Yum, tasty mutations...

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 no
known variant Reference ID: rs9394021
databasehomozygous (A/A)heterozygousallele carriers
1000G46910341503
ExAC58662044226308
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.2460.997
3.9760.994
(flanking)-1.380.564
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased17105wt: 0.24 / mu: 0.39wt: GGGCTCTCCGAGCCA
mu: GGGCTCTCCAAGCCA		 GCTC|tccg
Donor gained171140.33mu: AAGCCACGTACCAGC GCCA|cgta
distance from splice site 36
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      777VQEVVQVLRALRATYQLTKARPRV
mutated  all conserved    777VQEVVQVLRALQATY
Ptroglodytes  all identical  ENSPTRG00000034497  926VQEVVQVLRALRATY
Mmulatta  all identical  ENSMMUG00000018609  918VQEVVQVLRALRAT
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000038838  918VQEVVQALRALRAT
Ggallus  no homologue    
Trubripes  no alignment  ENSTRUG00000005264  n/a
Drerio  all identical  ENSDARG00000056717  911VQEVVRVTRLLRAQCQMTKEKPD
Dmelanogaster  all conserved  FBgn0035942  847IVNICHNVRQVKSRNEISKRHHPQ
Celegans  all identical  ZC513.4  826ITAMMAAIRSTRQTLQL
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 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 0.33 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