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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000254108
Querying Taster for transcript #2: ENST00000380244
Querying Taster for transcript #3: ENST00000568685
MT speed 0 s - this script 4.246262 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
FUS	disease_causing_automatic	0.962491256665302	simple_aae		affected	0	R522H	single base exchange	rs121909671		show file
FUS	disease_causing_automatic	0.993646262171402	simple_aae		affected	0	R520H	single base exchange	rs121909671		show file
FUS	disease_causing_automatic	0.993646262171402	simple_aae		affected	0	R521H	single base exchange	rs121909671		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.962491256665302 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM091091)
known disease mutation at this position (HGMD CM104703)
known disease mutation: rs16225 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr16:31202740G>AN/A show variant in all transcripts IGV

HGNC symbol

FUS

Ensembl transcript ID

ENST00000568685

Genbank transcript ID

N/A

UniProt peptide

P35637

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1565G>A
cDNA.1629G>A
g.11310G>A

AA changes

R522H Score: 29 explain score(s)

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

522

frameshift

known variant

Reference ID: rs121909671
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs16225 (pathogenic for Amyotrophic lateral sclerosis 6, with or without frontotemporal dementia) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM091091)

known disease mutation at this position, please check HGMD for details (HGMD ID CM091091)
known disease mutation at this position, please check HGMD for details (HGMD ID CM104703)

known disease mutation at this position, please check HGMD for details (HGMD ID CM091091)
known disease mutation at this position, please check HGMD for details (HGMD ID CM104703)
known disease mutation at this position, please check HGMD for details (HGMD ID CM091091)

known disease mutation at this position, please check HGMD for details (HGMD ID CM091091)
known disease mutation at this position, please check HGMD for details (HGMD ID CM104703)
known disease mutation at this position, please check HGMD for details (HGMD ID CM091091)
known disease mutation at this position, please check HGMD for details (HGMD ID CM104703)

regulatory features

PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.165	0.967
	1.239	0.971
(flanking)	0.103	0.966

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 marginally increased	11313	wt: 0.9717 / mu: 0.9902 (marginal change - not scored)	wt: TCGCAGGGAGAGGCC mu: TCACAGGGAGAGGCC	GCAG\|ggag
Donor marginally increased	11312	wt: 0.8577 / mu: 0.8853 (marginal change - not scored)	wt: ATCGCAGGGAGAGGC mu: ATCACAGGGAGAGGC	CGCA\|ggga
Donor increased	11311	wt: 0.31 / mu: 0.65	wt: GATCGCAGGGAGAGG mu: GATCACAGGGAGAGG	TCGC\|aggg
Donor increased	11314	wt: 0.87 / mu: 0.96	wt: CGCAGGGAGAGGCCG mu: CACAGGGAGAGGCCG	CAGG\|gaga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

522

mutated

not conserved

522

Ptroglodytes

all identical

ENSPTRG00000008038

515

Mmulatta

all identical

ENSMMUG00000019637

517

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000030795

513

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000037968

537

Dmelanogaster

all identical

FBgn0011571

374

Celegans

no alignment

C27H5.3

n/a

Xtropicalis

all identical

ENSXETG00000001951

534

protein features

start (aa)	end (aa)	feature	details
371	526	COMPBIAS	Arg/Gly-rich.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1584 / 1584

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

528 / 528

position of stopcodon in wt / mu cDNA

1648 / 1648

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

65 / 65

chromosome

strand

last intron/exon boundary

1609

theoretical NMD boundary in CDS

1494

length of CDS

1584

coding sequence (CDS) position

1565

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

1629

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

11310

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

31202740

original gDNA sequence snippet

GGGTGAGCACAGACAGGATCGCAGGGAGAGGCCGTATTAAT

altered gDNA sequence snippet

GGGTGAGCACAGACAGGATCACAGGGAGAGGCCGTATTAAT

original cDNA sequence snippet

GGGTGAGCACAGACAGGATCGCAGGGAGAGGCCGTATTAAT

altered cDNA sequence snippet

GGGTGAGCACAGACAGGATCACAGGGAGAGGCCGTATTAAT

wildtype AA sequence

MASNDYTQQA TQSYGAYPTQ PGQGYSQQSS QPYGQQSYSG YSQSTDTSGY GQSSYSSYGQ
SQNTGYGTQS TPQGYGSTGG YGSSQSSQSS YGQQSSYPGY GQQPAPSSTS GSYGSSSQSS
SYGQPQSGSY SQQPSYGGQQ QSYGQQQSYN PPQGYGQQNQ YNSSSGGGGG GGGGGNYGQD
QSSMSSGGGS GGGYGNQDQS GGGGSGGYGQ QDRGGRGRGG SGGGGGGGGG GYNRSSGGYE
PRGRGGGRGG RGGMGGSDRG GFNKFGGPRD QGSRHDSAEQ DNSDNNTIFV QGLGENVTIE
SVADYFKQIG IIKTNKKTGQ PMINLYTDRE TGKLKGEATV SFDDPPSAKA AIDWFDGKEF
SGNPIKVSFA TRRADFNRGG GNGRGGRGRG GPMGRGGYGG GGSGGGGRGG FPSGGGGGGG
QQRAGDWKCP NPTCENMNFS WRNECNQCKA PKPDGPGGGP GGSHMGGNYG DDRRGGRGGY
DRGGYRGRGG DRGGFRGGRG GGDRGGFGPG KMDSRGEHRQ DRRERPY*

mutated AA sequence

speed

0.93 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: 0.993646262171402 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM091091)
known disease mutation at this position (HGMD CM104703)
known disease mutation: rs16225 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr16:31202740G>AN/A show variant in all transcripts IGV

HGNC symbol

FUS

Ensembl transcript ID

ENST00000380244

Genbank transcript ID

N/A

UniProt peptide

P35637

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1559G>A
cDNA.1635G>A
g.11310G>A

AA changes

R520H Score: 29 explain score(s)

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

520

frameshift

known variant

regulatory features

PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.165	0.967
	1.239	0.971
(flanking)	0.103	0.966

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 marginally increased	11313	wt: 0.9717 / mu: 0.9902 (marginal change - not scored)	wt: TCGCAGGGAGAGGCC mu: TCACAGGGAGAGGCC	GCAG\|ggag
Donor marginally increased	11312	wt: 0.8577 / mu: 0.8853 (marginal change - not scored)	wt: ATCGCAGGGAGAGGC mu: ATCACAGGGAGAGGC	CGCA\|ggga
Donor increased	11311	wt: 0.31 / mu: 0.65	wt: GATCGCAGGGAGAGG mu: GATCACAGGGAGAGG	TCGC\|aggg
Donor increased	11314	wt: 0.87 / mu: 0.96	wt: CGCAGGGAGAGGCCG mu: CACAGGGAGAGGCCG	CAGG\|gaga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

520

mutated

not conserved

520

Ptroglodytes

all identical

ENSPTRG00000008038

515

Mmulatta

all identical

ENSMMUG00000019637

517

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000030795

513

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000037968

537

Dmelanogaster

all identical

FBgn0011571

374

Celegans

no alignment

C27H5.3

n/a

Xtropicalis

all identical

ENSXETG00000001951

534

protein features

start (aa)	end (aa)	feature	details
371	526	COMPBIAS	Arg/Gly-rich.	lost
514	521	HELIX		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1578 / 1578

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

526 / 526

position of stopcodon in wt / mu cDNA

1654 / 1654

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

77 / 77

chromosome

strand

last intron/exon boundary

1615

theoretical NMD boundary in CDS

1488

length of CDS

1578

coding sequence (CDS) position

1559

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

1635

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

11310

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

31202740

original gDNA sequence snippet

GGGTGAGCACAGACAGGATCGCAGGGAGAGGCCGTATTAAT

altered gDNA sequence snippet

GGGTGAGCACAGACAGGATCACAGGGAGAGGCCGTATTAAT

original cDNA sequence snippet

GGGTGAGCACAGACAGGATCGCAGGGAGAGGCCGTATTAAT

altered cDNA sequence snippet

GGGTGAGCACAGACAGGATCACAGGGAGAGGCCGTATTAAT

wildtype AA sequence

MASNDYTQQA TQSYGAYPTQ PGQGYSQQSS QPYGQQSYSG YSQSTDTSGY GQSSYSSYGQ
SQNSYGTQST PQGYGSTGGY GSSQSSQSSY GQQSSYPGYG QQPAPSSTSG SYGSSSQSSS
YGQPQSGSYS QQPSYGGQQQ SYGQQQSYNP PQGYGQQNQY NSSSGGGGGG GGGGNYGQDQ
SSMSSGGGSG GGYGNQDQSG GGGSGGYGQQ DRGGRGRGGS GGGGGGGGGG YNRSSGGYEP
RGRGGGRGGR GGMGGSDRGG FNKFGGPRDQ GSRHDSEQDN SDNNTIFVQG LGENVTIESV
ADYFKQIGII KTNKKTGQPM INLYTDRETG KLKGEATVSF DDPPSAKAAI DWFDGKEFSG
NPIKVSFATR RADFNRGGGN GRGGRGRGGP MGRGGYGGGG SGGGGRGGFP SGGGGGGGQQ
RAGDWKCPNP TCENMNFSWR NECNQCKAPK PDGPGGGPGG SHMGGNYGDD RRGGRGGYDR
GGYRGRGGDR GGFRGGRGGG DRGGFGPGKM DSRGEHRQDR RERPY*

mutated AA sequence

speed

1.24 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.993646262171402 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM091091)
known disease mutation at this position (HGMD CM104703)
known disease mutation: rs16225 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr16:31202740G>AN/A show variant in all transcripts IGV

HGNC symbol

FUS

Ensembl transcript ID

ENST00000254108

Genbank transcript ID

NM_001170634

UniProt peptide

P35637

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1562G>A
cDNA.1667G>A
g.11310G>A

AA changes

R521H Score: 29 explain score(s)

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

521

frameshift

known variant

regulatory features

PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.165	0.967
	1.239	0.971
(flanking)	0.103	0.966

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 marginally increased	11313	wt: 0.9717 / mu: 0.9902 (marginal change - not scored)	wt: TCGCAGGGAGAGGCC mu: TCACAGGGAGAGGCC	GCAG\|ggag
Donor marginally increased	11312	wt: 0.8577 / mu: 0.8853 (marginal change - not scored)	wt: ATCGCAGGGAGAGGC mu: ATCACAGGGAGAGGC	CGCA\|ggga
Donor increased	11311	wt: 0.31 / mu: 0.65	wt: GATCGCAGGGAGAGG mu: GATCACAGGGAGAGG	TCGC\|aggg
Donor increased	11314	wt: 0.87 / mu: 0.96	wt: CGCAGGGAGAGGCCG mu: CACAGGGAGAGGCCG	CAGG\|gaga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

521

mutated

not conserved

521

Ptroglodytes

all identical

ENSPTRG00000008038

515

Mmulatta

all identical

ENSMMUG00000019637

517

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000030795

513

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000037968

537

Dmelanogaster

all identical

FBgn0011571

374

Celegans

no alignment

C27H5.3

n/a

Xtropicalis

all identical

ENSXETG00000001951

534

protein features

start (aa)	end (aa)	feature	details
371	526	COMPBIAS	Arg/Gly-rich.	lost
514	521	HELIX		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1581 / 1581

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

527 / 527

position of stopcodon in wt / mu cDNA

1686 / 1686

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

106 / 106

chromosome

strand

last intron/exon boundary

1647

theoretical NMD boundary in CDS

1491

length of CDS

1581

coding sequence (CDS) position

1562

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

1667

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

11310

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

31202740

original gDNA sequence snippet

GGGTGAGCACAGACAGGATCGCAGGGAGAGGCCGTATTAAT

altered gDNA sequence snippet

GGGTGAGCACAGACAGGATCACAGGGAGAGGCCGTATTAAT

original cDNA sequence snippet

GGGTGAGCACAGACAGGATCGCAGGGAGAGGCCGTATTAAT

altered cDNA sequence snippet

GGGTGAGCACAGACAGGATCACAGGGAGAGGCCGTATTAAT

wildtype AA sequence

MASNDYTQQA TQSYGAYPTQ PGQGYSQQSS QPYGQQSYSG YSQSTDTSGY GQSSYSSYGQ
SQNTGYGTQS TPQGYGSTGG YGSSQSSQSS YGQQSSYPGY GQQPAPSSTS GSYGSSSQSS
SYGQPQSGSY SQQPSYGGQQ QSYGQQQSYN PPQGYGQQNQ YNSSSGGGGG GGGGGNYGQD
QSSMSSGGGS GGGYGNQDQS GGGGSGGYGQ QDRGGRGRGG SGGGGGGGGG GYNRSSGGYE
PRGRGGGRGG RGGMGGSDRG GFNKFGGPRD QGSRHDSEQD NSDNNTIFVQ GLGENVTIES
VADYFKQIGI IKTNKKTGQP MINLYTDRET GKLKGEATVS FDDPPSAKAA IDWFDGKEFS
GNPIKVSFAT RRADFNRGGG NGRGGRGRGG PMGRGGYGGG GSGGGGRGGF PSGGGGGGGQ
QRAGDWKCPN PTCENMNFSW RNECNQCKAP KPDGPGGGPG GSHMGGNYGD DRRGGRGGYD
RGGYRGRGGD RGGFRGGRGG GDRGGFGPGK MDSRGEHRQD RRERPY*

mutated AA sequence

MASNDYTQQA TQSYGAYPTQ PGQGYSQQSS QPYGQQSYSG YSQSTDTSGY GQSSYSSYGQ
SQNTGYGTQS TPQGYGSTGG YGSSQSSQSS YGQQSSYPGY GQQPAPSSTS GSYGSSSQSS
SYGQPQSGSY SQQPSYGGQQ QSYGQQQSYN PPQGYGQQNQ YNSSSGGGGG GGGGGNYGQD
QSSMSSGGGS GGGYGNQDQS GGGGSGGYGQ QDRGGRGRGG SGGGGGGGGG GYNRSSGGYE
PRGRGGGRGG RGGMGGSDRG GFNKFGGPRD QGSRHDSEQD NSDNNTIFVQ GLGENVTIES
VADYFKQIGI IKTNKKTGQP MINLYTDRET GKLKGEATVS FDDPPSAKAA IDWFDGKEFS
GNPIKVSFAT RRADFNRGGG NGRGGRGRGG PMGRGGYGGG GSGGGGRGGF PSGGGGGGGQ
QRAGDWKCPN PTCENMNFSW RNECNQCKAP KPDGPGGGPG GSHMGGNYGD DRRGGRGGYD
RGGYRGRGGD RGGFRGGRGG GDRGGFGPGK MDSRGEHRQD HRERPY*

speed

0.95 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems