MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000293780
MT speed 0 s - this script 3.137246 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CHRNE	disease_causing_automatic	0.998853829398696	simple_aae		affected	0	A431P	single base exchange	rs121909517		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.998853829398696 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM004693)
known disease mutation: rs18361 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:4802331C>GN/A show variant in all transcripts IGV

HGNC symbol

CHRNE

Ensembl transcript ID

ENST00000293780

Genbank transcript ID

NM_000080

UniProt peptide

Q04844

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1291G>C
cDNA.1302G>C
g.4039G>C

AA changes

A431P Score: 27 explain score(s)

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

431

frameshift

known variant

Reference ID: rs121909517

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

known disease mutation: rs18361 (pathogenic for Myasthenic syndrome, congenital, 4b, fast-channel) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM004693)

known disease mutation at this position, please check HGMD for details (HGMD ID CM004693)
known disease mutation at this position, please check HGMD for details (HGMD ID CM004693)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.514	1
	2.701	1
(flanking)	1.032	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 increased	4040	wt: 0.50 / mu: 0.80	wt: CGTGGCCGAGAGCAC mu: CGTGCCCGAGAGCAC	TGGC\|cgag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

431

mutated

not conserved

431

Ptroglodytes

no alignment

ENSPTRG00000008612

n/a

Mmulatta

all identical

ENSMMUG00000002409

431

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000014609

432

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000034307

451

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000014957

441

protein features

start (aa)	end (aa)	feature	details
329	456	TOPO_DOM	Cytoplasmic (Potential).	lost
457	480	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
481	493	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1482 / 1482

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

494 / 494

position of stopcodon in wt / mu cDNA

1493 / 1493

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

12 / 12

chromosome

strand

-1

last intron/exon boundary

1338

theoretical NMD boundary in CDS

1276

length of CDS

1482

coding sequence (CDS) position

1291

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

1302

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

4039

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

4802331

original gDNA sequence snippet

TGGATGCCGTGAACTTCGTGGCCGAGAGCACGAGAGATCAG

altered gDNA sequence snippet

TGGATGCCGTGAACTTCGTGCCCGAGAGCACGAGAGATCAG

original cDNA sequence snippet

TGGATGCCGTGAACTTCGTGGCCGAGAGCACGAGAGATCAG

altered cDNA sequence snippet

TGGATGCCGTGAACTTCGTGCCCGAGAGCACGAGAGATCAG

wildtype AA sequence

MARAPLGVLL LLGLLGRGVG KNEELRLYHH LFNNYDPGSR PVREPEDTVT ISLKVTLTNL
ISLNEKEETL TTSVWIGIDW QDYRLNYSKD DFGGIETLRV PSELVWLPEI VLENNIDGQF
GVAYDANVLV YEGGSVTWLP PAIYRSVCAV EVTYFPFDWQ NCSLIFRSQT YNAEEVEFTF
AVDNDGKTIN KIDIDTEAYT ENGEWAIDFC PGVIRRHHGG ATDGPGETDV IYSLIIRRKP
LFYVINIIVP CVLISGLVLL AYFLPAQAGG QKCTVSINVL LAQTVFLFLI AQKIPETSLS
VPLLGRFLIF VMVVATLIVM NCVIVLNVSQ RTPTTHAMSP RLRHVLLELL PRLLGSPPPP
EAPRAASPPR RASSVGLLLR AEELILKKPR SELVFEGQRH RQGTWTAAFC QSLGAAAPEV
RCCVDAVNFV AESTRDQEAT GEEVSDWVRM GNALDNICFW AALVLFSVGS SLIFLGAYFN
RVPDLPYAPC IQP*

mutated AA sequence

MARAPLGVLL LLGLLGRGVG KNEELRLYHH LFNNYDPGSR PVREPEDTVT ISLKVTLTNL
ISLNEKEETL TTSVWIGIDW QDYRLNYSKD DFGGIETLRV PSELVWLPEI VLENNIDGQF
GVAYDANVLV YEGGSVTWLP PAIYRSVCAV EVTYFPFDWQ NCSLIFRSQT YNAEEVEFTF
AVDNDGKTIN KIDIDTEAYT ENGEWAIDFC PGVIRRHHGG ATDGPGETDV IYSLIIRRKP
LFYVINIIVP CVLISGLVLL AYFLPAQAGG QKCTVSINVL LAQTVFLFLI AQKIPETSLS
VPLLGRFLIF VMVVATLIVM NCVIVLNVSQ RTPTTHAMSP RLRHVLLELL PRLLGSPPPP
EAPRAASPPR RASSVGLLLR AEELILKKPR SELVFEGQRH RQGTWTAAFC QSLGAAAPEV
RCCVDAVNFV PESTRDQEAT GEEVSDWVRM GNALDNICFW AALVLFSVGS SLIFLGAYFN
RVPDLPYAPC IQP*

speed

1.08 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
back to results table

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

Problems