mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999996899491138 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
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

ENST00000413720

Genbank transcript ID

NM_001190794

UniProt peptide

P19878

alteration type

single base exchange

alteration region

CDS

DNA changes

c.407A>G
cDNA.682A>G
g.17625A>G

AA changes

K136R Score: 26 explain score(s)

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

136

frameshift

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

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

136

mutated

all conserved

136

Ptroglodytes

all conserved

ENSPTRG00000001766

181

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000026480

181

Ggallus

no homologue

Trubripes

not conserved

ENSTRUG00000004299

181

Drerio

not conserved

ENSDARG00000005821

181

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000012530

182

protein features

start (aa)	end (aa)	feature	details
121	154	REPEAT	TPR 3.	lost
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

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1446 / 1446

position (AA) of stopcodon in wt / mu AA sequence

482 / 482

position of stopcodon in wt / mu cDNA

1721 / 1721

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

1609

theoretical NMD boundary in CDS

1283

length of CDS

1446

coding sequence (CDS) position

407

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

682

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

AGTGGTGATCCCTGTGGGCAAGCTGTTTCGACCAAATGAGA

altered cDNA sequence snippet

AGTGGTGATCCCTGTGGGCAGGCTGTTTCGACCAAATGAGA

wildtype AA sequence

MSLVEAISLW NEGVLAADKK DWKGALDAFS AVQDPHSRIC FNIGCMYTIL KNMTEAEKAF
TRSINRDKHL AVAYFQRGML YYQTEKYDLA IKDLKEALIQ LRGNQLIDYK ILGLQFKLFA
CEKQKLYEPV VIPVGKLFRP NERQVAQLAK KDYLGKATVV ASVVDQDSFS GFAPLQPQAA
EPPPRPKTPE IFRALEGEAH RVLFGFVPET KEELQVMPGN IVFVLKKGND NWATVMFNGQ
KGLVPCNYLE PVELRIHPQQ QPQEESSPQS DIPAPPSSKA PGRPQLSPGQ KQKEEPKEVK
LSVPMPYTLK VHYKYTVVMK TQPGLPYSQV RDMVSKKLEL RLEHTKLSYR PRDSNELVPL
SEDSMKDAWG QVKNYCLTLW CENTVGDQGF PDEPKESEKA DANNQTTEPQ LKKGSQVEAL
FSYEATQPED LEFQEGDIIL VLSKVNEEWL EGECKGKVGI FPKVFVEDCA TTDLESTRRE
V*

mutated AA sequence

MSLVEAISLW NEGVLAADKK DWKGALDAFS AVQDPHSRIC FNIGCMYTIL KNMTEAEKAF
TRSINRDKHL AVAYFQRGML YYQTEKYDLA IKDLKEALIQ LRGNQLIDYK ILGLQFKLFA
CEKQKLYEPV VIPVGRLFRP NERQVAQLAK KDYLGKATVV ASVVDQDSFS GFAPLQPQAA
EPPPRPKTPE IFRALEGEAH RVLFGFVPET KEELQVMPGN IVFVLKKGND NWATVMFNGQ
KGLVPCNYLE PVELRIHPQQ QPQEESSPQS DIPAPPSSKA PGRPQLSPGQ KQKEEPKEVK
LSVPMPYTLK VHYKYTVVMK TQPGLPYSQV RDMVSKKLEL RLEHTKLSYR PRDSNELVPL
SEDSMKDAWG QVKNYCLTLW CENTVGDQGF PDEPKESEKA DANNQTTEPQ LKKGSQVEAL
FSYEATQPED LEFQEGDIIL VLSKVNEEWL EGECKGKVGI FPKVFVEDCA TTDLESTRRE
V*

speed

1.13 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