mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 0.000114072781583659 (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)

chr2:74725178G>AN/A show variant in all transcripts IGV

HGNC symbol

LBX2

Ensembl transcript ID

ENST00000341396

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

3'UTR

DNA changes

cDNA.417C>T
g.7015C>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs17009998

database	homozygous (A/A)	heterozygous	allele carriers
1000G	451	766	1217
ExAC	4804	16272	21076

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
TAF1, Transcription Factor, TAF1 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.56	0.629
	1.157	0.681
(flanking)	-0.109	0.687

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

splice sites

splice site change occurs after stopcodon (at aa 99)

effect	gDNA position	score	detection sequence	exon-intron border
Acc increased	7019	wt: 0.26 / mu: 0.37	wt: TCGCTACGCGCGTTGTCCCCGGAAGTCCTGTGCAGCTTAGC mu: TCGCTACGCGCGTTGTTCCCGGAAGTCCTGTGCAGCTTAGC	cccg\|GAAG
Acc marginally increased	7018	wt: 0.2809 / mu: 0.3237 (marginal change - not scored)	wt: CTCGCTACGCGCGTTGTCCCCGGAAGTCCTGTGCAGCTTAG mu: CTCGCTACGCGCGTTGTTCCCGGAAGTCCTGTGCAGCTTAG	cccc\|GGAA
Acc marginally increased	7020	wt: 0.4759 / mu: 0.5471 (marginal change - not scored)	wt: CGCTACGCGCGTTGTCCCCGGAAGTCCTGTGCAGCTTAGCA mu: CGCTACGCGCGTTGTTCCCGGAAGTCCTGTGCAGCTTAGCA	ccgg\|AAGT
Donor marginally increased	7017	wt: 0.9905 / mu: 0.9929 (marginal change - not scored)	wt: TGTCCCCGGAAGTCC mu: TGTTCCCGGAAGTCC	TCCC\|cgga

distance from splice site

268

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

126 / 126

chromosome

strand

-1

last intron/exon boundary

150

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

174

coding sequence (CDS) position

N/A

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

417

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

7015

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

74725178

original gDNA sequence snippet

CGCCTCGCTACGCGCGTTGTCCCCGGAAGTCCTGTGCAGCT

altered gDNA sequence snippet

CGCCTCGCTACGCGCGTTGTTCCCGGAAGTCCTGTGCAGCT

original cDNA sequence snippet

CGCCTCGCTACGCGCGTTGTCCCCGGAAGTCCTGTGCAGCT

altered cDNA sequence snippet

CGCCTCGCTACGCGCGTTGTTCCCGGAAGTCCTGTGCAGCT

wildtype AA sequence

MGKRTSLEGG QVRTRWALVP SAANGASHAL RSPRNRCWSW SGASSSRSTW RRPSETG*

mutated AA sequence

N/A

speed

0.44 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