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: ENST00000372648
Querying Taster for transcript #2: ENST00000223865
Querying Taster for transcript #3: ENST00000539497
MT speed 0 s - this script 3.851577 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
TBC1D13	polymorphism_automatic	4.9960036108132e-15	simple_aae				V9A	single base exchange	rs1572912		show file
TBC1D13	polymorphism_automatic	8.40438829641244e-14	simple_aae				V190A	single base exchange	rs1572912		show file
TBC1D13	polymorphism_automatic	1.77569008052991e-07	without_aae					single base exchange	rs1572912		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999995 (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)

chr9:131565554T>CN/A show variant in all transcripts IGV

HGNC symbol

TBC1D13

Ensembl transcript ID

ENST00000539497

Genbank transcript ID

N/A

UniProt peptide

Q9NVG8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.26T>C
cDNA.330T>C
g.16072T>C

AA changes

V9A Score: 64 explain score(s)

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

frameshift

known variant

Reference ID: rs1572912

database	homozygous (C/C)	heterozygous	allele carriers
1000G	824	872	1696
ExAC	8873	15021	23894

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.819	0
	0.439	0
(flanking)	-1.337	0

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

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

ENSPTRG00000021440

190

Mmulatta

all identical

ENSMMUG00000019179

190

Fcatus

not conserved

ENSFCAG00000005857

190

Mmusculus

not conserved

ENSMUSG00000039678

190

Ggallus

not conserved

ENSGALG00000004645

190

Trubripes

not conserved

ENSTRUG00000012856

190

KAL

Drerio

no alignment

ENSDARG00000078274

n/a

Dmelanogaster

no alignment

FBgn0035916

n/a

Celegans

all conserved

F45E6.3

223

Xtropicalis

not conserved

ENSXETG00000032711

190

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

660 / 660

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

220 / 220

position of stopcodon in wt / mu cDNA

964 / 964

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

305 / 305

chromosome

strand

last intron/exon boundary

899

theoretical NMD boundary in CDS

544

length of CDS

660

coding sequence (CDS) position

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

330

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

16072

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

131565554

original gDNA sequence snippet

CTCCCCACACAAGAACTCTGTGCCATCATCCCTAAATGAGT

altered gDNA sequence snippet

CTCCCCACACAAGAACTCTGCGCCATCATCCCTAAATGAGT

original cDNA sequence snippet

CTCCCCACACAAGAACTCTGTGCCATCATCCCTAAATGAGT

altered cDNA sequence snippet

CTCCCCACACAAGAACTCTGCGCCATCATCCCTAAATGAGT

wildtype AA sequence

MSSPHKNSVP SSLNEYEVLP NGCEAHWEVV ERILFIYAKL NPGIAYVQGM NEIVGPLYYT
FATDPNSEWK EHAEADTFFC FTNLMAEIRD NFIKSLDDSQ CGITYKMEKV YSTLKDKDVE
LYLKLQEQNI KPQFFAFRWL TLLLSQEFLL PDVIRIWDSL FADDNRFDFL LLVCCAMLML
IREQLLEGDF TVNMRLLQDY PITDVCQILQ KAKELQDSK*

mutated AA sequence

MSSPHKNSAP SSLNEYEVLP NGCEAHWEVV ERILFIYAKL NPGIAYVQGM NEIVGPLYYT
FATDPNSEWK EHAEADTFFC FTNLMAEIRD NFIKSLDDSQ CGITYKMEKV YSTLKDKDVE
LYLKLQEQNI KPQFFAFRWL TLLLSQEFLL PDVIRIWDSL FADDNRFDFL LLVCCAMLML
IREQLLEGDF TVNMRLLQDY PITDVCQILQ KAKELQDSK*

speed

1.06 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: 0.999999999999916 (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)

chr9:131565554T>CN/A show variant in all transcripts IGV

HGNC symbol

TBC1D13

Ensembl transcript ID

ENST00000372648

Genbank transcript ID

NM_018201

UniProt peptide

Q9NVG8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.569T>C
cDNA.719T>C
g.16072T>C

AA changes

V190A Score: 64 explain score(s)

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

190

frameshift

known variant

Reference ID: rs1572912

database	homozygous (C/C)	heterozygous	allele carriers
1000G	824	872	1696
ExAC	8873	15021	23894

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.819	0
	0.439	0
(flanking)	-1.337	0

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

190

mutated

not conserved

190

Ptroglodytes

not conserved

ENSPTRG00000021440

190

Mmulatta

all identical

ENSMMUG00000019179

190

Fcatus

not conserved

ENSFCAG00000005857

190

Mmusculus

not conserved

ENSMUSG00000039678

190

Ggallus

not conserved

ENSGALG00000004645

190

Trubripes

not conserved

ENSTRUG00000012856

190

KAL

Drerio

not conserved

ENSDARG00000078274

Dmelanogaster

all identical

FBgn0035916

200

Celegans

not conserved

F45E6.3

184

IVGCVK

AKQ

SEFHWHQFFEYSYKFSQESLVFR

Xtropicalis

not conserved

ENSXETG00000032711

190

protein features

start (aa)	end (aa)	feature	details
35	345	DOMAIN	Rab-GAP TBC.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1203 / 1203

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

401 / 401

position of stopcodon in wt / mu cDNA

1353 / 1353

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

151 / 151

chromosome

strand

last intron/exon boundary

1288

theoretical NMD boundary in CDS

1087

length of CDS

1203

coding sequence (CDS) position

569

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

719

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

16072

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

131565554

original gDNA sequence snippet

CTCCCCACACAAGAACTCTGTGCCATCATCCCTAAATGAGT

altered gDNA sequence snippet

CTCCCCACACAAGAACTCTGCGCCATCATCCCTAAATGAGT

original cDNA sequence snippet

CTCCCCACACAAGAACTCTGTGCCATCATCCCTAAATGAGT

altered cDNA sequence snippet

CTCCCCACACAAGAACTCTGCGCCATCATCCCTAAATGAGT

wildtype AA sequence

MSSLHKSRIA DFQDVLKEPS IALEKLRELS FSGIPCEGGL RCLCWKILLN YLPLERASWT
SILAKQRELY AQFLREMIIQ PGIAKANMGV SREDVTFEDH PLNPNPDSRW NTYFKDNEVL
LQIDKDVRRL CPDISFFQRA TDYPCLLILD PQNEFETLRK RVEQTTLKSQ TVARNRSGVT
NMSSPHKNSV PSSLNEYEVL PNGCEAHWEV VERILFIYAK LNPGIAYVQG MNEIVGPLYY
TFATDPNSEW KEHAEADTFF CFTNLMAEIR DNFIKSLDDS QCGITYKMEK VYSTLKDKDV
ELYLKLQEQN IKPQFFAFRW LTLLLSQEFL LPDVIRIWDS LFADDNRFDF LLLVCCAMLM
LIREQLLEGD FTVNMRLLQD YPITDVCQIL QKAKELQDSK *

mutated AA sequence

MSSLHKSRIA DFQDVLKEPS IALEKLRELS FSGIPCEGGL RCLCWKILLN YLPLERASWT
SILAKQRELY AQFLREMIIQ PGIAKANMGV SREDVTFEDH PLNPNPDSRW NTYFKDNEVL
LQIDKDVRRL CPDISFFQRA TDYPCLLILD PQNEFETLRK RVEQTTLKSQ TVARNRSGVT
NMSSPHKNSA PSSLNEYEVL PNGCEAHWEV VERILFIYAK LNPGIAYVQG MNEIVGPLYY
TFATDPNSEW KEHAEADTFF CFTNLMAEIR DNFIKSLDDS QCGITYKMEK VYSTLKDKDV
ELYLKLQEQN IKPQFFAFRW LTLLLSQEFL LPDVIRIWDS LFADDNRFDF LLLVCCAMLM
LIREQLLEGD FTVNMRLLQD YPITDVCQIL QKAKELQDSK *

speed

0.77 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.999999822430992 (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)

chr9:131565554T>CN/A show variant in all transcripts IGV

HGNC symbol

TBC1D13

Ensembl transcript ID

ENST00000223865

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.16072T>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs1572912

database	homozygous (C/C)	heterozygous	allele carriers
1000G	824	872	1696
ExAC	8873	15021	23894

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.819	0
	0.439	0
(flanking)	-1.337	0

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

2584

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

6 / 6

chromosome

strand

last intron/exon boundary

768

theoretical NMD boundary in CDS

712

length of CDS

828

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)

16072

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

131565554

original gDNA sequence snippet

CTCCCCACACAAGAACTCTGTGCCATCATCCCTAAATGAGT

altered gDNA sequence snippet

CTCCCCACACAAGAACTCTGCGCCATCATCCCTAAATGAGT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MSSLHKSRIA DFQDVLKEPS IALEKLRELS FSGIPCEGGL RCLCWKILLN YLPLERASWT
SILAKQRELY AQFLREMIIQ PGIAKANMGV SREDVTFEDH PLNPNPDSRW NTYFKDNEVL
LQIDKDVRRL CPDISFFQRA TDYPCLLILD PQNEFETLRK RVEQTTLKSQ TVARNRSGVT
NQEQNIKPQF FAFRWLTLLL SQEFLLPDVI RIWDSLFADD NRFDFLLLVC CAMLMLIREQ
LLEGDFTVNM RLLQDYPITD VCQILQKAKE LQDSK*

mutated AA sequence

N/A

speed

0.73 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