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: ENST00000375326
Querying Taster for transcript #2: ENST00000415431
MT speed 0 s - this script 3.719165 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
FBP1	disease_causing_automatic	0.999999396188734	simple_aae			0	A177D	single base exchange	rs121918189		show file
FBP1	disease_causing_automatic	0.999999396188734	simple_aae			0	A177D	single base exchange	rs121918189		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999396188734 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM970525)
known disease mutation: rs869 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:97372240G>TN/A show variant in all transcripts IGV

HGNC symbol

FBP1

Ensembl transcript ID

ENST00000375326

Genbank transcript ID

NM_000507

UniProt peptide

P09467

alteration type

single base exchange

alteration region

CDS

DNA changes

c.530C>A
cDNA.727C>A
g.30292C>A

AA changes

A177D Score: 126 explain score(s)

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

177

frameshift

known variant

Reference ID: rs121918189
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs869 (pathogenic for Fructose-biphosphatase deficiency) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970525)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970525)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970525)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.433	0.996
	4.508	1
(flanking)	3.932	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	30292	wt: 0.3812 / mu: 0.3962 (marginal change - not scored)	wt: TGCCACCATGCTGGTCCTTGCCATGGACTGTGGGGTCAACT mu: TGCCACCATGCTGGTCCTTGACATGGACTGTGGGGTCAACT	ttgc\|CATG
Acc marginally increased	30295	wt: 0.8891 / mu: 0.9143 (marginal change - not scored)	wt: CACCATGCTGGTCCTTGCCATGGACTGTGGGGTCAACTGCT mu: CACCATGCTGGTCCTTGACATGGACTGTGGGGTCAACTGCT	ccat\|GGAC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

177

mutated

not conserved

177

Ptroglodytes

all identical

ENSPTRG00000021138

177

Mmulatta

all identical

ENSMMUG00000022536

177

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000069805

177

Ggallus

all identical

ENSGALG00000012613

187

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

not conserved

FBgn0032820

188

Celegans

all conserved

K07A3.1

181

Xtropicalis

all identical

ENSXETG00000033240

119

protein features

start (aa)	end (aa)	feature	details
161	178	STRAND		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1017 / 1017

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

339 / 339

position of stopcodon in wt / mu cDNA

1214 / 1214

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

198 / 198

chromosome

strand

-1

last intron/exon boundary

1023

theoretical NMD boundary in CDS

775

length of CDS

1017

coding sequence (CDS) position

530

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

727

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

30292

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

97372240

original gDNA sequence snippet

TGCCACCATGCTGGTCCTTGCCATGGACTGTGGGGTCAACT

altered gDNA sequence snippet

TGCCACCATGCTGGTCCTTGACATGGACTGTGGGGTCAACT

original cDNA sequence snippet

TGCCACCATGCTGGTCCTTGCCATGGACTGTGGGGTCAACT

altered cDNA sequence snippet

TGCCACCATGCTGGTCCTTGACATGGACTGTGGGGTCAACT

wildtype AA sequence

MADQAPFDTD VNTLTRFVME EGRKARGTGE LTQLLNSLCT AVKAISSAVR KAGIAHLYGI
AGSTNVTGDQ VKKLDVLSND LVMNMLKSSF ATCVLVSEED KHAIIVEPEK RGKYVVCFDP
LDGSSNIDCL VSVGTIFGIY RKKSTDEPSE KDALQPGRNL VAAGYALYGS ATMLVLAMDC
GVNCFMLDPA IGEFILVDKD VKIKKKGKIY SLNEGYARDF DPAVTEYIQR KKFPPDNSAP
YGARYVGSMV ADVHRTLVYG GIFLYPANKK SPNGKLRLLY ECNPMAYVME KAGGMATTGK
EAVLDVIPTD IHQRAPVILG SPDDVLEFLK VYEKHSAQ*

mutated AA sequence

MADQAPFDTD VNTLTRFVME EGRKARGTGE LTQLLNSLCT AVKAISSAVR KAGIAHLYGI
AGSTNVTGDQ VKKLDVLSND LVMNMLKSSF ATCVLVSEED KHAIIVEPEK RGKYVVCFDP
LDGSSNIDCL VSVGTIFGIY RKKSTDEPSE KDALQPGRNL VAAGYALYGS ATMLVLDMDC
GVNCFMLDPA IGEFILVDKD VKIKKKGKIY SLNEGYARDF DPAVTEYIQR KKFPPDNSAP
YGARYVGSMV ADVHRTLVYG GIFLYPANKK SPNGKLRLLY ECNPMAYVME KAGGMATTGK
EAVLDVIPTD IHQRAPVILG SPDDVLEFLK VYEKHSAQ*

speed

0.90 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: 0.999999396188734 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM970525)
known disease mutation: rs869 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:97372240G>TN/A show variant in all transcripts IGV

HGNC symbol

FBP1

Ensembl transcript ID

ENST00000415431

Genbank transcript ID

NM_001127628

UniProt peptide

P09467

alteration type

single base exchange

alteration region

CDS

DNA changes

c.530C>A
cDNA.760C>A
g.30292C>A

AA changes

A177D Score: 126 explain score(s)

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

177

frameshift

known variant

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.433	0.996
	4.508	1
(flanking)	3.932	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	30292	wt: 0.3812 / mu: 0.3962 (marginal change - not scored)	wt: TGCCACCATGCTGGTCCTTGCCATGGACTGTGGGGTCAACT mu: TGCCACCATGCTGGTCCTTGACATGGACTGTGGGGTCAACT	ttgc\|CATG
Acc marginally increased	30295	wt: 0.8891 / mu: 0.9143 (marginal change - not scored)	wt: CACCATGCTGGTCCTTGCCATGGACTGTGGGGTCAACTGCT mu: CACCATGCTGGTCCTTGACATGGACTGTGGGGTCAACTGCT	ccat\|GGAC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

177

mutated

not conserved

177

Ptroglodytes

all identical

ENSPTRG00000021138

177

Mmulatta

all identical

ENSMMUG00000022536

177

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000069805

177

Ggallus

all identical

ENSGALG00000012613

187

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

not conserved

FBgn0032820

188

Celegans

all conserved

K07A3.1

181

Xtropicalis

all identical

ENSXETG00000033240

119

protein features

start (aa)	end (aa)	feature	details
161	178	STRAND		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1017 / 1017

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

339 / 339

position of stopcodon in wt / mu cDNA

1247 / 1247

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

231 / 231

chromosome

strand

-1

last intron/exon boundary

1056

theoretical NMD boundary in CDS

775

length of CDS

1017

coding sequence (CDS) position

530

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

760

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

30292

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

97372240

original gDNA sequence snippet

TGCCACCATGCTGGTCCTTGCCATGGACTGTGGGGTCAACT

altered gDNA sequence snippet

TGCCACCATGCTGGTCCTTGACATGGACTGTGGGGTCAACT

original cDNA sequence snippet

TGCCACCATGCTGGTCCTTGCCATGGACTGTGGGGTCAACT

altered cDNA sequence snippet

TGCCACCATGCTGGTCCTTGACATGGACTGTGGGGTCAACT

wildtype AA sequence

mutated AA sequence

MADQAPFDTD VNTLTRFVME EGRKARGTGE LTQLLNSLCT AVKAISSAVR KAGIAHLYGI
AGSTNVTGDQ VKKLDVLSND LVMNMLKSSF ATCVLVSEED KHAIIVEPEK RGKYVVCFDP
LDGSSNIDCL VSVGTIFGIY RKKSTDEPSE KDALQPGRNL VAAGYALYGS ATMLVLDMDC
GVNCFMLDPA IGEFILVDKD VKIKKKGKIY SLNEGYARDF DPAVTEYIQR KKFPPDNSAP
YGARYVGSMV ADVHRTLVYG GIFLYPANKK SPNGKLRLLY ECNPMAYVME KAGGMATTGK
EAVLDVIPTD IHQRAPVILG SPDDVLEFLK VYEKHSAQ*

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