MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000264381
Querying Taster for transcript #2: ENST00000540653
MT speed 1.94 s - this script 3.971081 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
BCHE	disease_causing_automatic	0.999999999697187	simple_aae		affected	0	Y156C	single base exchange	rs121918558		show file
BCHE	disease_causing_automatic	1	without_aae		affected	0		single base exchange	rs121918558		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999697187 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM970162)
known disease mutation: rs13227 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:165548355T>CN/A show variant in all transcripts IGV

HGNC symbol

BCHE

Ensembl transcript ID

ENST00000264381

Genbank transcript ID

NM_000055

UniProt peptide

P06276

alteration type

single base exchange

alteration region

CDS

DNA changes

c.467A>G
cDNA.634A>G
g.6906A>G

AA changes

Y156C Score: 194 explain score(s)

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

156

frameshift

known variant

Reference ID: rs121918558
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs13227 (pathogenic for Deficiency of butyrylcholine esterase) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970162)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970162)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970162)

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.141	0.997
	4.641	1
(flanking)	4.641	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	6915	wt: 0.30 / mu: 0.38	wt: TTTACATGTTTATGATGGCAAGTTTCTGGCTCGGGTTGAAA mu: TTTACATGTTTGTGATGGCAAGTTTCTGGCTCGGGTTGAAA	gcaa\|GTTT
Acc increased	6905	wt: 0.44 / mu: 0.75	wt: GAACATCATCTTTACATGTTTATGATGGCAAGTTTCTGGCT mu: GAACATCATCTTTACATGTTTGTGATGGCAAGTTTCTGGCT	gttt\|ATGA
Acc marginally increased	6903	wt: 0.3791 / mu: 0.4011 (marginal change - not scored)	wt: TGGAACATCATCTTTACATGTTTATGATGGCAAGTTTCTGG mu: TGGAACATCATCTTTACATGTTTGTGATGGCAAGTTTCTGG	atgt\|TTAT
Donor gained	6905	0.81	mu: ATGTTTGTGATGGCA	GTTT\|gtga

