mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999999879164 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM080147)
known disease mutation: rs18388 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:175618323C>AN/A show variant in all transcripts IGV

HGNC symbol

CHRNA1

Ensembl transcript ID

ENST00000348749

Genbank transcript ID

NM_000079

UniProt peptide

P02708

alteration type

single base exchange

alteration region

CDS

DNA changes

c.686G>T
cDNA.764G>T
g.10878G>T

AA changes

R229L Score: 102 explain score(s)

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

229

frameshift

known variant

Reference ID: rs137852809

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

known disease mutation: rs18388 (pathogenic for Lethal multiple pterygium syndrome) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM080147)

known disease mutation at this position, please check HGMD for details (HGMD ID CM080147)
known disease mutation at this position, please check HGMD for details (HGMD ID CM080147)

regulatory features

H4K5ac, Histone, Histone 4 Lysine 5 Acetylation
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H2BK20ac, Histone, Histone 2B Lysine 20 Acetylation
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4ac, Histone, Histone 3 Lysine 4 Acetylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.064	0.993
	6.011	1
(flanking)	3.095	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 gained	10889	0.38	mu: TCATGCAGCTCCTGCCCCTCTACTTCATCGTCAACGTCATC	ctct\|ACTT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

229

mutated

not conserved

229

Ptroglodytes

all identical

ENSPTRG00000012658

254

Mmulatta

all identical

ENSMMUG00000021796

253

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000027107

229

Ggallus

all identical

ENSGALG00000009301

239

Trubripes

all identical

ENSTRUG00000008738

250

Drerio

all identical

ENSDARG00000009021

229

Dmelanogaster

no homologue

Celegans

all identical

K11G12.2

268

Xtropicalis

all identical

ENSXETG00000025418

229

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

1374 / 1374

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

458 / 458

position of stopcodon in wt / mu cDNA

1452 / 1452

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

79 / 79

chromosome

strand

-1

last intron/exon boundary

1321

theoretical NMD boundary in CDS

1192

length of CDS

1374

coding sequence (CDS) position

686

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

764

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

10878

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

175618323

original gDNA sequence snippet

CTACCACTTCGTCATGCAGCGCCTGCCCCTCTACTTCATCG

altered gDNA sequence snippet

CTACCACTTCGTCATGCAGCTCCTGCCCCTCTACTTCATCG

original cDNA sequence snippet

CTACCACTTCGTCATGCAGCGCCTGCCCCTCTACTTCATCG

altered cDNA sequence snippet

CTACCACTTCGTCATGCAGCTCCTGCCCCTCTACTTCATCG

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 EKMTLSISVL LSLTVFLLVI VELIPSTSSA VPLIGKYMLF
TMVFVIASII ITVIVINTHH RSPSTHVMPN WVRKVFIDTI PNIMFFSTMK RPSREKQDKK
IFTEDIDISD ISGKPGPPPM GFHSPLIKHP EVKSAIEGIK YIAETMKSDQ ESNNAAAEWK
YVAMVMDHIL LGVFMLVCII GTLAVFAGRL IELNQQG*

mutated AA sequence

MEPWPLLLLF SLCSAGLVLG SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL
INVDEVNQIV TTNVRLKQQW VDYNLKWNPD DYGGVKKIHI PSEKIWRPDL VLYNNADGDF
AIVKFTKVLL QYTGHITWTP PAIFKSYCEI IVTHFPFDEQ NCSMKLGTWT YDGSVVAINP
ESDQPDLSNF MESGEWVIKE SRGWKHSVTY SCCPDTPYLD ITYHFVMQLL PLYFIVNVII
PCLLFSFLTG LVFYLPTDSG EKMTLSISVL LSLTVFLLVI VELIPSTSSA VPLIGKYMLF
TMVFVIASII ITVIVINTHH RSPSTHVMPN WVRKVFIDTI PNIMFFSTMK RPSREKQDKK
IFTEDIDISD ISGKPGPPPM GFHSPLIKHP EVKSAIEGIK YIAETMKSDQ ESNNAAAEWK
YVAMVMDHIL LGVFMLVCII GTLAVFAGRL IELNQQG*

speed

0.75 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