mutation t@sting

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

ENST00000416670

Genbank transcript ID

NM_020442

UniProt peptide

Q5ST30

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2893G>A
cDNA.3060G>A
g.17410G>A

AA changes

A965T Score: 58 explain score(s)

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

965

frameshift

known variant

Reference ID: rs2252863

database	homozygous (A/A)	heterozygous	allele carriers
1000G	158	801	959
ExAC	6107	20553	26660

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-2.294	0
	-0.497	0
(flanking)	-0.016	0

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 marginally increased	17407	wt: 0.8365 / mu: 0.8666 (marginal change - not scored)	wt: CCCCAGGCGCAGCAG mu: CCCCAGGCACAGCAG	CCAG\|gcgc
Donor increased	17406	wt: 0.56 / mu: 0.90	wt: CCCCCAGGCGCAGCA mu: CCCCCAGGCACAGCA	CCCA\|ggcg
Donor increased	17402	wt: 0.60 / mu: 0.76	wt: GTTACCCCCAGGCGC mu: GTTACCCCCAGGCAC	TACC\|ccca
Donor increased	17412	wt: 0.28 / mu: 0.66	wt: GGCGCAGCAGCTCCC mu: GGCACAGCAGCTCCC	CGCA\|gcag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

965

mutated

not conserved

965

Ptroglodytes

all identical

ENSPTRG00000034497

974

Mmulatta

all identical

ENSMMUG00000018609

966

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000038838

966

Ggallus

no homologue

Trubripes

no alignment

ENSTRUG00000005264

n/a

Drerio

not conserved

ENSDARG00000056717

967

Dmelanogaster

no alignment

FBgn0035942

n/a

Celegans

no alignment

ZC513.4

n/a

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

2893

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

3060

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

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 QVLRALRATY QLTKARPRVL LQSSEPGDQG LFEAFLEPLG TLGYCGAVGL
LPPGTAAPSG WAQAPLSDTA QVYMELQGLV DPQIQLPLLA ARRYKLQKQL DSLTARTPSE
GEAGTQRQQK LSSLQLELSK LDKAASHLRQ LMDEPPAPGS PEL*

speed

0.23 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