MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000309971
Querying Taster for transcript #2: ENST00000372770
Querying Taster for transcript #3: ENST00000539582
MT speed 0 s - this script 3.475611 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GLE1	polymorphism_automatic	3.0400126860286e-12	simple_aae		affected		I243V	single base exchange	rs2275260		show file
GLE1	polymorphism_automatic	3.0400126860286e-12	simple_aae		affected		I243V	single base exchange	rs2275260		show file
GLE1	polymorphism_automatic	0.992549546542466	without_aae		affected			single base exchange	rs2275260		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999999999696 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:131285955A>GN/A show variant in all transcripts IGV

HGNC symbol

GLE1

Ensembl transcript ID

ENST00000309971

Genbank transcript ID

NM_001003722

UniProt peptide

Q53GS7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.727A>G
cDNA.833A>G
g.18977A>G

AA changes

I243V Score: 29 explain score(s)

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

243

frameshift

known variant

Reference ID: rs2275260

database	homozygous (G/G)	heterozygous	allele carriers
1000G	336	1068	1404
ExAC	4751	22810	27561

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.508	0.915
	0.353	0.155
(flanking)	0.439	0.056

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 increased	18971	wt: 0.85 / mu: 1.00	wt: AAGAAGGCCAGATCC mu: AAGAAGGCCAGGTCC	GAAG\|gcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

243

mutated

all conserved

243

Ptroglodytes

all conserved

ENSPTRG00000021431

243

Mmulatta

all conserved

ENSMMUG00000005989

243

Fcatus

all conserved

ENSFCAG00000005845

243

Mmusculus

all conserved

ENSMUSG00000019715

245

Ggallus

not conserved

ENSGALG00000004738

243

Trubripes

not conserved

ENSTRUG00000006713

256

Drerio

not conserved

ENSDARG00000043559

265

Dmelanogaster

not conserved

FBgn0033316

201

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
151	277	COILED	Potential.	lost
305	356	COILED	Potential.	might get lost (downstream of altered splice site)
444	483	REGION	Mediates the shuttling between the nucleus and the cytoplasm.	might get lost (downstream of altered splice site)
549	549	CONFLICT	R -> G (in Ref. 2; BAD96562).	might get lost (downstream of altered splice site)
656	698	REGION	Interaction with NUPL2.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2097 / 2097

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

699 / 699

position of stopcodon in wt / mu cDNA

2203 / 2203

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

107 / 107

chromosome

strand

last intron/exon boundary

2135

theoretical NMD boundary in CDS

1978

length of CDS

2097

coding sequence (CDS) position

727

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

833

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

18977

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

131285955

original gDNA sequence snippet

TTCGGAAGGAAGAAGGCCAGATCCGCCTGCGGGCCCTCTAT

altered gDNA sequence snippet

TTCGGAAGGAAGAAGGCCAGGTCCGCCTGCGGGCCCTCTAT

original cDNA sequence snippet

TTCGGAAGGAAGAAGGCCAGATCCGCCTGCGGGCCCTCTAT

altered cDNA sequence snippet

TTCGGAAGGAAGAAGGCCAGGTCCGCCTGCGGGCCCTCTAT

wildtype AA sequence

MPSEGRCWET LKALRSSDKG RLCYYRDWLL RREDVLEECM SLPKLSSYSG WVVEHVLPHM
QENQPLSETS PSSTSASALD QPSFVPKSPD ASSAFSPASP ATPNGTKGKD ESQHTESMVL
QSSRGIKVEG CVRMYELVHR MKGTEGLRLW QEEQERKVQA LSEMASEQLK RFDEWKELKQ
HKEFQDLREV MEKSSREALG HQEKLKAEHR HRAKILNLKL REAEQQRVKQ AEQERLRKEE
GQIRLRALYA LQEEMLQLSQ QLDASEQHKA LLKVDLAAFQ TRGNQLCSLI SGIIRASSES
SYPTAESQAE AERALREMRD LLMNLGQEIT RACEDKRRQD EEEAQVKLQE AQMQQGPEAH
KEPPAPSQGP GGKQNEDLQV KVQDITMQWY QQLQDASMQC VLTFEGLTNS KDSQAKKIKM
DLQKAATIPV SQISTIAGSK LKEIFDKIHS LLSGKPVQSG GRSVSVTLNP QGLDFVQYKL
AEKFVKQGEE EVASHHEAAF PIAVVASGIW ELHPRVGDLI LAHLHKKCPY SVPFYPTFKE
GMALEDYQRM LGYQVKDSKV EQQDNFLKRM SGMIRLYAAI IQLRWPYGNR QEIHPHGLNH
GWRWLAQILN MEPLSDVTAT LLFDFLEVCG NALMKQYQVQ FWKMLILIKE DYFPRIEAIT
SSGQMGSFIR LKQFLEKCLQ HKDIPVPKGF LTSSFWRS*

mutated AA sequence

MPSEGRCWET LKALRSSDKG RLCYYRDWLL RREDVLEECM SLPKLSSYSG WVVEHVLPHM
QENQPLSETS PSSTSASALD QPSFVPKSPD ASSAFSPASP ATPNGTKGKD ESQHTESMVL
QSSRGIKVEG CVRMYELVHR MKGTEGLRLW QEEQERKVQA LSEMASEQLK RFDEWKELKQ
HKEFQDLREV MEKSSREALG HQEKLKAEHR HRAKILNLKL REAEQQRVKQ AEQERLRKEE
GQVRLRALYA LQEEMLQLSQ QLDASEQHKA LLKVDLAAFQ TRGNQLCSLI SGIIRASSES
SYPTAESQAE AERALREMRD LLMNLGQEIT RACEDKRRQD EEEAQVKLQE AQMQQGPEAH
KEPPAPSQGP GGKQNEDLQV KVQDITMQWY QQLQDASMQC VLTFEGLTNS KDSQAKKIKM
DLQKAATIPV SQISTIAGSK LKEIFDKIHS LLSGKPVQSG GRSVSVTLNP QGLDFVQYKL
AEKFVKQGEE EVASHHEAAF PIAVVASGIW ELHPRVGDLI LAHLHKKCPY SVPFYPTFKE
GMALEDYQRM LGYQVKDSKV EQQDNFLKRM SGMIRLYAAI IQLRWPYGNR QEIHPHGLNH
GWRWLAQILN MEPLSDVTAT LLFDFLEVCG NALMKQYQVQ FWKMLILIKE DYFPRIEAIT
SSGQMGSFIR LKQFLEKCLQ HKDIPVPKGF LTSSFWRS*

speed

0.79 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: 0.99999999999696 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:131285955A>GN/A show variant in all transcripts IGV

HGNC symbol

GLE1

Ensembl transcript ID

ENST00000372770

Genbank transcript ID

NM_001499

UniProt peptide

Q53GS7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.727A>G
cDNA.802A>G
g.18977A>G

AA changes

I243V Score: 29 explain score(s)

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

243

frameshift

known variant

Reference ID: rs2275260

database	homozygous (G/G)	heterozygous	allele carriers
1000G	336	1068	1404
ExAC	4751	22810	27561

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.508	0.915
	0.353	0.155
(flanking)	0.439	0.056

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 increased	18971	wt: 0.85 / mu: 1.00	wt: AAGAAGGCCAGATCC mu: AAGAAGGCCAGGTCC	GAAG\|gcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

243

mutated

all conserved

243

Ptroglodytes

all conserved

ENSPTRG00000021431

243

Mmulatta

all conserved

ENSMMUG00000005989

243

Fcatus

all conserved

ENSFCAG00000005845

243

Mmusculus

all conserved

ENSMUSG00000019715

245

Ggallus

not conserved

ENSGALG00000004738

243

Trubripes

not conserved

ENSTRUG00000006713

256

Drerio

not conserved

ENSDARG00000043559

265

Dmelanogaster

not conserved

FBgn0033316

201

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
151	277	COILED	Potential.	lost
305	356	COILED	Potential.	might get lost (downstream of altered splice site)
444	483	REGION	Mediates the shuttling between the nucleus and the cytoplasm.	might get lost (downstream of altered splice site)
549	549	CONFLICT	R -> G (in Ref. 2; BAD96562).	might get lost (downstream of altered splice site)
656	698	REGION	Interaction with NUPL2.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1980 / 1980

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

660 / 660

position of stopcodon in wt / mu cDNA

2055 / 2055

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

76 / 76

chromosome

strand

last intron/exon boundary

1957

theoretical NMD boundary in CDS

1831

length of CDS

1980

coding sequence (CDS) position

727

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

802

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

18977

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

131285955

original gDNA sequence snippet

TTCGGAAGGAAGAAGGCCAGATCCGCCTGCGGGCCCTCTAT

altered gDNA sequence snippet

TTCGGAAGGAAGAAGGCCAGGTCCGCCTGCGGGCCCTCTAT

original cDNA sequence snippet

TTCGGAAGGAAGAAGGCCAGATCCGCCTGCGGGCCCTCTAT

altered cDNA sequence snippet

TTCGGAAGGAAGAAGGCCAGGTCCGCCTGCGGGCCCTCTAT

wildtype AA sequence

mutated AA sequence

MPSEGRCWET LKALRSSDKG RLCYYRDWLL RREDVLEECM SLPKLSSYSG WVVEHVLPHM
QENQPLSETS PSSTSASALD QPSFVPKSPD ASSAFSPASP ATPNGTKGKD ESQHTESMVL
QSSRGIKVEG CVRMYELVHR MKGTEGLRLW QEEQERKVQA LSEMASEQLK RFDEWKELKQ
HKEFQDLREV MEKSSREALG HQEKLKAEHR HRAKILNLKL REAEQQRVKQ AEQERLRKEE
GQVRLRALYA LQEEMLQLSQ QLDASEQHKA LLKVDLAAFQ TRGNQLCSLI SGIIRASSES
SYPTAESQAE AERALREMRD LLMNLGQEIT RACEDKRRQD EEEAQVKLQE AQMQQGPEAH
KEPPAPSQGP GGKQNEDLQV KVQDITMQWY QQLQDASMQC VLTFEGLTNS KDSQAKKIKM
DLQKAATIPV SQISTIAGSK LKEIFDKIHS LLSGKPVQSG GRSVSVTLNP QGLDFVQYKL
AEKFVKQGEE EVASHHEAAF PIAVVASGIW ELHPRVGDLI LAHLHKKCPY SVPFYPTFKE
GMALEDYQRM LGYQVKDSKV EQQDNFLKRM SGMIRLYAAI IQLRWPYGNR QEIHPHGLNH
GWRWLAQILN MEPLSDVTAT LLFDFLEVCG NALMKQYQVQ FWKMLILIKE DYFPRYQAC*

speed

0.85 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.00745045345753357 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:131285955A>GN/A show variant in all transcripts IGV

HGNC symbol

GLE1

Ensembl transcript ID

ENST00000539582

Genbank transcript ID

N/A

UniProt peptide

Q53GS7

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.578A>G
g.18977A>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs2275260

database	homozygous (G/G)	heterozygous	allele carriers
1000G	336	1068	1404
ExAC	4751	22810	27561

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.508	0.915
	0.353	0.155
(flanking)	0.439	0.056

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

splice sites

splice site change before start ATG (at aa -13) |

effect	gDNA position	score	detection sequence	exon-intron border
Donor increased	18971	wt: 0.85 / mu: 1.00	wt: AAGAAGGCCAGATCC mu: AAGAAGGCCAGGTCC	GAAG\|gcca

distance from splice site

Kozak consensus sequence altered?

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
1	29	REGION	Interaction with NUP155.	might get lost (downstream of altered splice site)
83	83	CONFLICT	S -> P (in Ref. 2; BAD96574).	might get lost (downstream of altered splice site)
88	88	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
151	277	COILED	Potential.	might get lost (downstream of altered splice site)
172	172	CONFLICT	F -> S (in Ref. 2; BAD96562).	might get lost (downstream of altered splice site)
305	356	COILED	Potential.	might get lost (downstream of altered splice site)
444	483	REGION	Mediates the shuttling between the nucleus and the cytoplasm.	might get lost (downstream of altered splice site)
549	549	CONFLICT	R -> G (in Ref. 2; BAD96562).	might get lost (downstream of altered splice site)
656	698	REGION	Interaction with NUPL2.	might get lost (downstream of altered splice site)

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

N/A

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

N/A

position of start ATG in wt / mu cDNA

614 / 614

chromosome

strand

last intron/exon boundary

1880

theoretical NMD boundary in CDS

1216

length of CDS

1335

coding sequence (CDS) position

N/A

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

578

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

18977

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

131285955

original gDNA sequence snippet

TTCGGAAGGAAGAAGGCCAGATCCGCCTGCGGGCCCTCTAT

altered gDNA sequence snippet

TTCGGAAGGAAGAAGGCCAGGTCCGCCTGCGGGCCCTCTAT

original cDNA sequence snippet

TTCGGAAGGAAGAAGGCCAGATCCGCCTGCGGGCCCTCTAT

altered cDNA sequence snippet

TTCGGAAGGAAGAAGGCCAGGTCCGCCTGCGGGCCCTCTAT

wildtype AA sequence

MLQLSQQLDA SEQHKALLKV DLAAFQTRGN QLCSLISGII RASSESSYPT AESQAEAERA
LREMRDLLMN LGQEITRACE DKRRQDEEEA QVKLQEAQMQ QGPEAHKEPP APSQGPGGKQ
NEDLQVKVQD ITMQWYQQLQ DASMQCVLTF EGLTNSKDSQ AKKIKMDLQK AATIPVSQIS
TIAGSKLKEI FDKIHSLLSG KPVQSGGRSV SVTLNPQGLD FVQYKLAEKF VKQGEEEVAS
HHEAAFPIAV VASGIWELHP RVGDLILAHL HKKCPYSVPF YPTFKEGMAL EDYQRMLGYQ
VKDSKVEQQD NFLKRMSGMI RLYAAIIQLR WPYGNRQEIH PHGLNHGWRW LAQILNMEPL
SDVTATLLFD FLEVCGNALM KQYQVQFWKM LILIKEDYFP RIEAITSSGQ MGSFIRLKQF
LEKCLQHKDI PVPKGFLTSS FWRS*

mutated AA sequence

N/A

speed

0.60 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