTDST PRDLDYSRYC
PTDQAAAGTD AEHVQQFYNL LTASIDVSRS WAEKIPGFTD LPKEDQTLLI ESAFLELFVL
RLSIRSNTAE DKFVFCNGLV LHRLQCLRGF GEWLDSIKDF SLNLQSLNLD IQALACLSAL
SMITERHGLK EPKRVEELCN KITSSLKDHQ SKGQALEPTE SKVLGALVEL RKICTLGLQR
IFYLKLEDLV SPPSIIDKLF LDTLPF*

speed

0.27 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: 0.993348975831345 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:102591042A>GN/A show variant in all transcripts IGV

HGNC symbol

NR4A3

Ensembl transcript ID

ENST00000338488

Genbank transcript ID

NM_173199

UniProt peptide

Q92570

alteration type

single base exchange

alteration region

CDS

DNA changes

c.718A>G
cDNA.1447A>G
g.6906A>G

AA changes

S240G Score: 56 explain score(s)

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

240

frameshift

known variant

Reference ID: rs12344570

database	homozygous (G/G)	heterozygous	allele carriers
1000G	385	1099	1484
ExAC	313	1257	1570

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.928	1
	0.678	1
(flanking)	2.201	1

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

234

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

240

mutated

not conserved

240

Ptroglodytes

not conserved

ENSPTRG00000021186

251

Mmulatta

not conserved

ENSMMUG00000011410

251

Fcatus

no alignment

ENSFCAG00000008621

n/a

Mmusculus

not conserved

ENSMUSG00000028341

271

Ggallus

all identical

ENSGALG00000013568

216

Trubripes

not conserved

ENSTRUG00000011235

204

SVSLH

Drerio

all identical

ENSDARG00000055854

209

Dmelanogaster

all identical

FBgn0014859

669

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
240	240	CONFLICT	S -> G (in Ref. 1 and 2).	lost

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

2061 / 2061

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

730 / 730

chromosome

strand

last intron/exon boundary

1811

theoretical NMD boundary in CDS

1031

length of CDS

1332

coding sequence (CDS) position

718

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

1447

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

6906

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

102591042

original gDNA sequence snippet

GCCAGGCCGCCGCGCTTGAGAGCCACCCGTACGGGCTGCCG

altered gDNA sequence snippet

GCCAGGCCGCCGCGCTTGAGGGCCACCCGTACGGGCTGCCG

original cDNA sequence snippet

GCCAGGCCGCCGCGCTTGAGAGCCACCCGTACGGGCTGCCG

altered cDNA sequence snippet

GCCAGGCCGCCGCGCTTGAGGGCCACCCGTACGGGCTGCCG

wildtype AA sequence

mutated AA sequence

MPCVQAQYSP SPPGSSYAAQ TYSSEYTTEI MNPDYTKLTM DLGSTEITAT ATTSLPSIST
FVEGYSSNYE LKPSCVYQMQ RPLIKVEEGR APSYHHHHHH HHHHHHHHQQ QHQQPSIPPA
SSPEDEVLPS TSMYFKQSPP STPTTPAFPP QAGALWDEAL PSAPGCIAPG PLLDPPMKAV
PTVAGARFPL FHFKPSPPHP PAPSPAGGHH LGYDPTAAAA LSLPLGAAAA AGSQAAALEG
HPYGLPLAKR AAPLAFPPLG LTPSPTASSL LGESPSLPSP PSRSSSSGEG TCAVCGDNAA
CQHYGVRTCE GCKGFFKRTV QKNAKYVCLA NKNCPVDKRR RNRCQYCRFQ KCLSVGMVKE
VVRTDSLKGR RGRLPSKPKS PLQQEPSQPS PPSPPICMMN ALVRALTDST PRDLDYSRVS
FMISCFQMND QGLYLWLLVI RVD*

speed

0.32 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.993348975831345 (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)

chr9:102591042A>GN/A show variant in all transcripts IGV

HGNC symbol

NR4A3

Ensembl transcript ID

ENST00000330847

Genbank transcript ID

NM_173200

UniProt peptide

Q92570

alteration type

single base exchange

alteration region

CDS

DNA changes

c.751A>G
cDNA.795A>G
g.6906A>G

AA changes

S251G Score: 56 explain score(s)

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

251

frameshift

known variant

Reference ID: rs12344570

database	homozygous (G/G)	heterozygous	allele carriers
1000G	385	1099	1484
ExAC	313	1257	1570

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.928	1
	0.678	1
(flanking)	2.201	1

