Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999985203 (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) chr6:30893428G>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.2473G>A
cDNA.2832G>A
g.17410G>A
AA changes A825T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 825
frameshift no
known variant Reference ID: rs2252863
databasehomozygous (A/A)heterozygousallele carriers
1000G158801959
ExAC61072055326660
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-2.2940
-0.4970
(flanking)-0.0160
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased17402wt: 0.60 / mu: 0.76wt: GTTACCCCCAGGCGC
mu: GTTACCCCCAGGCAC		 TACC|ccca
Donor marginally increased17407wt: 0.8365 / mu: 0.8666 (marginal change - not scored)wt: CCCCAGGCGCAGCAG
mu: CCCCAGGCACAGCAG		 CCAG|gcgc
Donor increased17412wt: 0.28 / mu: 0.66wt: GGCGCAGCAGCTCCC
mu: GGCACAGCAGCTCCC		 CGCA|gcag
Donor increased17406wt: 0.56 / mu: 0.90wt: CCCCCAGGCGCAGCA
mu: CCCCCAGGCACAGCA		 CCCA|ggcg
distance from splice site 69
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      825YCGAVGLLPPGAAAPSGWAQAPLS
mutated  not conserved    825YCGAVGLLPPGTAAPSGWAQAPL
Ptroglodytes  all identical  ENSPTRG00000034497  974YCGAVGLLPPGAAAPSGWAQAPL
Mmulatta  all identical  ENSMMUG00000018609  966HCGAVGLLPPGAAAPSGWAQAPL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000038838  966HCGAVGFLSPGAAAPSGWALTPL
Ggallus  no homologue    
Trubripes  no alignment  ENSTRUG00000005264  n/a
Drerio  not conserved  ENSDARG00000056717  965AGFSDCPPAKASAVGVVDHSL
Dmelanogaster  no alignment  FBgn0035942  n/a
Celegans  no alignment  ZC513.4  n/a
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
985985CONFLICTE -> 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 6
strand 1
last intron/exon boundary 3030
theoretical NMD boundary in CDS 2620
length of CDS 2772
coding sequence (CDS) position 2473
cDNA position
(for ins/del: last normal base / first normal base)		 2832
gDNA position
(for ins/del: last normal base / first normal base)		 17410
chromosomal position
(for ins/del: last normal base / first normal base)		 30893428
original gDNA sequence snippet TGGGCCTGTTACCCCCAGGCGCAGCAGCTCCCTCCGGCTGG
altered gDNA sequence snippet TGGGCCTGTTACCCCCAGGCACAGCAGCTCCCTCCGGCTGG
original cDNA sequence snippet TGGGCCTGTTACCCCCAGGCGCAGCAGCTCCCTCCGGCTGG
altered cDNA sequence snippet TGGGCCTGTTACCCCCAGGCACAGCAGCTCCCTCCGGCTGG
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 QVLRALRATY
QLTKARPRVL LQSSEPGDQG LFEAFLEPLG TLGYCGAVGL LPPGTAAPSG WAQAPLSDTA
QVYMELQGLV DPQIQLPLLA ARRYKLQKQL DSLTARTPSE GEAGTQRQQK LSSLQLELSK
LDKAASHLRQ LMDEPPAPGS PEL*
speed 1.12 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