mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999016917781389 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:184550501A>GN/A show variant in all transcripts IGV

HGNC symbol

VPS8

Ensembl transcript ID

ENST00000287546

Genbank transcript ID

N/A

UniProt peptide

Q8N3P4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.247A>G
cDNA.418A>G
g.20571A>G

AA changes

I83V Score: 29 explain score(s)

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

frameshift

known variant

Reference ID: rs9830734

database	homozygous (G/G)	heterozygous	allele carriers
1000G	815	1144	1959
ExAC	9529	13709	23238

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.357	1
	0.634	1
(flanking)	4.357	1

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
Acc marginally increased	20578	wt: 0.9078 / mu: 0.9515 (marginal change - not scored)	wt: AGATGAGTCTTTTATTCTTGAGGATCCTACATTGTTAAACA mu: AGATGAGTCTTTTGTTCTTGAGGATCCTACATTGTTAAACA	ttga\|GGAT
Acc marginally increased	20576	wt: 0.2731 / mu: 0.2838 (marginal change - not scored)	wt: GAAGATGAGTCTTTTATTCTTGAGGATCCTACATTGTTAAA mu: GAAGATGAGTCTTTTGTTCTTGAGGATCCTACATTGTTAAA	tctt\|GAGG
Acc marginally increased	20580	wt: 0.7669 / mu: 0.7957 (marginal change - not scored)	wt: ATGAGTCTTTTATTCTTGAGGATCCTACATTGTTAAACATT mu: ATGAGTCTTTTGTTCTTGAGGATCCTACATTGTTAAACATT	gagg\|ATCC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

no homologue

Mmulatta

all conserved

ENSMMUG00000000425

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000033653

Ggallus

no alignment

ENSGALG00000006704

n/a

Trubripes

all conserved

ENSTRUG00000003896

Drerio

all identical

ENSDARG00000060477

Dmelanogaster

not conserved

FBgn0035704

Celegans

not conserved

C42C1.4

Xtropicalis

no alignment

ENSXETG00000018613

n/a

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

4287 / 4287

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

1429 / 1429

position of stopcodon in wt / mu cDNA

4458 / 4458

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

172 / 172

chromosome

strand

last intron/exon boundary

4309

theoretical NMD boundary in CDS

4087

length of CDS

4287

coding sequence (CDS) position

247

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

418

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

20571

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

184550501

original gDNA sequence snippet

ATGATGAAGATGAGTCTTTTATTCTTGAGGATCCTACATTG

altered gDNA sequence snippet

ATGATGAAGATGAGTCTTTTGTTCTTGAGGATCCTACATTG

original cDNA sequence snippet

ATGATGAAGATGAGTCTTTTATTCTTGAGGATCCTACATTG

altered cDNA sequence snippet

ATGATGAAGATGAGTCTTTTGTTCTTGAGGATCCTACATTG

wildtype AA sequence

MENEPDHENV EQSLCAKTSE EELNKSFNLE ASLSKFSYID MDKELEFKND LIDDKEFDIP
QVDTPPTLES ILNETDDEDE SFILEDPTLL NIDTIDSHSY DTSSVASSDS GDRTNLKRKK
KLPDSFSLHG SVMRHSLLKG ISAQIVSAAD KVDAGLPTAI AVSSLIAVGT SHGLALIFGK
YQNQALRLCL GSTSVGGQYG AISALSINND CSRLLCGFAK GQITMWDLAS GKLLRSITDA
HPPGTAILHI KFTDDPTLAI CNDSGGSVFE LTFKRVMGVR TCESRCLFSG SKGEVCCIEP
LHSKPELKDH PITQFSLLAM ASLTKILVIG LKPSLKVWMT FPYGRMDPSS VPLLAWHFVA
VQNYVNPMLA FCRGDVVHFL LVKRDESGAI HVTKQKHLHL YYDLINFTWI NSRTVVLLDS
VEKLHVIDRQ TQEELETVEI SEVQLVYNSS HFKSLATGGN VSQALALVGE KACYQSISSY
GGQIFYLGTK SVYVMMLRSW RERVDHLLKQ DCLTEALALA WSFHEGKAKA VVGLSGDASK
RKAIVADRMV EILFHYADRA LKKCPDQGKI QVMEQHFQDM VPVIVDYCLL LQRKDLLFSQ
MYDKLSENSV AKGVFLECLE PYILSDKLVG ITPQVMKDLI VHFQDKKLME NVEALIVHMD
ITSLDIQQVV LMCWENRLYD AMIYVYNRGM NEFISPMEKL FRVIAPPLNA GKTLTDEQVV
MGNKLLVYIS CCLAGRAYPL GDIPEDLVPL VKNQVFEFLI RLHSAEASPE EEIYPYIRTL
LHFDTREFLN VLALTFEDFK NDKQAVEYQQ RIVDILLKVM VENSDFTPSQ VGCLFTFLAR
QLAKPDNTLF VNRTLFDQVL EFLCSPDDDS RHSERQQVLL ELLQAGGIVQ FEESRLIRMA
EKAEFYQICE FMYEREHQYD KIIDCYLRDP LREEEVFNYI HNILSIPGHS AEEKQSVWQK
AMDHIEELVS LKPCKAAELV ATHFSGHIET VIKKLQNQVL LFKFLRSLLD PREGIHVNQE
LLQISPCITE QFIELLCQFN PTQVIETLQV LECYRLEETI QITQKYQLHE VTAYLLEKKG
DIHGAFLIML ERLQSKLQEV THQGENTKED PSLKDVEDTM VETIALCQRN SHNLNQQQRE
ALWFPLLEAM MAPQKLSSSA IPHLHSEALK SLTMQVLNSM AAFIALPSIL QRILQDPVYG
KGKLGEIQGL ILGMLDTFNY EQTLLETTTS LLNQDLHWSL CNLRASVTRG LNPKQDYCSI
CLQQYKRRQE MADEIIVFSC GHLYHSFCLQ NKECTVEFEG QTRWTCYKCS SSNKVGKLSE
NSSEIKKGRI TPSQVKMSPS YHQSKGDPTA KKGTSEPVLD PQQIQAFDQL CRLYRGSSRL
ALLTELSQNR SSESYRPFSG SQSAPAFNSI FQNENFQLQL IPPPVTED*

mutated AA sequence

MENEPDHENV EQSLCAKTSE EELNKSFNLE ASLSKFSYID MDKELEFKND LIDDKEFDIP
QVDTPPTLES ILNETDDEDE SFVLEDPTLL NIDTIDSHSY DTSSVASSDS GDRTNLKRKK
KLPDSFSLHG SVMRHSLLKG ISAQIVSAAD KVDAGLPTAI AVSSLIAVGT SHGLALIFGK
YQNQALRLCL GSTSVGGQYG AISALSINND CSRLLCGFAK GQITMWDLAS GKLLRSITDA
HPPGTAILHI KFTDDPTLAI CNDSGGSVFE LTFKRVMGVR TCESRCLFSG SKGEVCCIEP
LHSKPELKDH PITQFSLLAM ASLTKILVIG LKPSLKVWMT FPYGRMDPSS VPLLAWHFVA
VQNYVNPMLA FCRGDVVHFL LVKRDESGAI HVTKQKHLHL YYDLINFTWI NSRTVVLLDS
VEKLHVIDRQ TQEELETVEI SEVQLVYNSS HFKSLATGGN VSQALALVGE KACYQSISSY
GGQIFYLGTK SVYVMMLRSW RERVDHLLKQ DCLTEALALA WSFHEGKAKA VVGLSGDASK
RKAIVADRMV EILFHYADRA LKKCPDQGKI QVMEQHFQDM VPVIVDYCLL LQRKDLLFSQ
MYDKLSENSV AKGVFLECLE PYILSDKLVG ITPQVMKDLI VHFQDKKLME NVEALIVHMD
ITSLDIQQVV LMCWENRLYD AMIYVYNRGM NEFISPMEKL FRVIAPPLNA GKTLTDEQVV
MGNKLLVYIS CCLAGRAYPL GDIPEDLVPL VKNQVFEFLI RLHSAEASPE EEIYPYIRTL
LHFDTREFLN VLALTFEDFK NDKQAVEYQQ RIVDILLKVM VENSDFTPSQ VGCLFTFLAR
QLAKPDNTLF VNRTLFDQVL EFLCSPDDDS RHSERQQVLL ELLQAGGIVQ FEESRLIRMA
EKAEFYQICE FMYEREHQYD KIIDCYLRDP LREEEVFNYI HNILSIPGHS AEEKQSVWQK
AMDHIEELVS LKPCKAAELV ATHFSGHIET VIKKLQNQVL LFKFLRSLLD PREGIHVNQE
LLQISPCITE QFIELLCQFN PTQVIETLQV LECYRLEETI QITQKYQLHE VTAYLLEKKG
DIHGAFLIML ERLQSKLQEV THQGENTKED PSLKDVEDTM VETIALCQRN SHNLNQQQRE
ALWFPLLEAM MAPQKLSSSA IPHLHSEALK SLTMQVLNSM AAFIALPSIL QRILQDPVYG
KGKLGEIQGL ILGMLDTFNY EQTLLETTTS LLNQDLHWSL CNLRASVTRG LNPKQDYCSI
CLQQYKRRQE MADEIIVFSC GHLYHSFCLQ NKECTVEFEG QTRWTCYKCS SSNKVGKLSE
NSSEIKKGRI TPSQVKMSPS YHQSKGDPTA KKGTSEPVLD PQQIQAFDQL CRLYRGSSRL
ALLTELSQNR SSESYRPFSG SQSAPAFNSI FQNENFQLQL IPPPVTED*

speed

1.06 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