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: ENST00000274773
Querying Taster for transcript #2: ENST00000334421
MT speed 0 s - this script 4.512316 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
TRIM7	polymorphism_automatic	3.18318604808354e-09	simple_aae				P73S	single base exchange	rs2770946		show file
TRIM7	polymorphism_automatic	3.18318604808354e-09	simple_aae				P73S	single base exchange	rs2770946		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999996816814 (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)

chr5:180631894G>AN/A show variant in all transcripts IGV

HGNC symbol

TRIM7

Ensembl transcript ID

ENST00000274773

Genbank transcript ID

NM_203293

UniProt peptide

Q9C029

alteration type

single base exchange

alteration region

CDS

DNA changes

c.217C>T
cDNA.279C>T
g.400C>T

AA changes

P73S Score: 74 explain score(s)

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

frameshift

known variant

Reference ID: rs2770946

database	homozygous (A/A)	heterozygous	allele carriers
1000G	167	403	570
ExAC	0	13	13

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
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
E2F1, Transcription Factor, E2F1 Transcription Factor Binding
TFIIIC-110, Transcription Factor, TFIIIC-110 Transcription Factor Binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.915	0.013
	1.268	0.017
(flanking)	-0.44	0.012

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 marginally increased	409	wt: 0.8400 / mu: 0.8650 (marginal change - not scored)	wt: CCCGCGCGCCCCCCTTCCCACTGCCCTGTCCGCAGTGCCGC mu: CCCGCGCGCCCTCCTTCCCACTGCCCTGTCCGCAGTGCCGC	ccac\|TGCC
Acc marginally increased	411	wt: 0.5985 / mu: 0.6425 (marginal change - not scored)	wt: CGCGCGCCCCCCTTCCCACTGCCCTGTCCGCAGTGCCGCGA mu: CGCGCGCCCTCCTTCCCACTGCCCTGTCCGCAGTGCCGCGA	actg\|CCCT
Acc marginally increased	406	wt: 0.8550 / mu: 0.8909 (marginal change - not scored)	wt: CCACCCGCGCGCCCCCCTTCCCACTGCCCTGTCCGCAGTGC mu: CCACCCGCGCGCCCTCCTTCCCACTGCCCTGTCCGCAGTGC	ttcc\|CACT
Acc marginally increased	408	wt: 0.7983 / mu: 0.8697 (marginal change - not scored)	wt: ACCCGCGCGCCCCCCTTCCCACTGCCCTGTCCGCAGTGCCG mu: ACCCGCGCGCCCTCCTTCCCACTGCCCTGTCCGCAGTGCCG	ccca\|CTGC
Acc marginally increased	404	wt: 0.2614 / mu: 0.2674 (marginal change - not scored)	wt: CGCCACCCGCGCGCCCCCCTTCCCACTGCCCTGTCCGCAGT mu: CGCCACCCGCGCGCCCTCCTTCCCACTGCCCTGTCCGCAGT	cctt\|CCCA
Acc marginally increased	410	wt: 0.6748 / mu: 0.7102 (marginal change - not scored)	wt: CCGCGCGCCCCCCTTCCCACTGCCCTGTCCGCAGTGCCGCG mu: CCGCGCGCCCTCCTTCCCACTGCCCTGTCCGCAGTGCCGCG	cact\|GCCC
Acc marginally increased	407	wt: 0.8606 / mu: 0.8700 (marginal change - not scored)	wt: CACCCGCGCGCCCCCCTTCCCACTGCCCTGTCCGCAGTGCC mu: CACCCGCGCGCCCTCCTTCCCACTGCCCTGTCCGCAGTGCC	tccc\|ACTG

distance from splice site

279

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000017649

Mmulatta

all identical

ENSMMUG00000003598

Fcatus

all identical

ENSFCAG00000003037

Mmusculus

all identical

ENSMUSG00000040350

Ggallus

not conserved

ENSGALG00000000107

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
29	82	ZN_FING	RING-type.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1536 / 1536

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

512 / 512

position of stopcodon in wt / mu cDNA

1598 / 1598

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

63 / 63

chromosome

strand

-1

last intron/exon boundary

1087

theoretical NMD boundary in CDS

974

length of CDS

1536

coding sequence (CDS) position

217

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

279

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

400

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

180631894

original gDNA sequence snippet

GGGCCGCCACCCGCGCGCCCCCCTTCCCACTGCCCTGTCCG

altered gDNA sequence snippet

GGGCCGCCACCCGCGCGCCCTCCTTCCCACTGCCCTGTCCG

original cDNA sequence snippet

GGGCCGCCACCCGCGCGCCCCCCTTCCCACTGCCCTGTCCG

altered cDNA sequence snippet

GGGCCGCCACCCGCGCGCCCTCCTTCCCACTGCCCTGTCCG

wildtype AA sequence

MAAVGPRTGP GTGAEALALA AELQGEATCS ICLELFREPV SVECGHSFCR ACIGRCWERP
GAGSVGAATR APPFPLPCPQ CREPARPSQL RPNRQLAAVA TLLRRFSLPA AAPGEHGSQA
AAARAAAARC GQHGEPFKLY CQDDGRAICV VCDRAREHRE HAVLPLDEAV QEAKELLESR
LRVLKKELED CEVFRSTEKK ESKELLKQMA AEQEKVGAEF QALRAFLVEQ EGRLLGRLEE
LSREVAQKQN ENLAQLGVEI TQLSKLSSQI QETAQKPDLD FLQEFKSTLS RCSNVPGPKP
TTVSSEMKNK VWNVSLKTFV LKGMLKKFKE DLRGELEKEE KVELTLDPDT ANPRLILSLD
LKGVRLGERA QDLPNHPCRF DTNTRVLASC GFSSGRHHWE VEVGSKDGWA FGVARESVRR
KGLTPFTPEE GVWALQLNGG QYWAVTSPER SPLSCGHLSR VRVALDLEVG AVSFYAVEDM
RHLYTFRVNF QERVFPLFSV CSTGTYLRIW P*

mutated AA sequence

MAAVGPRTGP GTGAEALALA AELQGEATCS ICLELFREPV SVECGHSFCR ACIGRCWERP
GAGSVGAATR APSFPLPCPQ CREPARPSQL RPNRQLAAVA TLLRRFSLPA AAPGEHGSQA
AAARAAAARC GQHGEPFKLY CQDDGRAICV VCDRAREHRE HAVLPLDEAV QEAKELLESR
LRVLKKELED CEVFRSTEKK ESKELLKQMA AEQEKVGAEF QALRAFLVEQ EGRLLGRLEE
LSREVAQKQN ENLAQLGVEI TQLSKLSSQI QETAQKPDLD FLQEFKSTLS RCSNVPGPKP
TTVSSEMKNK VWNVSLKTFV LKGMLKKFKE DLRGELEKEE KVELTLDPDT ANPRLILSLD
LKGVRLGERA QDLPNHPCRF DTNTRVLASC GFSSGRHHWE VEVGSKDGWA FGVARESVRR
KGLTPFTPEE GVWALQLNGG QYWAVTSPER SPLSCGHLSR VRVALDLEVG AVSFYAVEDM
RHLYTFRVNF QERVFPLFSV CSTGTYLRIW P*

speed

1.24 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: 0.999999996816814 (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)

chr5:180631894G>AN/A show variant in all transcripts IGV

HGNC symbol

TRIM7

Ensembl transcript ID

ENST00000334421

Genbank transcript ID

NM_033342

UniProt peptide

Q9C029

alteration type

single base exchange

alteration region

CDS

DNA changes

c.217C>T
cDNA.400C>T
g.400C>T

AA changes

P73S Score: 74 explain score(s)

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

frameshift

known variant

Reference ID: rs2770946

database	homozygous (A/A)	heterozygous	allele carriers
1000G	167	403	570
ExAC	0	13	13

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.915	0.013
	1.268	0.017
(flanking)	-0.44	0.012

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 marginally increased	409	wt: 0.8400 / mu: 0.8650 (marginal change - not scored)	wt: CCCGCGCGCCCCCCTTCCCACTGCCCTGTCCGCAGTGCCGC mu: CCCGCGCGCCCTCCTTCCCACTGCCCTGTCCGCAGTGCCGC	ccac\|TGCC
Acc marginally increased	411	wt: 0.5985 / mu: 0.6425 (marginal change - not scored)	wt: CGCGCGCCCCCCTTCCCACTGCCCTGTCCGCAGTGCCGCGA mu: CGCGCGCCCTCCTTCCCACTGCCCTGTCCGCAGTGCCGCGA	actg\|CCCT
Acc marginally increased	406	wt: 0.8550 / mu: 0.8909 (marginal change - not scored)	wt: CCACCCGCGCGCCCCCCTTCCCACTGCCCTGTCCGCAGTGC mu: CCACCCGCGCGCCCTCCTTCCCACTGCCCTGTCCGCAGTGC	ttcc\|CACT
Acc marginally increased	408	wt: 0.7983 / mu: 0.8697 (marginal change - not scored)	wt: ACCCGCGCGCCCCCCTTCCCACTGCCCTGTCCGCAGTGCCG mu: ACCCGCGCGCCCTCCTTCCCACTGCCCTGTCCGCAGTGCCG	ccca\|CTGC
Acc marginally increased	404	wt: 0.2614 / mu: 0.2674 (marginal change - not scored)	wt: CGCCACCCGCGCGCCCCCCTTCCCACTGCCCTGTCCGCAGT mu: CGCCACCCGCGCGCCCTCCTTCCCACTGCCCTGTCCGCAGT	cctt\|CCCA
Acc marginally increased	410	wt: 0.6748 / mu: 0.7102 (marginal change - not scored)	wt: CCGCGCGCCCCCCTTCCCACTGCCCTGTCCGCAGTGCCGCG mu: CCGCGCGCCCTCCTTCCCACTGCCCTGTCCGCAGTGCCGCG	cact\|GCCC
Acc marginally increased	407	wt: 0.8606 / mu: 0.8700 (marginal change - not scored)	wt: CACCCGCGCGCCCCCCTTCCCACTGCCCTGTCCGCAGTGCC mu: CACCCGCGCGCCCTCCTTCCCACTGCCCTGTCCGCAGTGCC	tccc\|ACTG

distance from splice site

306

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000017649

Mmulatta

all identical

ENSMMUG00000003598

Fcatus

all identical

ENSFCAG00000003037

Mmusculus

all identical

ENSMUSG00000040350

Ggallus

not conserved

ENSGALG00000000107

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
29	82	ZN_FING	RING-type.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

666 / 666

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

222 / 222

position of stopcodon in wt / mu cDNA

849 / 849

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

184 / 184

chromosome

strand

-1

last intron/exon boundary

706

theoretical NMD boundary in CDS

472

length of CDS

666

coding sequence (CDS) position

217

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

400

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

400

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

180631894

original gDNA sequence snippet

GGGCCGCCACCCGCGCGCCCCCCTTCCCACTGCCCTGTCCG

altered gDNA sequence snippet

GGGCCGCCACCCGCGCGCCCTCCTTCCCACTGCCCTGTCCG

original cDNA sequence snippet

GGGCCGCCACCCGCGCGCCCCCCTTCCCACTGCCCTGTCCG

altered cDNA sequence snippet

GGGCCGCCACCCGCGCGCCCTCCTTCCCACTGCCCTGTCCG

wildtype AA sequence

mutated AA sequence

speed

1.28 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems