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

ENST00000446204

Genbank transcript ID

N/A

UniProt peptide

Q8N3P4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.247A>G
cDNA.378A>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

4011 / 4011

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

1337 / 1337

position of stopcodon in wt / mu cDNA

4142 / 4142

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

132 / 132

chromosome

strand

last intron/exon boundary

3993

theoretical NMD boundary in CDS

3811

length of CDS

4011

coding sequence (CDS) position

247

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

378

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 SHGLALIFDQ
NQALRLCLGS TSVGGQYGAI SALSINNDCS RLLCGFAKGQ ITMWDLASGK LLRSITDAHP
PGTAILHIKF TDDPTLAICN DSGGSVFELT FKRVMGVRTC ESRCLFSGSK GEVCCIEPLH
SKPELKDHPI TQFSLLAMAS LTKILVIGLK PSLKVWMTFP YGRMDPSSVP LLAWHFVAVQ
NYVNPMLAFC RGDVVHFLLV KRDESGAIHV TKQKHLHLYY DLINFTWINS RTVVLLDSVE
KLHVIDRQTQ EELETVEISE VQLVYNSSHF KSLATGGNVS QALALVGEKA CYQSISSYGG
QIFYLGTKSV YVMMLRSWRE RVDHLLKQDC LTEALALAWS FHEGKAKAVV GLSGDASKRK
AIVADRMVEI LFHYADRALK KCPDQGKIQV MEQHFQVVLM CWENRLYDAM IYVYNRGMNE
FISPMEKLFR VIAPPLNAGK TLTDEQVVMG NKLLVYISCC LAGRAYPLGD IPEDLVPLVK
NQVFEFLIRL HSAEASPEEE IYPYIRTLLH FDTREFLNVL ALTFEDFKND KQAVEYQQRI
VDILLKVMVE NSDFTPSQVG CLFTFLARQL AKPDNTLFVN RTLFDQVLEF LCSPDDDSRH
SERQQVLLEL LQAGGIVQFE ESRLIRMAEK AEFYQICEFM YEREHQYDKI IDCYLRDPLR
EEEVFNYIHN ILSIPGHSAE EKQSVWQKAM DHIEELVSLK PCKAAELVAT HFSGHIETVI
KKLQNQVLLF KFLRSLLDPR EGIHVNQELL QISPCITEQF IELLCQFNPT QVIETLQVLE
CYRLEETIQI TQKYQLHEVT AYLLEKKGDI HGAFLIMLER LQSKLQEVTH QGENTKEDPS
LKDVEDTMVE TIALCQRNSH NLNQQQREAL WFPLLEAMMA PQKLSSSAIP HLHSEALKSL
TMQVLNSMAA FIALPSILQR ILQDPVYGKG KLGEIQGLIL GMLDTFNYEQ TLLETTTSLL
NQDLHWSLCN LRASVTRGLN PKQDYCSICL QQYKRRQEMA DEIIVFSCGH LYHSFCLQNK
ECTVEFEGQT RWTCYKCSSS NKVGKLSENS SEIKKGRITP SQVKMSPSYH QSKGDPTAKK
GTSEPVLDPQ QIQAFDQLCR LYRGSSRLAL LTELSQNRSS ESYRPFSGSQ SAPAFNSIFQ
NENFQLQLIP PPVTED*

mutated AA sequence

MENEPDHENV EQSLCAKTSE EELNKSFNLE ASLSKFSYID MDKELEFKND LIDDKEFDIP
QVDTPPTLES ILNETDDEDE SFVLEDPTLL NIDTIDSHSY DTSSVASSDS GDRTNLKRKK
KLPDSFSLHG SVMRHSLLKG ISAQIVSAAD KVDAGLPTAI AVSSLIAVGT SHGLALIFDQ
NQALRLCLGS TSVGGQYGAI SALSINNDCS RLLCGFAKGQ ITMWDLASGK LLRSITDAHP
PGTAILHIKF TDDPTLAICN DSGGSVFELT FKRVMGVRTC ESRCLFSGSK GEVCCIEPLH
SKPELKDHPI TQFSLLAMAS LTKILVIGLK PSLKVWMTFP YGRMDPSSVP LLAWHFVAVQ
NYVNPMLAFC RGDVVHFLLV KRDESGAIHV TKQKHLHLYY DLINFTWINS RTVVLLDSVE
KLHVIDRQTQ EELETVEISE VQLVYNSSHF KSLATGGNVS QALALVGEKA CYQSISSYGG
QIFYLGTKSV YVMMLRSWRE RVDHLLKQDC LTEALALAWS FHEGKAKAVV GLSGDASKRK
AIVADRMVEI LFHYADRALK KCPDQGKIQV MEQHFQVVLM CWENRLYDAM IYVYNRGMNE
FISPMEKLFR VIAPPLNAGK TLTDEQVVMG NKLLVYISCC LAGRAYPLGD IPEDLVPLVK
NQVFEFLIRL HSAEASPEEE IYPYIRTLLH FDTREFLNVL ALTFEDFKND KQAVEYQQRI
VDILLKVMVE NSDFTPSQVG CLFTFLARQL AKPDNTLFVN RTLFDQVLEF LCSPDDDSRH
SERQQVLLEL LQAGGIVQFE ESRLIRMAEK AEFYQICEFM YEREHQYDKI IDCYLRDPLR
EEEVFNYIHN ILSIPGHSAE EKQSVWQKAM DHIEELVSLK PCKAAELVAT HFSGHIETVI
KKLQNQVLLF KFLRSLLDPR EGIHVNQELL QISPCITEQF IELLCQFNPT QVIETLQVLE
CYRLEETIQI TQKYQLHEVT AYLLEKKGDI HGAFLIMLER LQSKLQEVTH QGENTKEDPS
LKDVEDTMVE TIALCQRNSH NLNQQQREAL WFPLLEAMMA PQKLSSSAIP HLHSEALKSL
TMQVLNSMAA FIALPSILQR ILQDPVYGKG KLGEIQGLIL GMLDTFNYEQ TLLETTTSLL
NQDLHWSLCN LRASVTRGLN PKQDYCSICL QQYKRRQEMA DEIIVFSCGH LYHSFCLQNK
ECTVEFEGQT RWTCYKCSSS NKVGKLSENS SEIKKGRITP SQVKMSPSYH QSKGDPTAKK
GTSEPVLDPQ QIQAFDQLCR LYRGSSRLAL LTELSQNRSS ESYRPFSGSQ SAPAFNSIFQ
NENFQLQLIP PPVTED*

speed

0.73 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