MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 4 transcript(s)...
Querying Taster for transcript #1: ENST00000346333
Querying Taster for transcript #2: ENST00000359244
Querying Taster for transcript #3: ENST00000426628
Querying Taster for transcript #4: ENST00000528685
MT speed 0 s - this script 3.363275 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
FAM86C1	polymorphism_automatic	2.73003841755326e-13	simple_aae		affected		A7S	single base exchange	rs12283300		show file
FAM86C1	polymorphism_automatic	2.73003841755326e-13	simple_aae		affected		A7S	single base exchange	rs12283300		show file
FAM86C1	polymorphism_automatic	2.73003841755326e-13	simple_aae		affected		A7S	single base exchange	rs12283300		show file
FAM86C1	polymorphism_automatic	2.73003841755326e-13	simple_aae		affected		A7S	single base exchange	rs12283300		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999727 (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)

chr11:71498601G>TN/A show variant in all transcripts IGV

HGNC symbol

FAM86C1

Ensembl transcript ID

ENST00000359244

Genbank transcript ID

NM_018172

UniProt peptide

Q9NVL1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.19G>T
cDNA.42G>T
g.46G>T

AA changes

A7S Score: 99 explain score(s)

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

frameshift

known variant

Reference ID: rs12283300

database	homozygous (T/T)	heterozygous	allele carriers
1000G	557	1129	1686
ExAC	2944	7826	10770

regulatory features

Cmyc, Transcription Factor, Cmyc TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F1, Transcription Factor, E2F1 Transcription Factor Binding
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Max, Transcription Factor, Max TF binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.695	0
	0.277	0
(flanking)	-1.471	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 increased	39	wt: 0.84 / mu: 0.96	wt: CCCGAGGAGAACGCG mu: CCCGAGGAGAACTCG	CGAG\|gaga
Donor increased	49	wt: 0.34 / mu: 0.60	wt: ACGCGGGGAGCGAAC mu: ACTCGGGGAGCGAAC	GCGG\|ggag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all identical

ENSPTRG00000007738

Mmulatta

all identical

ENSMMUG00000029240

Fcatus

no alignment

ENSFCAG00000018810

n/a

Mmusculus

not conserved

ENSMUSG00000022544

Ggallus

no alignment

ENSGALG00000002044

n/a

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000054950

n/a

Dmelanogaster

no alignment

FBgn0031003

n/a

Celegans

no alignment

R08D7.4

n/a

Xtropicalis

no alignment

ENSXETG00000033667

n/a

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

498 / 498

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

166 / 166

position of stopcodon in wt / mu cDNA

521 / 521

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

24 / 24

chromosome

strand

last intron/exon boundary

435

theoretical NMD boundary in CDS

361

length of CDS

498

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)

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

71498601

original gDNA sequence snippet

TCATGGCGCCCGAGGAGAACGCGGGGAGCGAACTCTTGCTG

altered gDNA sequence snippet

TCATGGCGCCCGAGGAGAACTCGGGGAGCGAACTCTTGCTG

original cDNA sequence snippet

TCATGGCGCCCGAGGAGAACGCGGGGAGCGAACTCTTGCTG

altered cDNA sequence snippet

TCATGGCGCCCGAGGAGAACTCGGGGAGCGAACTCTTGCTG

wildtype AA sequence

MAPEENAGSE LLLQSFKRRF LAARALRSFR WQSLEAKLRD SSDSELLRDI LQKHEAVHTE
PLDELYEVLV ETLMAKESTQ GHRSYLLTCC IAQKPSCRWS GSCGGWLPAG STSGLLNSTW
PLPSATQRCA SCSPPSYAGL GSDGKRKLIM TRNCFPTEST WRWQS*

mutated AA sequence

MAPEENSGSE LLLQSFKRRF LAARALRSFR WQSLEAKLRD SSDSELLRDI LQKHEAVHTE
PLDELYEVLV ETLMAKESTQ GHRSYLLTCC IAQKPSCRWS GSCGGWLPAG STSGLLNSTW
PLPSATQRCA SCSPPSYAGL GSDGKRKLIM TRNCFPTEST WRWQS*

speed

0.15 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: 0.999999999999727 (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)

chr11:71498601G>TN/A show variant in all transcripts IGV

HGNC symbol

FAM86C1

Ensembl transcript ID

ENST00000346333

Genbank transcript ID

NM_152563

UniProt peptide

Q9NVL1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.19G>T
cDNA.46G>T
g.46G>T

AA changes

A7S Score: 99 explain score(s)

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

frameshift

known variant

Reference ID: rs12283300

database	homozygous (T/T)	heterozygous	allele carriers
1000G	557	1129	1686
ExAC	2944	7826	10770

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.695	0
	0.277	0
(flanking)	-1.471	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 increased	39	wt: 0.84 / mu: 0.96	wt: CCCGAGGAGAACGCG mu: CCCGAGGAGAACTCG	CGAG\|gaga
Donor increased	49	wt: 0.34 / mu: 0.60	wt: ACGCGGGGAGCGAAC mu: ACTCGGGGAGCGAAC	GCGG\|ggag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all identical

ENSPTRG00000007738

Mmulatta

all identical

ENSMMUG00000029240

Fcatus

no alignment

ENSFCAG00000018810

n/a

Mmusculus

not conserved

ENSMUSG00000022544

Ggallus

no alignment

ENSGALG00000002044

n/a

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000054950

n/a

Dmelanogaster

no alignment

FBgn0031003

n/a

Celegans

no alignment

R08D7.4

n/a

Xtropicalis

no alignment

ENSXETG00000033667

n/a

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

396 / 396

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

132 / 132

position of stopcodon in wt / mu cDNA

423 / 423

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

28 / 28

chromosome

strand

last intron/exon boundary

337

theoretical NMD boundary in CDS

259

length of CDS

396

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)

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

71498601

original gDNA sequence snippet

TCATGGCGCCCGAGGAGAACGCGGGGAGCGAACTCTTGCTG

altered gDNA sequence snippet

TCATGGCGCCCGAGGAGAACTCGGGGAGCGAACTCTTGCTG

original cDNA sequence snippet

TCATGGCGCCCGAGGAGAACGCGGGGAGCGAACTCTTGCTG

altered cDNA sequence snippet

TCATGGCGCCCGAGGAGAACTCGGGGAGCGAACTCTTGCTG

wildtype AA sequence

MAPEENAGSE LLLQSFKRRF LAARALRSFR WQSLEAKLRD SSDSELLRDI LQKTCCIAQK
PSCRWSGSCG GWLPAGSTSG LLNSTWPLPS ATQRCASCSP PSYAGLGSDG KRKLIMTRNC
FPTESTWRWQ S*

mutated AA sequence

MAPEENSGSE LLLQSFKRRF LAARALRSFR WQSLEAKLRD SSDSELLRDI LQKTCCIAQK
PSCRWSGSCG GWLPAGSTSG LLNSTWPLPS ATQRCASCSP PSYAGLGSDG KRKLIMTRNC
FPTESTWRWQ S*

speed

0.14 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999727 (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)

chr11:71498601G>TN/A show variant in all transcripts IGV

HGNC symbol

FAM86C1

Ensembl transcript ID

ENST00000426628

Genbank transcript ID

NM_001099653

UniProt peptide

Q9NVL1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.19G>T
cDNA.38G>T
g.46G>T

AA changes

A7S Score: 99 explain score(s)

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

frameshift

known variant

Reference ID: rs12283300

database	homozygous (T/T)	heterozygous	allele carriers
1000G	557	1129	1686
ExAC	2944	7826	10770

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.695	0
	0.277	0
(flanking)	-1.471	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 increased	39	wt: 0.84 / mu: 0.96	wt: CCCGAGGAGAACGCG mu: CCCGAGGAGAACTCG	CGAG\|gaga
Donor increased	49	wt: 0.34 / mu: 0.60	wt: ACGCGGGGAGCGAAC mu: ACTCGGGGAGCGAAC	GCGG\|ggag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all identical

ENSPTRG00000007738

Mmulatta

all identical

ENSMMUG00000029240

Fcatus

no alignment

ENSFCAG00000018810

n/a

Mmusculus

not conserved

ENSMUSG00000022544

Ggallus

no alignment

ENSGALG00000002044

n/a

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000054950

n/a

Dmelanogaster

no alignment

FBgn0031003

n/a

Celegans

no alignment

R08D7.4

n/a

Xtropicalis

no alignment

ENSXETG00000033667

n/a

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

477 / 477

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

159 / 159

position of stopcodon in wt / mu cDNA

496 / 496

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

20 / 20

chromosome

strand

last intron/exon boundary

410

theoretical NMD boundary in CDS

340

length of CDS

477

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)

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

71498601

original gDNA sequence snippet

TCATGGCGCCCGAGGAGAACGCGGGGAGCGAACTCTTGCTG

altered gDNA sequence snippet

TCATGGCGCCCGAGGAGAACTCGGGGAGCGAACTCTTGCTG

original cDNA sequence snippet

TCATGGCGCCCGAGGAGAACGCGGGGAGCGAACTCTTGCTG

altered cDNA sequence snippet

TCATGGCGCCCGAGGAGAACTCGGGGAGCGAACTCTTGCTG

wildtype AA sequence

MAPEENAGSE LLLQSFKRRF LAARALRSFR WQSLEAKLRD SSDSELLRDI LQKTVKHPVC
VKHPPSVKYA RCFLSELIKK TCCIAQKPSC RWSGSCGGWL PAGSTSGLLN STWPLPSATQ
RCASCSPPSY AGLGSDGKRK LIMTRNCFPT ESTWRWQS*

mutated AA sequence

MAPEENSGSE LLLQSFKRRF LAARALRSFR WQSLEAKLRD SSDSELLRDI LQKTVKHPVC
VKHPPSVKYA RCFLSELIKK TCCIAQKPSC RWSGSCGGWL PAGSTSGLLN STWPLPSATQ
RCASCSPPSY AGLGSDGKRK LIMTRNCFPT ESTWRWQS*

speed

0.12 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999727 (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)

chr11:71498601G>TN/A show variant in all transcripts IGV

HGNC symbol

FAM86C1

Ensembl transcript ID

ENST00000528685

Genbank transcript ID

N/A

UniProt peptide

Q9NVL1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.19G>T
cDNA.19G>T
g.46G>T

AA changes

A7S Score: 99 explain score(s)

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

frameshift

known variant

Reference ID: rs12283300

database	homozygous (T/T)	heterozygous	allele carriers
1000G	557	1129	1686
ExAC	2944	7826	10770

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.695	0
	0.277	0
(flanking)	-1.471	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 increased	39	wt: 0.84 / mu: 0.96	wt: CCCGAGGAGAACGCG mu: CCCGAGGAGAACTCG	CGAG\|gaga
Donor increased	49	wt: 0.34 / mu: 0.60	wt: ACGCGGGGAGCGAAC mu: ACTCGGGGAGCGAAC	GCGG\|ggag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all identical

ENSPTRG00000007738

Mmulatta

all identical

ENSMMUG00000029240

Fcatus

no alignment

ENSFCAG00000018810

n/a

Mmusculus

not conserved

ENSMUSG00000022544

Ggallus

no alignment

ENSGALG00000002044

n/a

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000054950

n/a

Dmelanogaster

no alignment

FBgn0031003

n/a

Celegans

no alignment

R08D7.4

n/a

Xtropicalis

no alignment

ENSXETG00000033667

n/a

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

378 / 378

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

126 / 126

position of stopcodon in wt / mu cDNA

378 / 378

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

last intron/exon boundary

452

theoretical NMD boundary in CDS

401

length of CDS

378

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)

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

71498601

original gDNA sequence snippet

TCATGGCGCCCGAGGAGAACGCGGGGAGCGAACTCTTGCTG

altered gDNA sequence snippet

TCATGGCGCCCGAGGAGAACTCGGGGAGCGAACTCTTGCTG

original cDNA sequence snippet

ATGGCGCCCGAGGAGAACGCGGGGAGCGAACTCTTGCTG

altered cDNA sequence snippet

ATGGCGCCCGAGGAGAACTCGGGGAGCGAACTCTTGCTG

wildtype AA sequence

MAPEENAGSE LLLQSFKRRF LAARALRSFR WQSLEAKLRD SSDSELLRDI LQKTCCIAQK
PSCRWSGSCG GWLPAGSTSG LLNSTWPLPS ATQRCASCSP PSYVSPHAHP GLHGPQAVPT
GLQWK*

mutated AA sequence

MAPEENSGSE LLLQSFKRRF LAARALRSFR WQSLEAKLRD SSDSELLRDI LQKTCCIAQK
PSCRWSGSCG GWLPAGSTSG LLNSTWPLPS ATQRCASCSP PSYVSPHAHP GLHGPQAVPT
GLQWK*

speed

1.16 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems