mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999749171539 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM970305)
known disease mutation: rs18380 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:175614810C>AN/A show variant in all transcripts IGV

HGNC symbol

CHRNA1

Ensembl transcript ID

ENST00000409542

Genbank transcript ID

N/A

UniProt peptide

P02708

alteration type

single base exchange

alteration region

CDS

DNA changes

c.620G>T
cDNA.638G>T
g.14391G>T

AA changes

S207I Score: 142 explain score(s)

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

207

frameshift

known variant

Reference ID: rs137852802
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs18380 (pathogenic for Congenital myasthenic syndrome 1A) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970305)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970305)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970305)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.329	0.821
	4.248	1
(flanking)	2.409	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 increased	14397	wt: 0.33 / mu: 0.69	wt: CCCCTCCACGTCCAGTGCTGTGCCCTTGATTGGAAAATACA mu: CCCCTCCACGTCCATTGCTGTGCCCTTGATTGGAAAATACA	ctgt\|GCCC
Acc marginally increased	14392	wt: 0.2413 / mu: 0.2638 (marginal change - not scored)	wt: CTGATCCCCTCCACGTCCAGTGCTGTGCCCTTGATTGGAAA mu: CTGATCCCCTCCACGTCCATTGCTGTGCCCTTGATTGGAAA	cagt\|GCTG
Acc marginally increased	14387	wt: 0.3593 / mu: 0.3993 (marginal change - not scored)	wt: TGGAGCTGATCCCCTCCACGTCCAGTGCTGTGCCCTTGATT mu: TGGAGCTGATCCCCTCCACGTCCATTGCTGTGCCCTTGATT	acgt\|CCAG
Acc gained	14389	0.34	mu: GAGCTGATCCCCTCCACGTCCATTGCTGTGCCCTTGATTGG	gtcc\|ATTG
Acc gained	14396	0.51	mu: TCCCCTCCACGTCCATTGCTGTGCCCTTGATTGGAAAATAC	gctg\|TGCC
Acc gained	14393	0.80	mu: TGATCCCCTCCACGTCCATTGCTGTGCCCTTGATTGGAAAA	attg\|CTGT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

207

mutated

not conserved

207

Ptroglodytes

all identical

ENSPTRG00000012658

314

Mmulatta

all identical

ENSMMUG00000021796

313

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000027107

289

Ggallus

all identical

ENSGALG00000009301

299

Trubripes

all identical

ENSTRUG00000008738

310

Drerio

all identical

ENSDARG00000009021

289

Dmelanogaster

no homologue

Celegans

all conserved

K11G12.2

323

Xtropicalis

all identical

ENSXETG00000025418

289

protein features

start (aa)	end (aa)	feature	details
21	255	TOPO_DOM	Extracellular.	lost
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

1128 / 1128

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

376 / 376

position of stopcodon in wt / mu cDNA

1146 / 1146

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

19 / 19

chromosome

strand

-1

last intron/exon boundary

1015

theoretical NMD boundary in CDS

946

length of CDS

1128

coding sequence (CDS) position

620

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

638

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

14391

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

175614810

original gDNA sequence snippet

GCTGATCCCCTCCACGTCCAGTGCTGTGCCCTTGATTGGAA

altered gDNA sequence snippet

GCTGATCCCCTCCACGTCCATTGCTGTGCCCTTGATTGGAA

original cDNA sequence snippet

GCTGATCCCCTCCACGTCCAGTGCTGTGCCCTTGATTGGAA

altered cDNA sequence snippet

GCTGATCCCCTCCACGTCCATTGCTGTGCCCTTGATTGGAA

wildtype AA sequence

MEPWPLLLLF SLCSAGLVLG SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL
INVDEVNQIV TTNVRLKQNC SMKLGTWTYD GSVVAINPES DQPDLSNFME SGEWVIKESR
GWKHSVTYSC CPDTPYLDIT YHFVMQRLPL YFIVNVIIPC LLFSFLTGLV FYLPTDSGEK
MTLSISVLLS LTVFLLVIVE LIPSTSSAVP LIGKYMLFTM VFVIASIIIT VIVINTHHRS
PSTHVMPNWV RKVFIDTIPN IMFFSTMKRP SREKQDKKIF TEDIDISDIS GKPGPPPMGF
HSPLIKHPEV KSAIEGIKYI AETMKSDQES NNAAAEWKYV AMVMDHILLG VFMLVCIIGT
LAVFAGRLIE LNQQG*

mutated AA sequence

MEPWPLLLLF SLCSAGLVLG SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL
INVDEVNQIV TTNVRLKQNC SMKLGTWTYD GSVVAINPES DQPDLSNFME SGEWVIKESR
GWKHSVTYSC CPDTPYLDIT YHFVMQRLPL YFIVNVIIPC LLFSFLTGLV FYLPTDSGEK
MTLSISVLLS LTVFLLVIVE LIPSTSIAVP LIGKYMLFTM VFVIASIIIT VIVINTHHRS
PSTHVMPNWV RKVFIDTIPN IMFFSTMKRP SREKQDKKIF TEDIDISDIS GKPGPPPMGF
HSPLIKHPEV KSAIEGIKYI AETMKSDQES NNAAAEWKYV AMVMDHILLG VFMLVCIIGT
LAVFAGRLIE LNQQG*

speed

0.99 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