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

ENST00000436792

Genbank transcript ID

NM_015303

UniProt peptide

Q8N3P4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.247A>G
cDNA.390A>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

4281 / 4281

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

1427 / 1427

position of stopcodon in wt / mu cDNA

4424 / 4424

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

144 / 144

chromosome

strand

last intron/exon boundary

4275

theoretical NMD boundary in CDS

4081

length of CDS

4281

coding sequence (CDS) position

247

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

390

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 MEQHFQDMVP VIVDYCLLLQ RKDLLFSQMY
DKLSENSVAK GVFLECLEPY ILSDKLVGIT PQVMKDLIVH FQDKKLMENV EALIVHMDIT
SLDIQQVVLM 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 MEQHFQDMVP VIVDYCLLLQ RKDLLFSQMY
DKLSENSVAK GVFLECLEPY ILSDKLVGIT PQVMKDLIVH FQDKKLMENV EALIVHMDIT
SLDIQQVVLM 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

0.37 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