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: ENST00000313640
Querying Taster for transcript #2: ENST00000313624
MT speed 0 s - this script 3.175723 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
EPSTI1	polymorphism_automatic	0.00514176505355002	simple_aae		affected		N399K	single base exchange	rs1044856		show file
EPSTI1	polymorphism_automatic	0.999999994210631	without_aae		affected			single base exchange	rs1044856		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99485823494645 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr13:43462422A>TN/A show variant in all transcripts IGV

HGNC symbol

EPSTI1

Ensembl transcript ID

ENST00000313640

Genbank transcript ID

NM_001002264

UniProt peptide

Q96J88

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1197T>A
cDNA.1262T>A
g.103986T>A

AA changes

N399K Score: 94 explain score(s)

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

399

frameshift

known variant

Reference ID: rs1044856

database	homozygous (T/T)	heterozygous	allele carriers
1000G	99	590	689
ExAC	4943	22140	27083

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.235	0.913
	0.055	0.913
(flanking)	2.728	0.935

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	103981	0.60	mu: TCATATTTAAACTCT	ATAT\|ttaa

distance from splice site

217

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

399

mutated

not conserved

399

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000014926

399

Fcatus

no homologue

Mmusculus

no alignment

ENSMUSG00000022014

n/a

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000094578

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1233 / 1233

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

411 / 411

position of stopcodon in wt / mu cDNA

1298 / 1298

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

66 / 66

chromosome

strand

-1

last intron/exon boundary

1046

theoretical NMD boundary in CDS

930

length of CDS

1233

coding sequence (CDS) position

1197

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

1262

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

103986

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

43462422

original gDNA sequence snippet

ATTCCTGAACTCATATTTAATCTCTACTGCCAGGGAAATGC

altered gDNA sequence snippet

ATTCCTGAACTCATATTTAAACTCTACTGCCAGGGAAATGC

original cDNA sequence snippet

ATTCCTGAACTCATATTTAATCTCTACTGCCAGGGAAATGC

altered cDNA sequence snippet

ATTCCTGAACTCATATTTAAACTCTACTGCCAGGGAAATGC

wildtype AA sequence

MNTRNRVVNS GLGASPASRP TRDPQDPSGR QGELSPVEDQ REGLEAAPKG PSRESVVHAG
QRRTSAYTLI APNINRRNEI QRIAEQELAN LEKWKEQNRA KPVHLVPRRL GGSQSETEVR
QKQQLQLMQS KYKQKLKREE SVRIKKEAEE AELQKMKAIQ REKSNKLEEK KRLQENLRRE
AFREHQQYKT AEFLSKLNTE SPDRSACQSA VCGPQSSTWK LPILPRDHSW ARSWAYRDSL
KAEENRKLQK MKDEQHQKSE LLELKRQQQE QERAKIHQTE HRRVNNAFLD RLQGKSQPGG
LEQSGGCWNM NSGNSWGSLL VFSRHLRVYE KILTPIWPSS TDLEKPHEML FLNVILFSLT
VFTLISTAHT LDRAVRSDWL LLVLIYACLE ELIPELIFNL YCQGNATLFF *

mutated AA sequence

speed

0.35 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: without_aae, prob: 5.78936917459953e-09 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr13:43462422A>TN/A show variant in all transcripts IGV

HGNC symbol

EPSTI1

Ensembl transcript ID

ENST00000313624

Genbank transcript ID

NM_033255

UniProt peptide

N/A

alteration type

single base exchange

alteration region

3'UTR

DNA changes

cDNA.1216T>A
g.103986T>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs1044856

database	homozygous (T/T)	heterozygous	allele carriers
1000G	99	590	689
ExAC	4943	22140	27083

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.235	0.913
	0.055	0.913
(flanking)	2.728	0.935

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

splice site change occurs after stopcodon (at aa 376)

effect	gDNA position	score	detection sequence	exon-intron border
Donor gained	103981	0.60	mu: TCATATTTAAACTCT	ATAT\|ttaa

distance from splice site

217

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

poly(A) signal

signal is predicted to be ok

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

85 / 85

chromosome

strand

-1

last intron/exon boundary

1000

theoretical NMD boundary in CDS

865

length of CDS

924

coding sequence (CDS) position

N/A

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

1216

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

103986

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

43462422

original gDNA sequence snippet

ATTCCTGAACTCATATTTAATCTCTACTGCCAGGGAAATGC

altered gDNA sequence snippet

ATTCCTGAACTCATATTTAAACTCTACTGCCAGGGAAATGC

original cDNA sequence snippet

ATTCCTGAACTCATATTTAATCTCTACTGCCAGGGAAATGC

altered cDNA sequence snippet

ATTCCTGAACTCATATTTAAACTCTACTGCCAGGGAAATGC

wildtype AA sequence

MNTRNRVVNS GLGASPASRP TRDPQDPSGR QGELSPVEDQ REGLEAAPKG PSRESVVHAG
QRRTSAYTLI APNINRRNEI QRIAEQELAN LEKWKEQNRA KPVHLVPRRL GGSQSETEVR
QKQQLQLMQS KYKQKLKREE SVRIKKEAEE AELQKMKAIQ REKSNKLEEK KRLQENLRRE
AFREHQQYKT AEFLSKLNTE SPDRSACQSA VCGPQSSTWA RSWAYRDSLK AEENRKLQKM
KDEQHQKSEL LELKRQQQEQ ERAKIHQTEH RRVNNAFLDR LQGKSQPGGL EQSGGCWNMN
SGNSWGI*

mutated AA sequence

N/A

speed

0.88 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems