mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999996358 (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)

chr11:85436500T>CN/A show variant in all transcripts IGV

HGNC symbol

SYTL2

Ensembl transcript ID

ENST00000359152

Genbank transcript ID

N/A

UniProt peptide

Q9HCH5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2572A>G
cDNA.2572A>G
g.85685A>G

AA changes

M858V Score: 21 explain score(s)

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

858

frameshift

known variant

Reference ID: rs580459

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1167	1004	2171
ExAC	26493	-20219	6274

regulatory features

H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.034	0
	0.212	0.005
(flanking)	0.791	0.019

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 gained	85679	0.86	mu: ATTTGATTCAGGTGG	TTGA\|ttca

distance from splice site

1426

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

858

mutated

all conserved

858

Ptroglodytes

all identical

ENSPTRG00000004137

334

Mmulatta

all identical

ENSMMUG00000012449

855

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000030616

361

Ggallus

no alignment

ENSGALG00000014079

n/a

Trubripes

no alignment

ENSTRUG00000001148

n/a

Drerio

no alignment

ENSDARG00000061956

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000012793

n/a

protein features

start (aa)	end (aa)	feature	details
778	880	DOMAIN	C2 2.	lost
860	860	CONFLICT	A -> V (in Ref. 3; BAB13423).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

5343 / 5343

position (AA) of stopcodon in wt / mu AA sequence

1781 / 1781

position of stopcodon in wt / mu cDNA

5343 / 5343

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

1 / 1

chromosome

strand

-1

last intron/exon boundary

5198

theoretical NMD boundary in CDS

5147

length of CDS

5343

coding sequence (CDS) position

2572

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

2572

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

85685

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

85436500

original gDNA sequence snippet

GCACACAGAATTTGATTCAGATGGCTGCAGAAGATTCTCAT

altered gDNA sequence snippet

GCACACAGAATTTGATTCAGGTGGCTGCAGAAGATTCTCAT

original cDNA sequence snippet

GCACACAGAATTTGATTCAGATGGCTGCAGAAGATTCTCAT

altered cDNA sequence snippet

GCACACAGAATTTGATTCAGGTGGCTGCAGAAGATTCTCAT

wildtype AA sequence

MINSSLSMLF SYLEKYFYVA DELSHCVEPE PSQVPGGSSR DRQQGKPPPL PALKAKTSSR
SGPYATEIKK STDDSIFKVL DWFNRSSYSD DNKSFLQHPR GIESKEKTDS KSQVAVDLVT
DDTTLRENGS KTLSPSKIEL KPVRSDSPFQ AEGDMLVSES CQDNNVNIKS KFMNLSQKGT
PKEGPGILQP FESYGTPSQG SKNMDYSQDS KSPGKGNGAS PSNSNYSYSV LKESDAENQV
PCNTNNIGNL GEEEPKFHAH EENRGHSEVN FDSSTVVKEP GLKDNMNAER KSKVGNTYIL
KASLEPENIK STPGVANNGS PWKKPEVQFQ QEAGEVPKNQ VQREKYKRVS DRISFWEGEK
AGAKITHEKP TSSCSQEQPS AKAYQPVKKS QGVSSMDSLS TDQSEYNQAI PKRVVLDEDD
QASQLSNSYS SNKSKETKPQ IAGPSRYYLS AEQSDKVSLF QNKKNEPIKR SQVADSLPSR
RNITLPALQP PSNVGSERHA PLEKDRPLVR ESNANFKVMS LKERMDEPNA EQVYNPSQFE
NLRKFWDLEA NSNSKDNDKN ITTTSQKNSA PFNRQKHKEF SDIKLSGKNT HEAEVLLSPK
KVMAREEMEK LNSKGILQVL PDEITFPLSP LRKYTYQLPG NESSKENVEK NTEGIVTPVF
KEEKDYSEQE IQESIIKTNV LSKDCKDTFN DSLQKLLSET STPAIQPSGG KVHGKQVLEP
SVSENRTWPQ KTDFADTEEE VKGPEKIINE HVDKTVVHPK VKRNSLTASL DKLLKEATGT
SPSPLQAKLA PVITGTNSKL EEGRFFGKGI EQSHNTSADK REILAPFPVR DETFGNTALL
KKAESGECQL STQNLIQMAA EDSHPLDPTS QLSRKGSFGD VASPPQDMLF PQDAHLVPQA
RVHPSQTEIS ETVEKVILPP RPVLNDVSAA LQKLCGEVWL SYPAGREVGP GEVNPEFPEA
VQPVCSPLNP PGVISPWATM DTIVPDRKDF YSSNVVPDKT HEVGSYLAAQ MSPSDQTLSS
FASIVAQYGK GLPQEVEEIV RETIVQPKSE FLEFSAGLEK LLKEETETFP SKYESDTGNL
SPSKLIGSTE EPRRATSECH PEELKETVEK AEAPLITESA FDAGFEKLLK EITEAPPYQP
QVSVREETHE KESSQSEQTR FLGTVPHFYR AASQTSEMKD KSNGLESQVN QCDKMLGGDA
LVTDLLVDFC GSRSGVEIPR TPQLYVAHEI GTIKTVTPPE DRDSESGVAG GQGTLQEPGF
GEASEAISVS RNRQPIPLLM NKENSTKTSK VELTLASPYM KQEKEEEKEG FSESDFSDGN
TSSNAESWRN PSSSEEEPSP VLKTLERSAA RKMPSKSLED ISSDSSNQAK VDNQPEELVR
SAEDVSTVPT QPDNPFSHPD KLKRMSKSVP AFLQDESDDR ETDTASESSY QLSRHKKSPS
SLTNLSSSSG MTSLSSVSGS VMSVYSGDFG NLEVKGNIQF AIEYVESLKE LHVFVAQCKD
LAAADVKKQR SDPYVKAYLL PDKGKMGKKK TLVVKKTLNP VYNEILRYKI EKQILKTQKL
NLSIWHRDTF KRNSFLGEVE LDLETWDWDN KQNKQLRWYP LKRKTAPVAL EAENRGEMKL
ALQYVPEPVP GKKLPTTGEV HIWVKECLDL PLLRGSHLNS FVKCTILPDT SRKSRQKTRA
VGKTTNPIFN HTMVYDGFRP EDLMEACVEL TVWDHYKLTN QFLGGLRIGF GTGKSYGTEV
DWMDSTSEEV ALWEKMVNSP NTWIEATLPL RMLLIAKISK *

