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: ENST00000370038
Querying Taster for transcript #2: ENST00000415641
MT speed 0 s - this script 3.662047 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
NBPF4	polymorphism	6.14952533339874e-13	simple_aae		affected		A467V	single base exchange			show file
NBPF4	polymorphism	6.14952533339874e-13	simple_aae		affected		A467V	single base exchange			show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999385 (explain)

Summary

amino acid sequence changed
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:108774901G>AN/A show variant in all transcripts IGV

HGNC symbol

NBPF4

Ensembl transcript ID

ENST00000370038

Genbank transcript ID

N/A

UniProt peptide

Q96M43

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1400C>T
cDNA.1400C>T
g.11803C>T

AA changes

A467V Score: 64 explain score(s)

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

467

frameshift

known variant

Variant was neither found in ExAC nor 1000G.
Search ExAC.

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.288	0
	-0.415	0
(flanking)	-0.823	0

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	11812	wt: 0.47 / mu: 0.67	wt: GGATCAGCTTGCCTGCTCTGCTCTGGATGTAGCCTGTGAGT mu: GGATCAGCTTGTCTGCTCTGCTCTGGATGTAGCCTGTGAGT	ctgc\|TCTG
Acc increased	11814	wt: 0.67 / mu: 0.77	wt: ATCAGCTTGCCTGCTCTGCTCTGGATGTAGCCTGTGAGTAC mu: ATCAGCTTGTCTGCTCTGCTCTGGATGTAGCCTGTGAGTAC	gctc\|TGGA
Acc increased	11811	wt: 0.24 / mu: 0.47	wt: AGGATCAGCTTGCCTGCTCTGCTCTGGATGTAGCCTGTGAG mu: AGGATCAGCTTGTCTGCTCTGCTCTGGATGTAGCCTGTGAG	tctg\|CTCT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

467

mutated

not conserved

467

Ptroglodytes

all identical

ENSPTRG00000001028

405

Mmulatta

no homologue

Fcatus

not conserved

ENSFCAG00000009594

276

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
400	503	DOMAIN	NBPF 3.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1917 / 1917

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

639 / 639

position of stopcodon in wt / mu cDNA

1917 / 1917

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

1 / 1

chromosome

strand

-1

last intron/exon boundary

1876

theoretical NMD boundary in CDS

1825

length of CDS

1917

coding sequence (CDS) position

1400

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

1400

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

11803

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

108774901

original gDNA sequence snippet

CTCATTGGAGGATCAGCTTGCCTGCTCTGCTCTGGATGTAG

altered gDNA sequence snippet

CTCATTGGAGGATCAGCTTGTCTGCTCTGCTCTGGATGTAG

original cDNA sequence snippet

CTCATTGGAGGATCAGCTTGCCTGCTCTGCTCTGGATGTAG

altered cDNA sequence snippet

CTCATTGGAGGATCAGCTTGTCTGCTCTGCTCTGGATGTAG

wildtype AA sequence

MVVSADPLSS ERAEMNILEI NQELRSQLAE SNQQFRDLKE KFLITQATAY SLANQLKKYK
CEEYKDIIDS VLRDELQSME KLAEKLRQAE ELRQYKALVH SQAKELTQLR EKLREGRDAS
RWLNKHLKTL LTPDDPDKSQ GQDLREQLAE GHRLAEHLVH KLSPENDEDE DEDEDDKDEE
VEKVQESPAP REVQKTEEKE VPQDSLEECA VTCSNSHNPS NSNQPHRSTK ITFKEHEVDS
ALVVESEHPH DEEEEALNIP PENQNDHEEE EGKAPVPPRH HDKSNSYRHR EVSFLALDEQ
KVCSAQDVAR DYSNPKWDET SLGFLEKQSD LEEVKGQETV APRLSRGPLR VDKHEIPQES
LDGCCLTPSI LPDLTPSYHP YWSTLYSFED KQVSLALVDK IKKDQEEIED QSPPCPRLSQ
ELPEVKEQEV PEDSVNEVYL TPSVHHDVSD CHQPYSSTLS SLEDQLACSA LDVASPTEAA
CPQGTWSGDL SHHQSEVQVS QAQLEPSTLV PSCLRLQLDQ GFHCGNGLAQ RGLSSTTCSF
SANADSGNQW PFQELVLEPS LGMKNPPQLE DDALEGSASN TQGRQVTGRI RASLVLILKT
IRRRLPFSKW RLAFRFAGPH AESAEIPNTA GRTQRMAG*

mutated AA sequence

MVVSADPLSS ERAEMNILEI NQELRSQLAE SNQQFRDLKE KFLITQATAY SLANQLKKYK
CEEYKDIIDS VLRDELQSME KLAEKLRQAE ELRQYKALVH SQAKELTQLR EKLREGRDAS
RWLNKHLKTL LTPDDPDKSQ GQDLREQLAE GHRLAEHLVH KLSPENDEDE DEDEDDKDEE
VEKVQESPAP REVQKTEEKE VPQDSLEECA VTCSNSHNPS NSNQPHRSTK ITFKEHEVDS
ALVVESEHPH DEEEEALNIP PENQNDHEEE EGKAPVPPRH HDKSNSYRHR EVSFLALDEQ
KVCSAQDVAR DYSNPKWDET SLGFLEKQSD LEEVKGQETV APRLSRGPLR VDKHEIPQES
LDGCCLTPSI LPDLTPSYHP YWSTLYSFED KQVSLALVDK IKKDQEEIED QSPPCPRLSQ
ELPEVKEQEV PEDSVNEVYL TPSVHHDVSD CHQPYSSTLS SLEDQLVCSA LDVASPTEAA
CPQGTWSGDL SHHQSEVQVS QAQLEPSTLV PSCLRLQLDQ GFHCGNGLAQ RGLSSTTCSF
SANADSGNQW PFQELVLEPS LGMKNPPQLE DDALEGSASN TQGRQVTGRI RASLVLILKT
IRRRLPFSKW RLAFRFAGPH AESAEIPNTA GRTQRMAG*

speed

0.97 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

polymorphism

Model: simple_aae, prob: 0.999999999999385 (explain)

Summary

amino acid sequence changed
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:108774901G>AN/A show variant in all transcripts IGV

HGNC symbol

NBPF4

Ensembl transcript ID

ENST00000415641

Genbank transcript ID

NM_001143989

UniProt peptide

Q96M43

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1400C>T
cDNA.1618C>T
g.11803C>T

AA changes

A467V Score: 64 explain score(s)

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

467

frameshift

known variant

Variant was neither found in ExAC nor 1000G.
Search ExAC.

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.288	0
	-0.415	0
(flanking)	-0.823	0

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	11812	wt: 0.47 / mu: 0.67	wt: GGATCAGCTTGCCTGCTCTGCTCTGGATGTAGCCTGTGAGT mu: GGATCAGCTTGTCTGCTCTGCTCTGGATGTAGCCTGTGAGT	ctgc\|TCTG
Acc increased	11814	wt: 0.67 / mu: 0.77	wt: ATCAGCTTGCCTGCTCTGCTCTGGATGTAGCCTGTGAGTAC mu: ATCAGCTTGTCTGCTCTGCTCTGGATGTAGCCTGTGAGTAC	gctc\|TGGA
Acc increased	11811	wt: 0.24 / mu: 0.47	wt: AGGATCAGCTTGCCTGCTCTGCTCTGGATGTAGCCTGTGAG mu: AGGATCAGCTTGTCTGCTCTGCTCTGGATGTAGCCTGTGAG	tctg\|CTCT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

467

mutated

not conserved

467

Ptroglodytes

all identical

ENSPTRG00000001028

405

Mmulatta

no homologue

Fcatus

not conserved

ENSFCAG00000009594

276

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
400	503	DOMAIN	NBPF 3.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1917 / 1917

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

639 / 639

position of stopcodon in wt / mu cDNA

2135 / 2135

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

219 / 219

chromosome

strand

-1

last intron/exon boundary

2094

theoretical NMD boundary in CDS

1825

length of CDS

1917

coding sequence (CDS) position

1400

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

1618

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

11803

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

108774901

original gDNA sequence snippet

CTCATTGGAGGATCAGCTTGCCTGCTCTGCTCTGGATGTAG

altered gDNA sequence snippet

CTCATTGGAGGATCAGCTTGTCTGCTCTGCTCTGGATGTAG

original cDNA sequence snippet

CTCATTGGAGGATCAGCTTGCCTGCTCTGCTCTGGATGTAG

altered cDNA sequence snippet

CTCATTGGAGGATCAGCTTGTCTGCTCTGCTCTGGATGTAG

wildtype AA sequence

mutated AA sequence

MVVSADPLSS ERAEMNILEI NQELRSQLAE SNQQFRDLKE KFLITQATAY SLANQLKKYK
CEEYKDIIDS VLRDELQSME KLAEKLRQAE ELRQYKALVH SQAKELTQLR EKLREGRDAS
RWLNKHLKTL LTPDDPDKSQ GQDLREQLAE GHRLAEHLVH KLSPENDEDE DEDEDDKDEE
VEKVQESPAP REVQKTEEKE VPQDSLEECA VTCSNSHNPS NSNQPHRSTK ITFKEHEVDS
ALVVESEHPH DEEEEALNIP PENQNDHEEE EGKAPVPPRH HDKSNSYRHR EVSFLALDEQ
KVCSAQDVAR DYSNPKWDET SLGFLEKQSD LEEVKGQETV APRLSRGPLR VDKHEIPQES
LDGCCLTPSI LPDLTPSYHP YWSTLYSFED KQVSLALVDK IKKDQEEIED QSPPCPRLSQ
ELPEVKEQEV PEDSVNEVYL TPSVHHDVSD CHQPYSSTLS SLEDQLVCSA LDVASPTEAA
CPQGTWSGDL SHHQSEVQVS QAQLEPSTLV PSCLRLQLDQ GFHCGNGLAQ RGLSSTTCSF
SANADSGNQW PFQELVLEPS LGMKNPPQLE DDALEGSASN TQGRQVTGRI RASLVLILKT
IRRRLPFSKW RLAFRFAGPH AESAEIPNTA GRTQRMAG*

speed

0.75 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems