mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 1.45576414213291e-10 (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)

chr1:183542387T>CN/A show variant in all transcripts IGV

HGNC symbol

NCF2

Ensembl transcript ID

ENST00000418089

Genbank transcript ID

NM_001190789

UniProt peptide

P19878

alteration type

single base exchange

alteration region

intron

DNA changes

g.17625A>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs2274064

database	homozygous (C/C)	heterozygous	allele carriers
1000G	624	1214	1838
ExAC	15075	2617	17692

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.732	1
	0.101	0.993
(flanking)	0.878	0.997

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	17621	wt: 0.33 / mu: 0.45	wt: AGCCAGTGGTGATCCCTGTGGGCAAGCTGTTTCGACCAAAT mu: AGCCAGTGGTGATCCCTGTGGGCAGGCTGTTTCGACCAAAT	gtgg\|GCAA

distance from splice site

2413

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
120	133	HELIX		might get lost (downstream of altered splice site)
121	154	REPEAT	TPR 3.	might get lost (downstream of altered splice site)
137	148	HELIX		might get lost (downstream of altered splice site)
154	157	HELIX		might get lost (downstream of altered splice site)
158	167	HELIX		might get lost (downstream of altered splice site)
187	191	HELIX		might get lost (downstream of altered splice site)
240	299	DOMAIN	SH3 1.	might get lost (downstream of altered splice site)
243	247	STRAND		might get lost (downstream of altered splice site)
255	258	STRAND		might get lost (downstream of altered splice site)
266	269	STRAND		might get lost (downstream of altered splice site)
274	276	STRAND		might get lost (downstream of altered splice site)
278	282	STRAND		might get lost (downstream of altered splice site)
285	289	STRAND		might get lost (downstream of altered splice site)
294	296	STRAND		might get lost (downstream of altered splice site)
351	429	DOMAIN	OPR.	might get lost (downstream of altered splice site)
352	366	STRAND		might get lost (downstream of altered splice site)
372	382	HELIX		might get lost (downstream of altered splice site)
387	389	HELIX		might get lost (downstream of altered splice site)
392	394	STRAND		might get lost (downstream of altered splice site)
407	409	TURN		might get lost (downstream of altered splice site)
410	414	HELIX		might get lost (downstream of altered splice site)
421	426	STRAND		might get lost (downstream of altered splice site)
457	516	DOMAIN	SH3 2.	might get lost (downstream of altered splice site)
460	463	STRAND		might get lost (downstream of altered splice site)
472	475	STRAND		might get lost (downstream of altered splice site)
483	493	STRAND		might get lost (downstream of altered splice site)
495	498	STRAND		might get lost (downstream of altered splice site)
503	506	STRAND		might get lost (downstream of altered splice site)
508	510	HELIX		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

276 / 276

chromosome

strand

-1

last intron/exon boundary

1501

theoretical NMD boundary in CDS

1175

length of CDS

1338

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)

17625

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

183542387

original gDNA sequence snippet

AGTGGTGATCCCTGTGGGCAAGCTGTTTCGACCAAATGAGA

altered gDNA sequence snippet

AGTGGTGATCCCTGTGGGCAGGCTGTTTCGACCAAATGAGA

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MSLVEAISLW NEGVLAADKK DWKGALDAFS AVQDPHSRIC FNIGCMYTIL KNMTEAEKAF
TRSINRDKHL AVAYFQRGML YYQTEKYDLA IKDLKEALIQ LRGNQLIDYK ILGLQFKLFA
CEVVASVVDQ DSFSGFAPLQ PQAAEPPPRP KTPEIFRALE GEAHRVLFGF VPETKEELQV
MPGNIVFVLK KGNDNWATVM FNGQKGLVPC NYLEPVELRI HPQQQPQEES SPQSDIPAPP
SSKAPGRPQL SPGQKQKEEP KEVKLSVPMP YTLKVHYKYT VVMKTQPGLP YSQVRDMVSK
KLELRLEHTK LSYRPRDSNE LVPLSEDSMK DAWGQVKNYC LTLWCENTVG DQGFPDEPKE
SEKADANNQT TEPQLKKGSQ VEALFSYEAT QPEDLEFQEG DIILVLSKVN EEWLEGECKG
KVGIFPKVFV EDCATTDLES TRREV*

mutated AA sequence

N/A

speed

0.89 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