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

234

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

251

mutated

not conserved

251

Ptroglodytes

not conserved

ENSPTRG00000021186

251

Mmulatta

not conserved

ENSMMUG00000011410

251

Fcatus

no alignment

ENSFCAG00000008621

n/a

Mmusculus

not conserved

ENSMUSG00000028341

271

Ggallus

all identical

ENSGALG00000013568

216

Trubripes

not conserved

ENSTRUG00000011235

204

SVSLH

Drerio

all identical

ENSDARG00000055854

209

Dmelanogaster

all identical

FBgn0014859

669

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1914 / 1914

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

638 / 638

position of stopcodon in wt / mu cDNA

1958 / 1958

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

45 / 45

chromosome

strand

last intron/exon boundary

1711

theoretical NMD boundary in CDS

1616

length of CDS

1914

coding sequence (CDS) position

751

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

795

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

6906

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

102591042

original gDNA sequence snippet

GCCAGGCCGCCGCGCTTGAGAGCCACCCGTACGGGCTGCCG

altered gDNA sequence snippet

GCCAGGCCGCCGCGCTTGAGGGCCACCCGTACGGGCTGCCG

original cDNA sequence snippet

GCCAGGCCGCCGCGCTTGAGAGCCACCCGTACGGGCTGCCG

altered cDNA sequence snippet

GCCAGGCCGCCGCGCTTGAGGGCCACCCGTACGGGCTGCCG

wildtype AA sequence

MHDSIRFGNV DMPCVQAQYS PSPPGSSYAA QTYSSEYTTE IMNPDYTKLT MDLGSTEITA
TATTSLPSIS TFVEGYSSNY ELKPSCVYQM QRPLIKVEEG RAPSYHHHHH HHHHHHHHHQ
QQHQQPSIPP ASSPEDEVLP STSMYFKQSP PSTPTTPAFP PQAGALWDEA LPSAPGCIAP
GPLLDPPMKA VPTVAGARFP LFHFKPSPPH PPAPSPAGGH HLGYDPTAAA ALSLPLGAAA
AAGSQAAALE SHPYGLPLAK RAAPLAFPPL GLTPSPTASS LLGESPSLPS PPSRSSSSGE
GTCAVCGDNA ACQHYGVRTC EGCKGFFKRT VQKNAKYVCL ANKNCPVDKR RRNRCQYCRF
QKCLSVGMVK EVVRTDSLKG RRGRLPSKPK SPLQQEPSQP SPPSPPICMM NALVRALTDS
TPRDLDYSRY CPTDQAAAGT DAEHVQQFYN LLTASIDVSR SWAEKIPGFT DLPKEDQTLL
IESAFLELFV LRLSIRSNTA EDKFVFCNGL VLHRLQCLRG FGEWLDSIKD FSLNLQSLNL
DIQALACLSA LSMITERHGL KEPKRVEELC NKITSSLKDH QSKGQALEPT ESKVLGALVE
LRKICTLGLQ RIFYLKLEDL VSPPSIIDKL FLDTLPF*

mutated AA sequence

MHDSIRFGNV DMPCVQAQYS PSPPGSSYAA QTYSSEYTTE IMNPDYTKLT MDLGSTEITA
TATTSLPSIS TFVEGYSSNY ELKPSCVYQM QRPLIKVEEG RAPSYHHHHH HHHHHHHHHQ
QQHQQPSIPP ASSPEDEVLP STSMYFKQSP PSTPTTPAFP PQAGALWDEA LPSAPGCIAP
GPLLDPPMKA VPTVAGARFP LFHFKPSPPH PPAPSPAGGH HLGYDPTAAA ALSLPLGAAA
AAGSQAAALE GHPYGLPLAK RAAPLAFPPL GLTPSPTASS LLGESPSLPS PPSRSSSSGE
GTCAVCGDNA ACQHYGVRTC EGCKGFFKRT VQKNAKYVCL ANKNCPVDKR RRNRCQYCRF
QKCLSVGMVK EVVRTDSLKG RRGRLPSKPK SPLQQEPSQP SPPSPPICMM NALVRALTDS
TPRDLDYSRY CPTDQAAAGT DAEHVQQFYN LLTASIDVSR SWAEKIPGFT DLPKEDQTLL
IESAFLELFV LRLSIRSNTA EDKFVFCNGL VLHRLQCLRG FGEWLDSIKD FSLNLQSLNL
DIQALACLSA LSMITERHGL KEPKRVEELC NKITSSLKDH QSKGQALEPT ESKVLGALVE
LRKICTLGLQ RIFYLKLEDL VSPPSIIDKL FLDTLPF*

speed

0.12 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