distance from splice site

475

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

156

mutated

not conserved

156

Ptroglodytes

all identical

ENSPTRG00000015593

156

Mmulatta

all identical

ENSMMUG00000003742

156

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000027792

157

Ggallus

all identical

ENSGALG00000009478

156

Trubripes

all identical

ENSTRUG00000005322

152

Drerio

no homologue

Dmelanogaster

all identical

FBgn0000024

186

Celegans

all identical

W09B12.1

145

Xtropicalis

all identical

ENSXETG00000006497

158

protein features

start (aa)	end (aa)	feature	details
154	156	HELIX		lost
159	165	HELIX		might get lost (downstream of altered splice site)
168	172	STRAND		might get lost (downstream of altered splice site)
177	181	HELIX		might get lost (downstream of altered splice site)
190	192	STRAND		might get lost (downstream of altered splice site)
194	209	HELIX		might get lost (downstream of altered splice site)
210	213	HELIX		might get lost (downstream of altered splice site)
215	225	STRAND		might get lost (downstream of altered splice site)
226	226	ACT_SITE	Acyl-ester intermediate.	might get lost (downstream of altered splice site)
227	237	HELIX		might get lost (downstream of altered splice site)
239	244	HELIX		might get lost (downstream of altered splice site)
246	252	STRAND		might get lost (downstream of altered splice site)
258	260	TURN		might get lost (downstream of altered splice site)
264	277	HELIX		might get lost (downstream of altered splice site)
269	269	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
280	280	DISULFID		might get lost (downstream of altered splice site)
284	284	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
285	292	HELIX		might get lost (downstream of altered splice site)
291	291	DISULFID		might get lost (downstream of altered splice site)
297	304	HELIX		might get lost (downstream of altered splice site)
305	307	HELIX		might get lost (downstream of altered splice site)
308	310	STRAND		might get lost (downstream of altered splice site)
324	326	STRAND		might get lost (downstream of altered splice site)
331	336	HELIX		might get lost (downstream of altered splice site)
345	350	STRAND		might get lost (downstream of altered splice site)
352	354	STRAND		might get lost (downstream of altered splice site)
353	353	ACT_SITE	Charge relay system.	might get lost (downstream of altered splice site)
355	358	HELIX		might get lost (downstream of altered splice site)
359	361	TURN		might get lost (downstream of altered splice site)
367	369	STRAND		might get lost (downstream of altered splice site)
369	369	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
375	385	HELIX		might get lost (downstream of altered splice site)
387	389	STRAND		might get lost (downstream of altered splice site)
391	401	HELIX		might get lost (downstream of altered splice site)
405	408	TURN		might get lost (downstream of altered splice site)
412	425	HELIX		might get lost (downstream of altered splice site)
427	438	HELIX		might get lost (downstream of altered splice site)
428	428	DISULFID		might get lost (downstream of altered splice site)
439	441	TURN		might get lost (downstream of altered splice site)
444	449	STRAND		might get lost (downstream of altered splice site)
460	462	HELIX		might get lost (downstream of altered splice site)
466	466	ACT_SITE	Charge relay system.	might get lost (downstream of altered splice site)
466	469	TURN		might get lost (downstream of altered splice site)
470	473	HELIX		might get lost (downstream of altered splice site)
476	478	HELIX		might get lost (downstream of altered splice site)
480	482	HELIX		might get lost (downstream of altered splice site)
483	483	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
486	505	HELIX		might get lost (downstream of altered splice site)
509	509	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
511	514	TURN		might get lost (downstream of altered splice site)
513	513	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
514	514	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
523	525	TURN		might get lost (downstream of altered splice site)
527	531	STRAND		might get lost (downstream of altered splice site)
538	541	STRAND		might get lost (downstream of altered splice site)
544	551	HELIX		might get lost (downstream of altered splice site)
547	547	DISULFID		might get lost (downstream of altered splice site)
552	555	TURN		might get lost (downstream of altered splice site)
599	599	DISULFID	Interchain.	might get lost (downstream of altered splice site)
599	599	DISULFID	Interchain.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1809 / 1809

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

603 / 603

position of stopcodon in wt / mu cDNA

1976 / 1976

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

168 / 168

chromosome

strand

-1

last intron/exon boundary

1852

theoretical NMD boundary in CDS

1634

length of CDS

1809

coding sequence (CDS) position

467

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

634

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

6906

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

165548355

original gDNA sequence snippet

AACATCATCTTTACATGTTTATGATGGCAAGTTTCTGGCTC

altered gDNA sequence snippet

AACATCATCTTTACATGTTTGTGATGGCAAGTTTCTGGCTC

original cDNA sequence snippet

AACATCATCTTTACATGTTTATGATGGCAAGTTTCTGGCTC

altered cDNA sequence snippet

AACATCATCTTTACATGTTTGTGATGGCAAGTTTCTGGCTC

wildtype AA sequence

MHSKVTIICI RFLFWFLLLC MLIGKSHTED DIIIATKNGK VRGMNLTVFG GTVTAFLGIP
YAQPPLGRLR FKKPQSLTKW SDIWNATKYA NSCCQNIDQS FPGFHGSEMW NPNTDLSEDC
LYLNVWIPAP KPKNATVLIW IYGGGFQTGT SSLHVYDGKF LARVERVIVV SMNYRVGALG
FLALPGNPEA PGNMGLFDQQ LALQWVQKNI AAFGGNPKSV TLFGESAGAA SVSLHLLSPG
SHSLFTRAIL QSGSFNAPWA VTSLYEARNR TLNLAKLTGC SRENETEIIK CLRNKDPQEI
LLNEAFVVPY GTPLSVNFGP TVDGDFLTDM PDILLELGQF KKTQILVGVN KDEGTAFLVY
GAPGFSKDNN SIITRKEFQE GLKIFFPGVS EFGKESILFH YTDWVDDQRP ENYREALGDV
VGDYNFICPA LEFTKKFSEW GNNAFFYYFE HRSSKLPWPE WMGVMHGYEI EFVFGLPLER
RDNYTKAEEI LSRSIVKRWA NFAKYGNPNE TQNNSTSWPV FKSTEQKYLT LNTESTRIMT
KLRAQQCRFW TSFFPKVLEM TGNIDEAEWE WKAGFHRWNN YMMDWKNQFN DYTSKKESCV
GL*

mutated AA sequence

MHSKVTIICI RFLFWFLLLC MLIGKSHTED DIIIATKNGK VRGMNLTVFG GTVTAFLGIP
YAQPPLGRLR FKKPQSLTKW SDIWNATKYA NSCCQNIDQS FPGFHGSEMW NPNTDLSEDC
LYLNVWIPAP KPKNATVLIW IYGGGFQTGT SSLHVCDGKF LARVERVIVV SMNYRVGALG
FLALPGNPEA PGNMGLFDQQ LALQWVQKNI AAFGGNPKSV TLFGESAGAA SVSLHLLSPG
SHSLFTRAIL QSGSFNAPWA VTSLYEARNR TLNLAKLTGC SRENETEIIK CLRNKDPQEI
LLNEAFVVPY GTPLSVNFGP TVDGDFLTDM PDILLELGQF KKTQILVGVN KDEGTAFLVY
GAPGFSKDNN SIITRKEFQE GLKIFFPGVS EFGKESILFH YTDWVDDQRP ENYREALGDV
VGDYNFICPA LEFTKKFSEW GNNAFFYYFE HRSSKLPWPE WMGVMHGYEI EFVFGLPLER
RDNYTKAEEI LSRSIVKRWA NFAKYGNPNE TQNNSTSWPV FKSTEQKYLT LNTESTRIMT
KLRAQQCRFW TSFFPKVLEM TGNIDEAEWE WKAGFHRWNN YMMDWKNQFN DYTSKKESCV
GL*

speed

1.06 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 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM970162)
known disease mutation: rs13227 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:165548355T>CN/A show variant in all transcripts IGV

HGNC symbol

BCHE

Ensembl transcript ID

ENST00000540653

Genbank transcript ID

N/A

UniProt peptide

P06276

alteration type

single base exchange

alteration region

intron

DNA changes

g.6906A>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.141	0.997
	4.641	1
(flanking)	4.641	1

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

splice sites

splice site change before start ATG (at aa -31) |

effect	gDNA position	score	detection sequence	exon-intron border
Acc increased	6915	wt: 0.30 / mu: 0.38	wt: TTTACATGTTTATGATGGCAAGTTTCTGGCTCGGGTTGAAA mu: TTTACATGTTTGTGATGGCAAGTTTCTGGCTCGGGTTGAAA	gcaa\|GTTT
Acc increased	6905	wt: 0.44 / mu: 0.75	wt: GAACATCATCTTTACATGTTTATGATGGCAAGTTTCTGGCT mu: GAACATCATCTTTACATGTTTGTGATGGCAAGTTTCTGGCT	gttt\|ATGA
Acc marginally increased	6903	wt: 0.3791 / mu: 0.4011 (marginal change - not scored)	wt: TGGAACATCATCTTTACATGTTTATGATGGCAAGTTTCTGG mu: TGGAACATCATCTTTACATGTTTGTGATGGCAAGTTTCTGG	atgt\|TTAT
Donor gained	6905	0.81	mu: ATGTTTGTGATGGCA	GTTT\|gtga

distance from splice site

6747

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
1	28	SIGNAL		might get lost (downstream of altered splice site)
33	36	STRAND		might get lost (downstream of altered splice site)
39	42	STRAND		might get lost (downstream of altered splice site)
44	48	STRAND		might get lost (downstream of altered splice site)
45	45	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
51	60	STRAND		might get lost (downstream of altered splice site)
67	69	HELIX		might get lost (downstream of altered splice site)
82	85	STRAND		might get lost (downstream of altered splice site)
85	85	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
93	93	DISULFID		might get lost (downstream of altered splice site)
105	108	HELIX		might get lost (downstream of altered splice site)
116	118	STRAND		might get lost (downstream of altered splice site)
120	120	DISULFID		might get lost (downstream of altered splice site)
122	130	STRAND		might get lost (downstream of altered splice site)
133	141	STRAND		might get lost (downstream of altered splice site)
134	134	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
144	145	REGION	Substrate binding.	might get lost (downstream of altered splice site)
145	147	TURN		might get lost (downstream of altered splice site)
154	156	HELIX		might get lost (downstream of altered splice site)
159	165	HELIX		might get lost (downstream of altered splice site)
168	172	STRAND		might get lost (downstream of altered splice site)
177	181	HELIX		might get lost (downstream of altered splice site)
190	192	STRAND		might get lost (downstream of altered splice site)
194	209	HELIX		might get lost (downstream of altered splice site)
210	213	HELIX		might get lost (downstream of altered splice site)
215	225	STRAND		might get lost (downstream of altered splice site)
226	226	ACT_SITE	Acyl-ester intermediate.	might get lost (downstream of altered splice site)
227	237	HELIX		might get lost (downstream of altered splice site)
239	244	HELIX		might get lost (downstream of altered splice site)
246	252	STRAND		might get lost (downstream of altered splice site)
258	260	TURN		might get lost (downstream of altered splice site)
264	277	HELIX		might get lost (downstream of altered splice site)
269	269	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
280	280	DISULFID		might get lost (downstream of altered splice site)
284	284	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
285	292	HELIX		might get lost (downstream of altered splice site)
291	291	DISULFID		might get lost (downstream of altered splice site)
297	304	HELIX		might get lost (downstream of altered splice site)
305	307	HELIX		might get lost (downstream of altered splice site)
308	310	STRAND		might get lost (downstream of altered splice site)
324	326	STRAND		might get lost (downstream of altered splice site)
331	336	HELIX		might get lost (downstream of altered splice site)
345	350	STRAND		might get lost (downstream of altered splice site)
352	354	STRAND		might get lost (downstream of altered splice site)
353	353	ACT_SITE	Charge relay system.	might get lost (downstream of altered splice site)
355	358	HELIX		might get lost (downstream of altered splice site)
359	361	TURN		might get lost (downstream of altered splice site)
367	369	STRAND		might get lost (downstream of altered splice site)
369	369	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
375	385	HELIX		might get lost (downstream of altered splice site)
387	389	STRAND		might get lost (downstream of altered splice site)
391	401	HELIX		might get lost (downstream of altered splice site)
405	408	TURN		might get lost (downstream of altered splice site)
412	425	HELIX		might get lost (downstream of altered splice site)
427	438	HELIX		might get lost (downstream of altered splice site)
428	428	DISULFID		might get lost (downstream of altered splice site)
439	441	TURN		might get lost (downstream of altered splice site)
444	449	STRAND		might get lost (downstream of altered splice site)
460	462	HELIX		might get lost (downstream of altered splice site)
466	466	ACT_SITE	Charge relay system.	might get lost (downstream of altered splice site)
466	469	TURN		might get lost (downstream of altered splice site)
470	473	HELIX		might get lost (downstream of altered splice site)
476	478	HELIX		might get lost (downstream of altered splice site)
480	482	HELIX		might get lost (downstream of altered splice site)
483	483	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
486	505	HELIX		might get lost (downstream of altered splice site)
509	509	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
511	514	TURN		might get lost (downstream of altered splice site)
513	513	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
514	514	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
523	525	TURN		might get lost (downstream of altered splice site)
527	531	STRAND		might get lost (downstream of altered splice site)
538	541	STRAND		might get lost (downstream of altered splice site)
544	551	HELIX		might get lost (downstream of altered splice site)
547	547	DISULFID		might get lost (downstream of altered splice site)
552	555	TURN		might get lost (downstream of altered splice site)
599	599	DISULFID	Interchain.	might get lost (downstream of altered splice site)
599	599	DISULFID	Interchain.	might get lost (downstream of altered splice site)

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

205 / 205

chromosome

strand

-1

last intron/exon boundary

275

theoretical NMD boundary in CDS

length of CDS

195

coding sequence (CDS) position

N/A

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

N/A

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

6906

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

165548355

original gDNA sequence snippet

AACATCATCTTTACATGTTTATGATGGCAAGTTTCTGGCTC

altered gDNA sequence snippet

AACATCATCTTTACATGTTTGTGATGGCAAGTTTCTGGCTC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MTKLRAQQCR FWTSFFPKVL EMTGNIDEAE WEWKAGFHRW NNYMMDWKNQ FNDYTSKKES
CVGL*

mutated AA sequence

N/A

speed

0.88 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems