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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000377139
Querying Taster for transcript #2: ENST00000309877
Querying Taster for transcript #3: ENST00000377135
MT speed 0 s - this script 4.703188 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
IRF3	polymorphism_automatic	7.50510764646606e-14	simple_aae				S427T	single base exchange	rs7251		show file
IRF3	polymorphism_automatic	7.50510764646606e-14	simple_aae				S427T	single base exchange	rs7251		show file
IRF3	polymorphism_automatic	9.80326930744013e-14	simple_aae				S300T	single base exchange	rs7251		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999925 (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)

chr19:50162909C>GN/A show variant in all transcripts IGV

HGNC symbol

IRF3

Ensembl transcript ID

ENST00000377139

Genbank transcript ID

NM_001197122

UniProt peptide

Q14653

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1280G>C
cDNA.1533G>C
g.6224G>C

AA changes

S427T Score: 58 explain score(s)

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

427

frameshift

known variant

Reference ID: rs7251

database	homozygous (G/G)	heterozygous	allele carriers
1000G	652	1123	1775
ExAC	9492	13783	23275

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.121	0.125
	-0.381	0.002
(flanking)	-0.882	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
Donor marginally increased	6216	wt: 0.9707 / mu: 0.9796 (marginal change - not scored)	wt: GGCCCTGGGGAGAGC mu: GGCCCTGGGGAGACC	CCCT\|gggg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

427

mutated

all conserved

427

Ptroglodytes

all conserved

ENSPTRG00000011309

212

Mmulatta

all conserved

ENSMMUG00000022735

422

Fcatus

no alignment

ENSFCAG00000006074

n/a

Mmusculus

no alignment

ENSMUSG00000003184

n/a

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000076251

n/a

Dmelanogaster

no homologue

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

1284 / 1284

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

428 / 428

position of stopcodon in wt / mu cDNA

1537 / 1537

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

254 / 254

chromosome

strand

-1

last intron/exon boundary

1352

theoretical NMD boundary in CDS

1048

length of CDS

1284

coding sequence (CDS) position

1280

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

1533

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

6224

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

50162909

original gDNA sequence snippet

TTTCCAGGGCCCTGGGGAGAGCTGAGCCCTCGCTCCTCATG

altered gDNA sequence snippet

TTTCCAGGGCCCTGGGGAGACCTGAGCCCTCGCTCCTCATG

original cDNA sequence snippet

TTTCCAGGGCCCTGGGGAGAGCTGAGCCCTCGCTCCTCATG

altered cDNA sequence snippet

TTTCCAGGGCCCTGGGGAGACCTGAGCCCTCGCTCCTCATG

wildtype AA sequence

MGTPKPRILP WLVSQLDLGQ LEGVAWVNKS RTRFRIPWKH GLRQDAQQED FGIFQAWAEA
TGAYVPGRDK PDLPTWKRNF RSALNRKEGL RLAEDRSKDP HDPHKIYEFV NSGVGDFSQP
DTSPDTNGGG STSDTQEDIL DELLGNMVLA PLPDPGPPSL AVAPEPCPQP LRSPSLDNPT
PFPNLGPSEN PLKRLLVPGE EWEFEVTAFY RGRQVFQQTI SCPEGLRLVG SEVGDRTLPG
WPVTLPDPGM SLTDRGVMSY VRHVLSCLGG GLALWRAGQW LWAQRLGHCH TYWAVSEELL
PNSGHGPDGE VPKDKEGGVF DLGPFIVDLI TFTEGSGRSP RYALWFCVGE SWPQDQPWTK
RLVMVKVVPT CLRALVEMAR VGGASSLENT VDLHISNSHP LSLTSDQYKA YLQDLVEGMD
FQGPGES*

mutated AA sequence

speed

1.35 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: 0.999999999999925 (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)

chr19:50162909C>GN/A show variant in all transcripts IGV

HGNC symbol

IRF3

Ensembl transcript ID

ENST00000309877

Genbank transcript ID

N/A

UniProt peptide

Q14653

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1280G>C
cDNA.1611G>C
g.6224G>C

AA changes

S427T Score: 58 explain score(s)

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

427

frameshift

known variant

Reference ID: rs7251

database	homozygous (G/G)	heterozygous	allele carriers
1000G	652	1123	1775
ExAC	9492	13783	23275

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.121	0.125
	-0.381	0.002
(flanking)	-0.882	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
Donor marginally increased	6216	wt: 0.9707 / mu: 0.9796 (marginal change - not scored)	wt: GGCCCTGGGGAGAGC mu: GGCCCTGGGGAGACC	CCCT\|gggg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

427

mutated

all conserved

427

Ptroglodytes

all conserved

ENSPTRG00000011309

212

Mmulatta

all conserved

ENSMMUG00000022735

422

Fcatus

no alignment

ENSFCAG00000006074

n/a

Mmusculus

no alignment

ENSMUSG00000003184

n/a

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000076251

n/a

Dmelanogaster

no homologue

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

1284 / 1284

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

428 / 428

position of stopcodon in wt / mu cDNA

1615 / 1615

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

332 / 332

chromosome

strand

-1

last intron/exon boundary

1430

theoretical NMD boundary in CDS

1048

length of CDS

1284

coding sequence (CDS) position

1280

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

1611

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

6224

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

50162909

original gDNA sequence snippet

TTTCCAGGGCCCTGGGGAGAGCTGAGCCCTCGCTCCTCATG

altered gDNA sequence snippet

TTTCCAGGGCCCTGGGGAGACCTGAGCCCTCGCTCCTCATG

original cDNA sequence snippet

TTTCCAGGGCCCTGGGGAGAGCTGAGCCCTCGCTCCTCATG

altered cDNA sequence snippet

TTTCCAGGGCCCTGGGGAGACCTGAGCCCTCGCTCCTCATG

wildtype AA sequence

mutated AA sequence

speed

0.54 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999902 (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)

chr19:50162909C>GN/A show variant in all transcripts IGV

HGNC symbol

IRF3

Ensembl transcript ID

ENST00000377135

Genbank transcript ID

N/A

UniProt peptide

Q14653

alteration type

single base exchange

alteration region

CDS

DNA changes

c.899G>C
cDNA.899G>C
g.6224G>C

AA changes

S300T Score: 58 explain score(s)

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

300

frameshift

known variant

Reference ID: rs7251

database	homozygous (G/G)	heterozygous	allele carriers
1000G	652	1123	1775
ExAC	9492	13783	23275

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.121	0.125
	-0.381	0.002
(flanking)	-0.882	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
Donor marginally increased	6216	wt: 0.9707 / mu: 0.9796 (marginal change - not scored)	wt: GGCCCTGGGGAGAGC mu: GGCCCTGGGGAGACC	CCCT\|gggg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

300

mutated

all conserved

300

Ptroglodytes

all conserved

ENSPTRG00000011309

212

Mmulatta

all conserved

ENSMMUG00000022735

422

Fcatus

no alignment

ENSFCAG00000006074

n/a

Mmusculus

no alignment

ENSMUSG00000003184

n/a

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000076251

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
200	360	REGION	Involved in HERC5 binding.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

903 / 903

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

301 / 301

position of stopcodon in wt / mu cDNA

903 / 903

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

718

theoretical NMD boundary in CDS

667

length of CDS

903

coding sequence (CDS) position

899

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

899

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

6224

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

50162909

original gDNA sequence snippet

TTTCCAGGGCCCTGGGGAGAGCTGAGCCCTCGCTCCTCATG

altered gDNA sequence snippet

TTTCCAGGGCCCTGGGGAGACCTGAGCCCTCGCTCCTCATG

original cDNA sequence snippet

TTTCCAGGGCCCTGGGGAGAGCTGA

altered cDNA sequence snippet

TTTCCAGGGCCCTGGGGAGACCTGA

wildtype AA sequence

MGTPKPRILP WLVSQLDLGQ LEGVAWVNKS RTRFRIPWKH GLRQDAQQED FGIFQAWAEA
TGAYVPGRDK PDLPTWKRNF RSALNRKEGL RLAEDRSKDP HDPHKIYEFV NSGVGDFSQP
DTSPDTNGGG STSDTQEDIL DELLGNMVLA PLPDPGPPSL AVAPEPCPQP LRSPSLDNPT
PFPNLGPSEN PLKRLLVPGE DLITFTEGSG RSPRYALWFC VGESWPQDQP WTKRLVMVKV
VPTCLRALVE MARVGGASSL ENTVDLHISN SHPLSLTSDQ YKAYLQDLVE GMDFQGPGES
*

mutated AA sequence

MGTPKPRILP WLVSQLDLGQ LEGVAWVNKS RTRFRIPWKH GLRQDAQQED FGIFQAWAEA
TGAYVPGRDK PDLPTWKRNF RSALNRKEGL RLAEDRSKDP HDPHKIYEFV NSGVGDFSQP
DTSPDTNGGG STSDTQEDIL DELLGNMVLA PLPDPGPPSL AVAPEPCPQP LRSPSLDNPT
PFPNLGPSEN PLKRLLVPGE DLITFTEGSG RSPRYALWFC VGESWPQDQP WTKRLVMVKV
VPTCLRALVE MARVGGASSL ENTVDLHISN SHPLSLTSDQ YKAYLQDLVE GMDFQGPGET
*

speed

1.35 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