mutated AA sequence

MINSSLSMLF SYLEKYFYVA DELSHCVEPE PSQVPGGSSR DRQQGKPPPL PALKAKTSSR
SGPYATEIKK STDDSIFKVL DWFNRSSYSD DNKSFLQHPR GIESKEKTDS KSQVAVDLVT
DDTTLRENGS KTLSPSKIEL KPVRSDSPFQ AEGDMLVSES CQDNNVNIKS KFMNLSQKGT
PKEGPGILQP FESYGTPSQG SKNMDYSQDS KSPGKGNGAS PSNSNYSYSV LKESDAENQV
PCNTNNIGNL GEEEPKFHAH EENRGHSEVN FDSSTVVKEP GLKDNMNAER KSKVGNTYIL
KASLEPENIK STPGVANNGS PWKKPEVQFQ QEAGEVPKNQ VQREKYKRVS DRISFWEGEK
AGAKITHEKP TSSCSQEQPS AKAYQPVKKS QGVSSMDSLS TDQSEYNQAI PKRVVLDEDD
QASQLSNSYS SNKSKETKPQ IAGPSRYYLS AEQSDKVSLF QNKKNEPIKR SQVADSLPSR
RNITLPALQP PSNVGSERHA PLEKDRPLVR ESNANFKVMS LKERMDEPNA EQVYNPSQFE
NLRKFWDLEA NSNSKDNDKN ITTTSQKNSA PFNRQKHKEF SDIKLSGKNT HEAEVLLSPK
KVMAREEMEK LNSKGILQVL PDEITFPLSP LRKYTYQLPG NESSKENVEK NTEGIVTPVF
KEEKDYSEQE IQESIIKTNV LSKDCKDTFN DSLQKLLSET STPAIQPSGG KVHGKQVLEP
SVSENRTWPQ KTDFADTEEE VKGPEKIINE HVDKTVVHPK VKRNSLTASL DKLLKEATGT
SPSPLQAKLA PVITGTNSKL EEGRFFGKGI EQSHNTSADK REILAPFPVR DETFGNTALL
KKAESGECQL STQNLIQVAA EDSHPLDPTS QLSRKGSFGD VASPPQDMLF PQDAHLVPQA
RVHPSQTEIS ETVEKVILPP RPVLNDVSAA LQKLCGEVWL SYPAGREVGP GEVNPEFPEA
VQPVCSPLNP PGVISPWATM DTIVPDRKDF YSSNVVPDKT HEVGSYLAAQ MSPSDQTLSS
FASIVAQYGK GLPQEVEEIV RETIVQPKSE FLEFSAGLEK LLKEETETFP SKYESDTGNL
SPSKLIGSTE EPRRATSECH PEELKETVEK AEAPLITESA FDAGFEKLLK EITEAPPYQP
QVSVREETHE KESSQSEQTR FLGTVPHFYR AASQTSEMKD KSNGLESQVN QCDKMLGGDA
LVTDLLVDFC GSRSGVEIPR TPQLYVAHEI GTIKTVTPPE DRDSESGVAG GQGTLQEPGF
GEASEAISVS RNRQPIPLLM NKENSTKTSK VELTLASPYM KQEKEEEKEG FSESDFSDGN
TSSNAESWRN PSSSEEEPSP VLKTLERSAA RKMPSKSLED ISSDSSNQAK VDNQPEELVR
SAEDVSTVPT QPDNPFSHPD KLKRMSKSVP AFLQDESDDR ETDTASESSY QLSRHKKSPS
SLTNLSSSSG MTSLSSVSGS VMSVYSGDFG NLEVKGNIQF AIEYVESLKE LHVFVAQCKD
LAAADVKKQR SDPYVKAYLL PDKGKMGKKK TLVVKKTLNP VYNEILRYKI EKQILKTQKL
NLSIWHRDTF KRNSFLGEVE LDLETWDWDN KQNKQLRWYP LKRKTAPVAL EAENRGEMKL
ALQYVPEPVP GKKLPTTGEV HIWVKECLDL PLLRGSHLNS FVKCTILPDT SRKSRQKTRA
VGKTTNPIFN HTMVYDGFRP EDLMEACVEL TVWDHYKLTN QFLGGLRIGF GTGKSYGTEV
DWMDSTSEEV ALWEKMVNSP NTWIEATLPL RMLLIAKISK *

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