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mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999997267495673 (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) chr6:30888161T>CN/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.925T>C
cDNA.1284T>C
g.12143T>C
AA changes W309R Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 309
frameshift no
known variant Reference ID: rs2249464
databasehomozygous (C/C)heterozygousallele carriers
1000G10449982042
ExAC22808-128499959
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0120.992
0.9390.994
(flanking)0.4270.995
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 52
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      309AREKIMSVLSEWGLFRGLQNHPMV
mutated  not conserved    309KIMSVLSERGLFRGLQNHPM
Ptroglodytes  not conserved  ENSPTRG00000034497  479KIMSVLSERGLFRGLQNHPM
Mmulatta  not conserved  ENSMMUG00000018609  450EKIVSVLSERGLFRGLQNHPM
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000038838  449KIMCTLREQGLFRGLQEHPM
Ggallus  no homologue    
Trubripes  no alignment  ENSTRUG00000005264  n/a
Drerio  not conserved  ENSDARG00000056717  435RVISALMERKLFRGKKDHPM
Dmelanogaster  not conserved  FBgn0035942  393ARDLIVNRLEEMDLLRQVRSHTM
Celegans  not conserved  ZC513.4  378AREKVIQKLSELGNYNGLMKHEG
Xtropicalis  no homologue    
protein features no protein features affected
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 6
strand 1
last intron/exon boundary 3030
theoretical NMD boundary in CDS 2620
length of CDS 2772
coding sequence (CDS) position 925
cDNA position
(for ins/del: last normal base / first normal base)		 1284
gDNA position
(for ins/del: last normal base / first normal base)		 12143
chromosomal position
(for ins/del: last normal base / first normal base)		 30888161
original gDNA sequence snippet TAATGTCTGTGCTGAGTGAATGGGGCCTGTTCCGGGGCCTC
altered gDNA sequence snippet TAATGTCTGTGCTGAGTGAACGGGGCCTGTTCCGGGGCCTC
original cDNA sequence snippet TAATGTCTGTGCTGAGTGAATGGGGCCTGTTCCGGGGCCTC
altered cDNA sequence snippet TAATGTCTGTGCTGAGTGAACGGGGCCTGTTCCGGGGCCTC
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
KIMSVLSERG 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*
speed 1.30 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