MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000376257
Querying Taster for transcript #2: ENST00000376255
MT speed 1.34 s - this script 3.320472 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
TCF19	polymorphism_automatic	0	simple_aae		affected		M211V	single base exchange	rs2073721		show file
TCF19	polymorphism_automatic	0	simple_aae		affected		M211V	single base exchange	rs2073721		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 1 (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)

chr6:31129616A>GN/A show variant in all transcripts IGV

HGNC symbol

TCF19

Ensembl transcript ID

ENST00000376257

Genbank transcript ID

NM_007109

UniProt peptide

Q9Y242

alteration type

single base exchange

alteration region

CDS

DNA changes

c.631A>G
cDNA.1385A>G
g.3298A>G

AA changes

M211V Score: 21 explain score(s)

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

211

frameshift

known variant

Reference ID: rs2073721

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1508	836	2344
ExAC	-	-	-

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.17	0
	1.074	0.001
(flanking)	-1.476	0

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	3291	wt: 0.9905 / mu: 0.9915 (marginal change - not scored)	wt: CTGCCTGTTCCCGCCCCACCTGGGGAAATGGGGACCACGCC mu: CTGCCTGTTCCCGCCCCACCTGGGGAAGTGGGGACCACGCC	acct\|GGGG
Acc increased	3289	wt: 0.55 / mu: 0.64	wt: GCCTGCCTGTTCCCGCCCCACCTGGGGAAATGGGGACCACG mu: GCCTGCCTGTTCCCGCCCCACCTGGGGAAGTGGGGACCACG	ccac\|CTGG
Acc marginally increased	3293	wt: 0.6010 / mu: 0.6199 (marginal change - not scored)	wt: GCCTGTTCCCGCCCCACCTGGGGAAATGGGGACCACGCCTT mu: GCCTGTTCCCGCCCCACCTGGGGAAGTGGGGACCACGCCTT	ctgg\|GGAA
Donor marginally increased	3292	wt: 0.9412 / mu: 0.9952 (marginal change - not scored)	wt: CACCTGGGGAAATGG mu: CACCTGGGGAAGTGG	CCTG\|ggga
Donor gained	3297	0.38	mu: GGGGAAGTGGGGACC	GGAA\|gtgg

distance from splice site

167

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

211

mutated

all conserved

211

Ptroglodytes

all conserved

ENSPTRG00000017952

211

Mmulatta

all conserved

ENSMMUG00000015682

211

Fcatus

all conserved

ENSFCAG00000001077

211

Mmusculus

not conserved

ENSMUSG00000050410

210

Ggallus

no homologue

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000040036

245

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
187	300	COMPBIAS	Pro-rich.	lost
268	268	CONFLICT	R -> A (in Ref. 3; AAB60363).	might get lost (downstream of altered splice site)
296	339	ZN_FING	PHD-type.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1038 / 1038

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

346 / 346

position of stopcodon in wt / mu cDNA

1792 / 1792

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

755 / 755

chromosome

strand

last intron/exon boundary

1552

theoretical NMD boundary in CDS

747

length of CDS

1038

coding sequence (CDS) position

631

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

1385

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

3298

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

31129616

original gDNA sequence snippet

TTCCCGCCCCACCTGGGGAAATGGGGACCACGCCTTCTGCT

altered gDNA sequence snippet

TTCCCGCCCCACCTGGGGAAGTGGGGACCACGCCTTCTGCT

original cDNA sequence snippet

TTCCCGCCCCACCTGGGGAAATGGGGACCACGCCTTCTGCT

altered cDNA sequence snippet

TTCCCGCCCCACCTGGGGAAGTGGGGACCACGCCTTCTGCT

wildtype AA sequence

MLPCFQLLRI GGGRGGDLYT FHPPAGAGCT YRLGHRADLC DVALRPQQEP GLISGIHAEL
HAEPRGDDWR VSLEDHSSQG TLVNNVRLPR GHRLELSDGD LLTFGPEGPP GTSPSEFYFM
FQQVRVKPQD FAAITIPRSR GEARVGAGFR PMLPSQGAPQ RPLSTFSPAP KATLILNSIG
SLSKLRPQPL TFSPSWGGPK SLPVPAPPGE MGTTPSAPPQ RNRRKSVHRV LAELDDESEP
PENPPPVLME PRKKLRVDKA PLTPTGNRRG RPRKYPVSAP MAPPAVGGGE PCAAPCCCLP
QEETVAWVQC DGCDVWFHVA CVGCSIQAAR EADFRCPGCR AGIQT*

mutated AA sequence

MLPCFQLLRI GGGRGGDLYT FHPPAGAGCT YRLGHRADLC DVALRPQQEP GLISGIHAEL
HAEPRGDDWR VSLEDHSSQG TLVNNVRLPR GHRLELSDGD LLTFGPEGPP GTSPSEFYFM
FQQVRVKPQD FAAITIPRSR GEARVGAGFR PMLPSQGAPQ RPLSTFSPAP KATLILNSIG
SLSKLRPQPL TFSPSWGGPK SLPVPAPPGE VGTTPSAPPQ RNRRKSVHRV LAELDDESEP
PENPPPVLME PRKKLRVDKA PLTPTGNRRG RPRKYPVSAP MAPPAVGGGE PCAAPCCCLP
QEETVAWVQC DGCDVWFHVA CVGCSIQAAR EADFRCPGCR AGIQT*

speed

0.66 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: 1 (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)

chr6:31129616A>GN/A show variant in all transcripts IGV

HGNC symbol

TCF19

Ensembl transcript ID

ENST00000376255

Genbank transcript ID

NM_001077511

UniProt peptide

Q9Y242

alteration type

single base exchange

alteration region

CDS

DNA changes

c.631A>G
cDNA.1134A>G
g.3298A>G

AA changes

M211V Score: 21 explain score(s)

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

211

frameshift

known variant

Reference ID: rs2073721

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1508	836	2344
ExAC	-	-	-

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.17	0
	1.074	0.001
(flanking)	-1.476	0

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	3291	wt: 0.9905 / mu: 0.9915 (marginal change - not scored)	wt: CTGCCTGTTCCCGCCCCACCTGGGGAAATGGGGACCACGCC mu: CTGCCTGTTCCCGCCCCACCTGGGGAAGTGGGGACCACGCC	acct\|GGGG
Acc increased	3289	wt: 0.55 / mu: 0.64	wt: GCCTGCCTGTTCCCGCCCCACCTGGGGAAATGGGGACCACG mu: GCCTGCCTGTTCCCGCCCCACCTGGGGAAGTGGGGACCACG	ccac\|CTGG
Acc marginally increased	3293	wt: 0.6010 / mu: 0.6199 (marginal change - not scored)	wt: GCCTGTTCCCGCCCCACCTGGGGAAATGGGGACCACGCCTT mu: GCCTGTTCCCGCCCCACCTGGGGAAGTGGGGACCACGCCTT	ctgg\|GGAA
Donor marginally increased	3292	wt: 0.9412 / mu: 0.9952 (marginal change - not scored)	wt: CACCTGGGGAAATGG mu: CACCTGGGGAAGTGG	CCTG\|ggga
Donor gained	3297	0.38	mu: GGGGAAGTGGGGACC	GGAA\|gtgg

distance from splice site

167

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

211

mutated

all conserved

211

Ptroglodytes

all conserved

ENSPTRG00000017952

211

Mmulatta

all conserved

ENSMMUG00000015682

211

Fcatus

all conserved

ENSFCAG00000001077

211

Mmusculus

not conserved

ENSMUSG00000050410

210

Ggallus

no homologue

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000040036

245

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
187	300	COMPBIAS	Pro-rich.	lost
268	268	CONFLICT	R -> A (in Ref. 3; AAB60363).	might get lost (downstream of altered splice site)
296	339	ZN_FING	PHD-type.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1038 / 1038

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

346 / 346

position of stopcodon in wt / mu cDNA

1541 / 1541

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

504 / 504

chromosome

strand

last intron/exon boundary

1301

theoretical NMD boundary in CDS

747

length of CDS

1038

coding sequence (CDS) position

631

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

1134

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

3298

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

31129616

original gDNA sequence snippet

TTCCCGCCCCACCTGGGGAAATGGGGACCACGCCTTCTGCT

altered gDNA sequence snippet

TTCCCGCCCCACCTGGGGAAGTGGGGACCACGCCTTCTGCT

original cDNA sequence snippet

TTCCCGCCCCACCTGGGGAAATGGGGACCACGCCTTCTGCT

altered cDNA sequence snippet

TTCCCGCCCCACCTGGGGAAGTGGGGACCACGCCTTCTGCT

wildtype AA sequence

mutated AA sequence

MLPCFQLLRI GGGRGGDLYT FHPPAGAGCT YRLGHRADLC DVALRPQQEP GLISGIHAEL
HAEPRGDDWR VSLEDHSSQG TLVNNVRLPR GHRLELSDGD LLTFGPEGPP GTSPSEFYFM
FQQVRVKPQD FAAITIPRSR GEARVGAGFR PMLPSQGAPQ RPLSTFSPAP KATLILNSIG
SLSKLRPQPL TFSPSWGGPK SLPVPAPPGE VGTTPSAPPQ RNRRKSVHRV LAELDDESEP
PENPPPVLME PRKKLRVDKA PLTPTGNRRG RPRKYPVSAP MAPPAVGGGE PCAAPCCCLP
QEETVAWVQC DGCDVWFHVA CVGCSIQAAR EADFRCPGCR AGIQT*

speed

0.68 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems