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: ENST00000309971
Querying Taster for transcript #2: ENST00000539582
MT speed 0.99 s - this script 2.986554 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GLE1	disease_causing_automatic	0.999999837934903	simple_aae		affected	0	I430T	single base exchange	rs121434409		show file
GLE1	disease_causing_automatic	0.999999875534016	simple_aae		affected	0	I684T	single base exchange	rs121434409		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999837934903 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM080395)
known disease mutation: rs6465 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:131303403T>CN/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

CDS

DNA changes

c.1289T>C
cDNA.1902T>C
g.36425T>C

AA changes

I430T Score: 89 explain score(s)

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

430

frameshift

known variant

Reference ID: rs121434409

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	4	4

known disease mutation: rs6465 (pathogenic for Lethal arthrogryposis with anterior horn cell disease) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM080395)

known disease mutation at this position, please check HGMD for details (HGMD ID CM080395)
known disease mutation at this position, please check HGMD for details (HGMD ID CM080395)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.018	1
	4.426	1
(flanking)	0.076	0.996

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	36420	wt: 0.63 / mu: 0.81	wt: CACAAGGACATTCCT mu: CACAAGGACACTCCT	CAAG\|gaca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

430

mutated

not conserved

430

Ptroglodytes

all identical

ENSPTRG00000021431

683

Mmulatta

all identical

ENSMMUG00000005989

684

Fcatus

all identical

ENSFCAG00000005845

683

Mmusculus

all identical

ENSMUSG00000019715

685

Ggallus

all identical

ENSGALG00000004738

683

Trubripes

all identical

ENSTRUG00000006713

695

Drerio

all identical

ENSDARG00000043559

703

Dmelanogaster

all identical

FBgn0033316

668

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
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

1335 / 1335

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

445 / 445

position of stopcodon in wt / mu cDNA

1948 / 1948

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

1289

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

1902

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

36425

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

131303403

original gDNA sequence snippet

ATGTTTGCAACACAAGGACATTCCTGTCCCCAAGGGCTTTC

altered gDNA sequence snippet

ATGTTTGCAACACAAGGACACTCCTGTCCCCAAGGGCTTTC

original cDNA sequence snippet

ATGTTTGCAACACAAGGACATTCCTGTCCCCAAGGGCTTTC

altered cDNA sequence snippet

ATGTTTGCAACACAAGGACACTCCTGTCCCCAAGGGCTTTC

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

speed

0.49 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

disease causing

Model: simple_aae, prob: 0.999999875534016 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM080395)
known disease mutation: rs6465 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:131303403T>CN/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.2051T>C
cDNA.2157T>C
g.36425T>C

AA changes

I684T Score: 89 explain score(s)

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

684

frameshift

known variant

Reference ID: rs121434409

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	4	4

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.018	1
	4.426	1
(flanking)	0.076	0.996

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	36420	wt: 0.63 / mu: 0.81	wt: CACAAGGACATTCCT mu: CACAAGGACACTCCT	CAAG\|gaca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

684

mutated

not conserved

684

Ptroglodytes

all identical

ENSPTRG00000021431

683

Mmulatta

all identical

ENSMMUG00000005989

684

Fcatus

all identical

ENSFCAG00000005845

683

Mmusculus

all identical

ENSMUSG00000019715

685

Ggallus

all identical

ENSGALG00000004738

683

Trubripes

all identical

ENSTRUG00000006713

695

Drerio

all identical

ENSDARG00000043559

703

Dmelanogaster

all identical

FBgn0033316

668

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
656	698	REGION	Interaction with NUPL2.	lost

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

2051

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

2157

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

36425

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

131303403

original gDNA sequence snippet

ATGTTTGCAACACAAGGACATTCCTGTCCCCAAGGGCTTTC

altered gDNA sequence snippet

ATGTTTGCAACACAAGGACACTCCTGTCCCCAAGGGCTTTC

original cDNA sequence snippet

ATGTTTGCAACACAAGGACATTCCTGTCCCCAAGGGCTTTC

altered cDNA sequence snippet

ATGTTTGCAACACAAGGACACTCCTGTCCCCAAGGGCTTTC

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

speed

0.50 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems