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: ENST00000302068
Querying Taster for transcript #2: ENST00000509493
MT speed 0 s - this script 3.511856 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
FGB	disease_causing_automatic	0.999999737380955	simple_aae			0	L383R	single base exchange	rs121909621		show file
FGB	disease_causing_automatic	0.999999999694732	simple_aae			0	L164R	single base exchange	rs121909621		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999737380955 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM000156)
known disease mutation: rs16389 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr4:155490855T>GN/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.1148T>G
cDNA.1211T>G
g.6748T>G

AA changes

L383R Score: 102 explain score(s)

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

383

frameshift

known variant

Reference ID: rs121909621
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs16389 (pathogenic for Afibrinogenemia, congenital) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM000156)

known disease mutation at this position, please check HGMD for details (HGMD ID CM000156)
known disease mutation at this position, please check HGMD for details (HGMD ID CM000156)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H2AZ, Histone, Histone 2A variant Z

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.196	1
	5.19	1
(flanking)	0.008	0.965

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

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

383

mutated

not conserved

383

Ptroglodytes

all identical

ENSPTRG00000016534

366

Mmulatta

all identical

ENSMMUG00000021302

383

Fcatus

all identical

ENSFCAG00000013254

382

Mmusculus

all identical

ENSMUSG00000033831

373

Ggallus

all identical

ENSGALG00000009262

374

Trubripes

not conserved

ENSTRUG00000002645

388

Drerio

not conserved

ENSDARG00000008969

377

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000022431

383

protein features

start (aa)	end (aa)	feature	details
232	488	DOMAIN	Fibrinogen C-terminal.	lost
382	385	HELIX		lost

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

1148

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

1211

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

6748

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

155490855

original gDNA sequence snippet

AGGAACAGCCGGTAATGCCCTCATGGATGGAGCATCTCAGC

altered gDNA sequence snippet

AGGAACAGCCGGTAATGCCCGCATGGATGGAGCATCTCAGC

original cDNA sequence snippet

AGGAACAGCCGGTAATGCCCTCATGGATGGAGCATCTCAGC

altered cDNA sequence snippet

AGGAACAGCCGGTAATGCCCGCATGGATGGAGCATCTCAGC

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 NARMDGASQL MGENRTMTIH NGMFFSTYDR DNDGWLTSDP
RKQCSKEDGG GWWYNRCHAA NPNGRYYWGG QYTWDMAKHG TDDGVVWMNW KGSWYSMRKM
SMKIRPFFPQ Q*

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: simple_aae, prob: 0.999999999694732 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM000156)
known disease mutation: rs16389 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr4:155490855T>GN/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.491T>G
cDNA.765T>G
g.6748T>G

AA changes

L164R Score: 102 explain score(s)

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

164

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H2AZ, Histone, Histone 2A variant Z

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.196	1
	5.19	1
(flanking)	0.008	0.965

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

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

164

mutated

not conserved

164

Ptroglodytes

all identical

ENSPTRG00000016534

366

Mmulatta

all identical

ENSMMUG00000021302

383

Fcatus

all identical

ENSFCAG00000013254

382

Mmusculus

all identical

ENSMUSG00000033831

373

Ggallus

all identical

ENSGALG00000009262

374

Trubripes

not conserved

ENSTRUG00000002645

388

Drerio

not conserved

ENSDARG00000008969

377

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000022431

383

protein features

start (aa)	end (aa)	feature	details
147	167	HELIX		lost
157	222	COILED	Potential.	lost
163	164	SITE	Cleavage; by plasmin; to break down fibrin clots.	lost

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

491

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

765

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

6748

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

155490855

original gDNA sequence snippet

AGGAACAGCCGGTAATGCCCTCATGGATGGAGCATCTCAGC

altered gDNA sequence snippet

AGGAACAGCCGGTAATGCCCGCATGGATGGAGCATCTCAGC

original cDNA sequence snippet

AGGAACAGCCGGTAATGCCCTCATGGATGGAGCATCTCAGC

altered cDNA sequence snippet

AGGAACAGCCGGTAATGCCCGCATGGATGGAGCATCTCAGC

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 GNARMDGASQ LMGENRTMTI
HNGMFFSTYD RDNDGWLTSD PRKQCSKEDG GGWWYNRCHA ANPNGRYYWG GQYTWDMAKH
GTDDGVVWMN WKGSWYSMRK MSMKIRPFFP QQ*

speed

0.10 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems