MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000332624
Querying Taster for transcript #2: ENST00000430254
MT speed 0 s - this script 3.168764 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
TRAK2	polymorphism_automatic	0.0944985487518351	simple_aae		affected		V142I	single base exchange	rs13022344		show file
TRAK2	polymorphism_automatic	0.0944985487518351	simple_aae		affected		V142I	single base exchange	rs13022344		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.905501451248165 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM072094)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:202264156C>TN/A show variant in all transcripts IGV

HGNC symbol

TRAK2

Ensembl transcript ID

ENST00000332624

Genbank transcript ID

NM_015049

UniProt peptide

O60296

alteration type

single base exchange

alteration region

CDS

DNA changes

c.424G>A
cDNA.853G>A
g.52147G>A

AA changes

V142I Score: 29 explain score(s)

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

142

frameshift

known variant

Reference ID: rs13022344

database	homozygous (T/T)	heterozygous	allele carriers
1000G	778	1145	1923
ExAC	24071	-15375	8696

known disease mutation at this position, please check HGMD for details (HGMD ID CM072094)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.178	1
	0.979	1
(flanking)	0.796	1

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	52152	wt: 0.40 / mu: 0.64	wt: GTCTTATCTGAGCAG mu: ATCTTATCTGAGCAG	CTTA\|tctg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

142

mutated

all conserved

142

Ptroglodytes

all identical

ENSPTRG00000012804

142

Mmulatta

all identical

ENSMMUG00000023812

142

Fcatus

not conserved

ENSFCAG00000006099

Mmusculus

all identical

ENSMUSG00000026028

142

Ggallus

all conserved

ENSGALG00000008370

136

Trubripes

no homologue

Drerio

all identical

ENSDARG00000078872

118

Dmelanogaster

not conserved

FBgn0262872

315

Celegans

not conserved

T27A3.1

Xtropicalis

all conserved

ENSXETG00000032904

123

protein features

start (aa)	end (aa)	feature	details
48	353	DOMAIN	HAP1 N-terminal.	lost
134	354	COILED	Potential.	lost
301	311	CONFLICT	HVIEKEELKLH -> VGLFIHSTDIC (in Ref. 2).	might get lost (downstream of altered splice site)
312	914	CONFLICT	Missing (in Ref. 2).	might get lost (downstream of altered splice site)
359	509	REGION	Interaction with HGS (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2745 / 2745

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

915 / 915

position of stopcodon in wt / mu cDNA

3174 / 3174

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

430 / 430

chromosome

strand

-1

last intron/exon boundary

2499

theoretical NMD boundary in CDS

2019

length of CDS

2745

coding sequence (CDS) position

424

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

853

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

52147

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

202264156

original gDNA sequence snippet

CTCTCTTAAAGCGGAACCATGTCTTATCTGAGCAGAACGAA

altered gDNA sequence snippet

CTCTCTTAAAGCGGAACCATATCTTATCTGAGCAGAACGAA

original cDNA sequence snippet

CTCTCTTAAAGCGGAACCATGTCTTATCTGAGCAGAACGAA

altered cDNA sequence snippet

CTCTCTTAAAGCGGAACCATATCTTATCTGAGCAGAACGAA

wildtype AA sequence

MSQSQNAIFT SPTGEENLMN SNHRDSESIT DVCSNEDLPE VELVSLLEEQ LPQYRLKVDT
LFLYENQDWT QSPHQRQHAS DALSPVLAEE TFRYMILGTD RVEQMTKTYN DIDMVTHLLA
ERDRDLELAA RIGQALLKRN HVLSEQNESL EEQLGQAFDQ VNQLQHELCK KDELLRIVSI
ASEESETDSS CSTPLRFNES FSLSQGLLQL EMLQEKLKEL EEENMALRSK ACHIKTETVT
YEEKEQQLVS DCVKELRETN AQMSRMTEEL SGKSDELIRY QEELSSLLSQ IVDLQHKLKE
HVIEKEELKL HLQASKDAQR QLTMELHELQ DRNMECLGML HESQEEIKEL RSRSGPTAHL
YFSQSYGAFT GESLAAEIEG TMRKKLSLDE ESSLFKQKAQ QKRVFDTVRI ANDTRGRSIS
FPALLPIPGS NRSSVIMTAK PFESGLQQTE DKSLLNQGSS SEEVAGSSQK MGQPGPSGDS
DLATALHRLS LRRQNYLSEK QFFAEEWQRK IQVLADQKEG VSGCVTPTES LASLCTTQSE
ITDLSSASCL RGFMPEKLQI VKPLEGSQTL YHWQQLAQPN LGTILDPRPG VITKGFTQLP
GDAIYHISDL EEDEEEGITF QVQQPLEVEE KLSTSKPVTG IFLPPITSAG GPVTVATANP
GKCLSCTNST FTFTTCRILH PSDITQVTPS SGFPSLSCGS SGSSSSNTAV NSPALSYRLS
IGESITNRRD STTTFSSTMS LAKLLQERGI SAKVYHSPIS ENPLQPLPKS LAIPSTPPNS
PSHSPCPSPL PFEPRVHLSE NFLASRPAET FLQEMYGLRP SRNPPDVGQL KMNLVDRLKR
LGIARVVKNP GAQENGRCQE AEIGPQKPDS AVYLNSGSSL LGGLRRNQSL PVIMGSFAAP
VCTSSPKMGV LKED*

mutated AA sequence

MSQSQNAIFT SPTGEENLMN SNHRDSESIT DVCSNEDLPE VELVSLLEEQ LPQYRLKVDT
LFLYENQDWT QSPHQRQHAS DALSPVLAEE TFRYMILGTD RVEQMTKTYN DIDMVTHLLA
ERDRDLELAA RIGQALLKRN HILSEQNESL EEQLGQAFDQ VNQLQHELCK KDELLRIVSI
ASEESETDSS CSTPLRFNES FSLSQGLLQL EMLQEKLKEL EEENMALRSK ACHIKTETVT
YEEKEQQLVS DCVKELRETN AQMSRMTEEL SGKSDELIRY QEELSSLLSQ IVDLQHKLKE
HVIEKEELKL HLQASKDAQR QLTMELHELQ DRNMECLGML HESQEEIKEL RSRSGPTAHL
YFSQSYGAFT GESLAAEIEG TMRKKLSLDE ESSLFKQKAQ QKRVFDTVRI ANDTRGRSIS
FPALLPIPGS NRSSVIMTAK PFESGLQQTE DKSLLNQGSS SEEVAGSSQK MGQPGPSGDS
DLATALHRLS LRRQNYLSEK QFFAEEWQRK IQVLADQKEG VSGCVTPTES LASLCTTQSE
ITDLSSASCL RGFMPEKLQI VKPLEGSQTL YHWQQLAQPN LGTILDPRPG VITKGFTQLP
GDAIYHISDL EEDEEEGITF QVQQPLEVEE KLSTSKPVTG IFLPPITSAG GPVTVATANP
GKCLSCTNST FTFTTCRILH PSDITQVTPS SGFPSLSCGS SGSSSSNTAV NSPALSYRLS
IGESITNRRD STTTFSSTMS LAKLLQERGI SAKVYHSPIS ENPLQPLPKS LAIPSTPPNS
PSHSPCPSPL PFEPRVHLSE NFLASRPAET FLQEMYGLRP SRNPPDVGQL KMNLVDRLKR
LGIARVVKNP GAQENGRCQE AEIGPQKPDS AVYLNSGSSL LGGLRRNQSL PVIMGSFAAP
VCTSSPKMGV LKED*

speed

0.32 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: 0.905501451248165 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM072094)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:202264156C>TN/A show variant in all transcripts IGV

HGNC symbol

TRAK2

Ensembl transcript ID

ENST00000430254

Genbank transcript ID

N/A

UniProt peptide

O60296

alteration type

single base exchange

alteration region

CDS

DNA changes

c.424G>A
cDNA.774G>A
g.52147G>A

AA changes

V142I Score: 29 explain score(s)

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

142

frameshift

known variant

Reference ID: rs13022344

database	homozygous (T/T)	heterozygous	allele carriers
1000G	778	1145	1923
ExAC	24071	-15375	8696

known disease mutation at this position, please check HGMD for details (HGMD ID CM072094)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.178	1
	0.979	1
(flanking)	0.796	1

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	52152	wt: 0.40 / mu: 0.64	wt: GTCTTATCTGAGCAG mu: ATCTTATCTGAGCAG	CTTA\|tctg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

142

mutated

all conserved

142

Ptroglodytes

all identical

ENSPTRG00000012804

142

Mmulatta

all identical

ENSMMUG00000023812

142

Fcatus

not conserved

ENSFCAG00000006099

Mmusculus

all identical

ENSMUSG00000026028

142

Ggallus

all conserved

ENSGALG00000008370

136

Trubripes

no homologue

Drerio

all identical

ENSDARG00000078872

118

Dmelanogaster

not conserved

FBgn0262872

315

Celegans

not conserved

T27A3.1

Xtropicalis

all conserved

ENSXETG00000032904

123

protein features

start (aa)	end (aa)	feature	details
48	353	DOMAIN	HAP1 N-terminal.	lost
134	354	COILED	Potential.	lost
301	311	CONFLICT	HVIEKEELKLH -> VGLFIHSTDIC (in Ref. 2).	might get lost (downstream of altered splice site)
312	914	CONFLICT	Missing (in Ref. 2).	might get lost (downstream of altered splice site)
359	509	REGION	Interaction with HGS (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

936 / 936

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

312 / 312

position of stopcodon in wt / mu cDNA

1286 / 1286

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

351 / 351

chromosome

strand

-1

last intron/exon boundary

1120

theoretical NMD boundary in CDS

719

length of CDS

936

coding sequence (CDS) position

424

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

774

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

52147

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

202264156

original gDNA sequence snippet

CTCTCTTAAAGCGGAACCATGTCTTATCTGAGCAGAACGAA

altered gDNA sequence snippet

CTCTCTTAAAGCGGAACCATATCTTATCTGAGCAGAACGAA

original cDNA sequence snippet

CTCTCTTAAAGCGGAACCATGTCTTATCTGAGCAGAACGAA

altered cDNA sequence snippet

CTCTCTTAAAGCGGAACCATATCTTATCTGAGCAGAACGAA

wildtype AA sequence

mutated AA sequence

speed

0.85 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems