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 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 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      917VQEVVQVLRALRATYQLTKARPRV
mutated  all conserved    917VQEVVQVLRALQATYQLTKARPR
Ptroglodytes  all identical  ENSPTRG00000034497  926VQEVVQVLRALRATYQLTKARPR
Mmulatta  all identical  ENSMMUG00000018609  918VQEVVQVLRALRATYQLTKARPR
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000038838  918VQEVVQALRALRATYQLTKARPQ
Ggallus  no homologue    
Trubripes  no alignment  ENSTRUG00000005264  n/a
Drerio  all identical  ENSDARG00000056717  911VRVTRLLRAQCQMTKEKPD
Dmelanogaster  all conserved  FBgn0035942  847CHNVRQVKSRNEISKRHHPQ
Celegans  all identical  ZC513.4  827ITAMMAAIRSTRQTLQL
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 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 6
strand 1
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 0.59 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