mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999559954642 (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)

chr9:33941759T>CN/A show variant in all transcripts IGV

HGNC symbol

UBAP2

Ensembl transcript ID

ENST00000539807

Genbank transcript ID

N/A

UniProt peptide

Q5T6F2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1082A>G
cDNA.1338A>G
g.107189A>G

AA changes

N361S Score: 46 explain score(s)

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

361

frameshift

known variant

Reference ID: rs307658

database	homozygous (C/C)	heterozygous	allele carriers
1000G	387	1083	1470
ExAC	8980	14807	23787

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.869	1
	2.002	1
(flanking)	3.765	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 increased	107197	wt: 0.61 / mu: 0.68	wt: GCTCATCACTGAATTCTGCTAGTCCAGTAGCAATGTCTTCC mu: GCTCATCACTGAGTTCTGCTAGTCCAGTAGCAATGTCTTCC	gcta\|GTCC
Donor gained	107183	0.74	mu: CTCATCACTGAGTTC	CATC\|actg

distance from splice site

102

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

361

mutated

all conserved

361

Ptroglodytes

all conserved

ENSPTRG00000020871

606

Mmulatta

all conserved

ENSMMUG00000012597

574

Fcatus

all conserved

ENSFCAG00000009693

606

Mmusculus

all conserved

ENSMUSG00000028433

607

Ggallus

not conserved

ENSGALG00000013809

607

Trubripes

not conserved

ENSTRUG00000015263

623

Drerio

all conserved

ENSDARG00000088318

613

Dmelanogaster

not conserved

FBgn0020279

854

Celegans

no alignment

R119.4

n/a

Xtropicalis

not conserved

ENSXETG00000002157

601

VTATS

protein features

start (aa)	end (aa)	feature	details
432	432	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
439	439	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
473	473	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
633	633	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
839	839	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)
840	840	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)
862	862	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2625 / 2625

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

875 / 875

position of stopcodon in wt / mu cDNA

2881 / 2881

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

257 / 257

chromosome

strand

-1

last intron/exon boundary

2786

theoretical NMD boundary in CDS

2479

length of CDS

2625

coding sequence (CDS) position

1082

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

1338

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

107189

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

33941759

original gDNA sequence snippet

TCTGACAAGCTCATCACTGAATTCTGCTAGTCCAGTAGCAA

altered gDNA sequence snippet

TCTGACAAGCTCATCACTGAGTTCTGCTAGTCCAGTAGCAA

original cDNA sequence snippet

TCTGACAAGCTCATCACTGAATTCTGCTAGTCCAGTAGCAA

altered cDNA sequence snippet

TCTGACAAGCTCATCACTGAGTTCTGCTAGTCCAGTAGCAA

wildtype AA sequence

MRLAQVIFDK NDSDFEAKVK QLSETKVFTA SSAPAENHIL PGQSIDLVAL LQKPVPHSQA
SEANSFETSQ QQGFGQALVF TNSQHNNQMA PGTGSSTAVN SCSPQSLSSV LGSGFGELAP
PKMANITSSQ ILDQLKAPSL GQFTTTPSTQ QNSTSHPTTT TSWDLKPPTS QSSVLSHLDF
KSQPEPSPVL SQLSQRQQHQ SQAVTVPPPG LESFPSQAKL RESTPGDSPS TVNKLLQLPS
TTIENISVSV HQPQPKHIKL AKRRIPPASK IPASAVEMPG SADVTGLNVQ FGALEFGSEP
SLSEFGSAPS SENSNQIPIS LYSKSLSEPL NTSLSMTSAV QNSTYTTSVI TSCSLTSSSL
NSASPVAMSS SYDQSSVHNR IPYQSPVSSS ESAPGTIMNG HGGGRSQQTL DTPKTTGPPS
ALPSVSSLPS TTSCTALLPS TSQHTGDLTS SPLSQLSSSL SSHQSSLSAH AALSSSTSHT
HASVESASSH QSSATFSTAA TSVSSSASSG ASLSSSMNTA NSLCLGGTPA SASSSSSRAA
PLVTSGKAPP NLPQGVPPLL HNQYLVGPGG LLPAYPIYGY DELQMLQSRL PVDYYGIPFA
APTALASRDG SLANNPYPGD VTKFGRGDSA SPAPATTPAQ PQQSQSQTHH TAQQPFVNPA
LPPGYSYTGL PYYTGMPSAF QYGPTMFVPP ASAKQHGVNL STPTPPFQQA SGYGQHGYST
GYDDLTQGTA AGDYSKGGYA GSSQAPNKSA GSGPGKGVSV SSSTTGLPDM TGSVYNKTQT
FDKQGFHAGT PPPFSLPSVL GSTGPLASGA APGYAPPPFL HILPAHQQPH SQLLHHHLPQ
DAQSGSGQRS QPSSLQPKSQ ASKPAYGNSP YWTN*

mutated AA sequence

MRLAQVIFDK NDSDFEAKVK QLSETKVFTA SSAPAENHIL PGQSIDLVAL LQKPVPHSQA
SEANSFETSQ QQGFGQALVF TNSQHNNQMA PGTGSSTAVN SCSPQSLSSV LGSGFGELAP
PKMANITSSQ ILDQLKAPSL GQFTTTPSTQ QNSTSHPTTT TSWDLKPPTS QSSVLSHLDF
KSQPEPSPVL SQLSQRQQHQ SQAVTVPPPG LESFPSQAKL RESTPGDSPS TVNKLLQLPS
TTIENISVSV HQPQPKHIKL AKRRIPPASK IPASAVEMPG SADVTGLNVQ FGALEFGSEP
SLSEFGSAPS SENSNQIPIS LYSKSLSEPL NTSLSMTSAV QNSTYTTSVI TSCSLTSSSL
SSASPVAMSS SYDQSSVHNR IPYQSPVSSS ESAPGTIMNG HGGGRSQQTL DTPKTTGPPS
ALPSVSSLPS TTSCTALLPS TSQHTGDLTS SPLSQLSSSL SSHQSSLSAH AALSSSTSHT
HASVESASSH QSSATFSTAA TSVSSSASSG ASLSSSMNTA NSLCLGGTPA SASSSSSRAA
PLVTSGKAPP NLPQGVPPLL HNQYLVGPGG LLPAYPIYGY DELQMLQSRL PVDYYGIPFA
APTALASRDG SLANNPYPGD VTKFGRGDSA SPAPATTPAQ PQQSQSQTHH TAQQPFVNPA
LPPGYSYTGL PYYTGMPSAF QYGPTMFVPP ASAKQHGVNL STPTPPFQQA SGYGQHGYST
GYDDLTQGTA AGDYSKGGYA GSSQAPNKSA GSGPGKGVSV SSSTTGLPDM TGSVYNKTQT
FDKQGFHAGT PPPFSLPSVL GSTGPLASGA APGYAPPPFL HILPAHQQPH SQLLHHHLPQ
DAQSGSGQRS QPSSLQPKSQ ASKPAYGNSP YWTN*

speed

0.86 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