mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM960296)
known disease mutation: rs18373 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:7357648C>AN/A show variant in all transcripts IGV

HGNC symbol

CHRNB1

Ensembl transcript ID

ENST00000576360

Genbank transcript ID

N/A

UniProt peptide

P11230

alteration type

single base exchange

alteration region

intron

DNA changes

g.9269C>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs137852811
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs18373 (pathogenic for Myasthenic syndrome, congenital, 2a, slow-channel) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960296)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960296)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960296)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.193	1
	2.322	1
(flanking)	4.255	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
Acc marginally increased	9266	wt: 0.5598 / mu: 0.5986 (marginal change - not scored)	wt: TGGGGCTCTCAATCTTTGCCCTGCTGACCCTTACTGTGTTC mu: TGGGGCTCTCAATCTTTGCCCTGATGACCCTTACTGTGTTC	gccc\|TGCT
Acc gained	9268	0.43	mu: GGGCTCTCAATCTTTGCCCTGATGACCCTTACTGTGTTCCT	cctg\|ATGA
Donor gained	9265	0.53	mu: TTTGCCCTGATGACC	TGCC\|ctga

distance from splice site

115

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
24	244	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
210	210	CONFLICT	I -> N (in Ref. 1; CAA32939).	might get lost (downstream of altered splice site)
245	269	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
277	295	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
311	332	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
333	469	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
390	390	MOD_RES	Phosphotyrosine; by Tyr-kinases (By similarity).	might get lost (downstream of altered splice site)
470	488	TRANSMEM	Helical; (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

103 / 103

chromosome

strand

last intron/exon boundary

1105

theoretical NMD boundary in CDS

952

length of CDS

1143

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)

9269

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

7357648

original gDNA sequence snippet

GGCTCTCAATCTTTGCCCTGCTGACCCTTACTGTGTTCCTG

altered gDNA sequence snippet

GGCTCTCAATCTTTGCCCTGATGACCCTTACTGTGTTCCTG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MSTKVYLDLE WTDYRLSWDP AEHDGIDSLR ITAESVWLPD VVLLNNNDGN FDVALDISVV
VSSDGSVRWQ PPGIYRSSCS IQVTYFPFDW QNCTMVFSSY SYDSSEVSLQ TGLGPDGQGH
QEIHIHEGTF IENGQWEIIH KPSRLIQPPG DPRGGREGQR QEVIFYLIIR RKPLFYLVNV
IAPCILITLL AIFVFYLPPD AVILSVVVLN LHHRSPHTHQ MPLWVRQIFI HKLPLYLRLK
RPKPERDLMP EPPHCSSPGS GWGRGTDEYF IRKPPSDFLF PKPNRFQPEL SAPDLRRFID
GPNRAVALLP ELREVVSSIS YIARQLQEQE DHDALKEDWQ FVAMVVDRLF LWTFIIFTSV
GTLVIFLDAT YHLPPPDPFP *

mutated AA sequence

N/A

speed

0.78 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