mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999676915 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM970303)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:175618961C>TN/A show variant in all transcripts IGV

HGNC symbol

CHRNA1

Ensembl transcript ID

ENST00000409323

Genbank transcript ID

N/A

UniProt peptide

P02708

alteration type

single base exchange

alteration region

CDS

DNA changes

c.526G>A
cDNA.585G>A
g.10240G>A

AA changes

V176M Score: 21 explain score(s)

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

176

frameshift

known variant

Reference ID: rs137852799

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

known disease mutation at this position, please check HGMD for details (HGMD ID CM970303)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970303)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970303)

regulatory features

Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
USF1, Transcription Factor, USF1 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.872	1
	5.885	1
(flanking)	2.018	1

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 gained	10236	0.95	mu: GGCTCTGTCATGGCC	CTCT\|gtca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

176

mutated

all conserved

176

Ptroglodytes

all identical

ENSPTRG00000012658

201

Mmulatta

all identical

ENSMMUG00000021796

200

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000027107

176

Ggallus

all identical

ENSGALG00000009301

186

Trubripes

all identical

ENSTRUG00000008738

197

Drerio

all identical

ENSDARG00000009021

176

Dmelanogaster

no homologue

Celegans

all identical

K11G12.2

213

HWY

Xtropicalis

all identical

ENSXETG00000025418

176

protein features

start (aa)	end (aa)	feature	details
21	255	TOPO_DOM	Extracellular.	lost
186	186	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
187	187	DISULFID		might get lost (downstream of altered splice site)
237	237	DISULFID	Associated with receptor activation.	might get lost (downstream of altered splice site)
238	238	DISULFID	Associated with receptor activation.	might get lost (downstream of altered splice site)
256	280	TRANSMEM	Helical.	might get lost (downstream of altered splice site)
288	306	TRANSMEM	Helical.	might get lost (downstream of altered splice site)
322	341	TRANSMEM	Helical.	might get lost (downstream of altered splice site)
342	453	TOPO_DOM	Cytoplasmic.	might get lost (downstream of altered splice site)
415	415	CONFLICT	P -> F (in Ref. 4; AAD14247).	might get lost (downstream of altered splice site)
454	472	TRANSMEM	Helical.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

810 / 810

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

270 / 270

position of stopcodon in wt / mu cDNA

869 / 869

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

60 / 60

chromosome

strand

-1

last intron/exon boundary

600

theoretical NMD boundary in CDS

490

length of CDS

810

coding sequence (CDS) position

526

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

585

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

10240

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

175618961

original gDNA sequence snippet

GGACCTACGACGGCTCTGTCGTGGCCATCAACCCGGTAGGT

altered gDNA sequence snippet

GGACCTACGACGGCTCTGTCATGGCCATCAACCCGGTAGGT

original cDNA sequence snippet

GGACCTACGACGGCTCTGTCGTGGCCATCAACCCGGAAAGC

altered cDNA sequence snippet

GGACCTACGACGGCTCTGTCATGGCCATCAACCCGGAAAGC

wildtype AA sequence

MEPWPLLLLF SLCSAGLVLG SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL
INVDEVNQIV TTNVRLKQQW VDYNLKWNPD DYGGVKKIHI PSEKIWRPDL VLYNNADGDF
AIVKFTKVLL QYTGHITWTP PAIFKSYCEI IVTHFPFDEQ NCSMKLGTWT YDGSVVAINP
ESDQPDLSNF MESGEWVIKE SRGWKHSVTY SCCPDTPYLD ITYHFVMQRL PLYFIVNVII
PCLLFSFLTG LVFYLPTDSG GCGCHDCCC*

mutated AA sequence

MEPWPLLLLF SLCSAGLVLG SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL
INVDEVNQIV TTNVRLKQQW VDYNLKWNPD DYGGVKKIHI PSEKIWRPDL VLYNNADGDF
AIVKFTKVLL QYTGHITWTP PAIFKSYCEI IVTHFPFDEQ NCSMKLGTWT YDGSVMAINP
ESDQPDLSNF MESGEWVIKE SRGWKHSVTY SCCPDTPYLD ITYHFVMQRL PLYFIVNVII
PCLLFSFLTG LVFYLPTDSG GCGCHDCCC*

speed

0.45 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