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: ENST00000302068
Querying Taster for transcript #2: ENST00000509493
MT speed 0 s - this script 3.72776 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
FGB	disease_causing_automatic	0.999999999993784	simple_aae		affected	0	G430D	single base exchange	rs121909622		show file
FGB	disease_causing_automatic	0.999999999994895	simple_aae		affected	0	G211D	single base exchange	rs121909622		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999993784 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM000157)
known disease mutation: rs16390 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr4:155491615G>AN/A show variant in all transcripts IGV

HGNC symbol

FGB

Ensembl transcript ID

ENST00000302068

Genbank transcript ID

NM_005141

UniProt peptide

P02675

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1289G>A
cDNA.1352G>A
g.7508G>A

AA changes

G430D Score: 94 explain score(s)

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

430

frameshift

known variant

Reference ID: rs121909622
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs16390 (pathogenic for Afibrinogenemia, congenital) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM000157)

known disease mutation at this position, please check HGMD for details (HGMD ID CM000157)
known disease mutation at this position, please check HGMD for details (HGMD ID CM000157)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	6.114	1
	6.114	1
(flanking)	0.012	0.993

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	7504	wt: 0.65 / mu: 0.99	wt: AAGACGGTGGTGGAT mu: AAGACGGTGATGGAT	GACG\|gtgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

430

mutated

not conserved

430

Ptroglodytes

all identical

ENSPTRG00000016534

413

Mmulatta

all identical

ENSMMUG00000021302

430

Fcatus

all identical

ENSFCAG00000013254

429

Mmusculus

all identical

ENSMUSG00000033831

420

Ggallus

all identical

ENSGALG00000009262

421

Trubripes

all identical

ENSTRUG00000002645

435

Drerio

all identical

ENSDARG00000008969

424

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000022431

430

protein features

start (aa)	end (aa)	feature	details
232	488	DOMAIN	Fibrinogen C-terminal.	lost
424	428	TURN		might get lost (downstream of altered splice site)
435	437	STRAND		might get lost (downstream of altered splice site)
437	437	DISULFID		might get lost (downstream of altered splice site)
439	441	STRAND		might get lost (downstream of altered splice site)
448	451	STRAND		might get lost (downstream of altered splice site)
454	456	TURN		might get lost (downstream of altered splice site)
457	461	STRAND		might get lost (downstream of altered splice site)
464	467	STRAND		might get lost (downstream of altered splice site)
468	471	HELIX		might get lost (downstream of altered splice site)
473	475	STRAND		might get lost (downstream of altered splice site)
478	485	STRAND		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1476 / 1476

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

492 / 492

position of stopcodon in wt / mu cDNA

1539 / 1539

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

64 / 64

chromosome

strand

last intron/exon boundary

1308

theoretical NMD boundary in CDS

1194

length of CDS

1476

coding sequence (CDS) position

1289

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

1352

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

7508

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

155491615

original gDNA sequence snippet

GTGTTCTAAAGAAGACGGTGGTGGATGGTGGTATAATAGAT

altered gDNA sequence snippet

GTGTTCTAAAGAAGACGGTGATGGATGGTGGTATAATAGAT

original cDNA sequence snippet

GTGTTCTAAAGAAGACGGTGGTGGATGGTGGTATAATAGAT

altered cDNA sequence snippet

GTGTTCTAAAGAAGACGGTGATGGATGGTGGTATAATAGAT

wildtype AA sequence

MKRMVSWSFH KLKTMKHLLL LLLCVFLVKS QGVNDNEEGF FSARGHRPLD KKREEAPSLR
PAPPPISGGG YRARPAKAAA TQKKVERKAP DAGGCLHADP DLGVLCPTGC QLQEALLQQE
RPIRNSVDEL NNNVEAVSQT SSSSFQYMYL LKDLWQKRQK QVKDNENVVN EYSSELEKHQ
LYIDETVNSN IPTNLRVLRS ILENLRSKIQ KLESDVSAQM EYCRTPCTVS CNIPVVSGKE
CEEIIRKGGE TSEMYLIQPD SSVKPYRVYC DMNTENGGWT VIQNRQDGSV DFGRKWDPYK
QGFGNVATNT DGKNYCGLPG EYWLGNDKIS QLTRMGPTEL LIEMEDWKGD KVKAHYGGFT
VQNEANKYQI SVNKYRGTAG NALMDGASQL MGENRTMTIH NGMFFSTYDR DNDGWLTSDP
RKQCSKEDGG GWWYNRCHAA NPNGRYYWGG QYTWDMAKHG TDDGVVWMNW KGSWYSMRKM
SMKIRPFFPQ Q*

mutated AA sequence

MKRMVSWSFH KLKTMKHLLL LLLCVFLVKS QGVNDNEEGF FSARGHRPLD KKREEAPSLR
PAPPPISGGG YRARPAKAAA TQKKVERKAP DAGGCLHADP DLGVLCPTGC QLQEALLQQE
RPIRNSVDEL NNNVEAVSQT SSSSFQYMYL LKDLWQKRQK QVKDNENVVN EYSSELEKHQ
LYIDETVNSN IPTNLRVLRS ILENLRSKIQ KLESDVSAQM EYCRTPCTVS CNIPVVSGKE
CEEIIRKGGE TSEMYLIQPD SSVKPYRVYC DMNTENGGWT VIQNRQDGSV DFGRKWDPYK
QGFGNVATNT DGKNYCGLPG EYWLGNDKIS QLTRMGPTEL LIEMEDWKGD KVKAHYGGFT
VQNEANKYQI SVNKYRGTAG NALMDGASQL MGENRTMTIH NGMFFSTYDR DNDGWLTSDP
RKQCSKEDGD GWWYNRCHAA NPNGRYYWGG QYTWDMAKHG TDDGVVWMNW KGSWYSMRKM
SMKIRPFFPQ Q*

speed

0.48 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: simple_aae, prob: 0.999999999994895 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM000157)
known disease mutation: rs16390 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr4:155491615G>AN/A show variant in all transcripts IGV

HGNC symbol

FGB

Ensembl transcript ID

ENST00000509493

Genbank transcript ID

N/A

UniProt peptide

P02675

alteration type

single base exchange

alteration region

CDS

DNA changes

c.632G>A
cDNA.906G>A
g.7508G>A

AA changes

G211D Score: 94 explain score(s)

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

211

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	6.114	1
	6.114	1
(flanking)	0.012	0.993

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	7504	wt: 0.65 / mu: 0.99	wt: AAGACGGTGGTGGAT mu: AAGACGGTGATGGAT	GACG\|gtgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

211

mutated

not conserved

211

Ptroglodytes

all identical

ENSPTRG00000016534

413

Mmulatta

all identical

ENSMMUG00000021302

430

Fcatus

all identical

ENSFCAG00000013254

429

Mmusculus

all identical

ENSMUSG00000033831

420

Ggallus

all identical

ENSGALG00000009262

421

Trubripes

all identical

ENSTRUG00000002645

435

Drerio

all identical

ENSDARG00000008969

424

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000022431

430

protein features

start (aa)	end (aa)	feature	details
157	222	COILED	Potential.	lost
190	222	HELIX		lost
223	223	DISULFID	Interchain (with C-184 in alpha chain).	might get lost (downstream of altered splice site)
223	223	DISULFID	Interchain (with C-184 in alpha chain).	might get lost (downstream of altered splice site)
224	226	STRAND		might get lost (downstream of altered splice site)
227	227	DISULFID	Interchain (with C-161 in gamma chain).	might get lost (downstream of altered splice site)
227	227	DISULFID	Interchain (with C-161 in gamma chain).	might get lost (downstream of altered splice site)
231	231	DISULFID		might get lost (downstream of altered splice site)
232	488	DOMAIN	Fibrinogen C-terminal.	might get lost (downstream of altered splice site)
233	235	STRAND		might get lost (downstream of altered splice site)
238	240	STRAND		might get lost (downstream of altered splice site)
241	241	DISULFID		might get lost (downstream of altered splice site)
241	246	HELIX		might get lost (downstream of altered splice site)
253	257	STRAND		might get lost (downstream of altered splice site)
261	263	STRAND		might get lost (downstream of altered splice site)
266	271	STRAND		might get lost (downstream of altered splice site)
270	270	DISULFID		might get lost (downstream of altered splice site)
274	276	HELIX		might get lost (downstream of altered splice site)
279	288	STRAND		might get lost (downstream of altered splice site)
296	301	HELIX		might get lost (downstream of altered splice site)
302	304	STRAND		might get lost (downstream of altered splice site)
306	308	STRAND		might get lost (downstream of altered splice site)
311	315	STRAND		might get lost (downstream of altered splice site)
316	316	DISULFID		might get lost (downstream of altered splice site)
321	323	STRAND		might get lost (downstream of altered splice site)
326	334	HELIX		might get lost (downstream of altered splice site)
335	337	STRAND		might get lost (downstream of altered splice site)
339	345	STRAND		might get lost (downstream of altered splice site)
347	349	STRAND		might get lost (downstream of altered splice site)
351	361	STRAND		might get lost (downstream of altered splice site)
364	366	HELIX		might get lost (downstream of altered splice site)
370	379	STRAND		might get lost (downstream of altered splice site)
382	385	HELIX		might get lost (downstream of altered splice site)
388	390	STRAND		might get lost (downstream of altered splice site)
392	396	HELIX		might get lost (downstream of altered splice site)
394	394	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
404	407	STRAND		might get lost (downstream of altered splice site)
408	410	STRAND		might get lost (downstream of altered splice site)
420	422	HELIX		might get lost (downstream of altered splice site)
424	424	DISULFID		might get lost (downstream of altered splice site)
424	428	TURN		might get lost (downstream of altered splice site)
435	437	STRAND		might get lost (downstream of altered splice site)
437	437	DISULFID		might get lost (downstream of altered splice site)
439	441	STRAND		might get lost (downstream of altered splice site)
448	451	STRAND		might get lost (downstream of altered splice site)
454	456	TURN		might get lost (downstream of altered splice site)
457	461	STRAND		might get lost (downstream of altered splice site)
464	467	STRAND		might get lost (downstream of altered splice site)
468	471	HELIX		might get lost (downstream of altered splice site)
473	475	STRAND		might get lost (downstream of altered splice site)
478	485	STRAND		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

819 / 819

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

273 / 273

position of stopcodon in wt / mu cDNA

1093 / 1093

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

275 / 275

chromosome

strand

last intron/exon boundary

862

theoretical NMD boundary in CDS

537

length of CDS

819

coding sequence (CDS) position

632

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

906

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

7508

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

155491615

original gDNA sequence snippet

GTGTTCTAAAGAAGACGGTGGTGGATGGTGGTATAATAGAT

altered gDNA sequence snippet

GTGTTCTAAAGAAGACGGTGATGGATGGTGGTATAATAGAT

original cDNA sequence snippet

GTGTTCTAAAGAAGACGGTGGTGGATGGTGGTATAATAGAT

altered cDNA sequence snippet

GTGTTCTAAAGAAGACGGTGATGGATGGTGGTATAATAGAT

wildtype AA sequence

MEYCRTPCTV SCNIPVVSGK ECEEIIRKGG ETSEMYLIQP DSSVKPYRVY CDMNTENGGW
TVIQNRQDGS VDFGRKWDPY KQGFGNVATN TDGKNYCGLP GEYWLGNDKI SQLTRMGPTE
LLIEMEDWKG DKVKAHYGGF TVQNEANKYQ ISVNKYRGTA GNALMDGASQ LMGENRTMTI
HNGMFFSTYD RDNDGWLTSD PRKQCSKEDG GGWWYNRCHA ANPNGRYYWG GQYTWDMAKH
GTDDGVVWMN WKGSWYSMRK MSMKIRPFFP QQ*

mutated AA sequence

MEYCRTPCTV SCNIPVVSGK ECEEIIRKGG ETSEMYLIQP DSSVKPYRVY CDMNTENGGW
TVIQNRQDGS VDFGRKWDPY KQGFGNVATN TDGKNYCGLP GEYWLGNDKI SQLTRMGPTE
LLIEMEDWKG DKVKAHYGGF TVQNEANKYQ ISVNKYRGTA GNALMDGASQ LMGENRTMTI
HNGMFFSTYD RDNDGWLTSD PRKQCSKEDG DGWWYNRCHA ANPNGRYYWG GQYTWDMAKH
GTDDGVVWMN WKGSWYSMRK MSMKIRPFFP QQ*

speed

1.24 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems