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: ENST00000381365
MT speed 0 s - this script 4.089979 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CHRNE	disease_causing	0.99999921754203	simple_aae		affected		T284P	single base exchange	rs121909510		show file
C17orf107	disease_causing	1	without_aae		affected			single base exchange	rs121909510		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.99999921754203 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs18343 (probable pathogenic)
known disease mutation at this position (HGMD CM950260)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:4804155T>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.850A>C
cDNA.861A>C
g.2215A>C

AA changes

T284P Score: 38 explain score(s)

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

284

frameshift

known variant

Reference ID: rs121909510
Allele 'G' was neither found in ExAC nor 1000G.
known as potential disease variant: rs18343 (probable pathogenic for Myasthenic syndrome, congenital, 4a, slow-channel|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950260)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950260)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950260)

regulatory features

Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
H2BK20ac, Histone, Histone 2B Lysine 20 Acetylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.304	1
	4.381	1
(flanking)	1.815	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	2213	wt: 0.7138 / mu: 0.7272 (marginal change - not scored)	wt: CATCAACGTCCTGCTCGCCCAGACCGTCTTCTTGTTCCTCA mu: CATCAACGTCCTGCTCGCCCAGCCCGTCTTCTTGTTCCTCA	ccca\|GACC
Acc increased	2226	wt: 0.46 / mu: 0.60	wt: CTCGCCCAGACCGTCTTCTTGTTCCTCATTGCCCAGAAAAT mu: CTCGCCCAGCCCGTCTTCTTGTTCCTCATTGCCCAGAAAAT	cttg\|TTCC
Acc increased	2225	wt: 0.54 / mu: 0.77	wt: GCTCGCCCAGACCGTCTTCTTGTTCCTCATTGCCCAGAAAA mu: GCTCGCCCAGCCCGTCTTCTTGTTCCTCATTGCCCAGAAAA	tctt\|GTTC
Acc increased	2212	wt: 0.30 / mu: 0.41	wt: CCATCAACGTCCTGCTCGCCCAGACCGTCTTCTTGTTCCTC mu: CCATCAACGTCCTGCTCGCCCAGCCCGTCTTCTTGTTCCTC	gccc\|AGAC
Donor marginally increased	2208	wt: 0.8514 / mu: 0.9007 (marginal change - not scored)	wt: CTGCTCGCCCAGACC mu: CTGCTCGCCCAGCCC	GCTC\|gccc
Acc gained	2224	0.37	mu: TGCTCGCCCAGCCCGTCTTCTTGTTCCTCATTGCCCAGAAA	ttct\|TGTT
Acc gained	2217	0.71	mu: AACGTCCTGCTCGCCCAGCCCGTCTTCTTGTTCCTCATTGC	gccc\|GTCT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

284

mutated

not conserved

284

Ptroglodytes

all identical

ENSPTRG00000008612

284

Mmulatta

all identical

ENSMMUG00000002409

284

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000014609

284

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000034307

289

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000014957

293

protein features

start (aa)	end (aa)	feature	details
273	291	TRANSMEM	Helical; (Potential).	lost
292	306	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
307	328	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
329	456	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
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

850

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

861

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

2215

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

4804155

original gDNA sequence snippet

TCAACGTCCTGCTCGCCCAGACCGTCTTCTTGTTCCTCATT

altered gDNA sequence snippet

TCAACGTCCTGCTCGCCCAGCCCGTCTTCTTGTTCCTCATT

original cDNA sequence snippet

TCAACGTCCTGCTCGCCCAGACCGTCTTCTTGTTCCTCATT

altered cDNA sequence snippet

TCAACGTCCTGCTCGCCCAGCCCGTCTTCTTGTTCCTCATT

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 LAQPVFLFLI AQKIPETSLS
VPLLGRFLIF VMVVATLIVM NCVIVLNVSQ RTPTTHAMSP RLRHVLLELL PRLLGSPPPP
EAPRAASPPR RASSVGLLLR AEELILKKPR SELVFEGQRH RQGTWTAAFC QSLGAAAPEV
RCCVDAVNFV AESTRDQEAT GEEVSDWVRM GNALDNICFW AALVLFSVGS SLIFLGAYFN
RVPDLPYAPC IQP*

speed

0.98 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: rs18343 (probable pathogenic)
known disease mutation at this position (HGMD CM950260)
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:4804155T>GN/A show variant in all transcripts IGV

HGNC symbol

C17orf107

Ensembl transcript ID

ENST00000381365

Genbank transcript ID

NM_001145536

UniProt peptide

N/A

alteration type

single base exchange

alteration region

3'UTR

DNA changes

cDNA.1127T>G
g.1443T>G

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)	5.304	1
	4.381	1
(flanking)	1.815	1

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

splice sites

splice site change occurs after stopcodon (at aa 297) splice site change occurs after stopcodon (at aa 298)

effect	gDNA position	score	detection sequence	exon-intron border
Donor increased	1435	wt: 0.75 / mu: 0.85	wt: AACAAGAAGACGGTC mu: AACAAGAAGACGGGC	CAAG\|aaga
Donor gained	1437	0.81	mu: CAAGAAGACGGGCTG	AGAA\|gacg

distance from splice site

624

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

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

signal is predicted to be ok

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

228 / 228

chromosome

strand

last intron/exon boundary

504

theoretical NMD boundary in CDS

226

length of CDS

573

coding sequence (CDS) position

N/A

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

1127

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

1443

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

4804155

original gDNA sequence snippet

AATGAGGAACAAGAAGACGGTCTGGGCGAGCAGGACGTTGA

altered gDNA sequence snippet

AATGAGGAACAAGAAGACGGGCTGGGCGAGCAGGACGTTGA

original cDNA sequence snippet

AATGAGGAACAAGAAGACGGTCTGGGCGAGCAGGACGTTGA

altered cDNA sequence snippet

AATGAGGAACAAGAAGACGGGCTGGGCGAGCAGGACGTTGA

wildtype AA sequence

MKGTPSSLDT LMWIYHFHSS TEVALQPPLL SSLELSVAAA HEYLEQRFRE LKSLEPPEPK
MQGMLPAPKP TLGLVLREAT ASLVSFGTTL LEISALWLQQ EARRLDGSAG PAPDGRDPGA
ALSRVAQAAG QGVRQAGAAV GASARLLVQG AWLCLCGRGL QGSASFLRQS QQQLGLGIPG
EPVSSGHGVS *

mutated AA sequence

N/A

speed

0.92 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems