MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000293780
Querying Taster for transcript #2: ENST00000521575
MT speed 0 s - this script 3.412793 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CHRNE	disease_causing	0.999695975440594	simple_aae		affected		R331W	single base exchange	rs121909515		show file
C17orf107	disease_causing	1	without_aae		affected			single base exchange	rs121909515		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999695975440594 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs18358 (probable pathogenic)
known disease mutation at this position (HGMD CM970309)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:4802804G>AN/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.991C>T
cDNA.1002C>T
g.3566C>T

AA changes

R331W Score: 101 explain score(s)

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

331

frameshift

known variant

Reference ID: rs121909515
Allele 'A' was neither found in ExAC nor 1000G.
known as potential disease variant: rs18358 (probable pathogenic for Congenital myasthenic syndrome 4C|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970309)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970309)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970309)

regulatory features

Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K36ac, Histone, Histone 3 Lysine 36 Acetylation
H2AZ, Histone, Histone 2A variant Z
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H2BK20ac, Histone, Histone 2B Lysine 20 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K4ac, Histone, Histone 3 Lysine 4 Acetylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.182	1
	1.315	0.959
(flanking)	0.332	0.709

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	3564	wt: 0.35 / mu: 0.66	wt: CATCGTGCTCAACGTGTCCCAGCGGACGCCCACCACCCACG mu: CATCGTGCTCAACGTGTCCCAGTGGACGCCCACCACCCACG	ccca\|GCGG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

331

mutated

not conserved

331

Ptroglodytes

no alignment

ENSPTRG00000008612

n/a

Mmulatta

all identical

ENSMMUG00000002409

331

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000014609

331

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000034307

336

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000014957

340

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

991

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

1002

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

3566

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

4802804

original gDNA sequence snippet

TCGTGCTCAACGTGTCCCAGCGGACGCCCACCACCCACGCC

altered gDNA sequence snippet

TCGTGCTCAACGTGTCCCAGTGGACGCCCACCACCCACGCC

original cDNA sequence snippet

TCGTGCTCAACGTGTCCCAGCGGACGCCCACCACCCACGCC

altered cDNA sequence snippet

TCGTGCTCAACGTGTCCCAGTGGACGCCCACCACCCACGCC

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 WTPTTHAMSP RLRHVLLELL PRLLGSPPPP
EAPRAASPPR RASSVGLLLR AEELILKKPR SELVFEGQRH RQGTWTAAFC QSLGAAAPEV
RCCVDAVNFV AESTRDQEAT GEEVSDWVRM GNALDNICFW AALVLFSVGS SLIFLGAYFN
RVPDLPYAPC IQP*

speed

0.46 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

mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (explain)

Summary

known as potential disease variant: rs18358 (probable pathogenic)
known disease mutation at this position (HGMD CM970309)
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:4802804G>AN/A show variant in all transcripts IGV

HGNC symbol

C17orf107

Ensembl transcript ID

ENST00000521575

Genbank transcript ID

N/A

UniProt peptide

Q6ZR85

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.92G>A
g.92G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.182	1
	1.315	0.959
(flanking)	0.332	0.709

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

splice site change before start ATG (at aa -83) |

effect	gDNA position	score	detection sequence	exon-intron border
Donor marginally increased	96	wt: 0.9835 / mu: 0.9902 (marginal change - not scored)	wt: CGCTGGGACACGTTG mu: CACTGGGACACGTTG	CTGG\|gaca
Donor gained	94	0.39	mu: TCCACTGGGACACGT	CACT\|ggga

distance from splice site

Kozak consensus sequence altered?

conservation
protein level for non-synonymous changes

N/A

protein features

no protein features affected

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

346 / 346

chromosome

strand

last intron/exon boundary

412

theoretical NMD boundary in CDS

length of CDS

297

coding sequence (CDS) position

N/A

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

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

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

4802804

original gDNA sequence snippet

GGCGTGGGTGGTGGGCGTCCGCTGGGACACGTTGAGCACGA

altered gDNA sequence snippet

GGCGTGGGTGGTGGGCGTCCACTGGGACACGTTGAGCACGA

original cDNA sequence snippet

GGCGTGGGTGGTGGGCGTCCGCTGGGACACGTTGAGCACGA

altered cDNA sequence snippet

GGCGTGGGTGGTGGGCGTCCACTGGGACACGTTGAGCACGA

wildtype AA sequence

MKGTPSSLDT LMWIYHFHSS TEVALQPPLL SSLELSVAAA HEYLEQRFRE LKSLEPPEPK
MQGMLPAPKP TLGLVLREAT ASLVSFGTTL LEVGYWGA*

mutated AA sequence

N/A

speed

0.97 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems