MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000040877
MT speed 0 s - this script 2.750868 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
TARBP1	polymorphism_automatic	9.9298347322474e-13	simple_aae		affected		R154G	single base exchange	rs117698521		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999007 (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
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:234614390G>CN/A show variant in all transcripts IGV

HGNC symbol

TARBP1

Ensembl transcript ID

ENST00000040877

Genbank transcript ID

NM_005646

UniProt peptide

Q13395

alteration type

single base exchange

alteration region

CDS

DNA changes

c.460C>G
cDNA.460C>G
g.460C>G

AA changes

R154G Score: 125 explain score(s)

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

154

frameshift

known variant

Reference ID: rs117698521

database	homozygous (C/C)	heterozygous	allele carriers
1000G	415	698	1113
ExAC	106	493	599

regulatory features

Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
Max, Transcription Factor, Max TF binding
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Srf, Transcription Factor, Srf TF binding
Cmyc, Transcription Factor, Cmyc TF binding
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
CTCF, Transcription Factor, CCCTC-binding factor
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
E2F1, Transcription Factor, E2F1 Transcription Factor Binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Rad21, Transcription Factor, Rad21 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.07	0.009
	-0.192	0.002
(flanking)	-0.842	0.004

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
Acc increased	456	wt: 0.24 / mu: 0.31	wt: GCCGTCGGGCCATGTTTGCGGCCCCGCGAGGACGGGCCGCT mu: GCCGTCGGGCCATGTTTGCGGCCCGGCGAGGACGGGCCGCT	gcgg\|CCCC
Acc marginally increased	452	wt: 0.2602 / mu: 0.3313 (marginal change - not scored)	wt: AGCAGCCGTCGGGCCATGTTTGCGGCCCCGCGAGGACGGGC mu: AGCAGCCGTCGGGCCATGTTTGCGGCCCGGCGAGGACGGGC	gttt\|GCGG
Donor increased	459	wt: 0.69 / mu: 0.99	wt: CGGCCCCGCGAGGAC mu: CGGCCCGGCGAGGAC	GCCC\|cgcg

distance from splice site

460

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

154

mutated

not conserved

154

Ptroglodytes

all identical

ENSPTRG00000002124

154

Mmulatta

all identical

ENSMMUG00000021703

154

Fcatus

no alignment

ENSFCAG00000014183

n/a

Mmusculus

not conserved

ENSMUSG00000090290

139

Ggallus

no alignment

ENSGALG00000011000

n/a

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000079055

n/a

Dmelanogaster

no alignment

FBgn0038953

n/a

Celegans

no alignment

T14B4.1

n/a

Xtropicalis

no alignment

ENSXETG00000016224

n/a

protein features

start (aa)	end (aa)	feature	details
99	219	COMPBIAS	Ala-rich.	lost
1442	1442	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1465	1467	STRAND		might get lost (downstream of altered splice site)
1474	1486	HELIX		might get lost (downstream of altered splice site)
1490	1495	STRAND		might get lost (downstream of altered splice site)
1497	1501	HELIX		might get lost (downstream of altered splice site)
1503	1509	HELIX		might get lost (downstream of altered splice site)
1512	1514	HELIX		might get lost (downstream of altered splice site)
1518	1520	STRAND		might get lost (downstream of altered splice site)
1523	1525	HELIX		might get lost (downstream of altered splice site)
1526	1535	HELIX		might get lost (downstream of altered splice site)
1539	1543	STRAND		might get lost (downstream of altered splice site)
1552	1554	HELIX		might get lost (downstream of altered splice site)
1559	1565	STRAND		might get lost (downstream of altered splice site)
1566	1566	BINDING	S-adenosyl-L-methionine; via carbonyl oxygen (By similarity).	might get lost (downstream of altered splice site)
1568	1570	TURN		might get lost (downstream of altered splice site)
1574	1577	HELIX		might get lost (downstream of altered splice site)
1581	1585	STRAND		might get lost (downstream of altered splice site)
1586	1586	BINDING	S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygen (By similarity).	might get lost (downstream of altered splice site)
1590	1593	STRAND		might get lost (downstream of altered splice site)
1595	1595	BINDING	S-adenosyl-L-methionine; via amide nitrogen (By similarity).	might get lost (downstream of altered splice site)
1597	1613	HELIX		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

4866 / 4866

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

1622 / 1622

position of stopcodon in wt / mu cDNA

4866 / 4866

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

-1

last intron/exon boundary

4698

theoretical NMD boundary in CDS

4647

length of CDS

4866

coding sequence (CDS) position

460

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

460

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

460

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

234614390

original gDNA sequence snippet

TCGGGCCATGTTTGCGGCCCCGCGAGGACGGGCCGCTACTG

altered gDNA sequence snippet

TCGGGCCATGTTTGCGGCCCGGCGAGGACGGGCCGCTACTG

original cDNA sequence snippet

TCGGGCCATGTTTGCGGCCCCGCGAGGACGGGCCGCTACTG

altered cDNA sequence snippet

TCGGGCCATGTTTGCGGCCCGGCGAGGACGGGCCGCTACTG

wildtype AA sequence

MEWVLAEALL SQSRDPRALL GALCQGEASA ERVETLRFLL QRLEDEEARG SGGAGALPEA
AREVAAGYLV PLLRSLRGRP AGGPDPSLQP RHRRRVLRAA GAALRSCVRL AGRPQLAAAL
AEEALRDLLA GWRAPGAEAA VEVLAAVGPC LRPREDGPLL ERVAGTAVAL ALGGGGDGDE
AGPAEDAAAL VAGRLLPVLV QCGGAALRAV WGGLAAPGAS LGSGRVEEKL LVLSALAEKL
LPEPGGDRAR GAREAGPDAR RCWRFWRTVQ AGLGQADALT RKRARYLLQR AVEVSAELGA
DCTCGPQEGN GPSLFWWSER KKDELLKFWE NYILIMETLE GNQIHVIKPV LPKLNNLFEY
AVSEENGCWL FHPSWHMCIY KRMFESENKI LSKEGVIHFL ELYETKILPF SPEFSEFIIG
PLMDALSESS LYSRSPGQPI GSCSPLGLKL QKFLVTYISL LPEEIKSSFL LKFIRKMTSR
HWCAVPILFL SKALANVPRH KALGIDGLLA LRDVIHCTMI THQILLRGAA QCYLLQTAMN
LLDVEKVSLS DVSTFLMSLR QEESLGRGTS LWTELCDWLR VNESYFKPSP TCSSIGLHKT
SLNAYVKSIV QEYVKSSAWE TGENCFMPDW FEAKLVSLMV LLAVDVEGMK TQYSGKQRTE
NVLRIFLDPL LDVLMKFSTN AYMPLLKTDR CLQLLLKLLN TCRLKGSSAQ DDEVSTVLQN
FFMSTTESIS EFILRRLTMN ELNSVSDLDR CHLYLMVLTE LINLHLKVGW KRGNPIWRVI
SLLKNASIQH LQEMDSGQEP TVGSQIQRVV SMAALAMVCE AIDQKPELQL DSLHAGPLES
FLSSLQLNQT LQKPHAEEQS SYAHPLECSS VLEESSSSQG WGKIVAQYIH DQWVCLSFLL
KKYHTLIPTT GSEILEPFLP AVQMPIRTLQ SALEALTVLS SDQVLPVFHC LKVLVPKLLT
SSESLCIESF DMAWKIISSL SNTQLIFWAN LKAFVQFVFD NKVLTIAAKI KGQAYFKIKE
IMYKIIEMSA IKTGVFNTLI SYCCQSWIVS ASNVSQGSLS SAKNYSELIL EACIFGTVFR
RDQRLVQDVQ TFIENLGHDC AANIVMENTK REDHYVRICA VKFLCLLDGS NMSHKLFIED
LAIKLLDKDE LVSKSKKRYY VNSLQHRVKN RVWQTLLVLF PRLDQNFLNG IIDRIFQAGF
TNNQASIKYF IEWIIILILH KFPQFLPKFW DCFSYGEENL KTSICTFLAV LSHLDIITQN
IPEKKLILKQ ALIVVLQWCF NHNFSVRLYA LVALKKLWTV CKVLSVEEFD ALTPVIESSL
HQVESMHGAG NAKKNWQRIQ EHFFFATFHP LKDYCLETIF YILPRLSGLI EDEWITIDKF
TRFTDVPLAA GFQWYLSQTQ LSKLKPGDWS QQDIGTNLVE ADNQAEWTDV QKKIIPWNSR
VSDLDLELLF QDRAARLGKS ISRLIVVASL IDKPTNLGGL CRTCEVFGAS VLVVGSLQCI
SDKQFQHLSV SAEQWLPLVE VKPPQLIDYL QQKKTEGYTI IGVEQTAKSL DLTQYCFPEK
SLLLLGNERE GIPANLIQQL DVCVEIPQQG IIRSLNVHVS GALLIWEYTR QQLLSHGDTK
P*

mutated AA sequence

MEWVLAEALL SQSRDPRALL GALCQGEASA ERVETLRFLL QRLEDEEARG SGGAGALPEA
AREVAAGYLV PLLRSLRGRP AGGPDPSLQP RHRRRVLRAA GAALRSCVRL AGRPQLAAAL
AEEALRDLLA GWRAPGAEAA VEVLAAVGPC LRPGEDGPLL ERVAGTAVAL ALGGGGDGDE
AGPAEDAAAL VAGRLLPVLV QCGGAALRAV WGGLAAPGAS LGSGRVEEKL LVLSALAEKL
LPEPGGDRAR GAREAGPDAR RCWRFWRTVQ AGLGQADALT RKRARYLLQR AVEVSAELGA
DCTCGPQEGN GPSLFWWSER KKDELLKFWE NYILIMETLE GNQIHVIKPV LPKLNNLFEY
AVSEENGCWL FHPSWHMCIY KRMFESENKI LSKEGVIHFL ELYETKILPF SPEFSEFIIG
PLMDALSESS LYSRSPGQPI GSCSPLGLKL QKFLVTYISL LPEEIKSSFL LKFIRKMTSR
HWCAVPILFL SKALANVPRH KALGIDGLLA LRDVIHCTMI THQILLRGAA QCYLLQTAMN
LLDVEKVSLS DVSTFLMSLR QEESLGRGTS LWTELCDWLR VNESYFKPSP TCSSIGLHKT
SLNAYVKSIV QEYVKSSAWE TGENCFMPDW FEAKLVSLMV LLAVDVEGMK TQYSGKQRTE
NVLRIFLDPL LDVLMKFSTN AYMPLLKTDR CLQLLLKLLN TCRLKGSSAQ DDEVSTVLQN
FFMSTTESIS EFILRRLTMN ELNSVSDLDR CHLYLMVLTE LINLHLKVGW KRGNPIWRVI
SLLKNASIQH LQEMDSGQEP TVGSQIQRVV SMAALAMVCE AIDQKPELQL DSLHAGPLES
FLSSLQLNQT LQKPHAEEQS SYAHPLECSS VLEESSSSQG WGKIVAQYIH DQWVCLSFLL
KKYHTLIPTT GSEILEPFLP AVQMPIRTLQ SALEALTVLS SDQVLPVFHC LKVLVPKLLT
SSESLCIESF DMAWKIISSL SNTQLIFWAN LKAFVQFVFD NKVLTIAAKI KGQAYFKIKE
IMYKIIEMSA IKTGVFNTLI SYCCQSWIVS ASNVSQGSLS SAKNYSELIL EACIFGTVFR
RDQRLVQDVQ TFIENLGHDC AANIVMENTK REDHYVRICA VKFLCLLDGS NMSHKLFIED
LAIKLLDKDE LVSKSKKRYY VNSLQHRVKN RVWQTLLVLF PRLDQNFLNG IIDRIFQAGF
TNNQASIKYF IEWIIILILH KFPQFLPKFW DCFSYGEENL KTSICTFLAV LSHLDIITQN
IPEKKLILKQ ALIVVLQWCF NHNFSVRLYA LVALKKLWTV CKVLSVEEFD ALTPVIESSL
HQVESMHGAG NAKKNWQRIQ EHFFFATFHP LKDYCLETIF YILPRLSGLI EDEWITIDKF
TRFTDVPLAA GFQWYLSQTQ LSKLKPGDWS QQDIGTNLVE ADNQAEWTDV QKKIIPWNSR
VSDLDLELLF QDRAARLGKS ISRLIVVASL IDKPTNLGGL CRTCEVFGAS VLVVGSLQCI
SDKQFQHLSV SAEQWLPLVE VKPPQLIDYL QQKKTEGYTI IGVEQTAKSL DLTQYCFPEK
SLLLLGNERE GIPANLIQQL DVCVEIPQQG IIRSLNVHVS GALLIWEYTR QQLLSHGDTK
P*

speed

0.68 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

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

Problems