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: ENST00000367627
Querying Taster for transcript #2: ENST00000352445
MT speed 0.85 s - this script 3.070513 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
TOR3A	polymorphism_automatic	1.0991207943789e-14	simple_aae				F13L	single base exchange	rs2296377		show file
TOR3A	polymorphism_automatic	1.0991207943789e-14	simple_aae				F13L	single base exchange	rs2296377		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999989 (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)

chr1:179051300T>CN/A show variant in all transcripts IGV

HGNC symbol

TOR3A

Ensembl transcript ID

ENST00000367627

Genbank transcript ID

NM_022371

UniProt peptide

Q9H497

alteration type

single base exchange

alteration region

CDS

DNA changes

c.37T>C
cDNA.789T>C
g.789T>C

AA changes

F13L Score: 22 explain score(s)

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

frameshift

known variant

Reference ID: rs2296377

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1527	788	2315
ExAC	7386	5844	13230

regulatory features

ELF1, Transcription Factor, ELF1 Transcription Factor Binding
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Cfos, Transcription Factor, Cfos TF binding
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
Max, Transcription Factor, Max TF binding
Gabp, Transcription Factor, Gabp TF binding
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
H2AZ, Histone, Histone 2A variant Z
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
E2F4, Transcription Factor, E2F4 Transcription Factor Binding
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Cmyc, Transcription Factor, Cmyc TF binding
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
USF1, Transcription Factor, USF1 Transcription Factor Binding
Ap2gamma, Transcription Factor, Ap2gamma Transcription Factor Binding
H2BK20ac, Histone, Histone 2B Lysine 20 Acetylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
E2F1, Transcription Factor, E2F1 Transcription Factor Binding
H3K4ac, Histone, Histone 3 Lysine 4 Acetylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.168	0
	-1.528	0
(flanking)	0.413	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 marginally increased	790	wt: 0.6085 / mu: 0.6293 (marginal change - not scored)	wt: GCGCCAGCTTTGGCTCTTTTTCCTGCTGCTGCTCCCGGGCG mu: GCGCCAGCTTTGGCTCTTTCTCCTGCTGCTGCTCCCGGGCG	tttt\|CCTG
Acc marginally increased	796	wt: 0.2010 / mu: 0.2189 (marginal change - not scored)	wt: GCTTTGGCTCTTTTTCCTGCTGCTGCTCCCGGGCGCGCCTG mu: GCTTTGGCTCTTTCTCCTGCTGCTGCTCCCGGGCGCGCCTG	tgct\|GCTG

distance from splice site

223

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

not conserved

ENSPTRG00000001726

Mmulatta

not conserved

ENSMMUG00000006261

LLLLLL

Fcatus

no alignment

ENSFCAG00000005304

n/a

Mmusculus

not conserved

ENSMUSG00000060519

Ggallus

no alignment

ENSGALG00000004216

n/a

Trubripes

no alignment

ENSTRUG00000004963

n/a

Drerio

no alignment

ENSDARG00000079308

n/a

Dmelanogaster

no alignment

FBgn0025615

n/a

Celegans

no alignment

C18E9.11

n/a

Xtropicalis

all identical

ENSXETG00000012540

PCRLC

protein features

start (aa)	end (aa)	feature	details
1	25	SIGNAL	Potential.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1194 / 1194

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

398 / 398

position of stopcodon in wt / mu cDNA

1946 / 1946

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

753 / 753

chromosome

strand

last intron/exon boundary

1696

theoretical NMD boundary in CDS

893

length of CDS

1194

coding sequence (CDS) position

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

789

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

789

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

179051300

original gDNA sequence snippet

GGCGCCAGCTTTGGCTCTTTTTCCTGCTGCTGCTCCCGGGC

altered gDNA sequence snippet

GGCGCCAGCTTTGGCTCTTTCTCCTGCTGCTGCTCCCGGGC

original cDNA sequence snippet

GGCGCCAGCTTTGGCTCTTTTTCCTGCTGCTGCTCCCGGGC

altered cDNA sequence snippet

GGCGCCAGCTTTGGCTCTTTCTCCTGCTGCTGCTCCCGGGC

wildtype AA sequence

MLRGPWRQLW LFFLLLLPGA PEPRGASRPW EGTDEPGSAW AWPGFQRLQE QLRAAGALSK
RYWTLFSCQV WPDDCDEDEE AATGPLGWRL PLLGQRYLDL LTTWYCSFKD CCPRGDCRIS
NNFTGLEWDL NVRLHGQHLV QQLVLRTVRG YLETPQPEKA LALSFHGWSG TGKNFVARML
VENLYRDGLM SDCVRMFIAT FHFPHPKYVD LYKEQLMSQI RETQQLCHQT LFIFDEAEKL
HPGLLEVLGP HLERRAPEGH RAESPWTIFL FLSNLRGDII NEVVLKLLKA GWSREEITME
HLEPHLQAEI VETIDNGFGH SRLVKENLID YFIPFLPLEY RHVRLCARDA FLSQELLYKE
ETLDEIAQMM VYVPKEEQLF SSQGCKSISQ RINYFLS*

mutated AA sequence

MLRGPWRQLW LFLLLLLPGA PEPRGASRPW EGTDEPGSAW AWPGFQRLQE QLRAAGALSK
RYWTLFSCQV WPDDCDEDEE AATGPLGWRL PLLGQRYLDL LTTWYCSFKD CCPRGDCRIS
NNFTGLEWDL NVRLHGQHLV QQLVLRTVRG YLETPQPEKA LALSFHGWSG TGKNFVARML
VENLYRDGLM SDCVRMFIAT FHFPHPKYVD LYKEQLMSQI RETQQLCHQT LFIFDEAEKL
HPGLLEVLGP HLERRAPEGH RAESPWTIFL FLSNLRGDII NEVVLKLLKA GWSREEITME
HLEPHLQAEI VETIDNGFGH SRLVKENLID YFIPFLPLEY RHVRLCARDA FLSQELLYKE
ETLDEIAQMM VYVPKEEQLF SSQGCKSISQ RINYFLS*

speed

0.43 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: 0.999999999999989 (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)

chr1:179051300T>CN/A show variant in all transcripts IGV

HGNC symbol

TOR3A

Ensembl transcript ID

ENST00000352445

Genbank transcript ID

N/A

UniProt peptide

Q9H497

alteration type

single base exchange

alteration region

CDS

DNA changes

c.37T>C
cDNA.80T>C
g.789T>C

AA changes

F13L Score: 22 explain score(s)

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

frameshift

known variant

Reference ID: rs2296377

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1527	788	2315
ExAC	7386	5844	13230

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.168	0
	-1.528	0
(flanking)	0.413	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 marginally increased	790	wt: 0.6085 / mu: 0.6293 (marginal change - not scored)	wt: GCGCCAGCTTTGGCTCTTTTTCCTGCTGCTGCTCCCGGGCG mu: GCGCCAGCTTTGGCTCTTTCTCCTGCTGCTGCTCCCGGGCG	tttt\|CCTG
Acc marginally increased	796	wt: 0.2010 / mu: 0.2189 (marginal change - not scored)	wt: GCTTTGGCTCTTTTTCCTGCTGCTGCTCCCGGGCGCGCCTG mu: GCTTTGGCTCTTTCTCCTGCTGCTGCTCCCGGGCGCGCCTG	tgct\|GCTG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

not conserved

ENSPTRG00000001726

Mmulatta

not conserved

ENSMMUG00000006261

LLLLLL

Fcatus

no alignment

ENSFCAG00000005304

n/a

Mmusculus

not conserved

ENSMUSG00000060519

Ggallus

no alignment

ENSGALG00000004216

n/a

Trubripes

no alignment

ENSTRUG00000004963

n/a

Drerio

no alignment

ENSDARG00000079308

n/a

Dmelanogaster

no alignment

FBgn0025615

n/a

Celegans

no alignment

C18E9.11

n/a

Xtropicalis

all identical

ENSXETG00000012540

PCRLC

protein features

start (aa)	end (aa)	feature	details
1	25	SIGNAL	Potential.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1011 / 1011

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

337 / 337

position of stopcodon in wt / mu cDNA

1054 / 1054

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

44 / 44

chromosome

strand

last intron/exon boundary

987

theoretical NMD boundary in CDS

893

length of CDS

1011

coding sequence (CDS) position

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

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

789

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

179051300

original gDNA sequence snippet

GGCGCCAGCTTTGGCTCTTTTTCCTGCTGCTGCTCCCGGGC

altered gDNA sequence snippet

GGCGCCAGCTTTGGCTCTTTCTCCTGCTGCTGCTCCCGGGC

original cDNA sequence snippet

GGCGCCAGCTTTGGCTCTTTTTCCTGCTGCTGCTCCCGGGC

altered cDNA sequence snippet

GGCGCCAGCTTTGGCTCTTTCTCCTGCTGCTGCTCCCGGGC

wildtype AA sequence

mutated AA sequence

speed

0.42 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems