MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000341010
Querying Taster for transcript #2: ENST00000393197
Querying Taster for transcript #3: ENST00000337569
MT speed 0 s - this script 2.703187 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
IL1F10	polymorphism_automatic	8.69878349996078e-06	simple_aae		affected		A51D	single base exchange	rs6743376		show file
IL1F10	polymorphism_automatic	8.69878349996078e-06	simple_aae		affected		A51D	single base exchange	rs6743376		show file
IL1F10	polymorphism_automatic	8.69878349996078e-06	simple_aae		affected		A51D	single base exchange	rs6743376		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.9999913012165 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:113832333C>AN/A show variant in all transcripts IGV

HGNC symbol

IL1F10

Ensembl transcript ID

ENST00000341010

Genbank transcript ID

NM_173161

UniProt peptide

Q8WWZ1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.152C>A
cDNA.227C>A
g.6787C>A

AA changes

A51D Score: 126 explain score(s)

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

frameshift

known variant

Reference ID: rs6743376

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1327	979	2306
ExAC	29482	-26197	3285

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.755	0.994
	0.682	0.957
(flanking)	-0.334	0.887

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	6778	wt: 0.41 / mu: 0.51	wt: GATCTGCATACTTCCTAACAGAGGCTTGGCCCGCACCAAGG mu: GATCTGCATACTTCCTAACAGAGGCTTGGACCGCACCAAGG	acag\|AGGC
Donor increased	6791	wt: 0.78 / mu: 0.89	wt: GCCCGCACCAAGGTC mu: GACCGCACCAAGGTC	CCGC\|acca
Donor marginally increased	6792	wt: 0.9658 / mu: 0.9823 (marginal change - not scored)	wt: CCCGCACCAAGGTCC mu: ACCGCACCAAGGTCC	CGCA\|ccaa

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

ENSPTRG00000012377

Mmulatta

not conserved

ENSMMUG00000018203

Fcatus

not conserved

ENSFCAG00000009572

Mmusculus

not conserved

ENSMUSG00000046845

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

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

459 / 459

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

153 / 153

position of stopcodon in wt / mu cDNA

534 / 534

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

76 / 76

chromosome

strand

last intron/exon boundary

322

theoretical NMD boundary in CDS

196

length of CDS

459

coding sequence (CDS) position

152

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

227

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

6787

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

113832333

original gDNA sequence snippet

ACTTCCTAACAGAGGCTTGGCCCGCACCAAGGTCCCCATTT

altered gDNA sequence snippet

ACTTCCTAACAGAGGCTTGGACCGCACCAAGGTCCCCATTT

original cDNA sequence snippet

ACTTCCTAACAGAGGCTTGGCCCGCACCAAGGTCCCCATTT

altered cDNA sequence snippet

ACTTCCTAACAGAGGCTTGGACCGCACCAAGGTCCCCATTT

wildtype AA sequence

MCSLPMARYY IIKYADQKAL YTRDGQLLVG DPVADNCCAE KICILPNRGL ARTKVPIFLG
IQGGSRCLAC VETEEGPSLQ LEDVNIEELY KGGEEATRFT FFQSSSGSAF RLEAAAWPGW
FLCGPAEPQQ PVQLTKESEP SARTKFYFEQ SW*

mutated AA sequence

MCSLPMARYY IIKYADQKAL YTRDGQLLVG DPVADNCCAE KICILPNRGL DRTKVPIFLG
IQGGSRCLAC VETEEGPSLQ LEDVNIEELY KGGEEATRFT FFQSSSGSAF RLEAAAWPGW
FLCGPAEPQQ PVQLTKESEP SARTKFYFEQ SW*

speed

0.37 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: 0.9999913012165 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:113832333C>AN/A show variant in all transcripts IGV

HGNC symbol

IL1F10

Ensembl transcript ID

ENST00000393197

Genbank transcript ID

NM_032556

UniProt peptide

Q8WWZ1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.152C>A
cDNA.573C>A
g.6787C>A

AA changes

A51D Score: 126 explain score(s)

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

frameshift

known variant

Reference ID: rs6743376

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1327	979	2306
ExAC	29482	-26197	3285

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.755	0.994
	0.682	0.957
(flanking)	-0.334	0.887

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	6778	wt: 0.41 / mu: 0.51	wt: GATCTGCATACTTCCTAACAGAGGCTTGGCCCGCACCAAGG mu: GATCTGCATACTTCCTAACAGAGGCTTGGACCGCACCAAGG	acag\|AGGC
Donor increased	6791	wt: 0.78 / mu: 0.89	wt: GCCCGCACCAAGGTC mu: GACCGCACCAAGGTC	CCGC\|acca
Donor marginally increased	6792	wt: 0.9658 / mu: 0.9823 (marginal change - not scored)	wt: CCCGCACCAAGGTCC mu: ACCGCACCAAGGTCC	CGCA\|ccaa

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

ENSPTRG00000012377

Mmulatta

not conserved

ENSMMUG00000018203

Fcatus

not conserved

ENSFCAG00000009572

Mmusculus

not conserved

ENSMUSG00000046845

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

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

459 / 459

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

153 / 153

position of stopcodon in wt / mu cDNA

880 / 880

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

422 / 422

chromosome

strand

last intron/exon boundary

668

theoretical NMD boundary in CDS

196

length of CDS

459

coding sequence (CDS) position

152

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

573

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

6787

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

113832333

original gDNA sequence snippet

ACTTCCTAACAGAGGCTTGGCCCGCACCAAGGTCCCCATTT

altered gDNA sequence snippet

ACTTCCTAACAGAGGCTTGGACCGCACCAAGGTCCCCATTT

original cDNA sequence snippet

ACTTCCTAACAGAGGCTTGGCCCGCACCAAGGTCCCCATTT

altered cDNA sequence snippet

ACTTCCTAACAGAGGCTTGGACCGCACCAAGGTCCCCATTT

wildtype AA sequence

MCSLPMARYY IIKYADQKAL YTRDGQLLVG DPVADNCCAE KICILPNRGL ARTKVPIFLG
IQGGSRCLAC VETEEGPSLQ LEDVNIEELY KGGEEATRFT FFQSSSGSAF RLEAAAWPGW
FLCGPAEPQQ PVQLTKESEP SARTKFYFEQ SW*

mutated AA sequence

MCSLPMARYY IIKYADQKAL YTRDGQLLVG DPVADNCCAE KICILPNRGL DRTKVPIFLG
IQGGSRCLAC VETEEGPSLQ LEDVNIEELY KGGEEATRFT FFQSSSGSAF RLEAAAWPGW
FLCGPAEPQQ PVQLTKESEP SARTKFYFEQ SW*

speed

0.39 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.9999913012165 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:113832333C>AN/A show variant in all transcripts IGV

HGNC symbol

IL1F10

Ensembl transcript ID

ENST00000337569

Genbank transcript ID

N/A

UniProt peptide

Q8WWZ1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.152C>A
cDNA.227C>A
g.6787C>A

AA changes

A51D Score: 126 explain score(s)

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

frameshift

known variant

Reference ID: rs6743376

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1327	979	2306
ExAC	29482	-26197	3285

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.755	0.994
	0.682	0.957
(flanking)	-0.334	0.887

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	6778	wt: 0.41 / mu: 0.51	wt: GATCTGCATACTTCCTAACAGAGGCTTGGCCCGCACCAAGG mu: GATCTGCATACTTCCTAACAGAGGCTTGGACCGCACCAAGG	acag\|AGGC
Donor increased	6791	wt: 0.78 / mu: 0.89	wt: GCCCGCACCAAGGTC mu: GACCGCACCAAGGTC	CCGC\|acca
Donor marginally increased	6792	wt: 0.9658 / mu: 0.9823 (marginal change - not scored)	wt: CCCGCACCAAGGTCC mu: ACCGCACCAAGGTCC	CGCA\|ccaa

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

ENSPTRG00000012377

Mmulatta

not conserved

ENSMMUG00000018203

Fcatus

not conserved

ENSFCAG00000009572

Mmusculus

not conserved

ENSMUSG00000046845

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

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

459 / 459

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

153 / 153

position of stopcodon in wt / mu cDNA

534 / 534

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

76 / 76

chromosome

strand

last intron/exon boundary

322

theoretical NMD boundary in CDS

196

length of CDS

459

coding sequence (CDS) position

152

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

227

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

6787

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

113832333

original gDNA sequence snippet

ACTTCCTAACAGAGGCTTGGCCCGCACCAAGGTCCCCATTT

altered gDNA sequence snippet

ACTTCCTAACAGAGGCTTGGACCGCACCAAGGTCCCCATTT

original cDNA sequence snippet

ACTTCCTAACAGAGGCTTGGCCCGCACCAAGGTCCCCATTT

altered cDNA sequence snippet

ACTTCCTAACAGAGGCTTGGACCGCACCAAGGTCCCCATTT

wildtype AA sequence

MCSLPMARYY ISFLPEPLPA KSLQHGVPLS LDSSLSSLLE KICILPNRGL ARTKVPIFLG
IQGGSRCLAC VETEEGPSLQ LEDVNIEELY KGGEEATRFT FFQSSSGSAF RLEAAAWPGW
FLCGPAEPQQ PVQLTKESEP SARTKFYFEQ SW*

mutated AA sequence

MCSLPMARYY ISFLPEPLPA KSLQHGVPLS LDSSLSSLLE KICILPNRGL DRTKVPIFLG
IQGGSRCLAC VETEEGPSLQ LEDVNIEELY KGGEEATRFT FFQSSSGSAF RLEAAAWPGW
FLCGPAEPQQ PVQLTKESEP SARTKFYFEQ SW*

speed

0.33 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