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 2.620812 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
APOE	disease_causing_automatic	4.45018402400156e-06	simple_aae			0	R246C	single base exchange	rs121918395		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 4.45018402400156e-06 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM900022)
known disease mutation: rs17859 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:45412289C>TN/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.736C>T
cDNA.847C>T
g.3279C>T

AA changes

R246C Score: 180 explain score(s)

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

246

frameshift

known variant

Reference ID: rs121918395

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	3	3

known disease mutation: rs17859 (pathogenic for APOE2-DUNEDIN) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM900022)

known disease mutation at this position, please check HGMD for details (HGMD ID CM900022)
known disease mutation at this position, please check HGMD for details (HGMD ID CM900022)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.029	0.055
	0.332	0.019
(flanking)	-0.481	0.006

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	3273	wt: 0.3523 / mu: 0.4103 (marginal change - not scored)	wt: GGACCCGCGACCGCC mu: GGACCCGCGACTGCC	ACCC\|gcga

distance from splice site

362

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

246

mutated

not conserved

246

Ptroglodytes

all identical

ENSPTRG00000011127

246

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000002985

238

Ggallus

no homologue

Trubripes

not conserved

ENSTRUG00000000934

247

Drerio

not conserved

ENSDARG00000040295

215

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000019317

220

protein features

start (aa)	end (aa)	feature	details
80	255	REGION	8 X 22 AA approximate tandem repeats.	lost
234	255	REPEAT	8.	lost

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

736

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

847

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

3279

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

45412289

original gDNA sequence snippet

TGGGCAGCCGGACCCGCGACCGCCTGGACGAGGTGAAGGAG

altered gDNA sequence snippet

TGGGCAGCCGGACCCGCGACTGCCTGGACGAGGTGAAGGAG

original cDNA sequence snippet

TGGGCAGCCGGACCCGCGACCGCCTGGACGAGGTGAAGGAG

altered cDNA sequence snippet

TGGGCAGCCGGACCCGCGACTGCCTGGACGAGGTGAAGGAG

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 LRVRLASHLR KLRKRLLRDA DDLQKRLAVY
QAGAREGAER GLSAIRERLG PLVEQGRVRA ATVGSLAGQP LQERAQAWGE RLRARMEEMG
SRTRDCLDEV KEQVAEVRAK LEEQAQQIRL QAEAFQARLK SWFEPLVEDM QRQWAGLVEK
VQAAVGTSAA PVPSDNH*

speed

0.61 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