mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 4.4013353304463e-05 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:48151822C>GN/A show variant in all transcripts IGV

HGNC symbol

RAPGEF3

Ensembl transcript ID

ENST00000548919

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.224G>C
g.13002G>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs11168230

database	homozygous (G/G)	heterozygous	allele carriers
1000G	242	1003	1245
ExAC	2414	10976	13390

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.028	0.758
	0.462	0.676
(flanking)	-0.335	0.603

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	13004	wt: 0.9799 / mu: 0.9902 (marginal change - not scored)	wt: CTGGCTGTGGAGGAT mu: CTGCCTGTGGAGGAT	GGCT\|gtgg

distance from splice site

Kozak consensus sequence altered?

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

N/A

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

N/A

position of start ATG in wt / mu cDNA

305 / 305

chromosome

strand

-1

last intron/exon boundary

2631

theoretical NMD boundary in CDS

2276

length of CDS

2445

coding sequence (CDS) position

N/A

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

224

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

13002

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

48151822

original gDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGGCTGTGGAGGATAGCCCAGCT

altered gDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGCCTGTGGAGGATAGCCCAGCT

original cDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGGCTGTGGAGGATAGCCCAGCT

altered cDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGCCTGTGGAGGATAGCCCAGCT

wildtype AA sequence

MVLRRMHRPR SCSYQLLLEH QRPSCIQGLR WTPLTNSEES LDFSESLEQA STERVLRAGR
QLHRHLLATC PNLIRDRKYH LRLYRQCCSG RELVDGILAL GLGVHSRSQV VGICQVLLDE
GALCHVKHDW AFQDRDAQFY RFPGPEPEPV RTHEMEEELA EAVALLSQRG PDALLTVALR
KPPGQRTDEE LDLIFEELLH IKAVAHLSNS VKRELAAVLL FEPHSKAGTV LFSQGDKGTS
WYIIWKGSVN VVTHGKGLVT TLHEGDDFGQ LALVNDAPRA ATIILREDNC HFLRVDKQDF
NRIIKDVEAK TMRLEEHGKV VLVLERASQG AGPSRPPTPG RNRYTVMSGT PEKILELLLE
AMGPDSSAHD PTETFLSDFL LTHRVFMPSA QLCAALLHHF HVEPAGGSEQ ERSTYVCNKR
QQILRLVSQW VALYGSMLHT DPVATSFLQK LSDLVGRDTR LSNLLREQWP ERRRCHRLEN
GCGNASPQMK ARNLPVWLPN QDEPLPGSSC AIQVGDKDAI GLQPDARGVA TSLGLNERLF
VVNPQEVHEL IPHPDQLGPT VGSAEGLDLV SAKDLAGQLT DHDWSLFNSI HQVELIHYVL
GPQHLRDVTT ANLERFMRRF NELQYWVATE LCLCPVPGPR AQLLRKFIKL AAHNSAISRL
AHTWERLPHK VRKLYSALER LLDPSWNHRV YRLALAKLSP PVIPFMPLLL KDMTFIHEGN
HTLVENLINF EKMRMMARAA RMLHHCRSHN PVPLSPLRSR VSHLHEDSQV ARISTCSEQS
LSTRSPASTW AYVQQLKVID NQRELSRLSR ELEP*

mutated AA sequence

N/A

speed

1.07 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