MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 4 transcript(s)...
Querying Taster for transcript #1: ENST00000321897
Querying Taster for transcript #2: ENST00000541562
Querying Taster for transcript #3: ENST00000416670
Querying Taster for transcript #4: ENST00000542001
MT speed 0 s - this script 4.096679 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
VARS2	polymorphism_automatic	0.999624175445277	simple_aae		affected		R947Q	single base exchange	rs9394021		show file
VARS2	polymorphism_automatic	0.999624175445277	simple_aae		affected		R917Q	single base exchange	rs9394021		show file
VARS2	polymorphism_automatic	0.999624175445277	simple_aae		affected		R917Q	single base exchange	rs9394021		show file
VARS2	polymorphism_automatic	0.999624175445277	simple_aae		affected		R777Q	single base exchange	rs9394021		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.000375824554722551 (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
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:30893127G>AN/A show variant in all transcripts IGV

HGNC symbol

VARS2

Ensembl transcript ID

ENST00000541562

Genbank transcript ID

NM_001167734

UniProt peptide

Q5ST30

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2840G>A
cDNA.2921G>A
g.17109G>A

AA changes

R947Q Score: 43 explain score(s)

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

947

frameshift

known variant

Reference ID: rs9394021

database	homozygous (A/A)	heterozygous	allele carriers
1000G	469	1034	1503
ExAC	5866	20442	26308

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.246	0.997
	3.976	0.994
(flanking)	-1.38	0.564

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	17105	wt: 0.24 / mu: 0.39	wt: GGGCTCTCCGAGCCA mu: GGGCTCTCCAAGCCA	GCTC\|tccg
Donor gained	17114	0.33	mu: AAGCCACGTACCAGC	GCCA\|cgta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

947

mutated

all conserved

947

Ptroglodytes

all identical

ENSPTRG00000034497

926

Mmulatta

all identical

ENSMMUG00000018609

918

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000038838

918

Ggallus

no homologue

Trubripes

no alignment

ENSTRUG00000005264

n/a

Drerio

all identical

ENSDARG00000056717

911

Dmelanogaster

all conserved

FBgn0035942

847

Celegans

all identical

ZC513.4

827

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
985	985	CONFLICT	E -> G (in Ref. 2; BAB15191).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3282 / 3282

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

1094 / 1094

position of stopcodon in wt / mu cDNA

3363 / 3363

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

82 / 82

chromosome

strand

last intron/exon boundary

3262

theoretical NMD boundary in CDS

3130

length of CDS

3282

coding sequence (CDS) position

2840

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

2921

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

17109

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

30893127

original gDNA sequence snippet

GCAGGTGCTAAGGGCTCTCCGAGCCACGTACCAGCTCACCA

altered gDNA sequence snippet

GCAGGTGCTAAGGGCTCTCCAAGCCACGTACCAGCTCACCA

original cDNA sequence snippet

GCAGGTGCTAAGGGCTCTCCGAGCCACGTACCAGCTCACCA

altered cDNA sequence snippet

GCAGGTGCTAAGGGCTCTCCAAGCCACGTACCAGCTCACCA

wildtype AA sequence

MGGKAWPRRA VGTAGGPCAE QISAPFQTLL MPHLPLASFR PPFWGLRHSR GLPRFHSVST
QSEPHGSPIS RRNREAKQKR LREKQATLEA EIAGESKSPA ESIKAWRPKE LVLYEIPTKP
GEKKDVSGPL PPAYSPRYVE AAWYPWWVRE GFFKPEYQAR LPQATGETFS MCIPPPNVTG
SLHIGHALTV AIQDALVRWH RMRGDQVLWV PGSDHAGIAT QAVVEKQLWK ERGVRRHELS
REAFLREVWQ WKEAKGGEIC EQLRALGASL DWDRECFTMD VGSSVAVTEA FVRLYKAGLL
YRNHQLVNWS CALRSAISDI EVENRPLPGH TQLRLPGCPT PVSFGLLFSV AFPVDGEPDA
EVVVGTTRPE TLPGDVAVAV HPDDSRYTHL HGRQLRHPLM GQPLPLITDY AVQPHVGTGA
VKVTPAHSPA DAEMGARHGL SPLNVIAEDG TMTSLCGDWL QGLHRFVARE KIMSVLSEWG
LFRGLQNHPM VLPICSRSGD VIEYLLKNQW FVRCQEMGAR AAKAVESGAL ELSPSFHQKN
WQHWFSHIGD WCVSRQLWWG HQIPAYLVVE DHAQGEEDCW VVGRSEAEAR EVAAELTGRP
GAELTLERDP DVLDTWFSSA LFPFSALGWP QETPDLARFY PLSLLETGSD LLLFWVGRMV
MLGTQLTGQL PFSKVLLHPM VRDRQGRKMS KSLGNVLDPR DIISGVEMQV LQEKLRSGNL
DPAELAIVAA AQKKDFPHGI PECGTDALRF TLCSHGVQAG DLHLSVSEVQ SCRHFCNKIW
NALRFILNAL GEKFVPQPAE ELSPSSPMDA WILSRLALAA QECERGFLTR ELSLVTHALH
HFWLHNLCDV YLEAVKPVLW HSPRPLGPPQ VLFSCADLGL RLLAPLMPFL AEELWQRLPP
RPGCPPAPSI SVAPYPSACS LEHWRQPELE RRFSRVQEVV QVLRALRATY QLTKARPRVL
LQSSEPGDQG LFEAFLEPLG TLGYCGAVGL LPPGAAAPSG WAQAPLSDTA QVYMELQGLV
DPQIQLPLLA ARRYKLQKQL DSLTARTPSE GEAGTQRQQK LSSLQLELSK LDKAASHLRQ
LMDEPPAPGS PEL*

mutated AA sequence

MGGKAWPRRA VGTAGGPCAE QISAPFQTLL MPHLPLASFR PPFWGLRHSR GLPRFHSVST
QSEPHGSPIS RRNREAKQKR LREKQATLEA EIAGESKSPA ESIKAWRPKE LVLYEIPTKP
GEKKDVSGPL PPAYSPRYVE AAWYPWWVRE GFFKPEYQAR LPQATGETFS MCIPPPNVTG
SLHIGHALTV AIQDALVRWH RMRGDQVLWV PGSDHAGIAT QAVVEKQLWK ERGVRRHELS
REAFLREVWQ WKEAKGGEIC EQLRALGASL DWDRECFTMD VGSSVAVTEA FVRLYKAGLL
YRNHQLVNWS CALRSAISDI EVENRPLPGH TQLRLPGCPT PVSFGLLFSV AFPVDGEPDA
EVVVGTTRPE TLPGDVAVAV HPDDSRYTHL HGRQLRHPLM GQPLPLITDY AVQPHVGTGA
VKVTPAHSPA DAEMGARHGL SPLNVIAEDG TMTSLCGDWL QGLHRFVARE KIMSVLSEWG
LFRGLQNHPM VLPICSRSGD VIEYLLKNQW FVRCQEMGAR AAKAVESGAL ELSPSFHQKN
WQHWFSHIGD WCVSRQLWWG HQIPAYLVVE DHAQGEEDCW VVGRSEAEAR EVAAELTGRP
GAELTLERDP DVLDTWFSSA LFPFSALGWP QETPDLARFY PLSLLETGSD LLLFWVGRMV
MLGTQLTGQL PFSKVLLHPM VRDRQGRKMS KSLGNVLDPR DIISGVEMQV LQEKLRSGNL
DPAELAIVAA AQKKDFPHGI PECGTDALRF TLCSHGVQAG DLHLSVSEVQ SCRHFCNKIW
NALRFILNAL GEKFVPQPAE ELSPSSPMDA WILSRLALAA QECERGFLTR ELSLVTHALH
HFWLHNLCDV YLEAVKPVLW HSPRPLGPPQ VLFSCADLGL RLLAPLMPFL AEELWQRLPP
RPGCPPAPSI SVAPYPSACS LEHWRQPELE RRFSRVQEVV QVLRALQATY QLTKARPRVL
LQSSEPGDQG LFEAFLEPLG TLGYCGAVGL LPPGAAAPSG WAQAPLSDTA QVYMELQGLV
DPQIQLPLLA ARRYKLQKQL DSLTARTPSE GEAGTQRQQK LSSLQLELSK LDKAASHLRQ
LMDEPPAPGS PEL*

speed

0.67 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: 0.000375824554722551 (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
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:30893127G>AN/A show variant in all transcripts IGV

HGNC symbol

VARS2

Ensembl transcript ID

ENST00000321897

Genbank transcript ID

N/A

UniProt peptide

Q5ST30

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2750G>A
cDNA.3382G>A
g.17109G>A

AA changes

R917Q Score: 43 explain score(s)

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

917

frameshift

known variant

Reference ID: rs9394021

database	homozygous (A/A)	heterozygous	allele carriers
1000G	469	1034	1503
ExAC	5866	20442	26308

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.246	0.997
	3.976	0.994
(flanking)	-1.38	0.564

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	17105	wt: 0.24 / mu: 0.39	wt: GGGCTCTCCGAGCCA mu: GGGCTCTCCAAGCCA	GCTC\|tccg
Donor gained	17114	0.33	mu: AAGCCACGTACCAGC	GCCA\|cgta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

917

mutated

all conserved

917

Ptroglodytes

all identical

ENSPTRG00000034497

926

Mmulatta

all identical

ENSMMUG00000018609

918

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000038838

918

Ggallus

no homologue

Trubripes

no alignment

ENSTRUG00000005264

n/a

Drerio

all identical

ENSDARG00000056717

911

Dmelanogaster

all conserved

FBgn0035942

847

Celegans

all identical

ZC513.4

827

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
985	985	CONFLICT	E -> G (in Ref. 2; BAB15191).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3192 / 3192

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

1064 / 1064

position of stopcodon in wt / mu cDNA

3824 / 3824

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

633 / 633

chromosome

strand

last intron/exon boundary

3723

theoretical NMD boundary in CDS

3040

length of CDS

3192

coding sequence (CDS) position

2750

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

3382

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

17109

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

30893127

original gDNA sequence snippet

GCAGGTGCTAAGGGCTCTCCGAGCCACGTACCAGCTCACCA

altered gDNA sequence snippet

GCAGGTGCTAAGGGCTCTCCAAGCCACGTACCAGCTCACCA

original cDNA sequence snippet

GCAGGTGCTAAGGGCTCTCCGAGCCACGTACCAGCTCACCA

altered cDNA sequence snippet

GCAGGTGCTAAGGGCTCTCCAAGCCACGTACCAGCTCACCA

wildtype AA sequence

MPHLPLASFR PPFWGLRHSR GLPRFHSVST QSEPHGSPIS RRNREAKQKR LREKQATLEA
EIAGESKSPA ESIKAWRPKE LVLYEIPTKP GEKKDVSGPL PPAYSPRYVE AAWYPWWVRE
GFFKPEYQAR LPQATGETFS MCIPPPNVTG SLHIGHALTV AIQDALVRWH RMRGDQVLWV
PGSDHAGIAT QAVVEKQLWK ERGVRRHELS REAFLREVWQ WKEAKGGEIC EQLRALGASL
DWDRECFTMD VGSSVAVTEA FVRLYKAGLL YRNHQLVNWS CALRSAISDI EVENRPLPGH
TQLRLPGCPT PVSFGLLFSV AFPVDGEPDA EVVVGTTRPE TLPGDVAVAV HPDDSRYTHL
HGRQLRHPLM GQPLPLITDY AVQPHVGTGA VKVTPAHSPA DAEMGARHGL SPLNVIAEDG
TMTSLCGDWL QGLHRFVARE KIMSVLSEWG LFRGLQNHPM VLPICSRSGD VIEYLLKNQW
FVRCQEMGAR AAKAVESGAL ELSPSFHQKN WQHWFSHIGD WCVSRQLWWG HQIPAYLVVE
DHAQGEEDCW VVGRSEAEAR EVAAELTGRP GAELTLERDP DVLDTWFSSA LFPFSALGWP
QETPDLARFY PLSLLETGSD LLLFWVGRMV MLGTQLTGQL PFSKVLLHPM VRDRQGRKMS
KSLGNVLDPR DIISGVEMQV LQEKLRSGNL DPAELAIVAA AQKKDFPHGI PECGTDALRF
TLCSHGVQAG DLHLSVSEVQ SCRHFCNKIW NALRFILNAL GEKFVPQPAE ELSPSSPMDA
WILSRLALAA QECERGFLTR ELSLVTHALH HFWLHNLCDV YLEAVKPVLW HSPRPLGPPQ
VLFSCADLGL RLLAPLMPFL AEELWQRLPP RPGCPPAPSI SVAPYPSACS LEHWRQPELE
RRFSRVQEVV QVLRALRATY QLTKARPRVL LQSSEPGDQG LFEAFLEPLG TLGYCGAVGL
LPPGAAAPSG WAQAPLSDTA QVYMELQGLV DPQIQLPLLA ARRYKLQKQL DSLTARTPSE
GEAGTQRQQK LSSLQLELSK LDKAASHLRQ LMDEPPAPGS PEL*

mutated AA sequence

MPHLPLASFR PPFWGLRHSR GLPRFHSVST QSEPHGSPIS RRNREAKQKR LREKQATLEA
EIAGESKSPA ESIKAWRPKE LVLYEIPTKP GEKKDVSGPL PPAYSPRYVE AAWYPWWVRE
GFFKPEYQAR LPQATGETFS MCIPPPNVTG SLHIGHALTV AIQDALVRWH RMRGDQVLWV
PGSDHAGIAT QAVVEKQLWK ERGVRRHELS REAFLREVWQ WKEAKGGEIC EQLRALGASL
DWDRECFTMD VGSSVAVTEA FVRLYKAGLL YRNHQLVNWS CALRSAISDI EVENRPLPGH
TQLRLPGCPT PVSFGLLFSV AFPVDGEPDA EVVVGTTRPE TLPGDVAVAV HPDDSRYTHL
HGRQLRHPLM GQPLPLITDY AVQPHVGTGA VKVTPAHSPA DAEMGARHGL SPLNVIAEDG
TMTSLCGDWL QGLHRFVARE KIMSVLSEWG LFRGLQNHPM VLPICSRSGD VIEYLLKNQW
FVRCQEMGAR AAKAVESGAL ELSPSFHQKN WQHWFSHIGD WCVSRQLWWG HQIPAYLVVE
DHAQGEEDCW VVGRSEAEAR EVAAELTGRP GAELTLERDP DVLDTWFSSA LFPFSALGWP
QETPDLARFY PLSLLETGSD LLLFWVGRMV MLGTQLTGQL PFSKVLLHPM VRDRQGRKMS
KSLGNVLDPR DIISGVEMQV LQEKLRSGNL DPAELAIVAA AQKKDFPHGI PECGTDALRF
TLCSHGVQAG DLHLSVSEVQ SCRHFCNKIW NALRFILNAL GEKFVPQPAE ELSPSSPMDA
WILSRLALAA QECERGFLTR ELSLVTHALH HFWLHNLCDV YLEAVKPVLW HSPRPLGPPQ
VLFSCADLGL RLLAPLMPFL AEELWQRLPP RPGCPPAPSI SVAPYPSACS LEHWRQPELE
RRFSRVQEVV QVLRALQATY QLTKARPRVL LQSSEPGDQG LFEAFLEPLG TLGYCGAVGL
LPPGAAAPSG WAQAPLSDTA QVYMELQGLV DPQIQLPLLA ARRYKLQKQL DSLTARTPSE
GEAGTQRQQK LSSLQLELSK LDKAASHLRQ LMDEPPAPGS PEL*

speed

0.69 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.000375824554722551 (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
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:30893127G>AN/A show variant in all transcripts IGV

HGNC symbol

VARS2

Ensembl transcript ID

ENST00000416670

Genbank transcript ID

NM_020442

UniProt peptide

Q5ST30

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2750G>A
cDNA.2917G>A
g.17109G>A

AA changes

R917Q Score: 43 explain score(s)

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

917

frameshift

known variant

Reference ID: rs9394021

database	homozygous (A/A)	heterozygous	allele carriers
1000G	469	1034	1503
ExAC	5866	20442	26308

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.246	0.997
	3.976	0.994
(flanking)	-1.38	0.564

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	17105	wt: 0.24 / mu: 0.39	wt: GGGCTCTCCGAGCCA mu: GGGCTCTCCAAGCCA	GCTC\|tccg
Donor gained	17114	0.33	mu: AAGCCACGTACCAGC	GCCA\|cgta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

917

mutated

all conserved

917

Ptroglodytes

all identical

ENSPTRG00000034497

926

Mmulatta

all identical

ENSMMUG00000018609

918

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000038838

918

Ggallus

no homologue

Trubripes

no alignment

ENSTRUG00000005264

n/a

Drerio

all identical

ENSDARG00000056717

911

Dmelanogaster

all conserved

FBgn0035942

847

Celegans

all identical

ZC513.4

827

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
985	985	CONFLICT	E -> G (in Ref. 2; BAB15191).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3192 / 3192

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

1064 / 1064

position of stopcodon in wt / mu cDNA

3359 / 3359

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

168 / 168

chromosome

strand

last intron/exon boundary

3258

theoretical NMD boundary in CDS

3040

length of CDS

3192

coding sequence (CDS) position

2750

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

2917

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

17109

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

30893127

original gDNA sequence snippet

GCAGGTGCTAAGGGCTCTCCGAGCCACGTACCAGCTCACCA

altered gDNA sequence snippet

GCAGGTGCTAAGGGCTCTCCAAGCCACGTACCAGCTCACCA

original cDNA sequence snippet

GCAGGTGCTAAGGGCTCTCCGAGCCACGTACCAGCTCACCA

altered cDNA sequence snippet

GCAGGTGCTAAGGGCTCTCCAAGCCACGTACCAGCTCACCA

wildtype AA sequence

mutated AA sequence

MPHLPLASFR PPFWGLRHSR GLPRFHSVST QSEPHGSPIS RRNREAKQKR LREKQATLEA
EIAGESKSPA ESIKAWRPKE LVLYEIPTKP GEKKDVSGPL PPAYSPRYVE AAWYPWWVRE
GFFKPEYQAR LPQATGETFS MCIPPPNVTG SLHIGHALTV AIQDALVRWH RMRGDQVLWV
PGSDHAGIAT QAVVEKQLWK ERGVRRHELS REAFLREVWQ WKEAKGGEIC EQLRALGASL
DWDRECFTMD VGSSVAVTEA FVRLYKAGLL YRNHQLVNWS CALRSAISDI EVENRPLPGH
TQLRLPGCPT PVSFGLLFSV AFPVDGEPDA EVVVGTTRPE TLPGDVAVAV HPDDSRYTHL
HGRQLRHPLM GQPLPLITDY AVQPHVGTGA VKVTPAHSPA DAEMGARHGL SPLNVIAEDG
TMTSLCGDWL QGLHRFVARE KIMSVLSEWG LFRGLQNHPM VLPICSRSGD VIEYLLKNQW
FVRCQEMGAR AAKAVESGAL ELSPSFHQKN WQHWFSHIGD WCVSRQLWWG HQIPAYLVVE
DHAQGEEDCW VVGRSEAEAR EVAAELTGRP GAELTLERDP DVLDTWFSSA LFPFSALGWP
QETPDLARFY PLSLLETGSD LLLFWVGRMV MLGTQLTGQL PFSKVLLHPM VRDRQGRKMS
KSLGNVLDPR DIISGVEMQV LQEKLRSGNL DPAELAIVAA AQKKDFPHGI PECGTDALRF
TLCSHGVQAG DLHLSVSEVQ SCRHFCNKIW NALRFILNAL GEKFVPQPAE ELSPSSPMDA
WILSRLALAA QECERGFLTR ELSLVTHALH HFWLHNLCDV YLEAVKPVLW HSPRPLGPPQ
VLFSCADLGL RLLAPLMPFL AEELWQRLPP RPGCPPAPSI SVAPYPSACS LEHWRQPELE
RRFSRVQEVV QVLRALQATY QLTKARPRVL LQSSEPGDQG LFEAFLEPLG TLGYCGAVGL
LPPGAAAPSG WAQAPLSDTA QVYMELQGLV DPQIQLPLLA ARRYKLQKQL DSLTARTPSE
GEAGTQRQQK LSSLQLELSK LDKAASHLRQ LMDEPPAPGS PEL*

speed

0.66 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.000375824554722551 (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
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:30893127G>AN/A show variant in all transcripts IGV

HGNC symbol

VARS2

Ensembl transcript ID

ENST00000542001

Genbank transcript ID

NM_001167733

UniProt peptide

Q5ST30

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2330G>A
cDNA.2689G>A
g.17109G>A

AA changes

R777Q Score: 43 explain score(s)

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

777

frameshift

known variant

Reference ID: rs9394021

database	homozygous (A/A)	heterozygous	allele carriers
1000G	469	1034	1503
ExAC	5866	20442	26308

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.246	0.997
	3.976	0.994
(flanking)	-1.38	0.564

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	17105	wt: 0.24 / mu: 0.39	wt: GGGCTCTCCGAGCCA mu: GGGCTCTCCAAGCCA	GCTC\|tccg
Donor gained	17114	0.33	mu: AAGCCACGTACCAGC	GCCA\|cgta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

777

mutated

all conserved

777

Ptroglodytes

all identical

ENSPTRG00000034497

926

Mmulatta

all identical

ENSMMUG00000018609

918

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000038838

918

Ggallus

no homologue

Trubripes

no alignment

ENSTRUG00000005264

n/a

Drerio

all identical

ENSDARG00000056717

911

Dmelanogaster

all conserved

FBgn0035942

847

Celegans

all identical

ZC513.4

826

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
985	985	CONFLICT	E -> G (in Ref. 2; BAB15191).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2772 / 2772

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

924 / 924

position of stopcodon in wt / mu cDNA

3131 / 3131

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

360 / 360

chromosome

strand

last intron/exon boundary

3030

theoretical NMD boundary in CDS

2620

length of CDS

2772

coding sequence (CDS) position

2330

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

2689

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

17109

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

30893127

original gDNA sequence snippet

GCAGGTGCTAAGGGCTCTCCGAGCCACGTACCAGCTCACCA

altered gDNA sequence snippet

GCAGGTGCTAAGGGCTCTCCAAGCCACGTACCAGCTCACCA

original cDNA sequence snippet

GCAGGTGCTAAGGGCTCTCCGAGCCACGTACCAGCTCACCA

altered cDNA sequence snippet

GCAGGTGCTAAGGGCTCTCCAAGCCACGTACCAGCTCACCA

wildtype AA sequence

MCIPPPNVTG SLHIGHALTV AIQDALVRWH RMRGDQVLWV PGSDHAGIAT QAVVEKQLWK
ERGVRRHELS REAFLREVWQ WKEAKGGEIC EQLRALGASL DWDRECFTMD VGSSVAVTEA
FVRLYKAGLL YRNHQLVNWS CALRSAISDI EVENRPLPGH TQLRLPGCPT PVSFGLLFSV
AFPVDGEPDA EVVVGTTRPE TLPGDVAVAV HPDDSRYTHL HGRQLRHPLM GQPLPLITDY
AVQPHVGTGA VKVTPAHSPA DAEMGARHGL SPLNVIAEDG TMTSLCGDWL QGLHRFVARE
KIMSVLSEWG LFRGLQNHPM VLPICSRSGD VIEYLLKNQW FVRCQEMGAR AAKAVESGAL
ELSPSFHQKN WQHWFSHIGD WCVSRQLWWG HQIPAYLVVE DHAQGEEDCW VVGRSEAEAR
EVAAELTGRP GAELTLERDP DVLDTWFSSA LFPFSALGWP QETPDLARFY PLSLLETGSD
LLLFWVGRMV MLGTQLTGQL PFSKVLLHPM VRDRQGRKMS KSLGNVLDPR DIISGVEMQV
LQEKLRSGNL DPAELAIVAA AQKKDFPHGI PECGTDALRF TLCSHGVQAG DLHLSVSEVQ
SCRHFCNKIW NALRFILNAL GEKFVPQPAE ELSPSSPMDA WILSRLALAA QECERGFLTR
ELSLVTHALH HFWLHNLCDV YLEAVKPVLW HSPRPLGPPQ VLFSCADLGL RLLAPLMPFL
AEELWQRLPP RPGCPPAPSI SVAPYPSACS LEHWRQPELE RRFSRVQEVV QVLRALRATY
QLTKARPRVL LQSSEPGDQG LFEAFLEPLG TLGYCGAVGL LPPGAAAPSG WAQAPLSDTA
QVYMELQGLV DPQIQLPLLA ARRYKLQKQL DSLTARTPSE GEAGTQRQQK LSSLQLELSK
LDKAASHLRQ LMDEPPAPGS PEL*

mutated AA sequence

MCIPPPNVTG SLHIGHALTV AIQDALVRWH RMRGDQVLWV PGSDHAGIAT QAVVEKQLWK
ERGVRRHELS REAFLREVWQ WKEAKGGEIC EQLRALGASL DWDRECFTMD VGSSVAVTEA
FVRLYKAGLL YRNHQLVNWS CALRSAISDI EVENRPLPGH TQLRLPGCPT PVSFGLLFSV
AFPVDGEPDA EVVVGTTRPE TLPGDVAVAV HPDDSRYTHL HGRQLRHPLM GQPLPLITDY
AVQPHVGTGA VKVTPAHSPA DAEMGARHGL SPLNVIAEDG TMTSLCGDWL QGLHRFVARE
KIMSVLSEWG LFRGLQNHPM VLPICSRSGD VIEYLLKNQW FVRCQEMGAR AAKAVESGAL
ELSPSFHQKN WQHWFSHIGD WCVSRQLWWG HQIPAYLVVE DHAQGEEDCW VVGRSEAEAR
EVAAELTGRP GAELTLERDP DVLDTWFSSA LFPFSALGWP QETPDLARFY PLSLLETGSD
LLLFWVGRMV MLGTQLTGQL PFSKVLLHPM VRDRQGRKMS KSLGNVLDPR DIISGVEMQV
LQEKLRSGNL DPAELAIVAA AQKKDFPHGI PECGTDALRF TLCSHGVQAG DLHLSVSEVQ
SCRHFCNKIW NALRFILNAL GEKFVPQPAE ELSPSSPMDA WILSRLALAA QECERGFLTR
ELSLVTHALH HFWLHNLCDV YLEAVKPVLW HSPRPLGPPQ VLFSCADLGL RLLAPLMPFL
AEELWQRLPP RPGCPPAPSI SVAPYPSACS LEHWRQPELE RRFSRVQEVV QVLRALQATY
QLTKARPRVL LQSSEPGDQG LFEAFLEPLG TLGYCGAVGL LPPGAAAPSG WAQAPLSDTA
QVYMELQGLV DPQIQLPLLA ARRYKLQKQL DSLTARTPSE GEAGTQRQQK LSSLQLELSK
LDKAASHLRQ LMDEPPAPGS PEL*

speed

0.65 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