mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 0.99999985948528 (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)

chr15:101120963T>CN/A show variant in all transcripts IGV

HGNC symbol

LINS1

Ensembl transcript ID

ENST00000560133

Genbank transcript ID

N/A

UniProt peptide

Q8NG48

alteration type

single base exchange

alteration region

intron

DNA changes

g.22473A>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs11247226

database	homozygous (C/C)	heterozygous	allele carriers
1000G	257	981	1238
ExAC	9489	13789	23278

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H2BK20ac, Histone, Histone 2B Lysine 20 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.185	0.004
	-0.872	0
(flanking)	-0.292	0.003

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	22481	wt: 0.69 / mu: 0.76	wt: AGCCATGATTACATCTTTTATCTCAACCCAGCAGTTTCAGA mu: AGCCATGATTACGTCTTTTATCTCAACCCAGCAGTTTCAGA	ttat\|CTCA
Acc marginally increased	22484	wt: 0.8675 / mu: 0.8883 (marginal change - not scored)	wt: CATGATTACATCTTTTATCTCAACCCAGCAGTTTCAGATCA mu: CATGATTACGTCTTTTATCTCAACCCAGCAGTTTCAGATCA	tctc\|AACC
Donor gained	22467	0.64	mu: GCCATGATTACGTCT	CATG\|atta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

no protein features affected

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

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

158 / 158

chromosome

strand

-1

last intron/exon boundary

432

theoretical NMD boundary in CDS

224

length of CDS

954

coding sequence (CDS) position

N/A

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

N/A

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

22473

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

101120963

original gDNA sequence snippet

AAAATGACAGCCATGATTACATCTTTTATCTCAACCCAGCA

altered gDNA sequence snippet

AAAATGACAGCCATGATTACGTCTTTTATCTCAACCCAGCA

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MKVFCEVLEE LYKKICMFQN SDKLLSHMAA QCLALLLYFQ LREKITLSNS WIAFCQKNLS
EYSESNKAIY CLWTLTAIIK EIFKDSCSQK TEILKQFLTH FDTIFEVFYN SLFSQHFENC
RDTSKIVNIL MCFLDLLELL IASRIHLKLH FTCQRILFLK PSCMLEVITW PIQAFVKRKV
IIFLKKCLLC KVGEDLCRGS VPALMPPDHH VAVDMLALAN AVLQAVNSGL LKTLSVYEKH
SFFGGDEVQP ECELITSPDH VILRAASLVI MKSLEIKFQN YSSASEVKGN SPNSFCMQCV
IIYLSTVIHN YQISGLV*

mutated AA sequence

N/A

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