mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 3.26210740356359e-50 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:100219374T>AN/A show variant in all transcripts IGV

HGNC symbol

HPSE2

Ensembl transcript ID

ENST00000370546

Genbank transcript ID

NM_001166246

UniProt peptide

N/A

alteration type

single base exchange

alteration region

3'UTR

DNA changes

cDNA.1806A>T
g.776246A>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs10883100

database	homozygous (A/A)	heterozygous	allele carriers
1000G	741	1175	1916
ExAC	15537	1693	17230

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gata2, Transcription Factor, Gata2 Transcription Factor Binding
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.692	1
	4.617	1
(flanking)	4.699	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

splice site change occurs after stopcodon (at aa 604) splice site change occurs after stopcodon (at aa 605) splice site change occurs after stopcodon (at aa 606)

effect	gDNA position	score	detection sequence	exon-intron border
Acc marginally increased	776249	wt: 0.8688 / mu: 0.8785 (marginal change - not scored)	wt: AGTCACCATGGGCTTTTATGTGGTCAAGAATGTCAATGCTT mu: AGTCACCATGGGCTTTTTTGTGGTCAAGAATGTCAATGCTT	atgt\|GGTC
Acc marginally increased	776239	wt: 0.4793 / mu: 0.5256 (marginal change - not scored)	wt: TCATCCCTCCAGTCACCATGGGCTTTTATGTGGTCAAGAAT mu: TCATCCCTCCAGTCACCATGGGCTTTTTTGTGGTCAAGAAT	atgg\|GCTT
Acc increased	776255	wt: 0.26 / mu: 0.79	wt: CATGGGCTTTTATGTGGTCAAGAATGTCAATGCTTTGGCCT mu: CATGGGCTTTTTTGTGGTCAAGAATGTCAATGCTTTGGCCT	tcaa\|GAAT
Acc marginally increased	776247	wt: 0.8379 / mu: 0.8408 (marginal change - not scored)	wt: CCAGTCACCATGGGCTTTTATGTGGTCAAGAATGTCAATGC mu: CCAGTCACCATGGGCTTTTTTGTGGTCAAGAATGTCAATGC	ttat\|GTGG
Acc gained	776254	0.61	mu: CCATGGGCTTTTTTGTGGTCAAGAATGTCAATGCTTTGGCC	gtca\|AGAA
Acc gained	776251	0.41	mu: TCACCATGGGCTTTTTTGTGGTCAAGAATGTCAATGCTTTG	gtgg\|TCAA

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

poly(A) signal

signal is predicted to be ok

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

1684

theoretical NMD boundary in CDS

1633

length of CDS

1647

coding sequence (CDS) position

N/A

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

1806

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

776246

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

100219374

original gDNA sequence snippet

TCCAGTCACCATGGGCTTTTATGTGGTCAAGAATGTCAATG

altered gDNA sequence snippet

TCCAGTCACCATGGGCTTTTTTGTGGTCAAGAATGTCAATG

original cDNA sequence snippet

TCCAGTCACCATGGGCTTTTATGTGGTCAAGAATGTCAATG

altered cDNA sequence snippet

TCCAGTCACCATGGGCTTTTTTGTGGTCAAGAATGTCAATG

wildtype AA sequence

MRVLCAFPEA MPSSNSRPPA CLAPGALYLA LLLHLSLSSQ AGDRRPLPVD RAAGLKEKTL
ILLDVSTKNP VRTVNENFLS LQLDPSIIHD GWLDFLSSKR LVTLARGLSP AFLRFGGKRT
DFLQFQNLRN PAKSRGGPGP DYYLKNYEDD IVRSDVALDK QKGCKIAQHP DVMLELQREK
AAQMHLVLLK EQFSNTYSNL ILTARSLDKL YNFADCSGLH LIFALNALRR NPNNSWNSSS
ALSLLKYSAS KKYNISWELG NEPNNYRTMH GRAVNGSQLG KDYIQLKSLL QPIRIYSRAS
LYGPNIGRPR KNVIALLDGF MKVAGSTVDA VTWQHCYIDG RVVKVMDFLK TRLLDTLSDQ
IRKIQKVVNT YTPGKKIWLE GVVTTSAGGT NNLSDSYAAG FLWLNTLGML ANQGIDVVIR
HSFFDHGYNH LVDQNFNPLP DYWLSLLYKR LIGPKVLAVH VAGLQRKPRP GRVIRDKLRI
YAHCTNHHNH NYVRGSITLF IINLHRSRKK IKLAGTLRDK LVHQYLLQPY GQEGLKSKTQ
RCQYCGII*

mutated AA sequence

N/A

speed

0.77 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