MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000361852
Querying Taster for transcript #2: ENST00000369805
Querying Taster for transcript #3: ENST00000361965
MT speed 0 s - this script 3.914932 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
EPS8L3	polymorphism_automatic	9.24378380506852e-08	simple_aae				H293Y	single base exchange	rs3818562		show file
EPS8L3	polymorphism_automatic	9.24378380506852e-08	simple_aae				H294Y	single base exchange	rs3818562		show file
EPS8L3	polymorphism_automatic	9.24378380506852e-08	simple_aae				H293Y	single base exchange	rs3818562		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999907562162 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:110300441G>AN/A show variant in all transcripts IGV

HGNC symbol

EPS8L3

Ensembl transcript ID

ENST00000361852

Genbank transcript ID

NM_024526

UniProt peptide

Q8TE67

alteration type

single base exchange

alteration region

CDS

DNA changes

c.877C>T
cDNA.1004C>T
g.6209C>T

AA changes

H293Y Score: 83 explain score(s)

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

293

frameshift

known variant

Reference ID: rs3818562

database	homozygous (A/A)	heterozygous	allele carriers
1000G	680	1010	1690
ExAC	15183	2401	17584

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.462	0.981
	0.194	0.985
(flanking)	1.7	0.999

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	6202	wt: 0.9848 / mu: 0.9903 (marginal change - not scored)	wt: CAGAAGATCAAGCAC mu: CAGAAGATCAAGTAC	GAAG\|atca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

293

mutated

all conserved

293

Ptroglodytes

all conserved

ENSPTRG00000001065

294

Mmulatta

all conserved

ENSMMUG00000008030

294

Fcatus

all conserved

ENSFCAG00000015600

322

Mmusculus

not conserved

ENSMUSG00000040600

302

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000006845

312

Drerio

not conserved

ENSDARG00000077296

346

Dmelanogaster

not conserved

FBgn0029095

395

Celegans

not conserved

Y57G11C.24

329

Xtropicalis

all conserved

ENSXETG00000002019

296

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1692 / 1692

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

564 / 564

position of stopcodon in wt / mu cDNA

1819 / 1819

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

128 / 128

chromosome

strand

-1

last intron/exon boundary

1808

theoretical NMD boundary in CDS

1630

length of CDS

1692

coding sequence (CDS) position

877

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

1004

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

6209

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

110300441

original gDNA sequence snippet

ACTGCTTCCAGAAGATCAAGCACAGCTTCAACCTCCTGGTA

altered gDNA sequence snippet

ACTGCTTCCAGAAGATCAAGTACAGCTTCAACCTCCTGGTA

original cDNA sequence snippet

ACTGCTTCCAGAAGATCAAGCACAGCTTCAACCTCCTGGGA

altered cDNA sequence snippet

ACTGCTTCCAGAAGATCAAGTACAGCTTCAACCTCCTGGGA

wildtype AA sequence

MSRPSSRAIY LHRKEYSQNL TSEPTLLQHR VEHLMTCKQG SQRVQGPEDA LQKLFEMDAQ
GRVWSQDLIL QVRDGWLQLL DIETKEELDS YRLDSIQAMN VALNTCSYNS ILSITVQEPG
LPGTSTLLFQ CQEVGAERLK TSLQKALEEE LEQRPRLGGL QPGQDRWRGP AMERPLPMEQ
ARYLEPGIPP EQPHQRTLEH SLPPSPRPLP RHTSAREPSA FTLPPPRRSS SPEDPERDEE
VLNHVLRDIE LFMGKLEKAQ AKTSRKKKFG KKNKDQGGLT QAQYIDCFQK IKHSFNLLGR
LATWLKETSA PELVHILFKS LNFILARCPE AGLAAQVISP LLTPKAINLL QSCLSPPESN
LWMGLGPAWT TSRADWTGDE PLPYQPTFSD DWQLPEPSSQ APLGYQDPVS LRPSSPKPAQ
PALKMQVLYE FEARNPRELT VVQGEKLEVL DHSKRWWLVK NEAGRSGYIP SNILEPLQPG
TPGTQGQSPS RVPMLRLSSR PEEVTDWLQA ENFSTATVRT LGSLTGSQLL RIRPGELQML
CPQEAPRILS RLEAVRRMLG ISP*

mutated AA sequence

MSRPSSRAIY LHRKEYSQNL TSEPTLLQHR VEHLMTCKQG SQRVQGPEDA LQKLFEMDAQ
GRVWSQDLIL QVRDGWLQLL DIETKEELDS YRLDSIQAMN VALNTCSYNS ILSITVQEPG
LPGTSTLLFQ CQEVGAERLK TSLQKALEEE LEQRPRLGGL QPGQDRWRGP AMERPLPMEQ
ARYLEPGIPP EQPHQRTLEH SLPPSPRPLP RHTSAREPSA FTLPPPRRSS SPEDPERDEE
VLNHVLRDIE LFMGKLEKAQ AKTSRKKKFG KKNKDQGGLT QAQYIDCFQK IKYSFNLLGR
LATWLKETSA PELVHILFKS LNFILARCPE AGLAAQVISP LLTPKAINLL QSCLSPPESN
LWMGLGPAWT TSRADWTGDE PLPYQPTFSD DWQLPEPSSQ APLGYQDPVS LRPSSPKPAQ
PALKMQVLYE FEARNPRELT VVQGEKLEVL DHSKRWWLVK NEAGRSGYIP SNILEPLQPG
TPGTQGQSPS RVPMLRLSSR PEEVTDWLQA ENFSTATVRT LGSLTGSQLL RIRPGELQML
CPQEAPRILS RLEAVRRMLG ISP*

speed

0.81 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: 0.999999907562162 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:110300441G>AN/A show variant in all transcripts IGV

HGNC symbol

EPS8L3

Ensembl transcript ID

ENST00000369805

Genbank transcript ID

NM_139053

UniProt peptide

Q8TE67

alteration type

single base exchange

alteration region

CDS

DNA changes

c.880C>T
cDNA.1110C>T
g.6209C>T

AA changes

H294Y Score: 83 explain score(s)

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

294

frameshift

known variant

Reference ID: rs3818562

database	homozygous (A/A)	heterozygous	allele carriers
1000G	680	1010	1690
ExAC	15183	2401	17584

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.462	0.981
	0.194	0.985
(flanking)	1.7	0.999

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	6202	wt: 0.9848 / mu: 0.9903 (marginal change - not scored)	wt: CAGAAGATCAAGCAC mu: CAGAAGATCAAGTAC	GAAG\|atca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

294

mutated

all conserved

294

Ptroglodytes

all conserved

ENSPTRG00000001065

294

Mmulatta

all conserved

ENSMMUG00000008030

294

Fcatus

all conserved

ENSFCAG00000015600

322

Mmusculus

not conserved

ENSMUSG00000040600

302

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000006845

312

Drerio

not conserved

ENSDARG00000077296

346

Dmelanogaster

not conserved

FBgn0029095

395

Celegans

not conserved

Y57G11C.24

329

Xtropicalis

all conserved

ENSXETG00000002019

296

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1785 / 1785

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

595 / 595

position of stopcodon in wt / mu cDNA

2015 / 2015

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

2004

theoretical NMD boundary in CDS

1723

length of CDS

1785

coding sequence (CDS) position

880

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

1110

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

6209

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

110300441

original gDNA sequence snippet

ACTGCTTCCAGAAGATCAAGCACAGCTTCAACCTCCTGGTA

altered gDNA sequence snippet

ACTGCTTCCAGAAGATCAAGTACAGCTTCAACCTCCTGGTA

original cDNA sequence snippet

ACTGCTTCCAGAAGATCAAGCACAGCTTCAACCTCCTGGGA

altered cDNA sequence snippet

ACTGCTTCCAGAAGATCAAGTACAGCTTCAACCTCCTGGGA

wildtype AA sequence

MSRPSSRAIY LHRKEYSQNL TSEPTLLQHR VEHLMTCKQG SQRVQGPEDA LQKLFEMDAQ
GRVWSQDLIL QVRDGWLQLL DIETKEELDS YRLDSIQAMN VALNTCSYNS ILSITVQEPG
LPGTSTLLFQ CQEVGAERLK TSLQKALEEE LEQSRPRLGG LQPGQDRWRG PAMERPLPME
QARYLEPGIP PEQPHQRTLE HSLPPSPRPL PRHTSAREPS AFTLPPPRRS SSPEDPERDE
EVLNHVLRDI ELFMGKLEKA QAKTSRKKKF GKKNKDQGGL TQAQYIDCFQ KIKHSFNLLG
RLATWLKETS APELVHILFK SLNFILARCP EAGLAAQVIS PLLTPKAINL LQSCLSPPES
NLWMGLGPAW TTSRADWTGD EPLPYQPTFS DDWQLPEPSS QAPLGYQDPV SLRRGSHRLG
STSHFPQEKT HNHDPQPGDP NSRPSSPKPA QPALKMQVLY EFEARNPREL TVVQGEKLEV
LDHSKRWWLV KNEAGRSGYI PSNILEPLQP GTPGTQGQSP SRVPMLRLSS RPEEVTDWLQ
AENFSTATVR TLGSLTGSQL LRIRPGELQM LCPQEAPRIL SRLEAVRRML GISP*

mutated AA sequence

MSRPSSRAIY LHRKEYSQNL TSEPTLLQHR VEHLMTCKQG SQRVQGPEDA LQKLFEMDAQ
GRVWSQDLIL QVRDGWLQLL DIETKEELDS YRLDSIQAMN VALNTCSYNS ILSITVQEPG
LPGTSTLLFQ CQEVGAERLK TSLQKALEEE LEQSRPRLGG LQPGQDRWRG PAMERPLPME
QARYLEPGIP PEQPHQRTLE HSLPPSPRPL PRHTSAREPS AFTLPPPRRS SSPEDPERDE
EVLNHVLRDI ELFMGKLEKA QAKTSRKKKF GKKNKDQGGL TQAQYIDCFQ KIKYSFNLLG
RLATWLKETS APELVHILFK SLNFILARCP EAGLAAQVIS PLLTPKAINL LQSCLSPPES
NLWMGLGPAW TTSRADWTGD EPLPYQPTFS DDWQLPEPSS QAPLGYQDPV SLRRGSHRLG
STSHFPQEKT HNHDPQPGDP NSRPSSPKPA QPALKMQVLY EFEARNPREL TVVQGEKLEV
LDHSKRWWLV KNEAGRSGYI PSNILEPLQP GTPGTQGQSP SRVPMLRLSS RPEEVTDWLQ
AENFSTATVR TLGSLTGSQL LRIRPGELQM LCPQEAPRIL SRLEAVRRML GISP*

speed

0.97 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999907562162 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:110300441G>AN/A show variant in all transcripts IGV

HGNC symbol

EPS8L3

Ensembl transcript ID

ENST00000361965

Genbank transcript ID

NM_133181

UniProt peptide

Q8TE67

alteration type

single base exchange

alteration region

CDS

DNA changes

c.877C>T
cDNA.984C>T
g.6209C>T

AA changes

H293Y Score: 83 explain score(s)

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

293

frameshift

known variant

Reference ID: rs3818562

database	homozygous (A/A)	heterozygous	allele carriers
1000G	680	1010	1690
ExAC	15183	2401	17584

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.462	0.981
	0.194	0.985
(flanking)	1.7	0.999

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	6202	wt: 0.9848 / mu: 0.9903 (marginal change - not scored)	wt: CAGAAGATCAAGCAC mu: CAGAAGATCAAGTAC	GAAG\|atca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

293

mutated

all conserved

293

Ptroglodytes

all conserved

ENSPTRG00000001065

294

Mmulatta

all conserved

ENSMMUG00000008030

294

Fcatus

all conserved

ENSFCAG00000015600

322

Mmusculus

not conserved

ENSMUSG00000040600

302

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000006845

312

Drerio

not conserved

ENSDARG00000077296

346

Dmelanogaster

not conserved

FBgn0029095

395

Celegans

not conserved

Y57G11C.24

329

Xtropicalis

all conserved

ENSXETG00000002019

296

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1782 / 1782

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

594 / 594

position of stopcodon in wt / mu cDNA

1889 / 1889

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

108 / 108

chromosome

strand

-1

last intron/exon boundary

1878

theoretical NMD boundary in CDS

1720

length of CDS

1782

coding sequence (CDS) position

877

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

984

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

6209

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

110300441

original gDNA sequence snippet

ACTGCTTCCAGAAGATCAAGCACAGCTTCAACCTCCTGGTA

altered gDNA sequence snippet

ACTGCTTCCAGAAGATCAAGTACAGCTTCAACCTCCTGGTA

original cDNA sequence snippet

ACTGCTTCCAGAAGATCAAGCACAGCTTCAACCTCCTGGGA

altered cDNA sequence snippet

ACTGCTTCCAGAAGATCAAGTACAGCTTCAACCTCCTGGGA

wildtype AA sequence

MSRPSSRAIY LHRKEYSQNL TSEPTLLQHR VEHLMTCKQG SQRVQGPEDA LQKLFEMDAQ
GRVWSQDLIL QVRDGWLQLL DIETKEELDS YRLDSIQAMN VALNTCSYNS ILSITVQEPG
LPGTSTLLFQ CQEVGAERLK TSLQKALEEE LEQRPRLGGL QPGQDRWRGP AMERPLPMEQ
ARYLEPGIPP EQPHQRTLEH SLPPSPRPLP RHTSAREPSA FTLPPPRRSS SPEDPERDEE
VLNHVLRDIE LFMGKLEKAQ AKTSRKKKFG KKNKDQGGLT QAQYIDCFQK IKHSFNLLGR
LATWLKETSA PELVHILFKS LNFILARCPE AGLAAQVISP LLTPKAINLL QSCLSPPESN
LWMGLGPAWT TSRADWTGDE PLPYQPTFSD DWQLPEPSSQ APLGYQDPVS LRRGSHRLGS
TSHFPQEKTH NHDPQPGDPN SRPSSPKPAQ PALKMQVLYE FEARNPRELT VVQGEKLEVL
DHSKRWWLVK NEAGRSGYIP SNILEPLQPG TPGTQGQSPS RVPMLRLSSR PEEVTDWLQA
ENFSTATVRT LGSLTGSQLL RIRPGELQML CPQEAPRILS RLEAVRRMLG ISP*

mutated AA sequence

MSRPSSRAIY LHRKEYSQNL TSEPTLLQHR VEHLMTCKQG SQRVQGPEDA LQKLFEMDAQ
GRVWSQDLIL QVRDGWLQLL DIETKEELDS YRLDSIQAMN VALNTCSYNS ILSITVQEPG
LPGTSTLLFQ CQEVGAERLK TSLQKALEEE LEQRPRLGGL QPGQDRWRGP AMERPLPMEQ
ARYLEPGIPP EQPHQRTLEH SLPPSPRPLP RHTSAREPSA FTLPPPRRSS SPEDPERDEE
VLNHVLRDIE LFMGKLEKAQ AKTSRKKKFG KKNKDQGGLT QAQYIDCFQK IKYSFNLLGR
LATWLKETSA PELVHILFKS LNFILARCPE AGLAAQVISP LLTPKAINLL QSCLSPPESN
LWMGLGPAWT TSRADWTGDE PLPYQPTFSD DWQLPEPSSQ APLGYQDPVS LRRGSHRLGS
TSHFPQEKTH NHDPQPGDPN SRPSSPKPAQ PALKMQVLYE FEARNPRELT VVQGEKLEVL
DHSKRWWLVK NEAGRSGYIP SNILEPLQPG TPGTQGQSPS RVPMLRLSSR PEEVTDWLQA
ENFSTATVRT LGSLTGSQLL RIRPGELQML CPQEAPRILS RLEAVRRMLG ISP*

speed

0.97 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems