mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 0.999972551862149 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

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)

chr12:65150485C>TN/A show variant in all transcripts IGV

HGNC symbol

GNS

Ensembl transcript ID

ENST00000542058

Genbank transcript ID

N/A

UniProt peptide

P15586

alteration type

single base exchange

alteration region

intron

DNA changes

g.2743G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs2620733

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1526	793	2319
ExAC	2267	2354	4621

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.066	0.103
	-0.067	0.013
(flanking)	0.133	0.005

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
Donor marginally increased	2743	wt: 0.9982 / mu: 0.9992 (marginal change - not scored)	wt: AGCTAGGACAAGAGC mu: AGCTAAGACAAGAGC	CTAG\|gaca
Donor increased	2738	wt: 0.91 / mu: 1.00	wt: GGAAGAGCTAGGACA mu: GGAAGAGCTAAGACA	AAGA\|gcta
Donor marginally increased	2745	wt: 0.8438 / mu: 0.9211 (marginal change - not scored)	wt: CTAGGACAAGAGCAT mu: CTAAGACAAGAGCAT	AGGA\|caag

distance from splice site

2380

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
91	91	MOD_RES	3-oxoalanine (Cys) (By similarity).	might get lost (downstream of altered splice site)
91	91	METAL	Calcium; via 3-oxoalanine (By similarity).	might get lost (downstream of altered splice site)
111	111	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
117	117	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
183	183	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
198	198	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
210	210	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
252	252	CONFLICT	F -> C (in Ref. 2; BAD97204).	might get lost (downstream of altered splice site)
279	279	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
317	317	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
326	326	METAL	Calcium (By similarity).	might get lost (downstream of altered splice site)
327	327	METAL	Calcium (By similarity).	might get lost (downstream of altered splice site)
362	362	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
387	387	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
405	405	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
422	422	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
449	449	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
480	480	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)

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

156 / 156

chromosome

strand

-1

last intron/exon boundary

1676

theoretical NMD boundary in CDS

1470

length of CDS

1599

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)

2743

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

65150485

original gDNA sequence snippet

GACTCCAAGGGGAAGAGCTAGGACAAGAGCATTTGAGAACT

altered gDNA sequence snippet

GACTCCAAGGGGAAGAGCTAAGACAAGAGCATTTGAGAACT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MRLLPLAPGR LRRGSPRHLP SCSPALLLLV LGGCLGVFGV AAGTRRPNVV LLLTDDQDEV
LGGMYVPSAL CCPSRASILT GKYPHNHHVV NNTLEGNCSS KSWQKIQEPN TFPAILRSMC
GYQTFFAGKY LNEYGAPDAG GLEHVPLGWS YWYALEKNSK YYNYTLSING KARKHGENYS
VDYLTDVLAN VSLDFLDYKS NFEPFFMMIA TPAPHSPWTA APQYQKAFQN VFAPRNKNFN
IHGTNKHWLI RQAKTPMTNS SIQFLDNAFR KRWQTLLSVD DLVEKLVKRL EFTGELNNTY
IFYTSDNGYH TGQFSLPIDK RQLYEFDIKV PLLVRGPGIK PNQTSKMLVA NIDLGPTILD
IAGYDLNKTQ MDGMSLLPIL RGASNLTWRS DVLVEYQGEG RNVTDPTCPS LSPGVSQCFP
DCVCEDAYNN TYACVRTMSA LWNLQYCEFD DQEVFVEVYN LTADPDQITN IAKTIDPELL
GKMNYRLMML QSCSGPTCRT PGVFDPGYRF DPRLMFSNRG SVRTRRFSKH LL*

mutated AA sequence

N/A

speed

0.83 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