MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000252486
MT speed 0 s - this script 2.432235 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
APOE	disease_causing_automatic	0.968183155272308	simple_aae		affected	0	R154S	single base exchange	rs121918393		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.968183155272308 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM880007)
known disease mutation at this position (HGMD CM940076)
known disease mutation: rs17850 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:45412013C>AN/A show variant in all transcripts IGV

HGNC symbol

APOE

Ensembl transcript ID

ENST00000252486

Genbank transcript ID

NM_000041

UniProt peptide

P02649

alteration type

single base exchange

alteration region

CDS

DNA changes

c.460C>A
cDNA.571C>A
g.3003C>A

AA changes

R154S Score: 110 explain score(s)

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

154

frameshift

known variant

Reference ID: rs121918393
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs17850 (pathogenic for Familial type 3 hyperlipoproteinemia) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM880007)

known disease mutation at this position, please check HGMD for details (HGMD ID CM880007)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940076)

known disease mutation at this position, please check HGMD for details (HGMD ID CM880007)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940076)
known disease mutation at this position, please check HGMD for details (HGMD ID CM880007)

known disease mutation at this position, please check HGMD for details (HGMD ID CM880007)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940076)
known disease mutation at this position, please check HGMD for details (HGMD ID CM880007)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940076)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.221	0.086
	1.627	0.595
(flanking)	3.133	0.634

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 gained	2998	0.64	mu: GCTGCGGGTGAGCCT	TGCG\|ggtg
Donor gained	3003	0.32	mu: GGGTGAGCCTCGCCT	GTGA\|gcct

distance from splice site

224

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

154

mutated

not conserved

154

Ptroglodytes

all identical

ENSPTRG00000011127

154

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000002985

146

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000000934

155

Drerio

all identical

ENSDARG00000040295

141

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000019317

143

protein features

start (aa)	end (aa)	feature	details
80	255	REGION	8 X 22 AA approximate tandem repeats.	lost
146	167	REPEAT	4.	lost
149	179	HELIX		lost
158	168	REGION	LDL receptor binding (Potential).	might get lost (downstream of altered splice site)
162	165	REGION	Heparin-binding.	might get lost (downstream of altered splice site)
168	189	REPEAT	5.	might get lost (downstream of altered splice site)
180	182	TURN		might get lost (downstream of altered splice site)
187	190	TURN		might get lost (downstream of altered splice site)
190	211	REPEAT	6.	might get lost (downstream of altered splice site)
193	198	HELIX		might get lost (downstream of altered splice site)
200	202	STRAND		might get lost (downstream of altered splice site)
209	217	HELIX		might get lost (downstream of altered splice site)
212	212	CARBOHYD	O-linked (GalNAc...).	might get lost (downstream of altered splice site)
212	233	REPEAT	7.	might get lost (downstream of altered splice site)
228	241	HELIX		might get lost (downstream of altered splice site)
229	236	REGION	Heparin-binding.	might get lost (downstream of altered splice site)
234	255	REPEAT	8.	might get lost (downstream of altered splice site)
257	283	HELIX		might get lost (downstream of altered splice site)
286	303	HELIX		might get lost (downstream of altered splice site)
307	307	CARBOHYD	O-linked (GalNAc...).	might get lost (downstream of altered splice site)
307	309	STRAND		might get lost (downstream of altered splice site)
308	308	CARBOHYD	O-linked (GalNAc...).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

954 / 954

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

318 / 318

position of stopcodon in wt / mu cDNA

1065 / 1065

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

112 / 112

chromosome

strand

last intron/exon boundary

348

theoretical NMD boundary in CDS

186

length of CDS

954

coding sequence (CDS) position

460

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

571

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

3003

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

45412013

original gDNA sequence snippet

GCACCGAGGAGCTGCGGGTGCGCCTCGCCTCCCACCTGCGC

altered gDNA sequence snippet

GCACCGAGGAGCTGCGGGTGAGCCTCGCCTCCCACCTGCGC

original cDNA sequence snippet

GCACCGAGGAGCTGCGGGTGCGCCTCGCCTCCCACCTGCGC

altered cDNA sequence snippet

GCACCGAGGAGCTGCGGGTGAGCCTCGCCTCCCACCTGCGC

wildtype AA sequence

MKVLWAALLV TFLAGCQAKV EQAVETEPEP ELRQQTEWQS GQRWELALGR FWDYLRWVQT
LSEQVQEELL SSQVTQELRA LMDETMKELK AYKSELEEQL TPVAEETRAR LSKELQAAQA
RLGADMEDVC GRLVQYRGEV QAMLGQSTEE LRVRLASHLR KLRKRLLRDA DDLQKRLAVY
QAGAREGAER GLSAIRERLG PLVEQGRVRA ATVGSLAGQP LQERAQAWGE RLRARMEEMG
SRTRDRLDEV KEQVAEVRAK LEEQAQQIRL QAEAFQARLK SWFEPLVEDM QRQWAGLVEK
VQAAVGTSAA PVPSDNH*

mutated AA sequence

MKVLWAALLV TFLAGCQAKV EQAVETEPEP ELRQQTEWQS GQRWELALGR FWDYLRWVQT
LSEQVQEELL SSQVTQELRA LMDETMKELK AYKSELEEQL TPVAEETRAR LSKELQAAQA
RLGADMEDVC GRLVQYRGEV QAMLGQSTEE LRVSLASHLR KLRKRLLRDA DDLQKRLAVY
QAGAREGAER GLSAIRERLG PLVEQGRVRA ATVGSLAGQP LQERAQAWGE RLRARMEEMG
SRTRDRLDEV KEQVAEVRAK LEEQAQQIRL QAEAFQARLK SWFEPLVEDM QRQWAGLVEK
VQAAVGTSAA PVPSDNH*

speed

0.38 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

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

Problems