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: ENST00000275227
Querying Taster for transcript #2: ENST00000367918
Querying Taster for transcript #3: ENST00000538764
MT speed 0 s - this script 3.504788 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SLC18B1	polymorphism_automatic	2.42495901137119e-09	simple_aae				V204I	single base exchange	rs6926101		show file
SLC18B1	polymorphism_automatic	2.42495901137119e-09	simple_aae				V78I	single base exchange	rs6926101		show file
SLC18B1	polymorphism_automatic	0.935010923720875	without_aae					single base exchange	rs6926101		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999997575041 (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)

chr6:133105120C>TN/A show variant in all transcripts IGV

HGNC symbol

SLC18B1

Ensembl transcript ID

ENST00000275227

Genbank transcript ID

NM_052831

UniProt peptide

Q6NT16

alteration type

single base exchange

alteration region

CDS

DNA changes

c.610G>A
cDNA.707G>A
g.14582G>A

AA changes

V204I Score: 29 explain score(s)

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

204

frameshift

known variant

Reference ID: rs6926101

database	homozygous (T/T)	heterozygous	allele carriers
1000G	201	532	733
ExAC	1383	8379	9762

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.857	0.575
	-2.147	0.04
(flanking)	1.116	0.795

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	14574	wt: 0.8879 / mu: 0.9641 (marginal change - not scored)	wt: TGTTCTGGGATGCGT mu: TGTTCTGGGATGCAT	TTCT\|ggga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

204

mutated

all conserved

204

Ptroglodytes

all conserved

ENSPTRG00000018616

204

Mmulatta

all conserved

ENSMMUG00000013236

204

Fcatus

all conserved

ENSFCAG00000011135

204

Mmusculus

all conserved

ENSMUSG00000037455

204

Ggallus

no alignment

ENSGALG00000019961

n/a

Trubripes

not conserved

ENSTRUG00000001854

185

VLPA

Drerio

all conserved

ENSDARG00000044047

195

Dmelanogaster

no homologue

Celegans

all identical

F55A4.8

396

Xtropicalis

all identical

ENSXETG00000000108

227

protein features

start (aa)	end (aa)	feature	details
196	216	TRANSMEM	Helical; (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1371 / 1371

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

457 / 457

position of stopcodon in wt / mu cDNA

1468 / 1468

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

98 / 98

chromosome

strand

-1

last intron/exon boundary

1402

theoretical NMD boundary in CDS

1254

length of CDS

1371

coding sequence (CDS) position

610

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

707

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

14582

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

133105120

original gDNA sequence snippet

CTTTTATTGTTCTGGGATGCGTCGTTTTGCTGATGGTACCA

altered gDNA sequence snippet

CTTTTATTGTTCTGGGATGCATCGTTTTGCTGATGGTACCA

original cDNA sequence snippet

CTTTTATTGTTCTGGGATGCGTCGTTTTGCTGATGGTACCA

altered cDNA sequence snippet

CTTTTATTGTTCTGGGATGCATCGTTTTGCTGATGGTACCA

wildtype AA sequence

MEALGDLEGP RAPGGDDPAG SAGETPGWLS REQVFVLISA ASVNLGSMMC YSILGPFFPK
EAEKKGASNT IIGMIFGCFA LFELLASLVF GNYLVHIGAK FMFVAGMFVS GGVTILFGVL
DRVPDGPVFI AMCFLVRVMD AVSFAAAMTA SSSILAKAFP NNVATVLGSL ETFSGLGLIL
GPPVGGFLYQ SFGYEVPFIV LGCVVLLMVP LNMYILPNYE SDPGEHSFWK LIALPKVGLI
AFVINSLSSC FGFLDPTLSL FVLEKFNLPA GYVGLVFLGM ALSYAISSPL FGLLSDKRPP
LRKWLLVFGN LITAGCYMLL GPVPILHIKS QLWLLVLILV VSGLSAGMSI IPTFPEILSC
AHENGFEEGL STLGLVSGLF SAMWSIGAFM GPTLGGFLYE KIGFEWAAAI QGLWALISGL
AMGLFYLLEY SRRKRSKSQN ILSTEEERTT LLPNET*

mutated AA sequence

MEALGDLEGP RAPGGDDPAG SAGETPGWLS REQVFVLISA ASVNLGSMMC YSILGPFFPK
EAEKKGASNT IIGMIFGCFA LFELLASLVF GNYLVHIGAK FMFVAGMFVS GGVTILFGVL
DRVPDGPVFI AMCFLVRVMD AVSFAAAMTA SSSILAKAFP NNVATVLGSL ETFSGLGLIL
GPPVGGFLYQ SFGYEVPFIV LGCIVLLMVP LNMYILPNYE SDPGEHSFWK LIALPKVGLI
AFVINSLSSC FGFLDPTLSL FVLEKFNLPA GYVGLVFLGM ALSYAISSPL FGLLSDKRPP
LRKWLLVFGN LITAGCYMLL GPVPILHIKS QLWLLVLILV VSGLSAGMSI IPTFPEILSC
AHENGFEEGL STLGLVSGLF SAMWSIGAFM GPTLGGFLYE KIGFEWAAAI QGLWALISGL
AMGLFYLLEY SRRKRSKSQN ILSTEEERTT LLPNET*

speed

0.93 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: 0.999999997575041 (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)

chr6:133105120C>TN/A show variant in all transcripts IGV

HGNC symbol

SLC18B1

Ensembl transcript ID

ENST00000538764

Genbank transcript ID

N/A

UniProt peptide

Q6NT16

alteration type

single base exchange

alteration region

CDS

DNA changes

c.232G>A
cDNA.568G>A
g.14582G>A

AA changes

V78I Score: 29 explain score(s)

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

frameshift

known variant

Reference ID: rs6926101

database	homozygous (T/T)	heterozygous	allele carriers
1000G	201	532	733
ExAC	1383	8379	9762

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.857	0.575
	-2.147	0.04
(flanking)	1.116	0.795

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	14574	wt: 0.8879 / mu: 0.9641 (marginal change - not scored)	wt: TGTTCTGGGATGCGT mu: TGTTCTGGGATGCAT	TTCT\|ggga

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 conserved

ENSPTRG00000018616

204

Mmulatta

all conserved

ENSMMUG00000013236

204

Fcatus

all conserved

ENSFCAG00000011135

204

Mmusculus

all conserved

ENSMUSG00000037455

204

Ggallus

no alignment

ENSGALG00000019961

n/a

Trubripes

not conserved

ENSTRUG00000001854

185

Drerio

all conserved

ENSDARG00000044047

195

Dmelanogaster

no homologue

Celegans

all identical

F55A4.8

396

Xtropicalis

all identical

ENSXETG00000000108

227

protein features

start (aa)	end (aa)	feature	details
71	91	TRANSMEM	Helical; (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

711 / 711

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

237 / 237

position of stopcodon in wt / mu cDNA

1047 / 1047

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

337 / 337

chromosome

strand

-1

last intron/exon boundary

948

theoretical NMD boundary in CDS

561

length of CDS

711

coding sequence (CDS) position

232

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

568

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

14582

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

133105120

original gDNA sequence snippet

CTTTTATTGTTCTGGGATGCGTCGTTTTGCTGATGGTACCA

altered gDNA sequence snippet

CTTTTATTGTTCTGGGATGCATCGTTTTGCTGATGGTACCA

original cDNA sequence snippet

CTTTTATTGTTCTGGGATGCGTCGTTTTGCTGATGGTACCA

altered cDNA sequence snippet

CTTTTATTGTTCTGGGATGCATCGTTTTGCTGATGGTACCA

wildtype AA sequence

MFCFVRVAGI LGIWKLSCTY WSKIYVCSRN VCLRRSYNSL WGSLETFSGL GLILGPPVGG
FLYQSFGYEV PFIVLGCVVL LMVPLNMYIL PNYESDPGEH SFWKLIALPK VGLIAFVINS
LSSCFGFLDP TLSLFVLEKF NLPAGYVGLV FLGMALSYAI SSPLFGLLSD KRPPLRKWLL
VFGNLITAGC YMLLGPVPIL HIKSQLWLLV LILVVSGLSA GMSIIPTFPE ILSCAQ*

mutated AA sequence

MFCFVRVAGI LGIWKLSCTY WSKIYVCSRN VCLRRSYNSL WGSLETFSGL GLILGPPVGG
FLYQSFGYEV PFIVLGCIVL LMVPLNMYIL PNYESDPGEH SFWKLIALPK VGLIAFVINS
LSSCFGFLDP TLSLFVLEKF NLPAGYVGLV FLGMALSYAI SSPLFGLLSD KRPPLRKWLL
VFGNLITAGC YMLLGPVPIL HIKSQLWLLV LILVVSGLSA GMSIIPTFPE ILSCAQ*

speed

0.61 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.0649890762791252 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:133105120C>TN/A show variant in all transcripts IGV

HGNC symbol

SLC18B1

Ensembl transcript ID

ENST00000367918

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.14582G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs6926101

database	homozygous (T/T)	heterozygous	allele carriers
1000G	201	532	733
ExAC	1383	8379	9762

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.857	0.575
	-2.147	0.04
(flanking)	1.116	0.795

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	14574	wt: 0.8879 / mu: 0.9641 (marginal change - not scored)	wt: TGTTCTGGGATGCGT mu: TGTTCTGGGATGCAT	TTCT\|ggga

distance from splice site

6243

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

67 / 67

chromosome

strand

-1

last intron/exon boundary

401

theoretical NMD boundary in CDS

284

length of CDS

324

coding sequence (CDS) position

N/A

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

N/A

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

14582

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

133105120

original gDNA sequence snippet

CTTTTATTGTTCTGGGATGCGTCGTTTTGCTGATGGTACCA

altered gDNA sequence snippet

CTTTTATTGTTCTGGGATGCATCGTTTTGCTGATGGTACCA

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MEALGDLEGP RAPGGDDPAG SAGETPGWLS REQVFVLISA ASVNLGSMMC YSILGPFFPK
EAEKKGASNT IIGMIFGFQF TSWICGTSIP GYGTVLCHLF TTIWSPK*

mutated AA sequence

N/A

speed

0.81 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