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: ENST00000167462
Querying Taster for transcript #2: ENST00000392550
Querying Taster for transcript #3: ENST00000577200
MT speed 1.74 s - this script 3.278114 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
LLGL2	polymorphism_automatic	0.947969008051972	simple_aae		affected		P759S	single base exchange	rs1661715		show file
LLGL2	polymorphism_automatic	0.947969008051972	simple_aae		affected		P759S	single base exchange	rs1661715		show file
LLGL2	polymorphism_automatic	0.947969008051972	simple_aae		affected		P759S	single base exchange	rs1661715		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.0520309919480284 (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)

chr17:73567846C>TN/A show variant in all transcripts IGV

HGNC symbol

LLGL2

Ensembl transcript ID

ENST00000167462

Genbank transcript ID

NM_004524

UniProt peptide

Q6P1M3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2275C>T
cDNA.2405C>T
g.46686C>T

AA changes

P759S Score: 74 explain score(s)

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

759

frameshift

known variant

Reference ID: rs1661715

database	homozygous (T/T)	heterozygous	allele carriers
1000G	305	942	1247
ExAC	5176	22415	27591

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2AZ, Histone, Histone 2A variant Z
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.229	0.994
	2.287	0.997
(flanking)	2.6	0.986

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	46679	wt: 0.87 / mu: 0.99	wt: AGAATGGATGAGCCT mu: AGAATGGATGAGTCT	AATG\|gatg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

759

mutated

not conserved

759

Ptroglodytes

all identical

ENSPTRG00000009647

759

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000020782

785

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000023920

756

Dmelanogaster

not conserved

FBgn0002121

754

TAATAVPSASGNAPP

Celegans

not conserved

F56F10.4

783

Xtropicalis

not conserved

ENSXETG00000012529

732

protein features

start (aa)	end (aa)	feature	details
713	769	REPEAT	WD 11.	lost
778	830	REPEAT	WD 12.	might get lost (downstream of altered splice site)
835	888	REPEAT	WD 13.	might get lost (downstream of altered splice site)
902	925	REPEAT	WD 14.	might get lost (downstream of altered splice site)
1015	1015	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3048 / 3048

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

1016 / 1016

position of stopcodon in wt / mu cDNA

3178 / 3178

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

131 / 131

chromosome

strand

last intron/exon boundary

3143

theoretical NMD boundary in CDS

2962

length of CDS

3048

coding sequence (CDS) position

2275

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

2405

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

46686

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

73567846

original gDNA sequence snippet

CCGAGCGGAGAATGGATGAGCCTGTGCGGGCAGAGCAGGGT

altered gDNA sequence snippet

CCGAGCGGAGAATGGATGAGTCTGTGCGGGCAGAGCAGGGT

original cDNA sequence snippet

CCGAGCGGAGAATGGATGAGCCTGTGCGGGCAGAGCAGGCC

altered cDNA sequence snippet

CCGAGCGGAGAATGGATGAGTCTGTGCGGGCAGAGCAGGCC

wildtype AA sequence

MRRFLRPGHD PVRERLKRDL FQFNKTVEHG FPHQPSALGY SPSLRILAIG TRSGAIKLYG
APGVEFMGLH QENNAVTQIH LLPGQCQLVT LLDDNSLHLW SLKVKGGASE LQEDESFTLR
GPPGAAPSAT QITVVLPHSS CELLYLGTES GNVFVVQLPA FRALEDRTIS SDAVLQRLPE
EARHRRVFEM VEALQEHPRD PNQILIGYSR GLVVIWDLQG SRVLYHFLSS QQLENIWWQR
DGRLLVSCHS DGSYCQWPVS SEAQQPEPLR SLVPYGPFPC KAITRILWLT TRQGLPFTIF
QGGMPRASYG DRHCISVIHD GQQTAFDFTS RVIGFTVLTE ADPAATFDDP YALVVLAEEE
LVVIDLQTAG WPPVQLPYLA SLHCSAITCS HHVSNIPLKL WERIIAAGSR QNAHFSTMEW
PIDGGTSLTP APPQRDLLLT GHEDGTVRFW DASGVCLRLL YKLSTVRVFL TDTDPNENFS
AQGEDEWPPL RKVGSFDPYS DDPRLGIQKI FLCKYSGYLA VAGTAGQVLV LELNDEAAEQ
AVEQVEADLL QDQEGYRWKG HERLAARSGP VRFEPGFQPF VLVQCQPPAV VTSLALHSEW
RLVAFGTSHG FGLFDHQQRR QVFVKCTLHP SDQLALEGPL SRVKSLKKSL RQSFRRMRRS
RVSSRKRHPA GPPGEAQEGS AKAERPGLQN MELAPVQRKI EARSAEDSFT GFVRTLYFAD
TYLKDSSRHC PSLWAGTNGG TIYAFSLRVP PAERRMDEPV RAEQAKEIQL MHRAPVVGIL
VLDGHSVPLP EPLEVAHDLS KSPDMQGSHQ LLVVSEEQFK VFTLPKVSAK LKLKLTALEG
SRVRRVSVAH FGSRRAEDYG EHHLAVLTNL GDIQVVSLPL LKPQVRYSCI RREDVSGIAS
CVFTKYGQGF YLISPSEFER FSLSTKWLVE PRCLVDSAET KNHRPGNGAG PKKAPSRARN
SGTQSDGEEK QPGLVMERAL LSDERAATGV HIEPPWGAAS AMAEQSEWLS VQAAR*

mutated AA sequence

MRRFLRPGHD PVRERLKRDL FQFNKTVEHG FPHQPSALGY SPSLRILAIG TRSGAIKLYG
APGVEFMGLH QENNAVTQIH LLPGQCQLVT LLDDNSLHLW SLKVKGGASE LQEDESFTLR
GPPGAAPSAT QITVVLPHSS CELLYLGTES GNVFVVQLPA FRALEDRTIS SDAVLQRLPE
EARHRRVFEM VEALQEHPRD PNQILIGYSR GLVVIWDLQG SRVLYHFLSS QQLENIWWQR
DGRLLVSCHS DGSYCQWPVS SEAQQPEPLR SLVPYGPFPC KAITRILWLT TRQGLPFTIF
QGGMPRASYG DRHCISVIHD GQQTAFDFTS RVIGFTVLTE ADPAATFDDP YALVVLAEEE
LVVIDLQTAG WPPVQLPYLA SLHCSAITCS HHVSNIPLKL WERIIAAGSR QNAHFSTMEW
PIDGGTSLTP APPQRDLLLT GHEDGTVRFW DASGVCLRLL YKLSTVRVFL TDTDPNENFS
AQGEDEWPPL RKVGSFDPYS DDPRLGIQKI FLCKYSGYLA VAGTAGQVLV LELNDEAAEQ
AVEQVEADLL QDQEGYRWKG HERLAARSGP VRFEPGFQPF VLVQCQPPAV VTSLALHSEW
RLVAFGTSHG FGLFDHQQRR QVFVKCTLHP SDQLALEGPL SRVKSLKKSL RQSFRRMRRS
RVSSRKRHPA GPPGEAQEGS AKAERPGLQN MELAPVQRKI EARSAEDSFT GFVRTLYFAD
TYLKDSSRHC PSLWAGTNGG TIYAFSLRVP PAERRMDESV RAEQAKEIQL MHRAPVVGIL
VLDGHSVPLP EPLEVAHDLS KSPDMQGSHQ LLVVSEEQFK VFTLPKVSAK LKLKLTALEG
SRVRRVSVAH FGSRRAEDYG EHHLAVLTNL GDIQVVSLPL LKPQVRYSCI RREDVSGIAS
CVFTKYGQGF YLISPSEFER FSLSTKWLVE PRCLVDSAET KNHRPGNGAG PKKAPSRARN
SGTQSDGEEK QPGLVMERAL LSDERAATGV HIEPPWGAAS AMAEQSEWLS VQAAR*

speed

0.54 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: 0.0520309919480284 (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)

chr17:73567846C>TN/A show variant in all transcripts IGV

HGNC symbol

LLGL2

Ensembl transcript ID

ENST00000392550

Genbank transcript ID

NM_001031803

UniProt peptide

Q6P1M3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2275C>T
cDNA.2392C>T
g.46686C>T

AA changes

P759S Score: 74 explain score(s)

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

759

frameshift

known variant

Reference ID: rs1661715

database	homozygous (T/T)	heterozygous	allele carriers
1000G	305	942	1247
ExAC	5176	22415	27591

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.229	0.994
	2.287	0.997
(flanking)	2.6	0.986

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	46679	wt: 0.87 / mu: 0.99	wt: AGAATGGATGAGCCT mu: AGAATGGATGAGTCT	AATG\|gatg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

759

mutated

not conserved

759

Ptroglodytes

all identical

ENSPTRG00000009647

759

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000020782

785

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000023920

756

Dmelanogaster

not conserved

FBgn0002121

754

TAATAVPSASGNAPP

Celegans

not conserved

F56F10.4

783

Xtropicalis

not conserved

ENSXETG00000012529

732

protein features

start (aa)	end (aa)	feature	details
713	769	REPEAT	WD 11.	lost
778	830	REPEAT	WD 12.	might get lost (downstream of altered splice site)
835	888	REPEAT	WD 13.	might get lost (downstream of altered splice site)
902	925	REPEAT	WD 14.	might get lost (downstream of altered splice site)
1015	1015	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3063 / 3063

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

1021 / 1021

position of stopcodon in wt / mu cDNA

3180 / 3180

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

118 / 118

chromosome

strand

last intron/exon boundary

3173

theoretical NMD boundary in CDS

3005

length of CDS

3063

coding sequence (CDS) position

2275

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

2392

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

46686

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

73567846

original gDNA sequence snippet

CCGAGCGGAGAATGGATGAGCCTGTGCGGGCAGAGCAGGGT

altered gDNA sequence snippet

CCGAGCGGAGAATGGATGAGTCTGTGCGGGCAGAGCAGGGT

original cDNA sequence snippet

CCGAGCGGAGAATGGATGAGCCTGTGCGGGCAGAGCAGGCC

altered cDNA sequence snippet

CCGAGCGGAGAATGGATGAGTCTGTGCGGGCAGAGCAGGCC

wildtype AA sequence

mutated AA sequence

MRRFLRPGHD PVRERLKRDL FQFNKTVEHG FPHQPSALGY SPSLRILAIG TRSGAIKLYG
APGVEFMGLH QENNAVTQIH LLPGQCQLVT LLDDNSLHLW SLKVKGGASE LQEDESFTLR
GPPGAAPSAT QITVVLPHSS CELLYLGTES GNVFVVQLPA FRALEDRTIS SDAVLQRLPE
EARHRRVFEM VEALQEHPRD PNQILIGYSR GLVVIWDLQG SRVLYHFLSS QQLENIWWQR
DGRLLVSCHS DGSYCQWPVS SEAQQPEPLR SLVPYGPFPC KAITRILWLT TRQGLPFTIF
QGGMPRASYG DRHCISVIHD GQQTAFDFTS RVIGFTVLTE ADPAATFDDP YALVVLAEEE
LVVIDLQTAG WPPVQLPYLA SLHCSAITCS HHVSNIPLKL WERIIAAGSR QNAHFSTMEW
PIDGGTSLTP APPQRDLLLT GHEDGTVRFW DASGVCLRLL YKLSTVRVFL TDTDPNENFS
AQGEDEWPPL RKVGSFDPYS DDPRLGIQKI FLCKYSGYLA VAGTAGQVLV LELNDEAAEQ
AVEQVEADLL QDQEGYRWKG HERLAARSGP VRFEPGFQPF VLVQCQPPAV VTSLALHSEW
RLVAFGTSHG FGLFDHQQRR QVFVKCTLHP SDQLALEGPL SRVKSLKKSL RQSFRRMRRS
RVSSRKRHPA GPPGEAQEGS AKAERPGLQN MELAPVQRKI EARSAEDSFT GFVRTLYFAD
TYLKDSSRHC PSLWAGTNGG TIYAFSLRVP PAERRMDESV RAEQAKEIQL MHRAPVVGIL
VLDGHSVPLP EPLEVAHDLS KSPDMQGSHQ LLVVSEEQFK VFTLPKVSAK LKLKLTALEG
SRVRRVSVAH FGSRRAEDYG EHHLAVLTNL GDIQVVSLPL LKPQVRYSCI RREDVSGIAS
CVFTKYGQGF YLISPSEFER FSLSTKWLVE PRCLVDSAET KNHRPGNGAG PKKAPSRARN
SGTQSDGEEK QPGLVMERAL LSDERVLKEI QSTLEGDRGS GNWRSHRAAV GCSLSNGGAE
*

speed

0.59 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.0520309919480284 (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)

chr17:73567846C>TN/A show variant in all transcripts IGV

HGNC symbol

LLGL2

Ensembl transcript ID

ENST00000577200

Genbank transcript ID

N/A

UniProt peptide

Q6P1M3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2275C>T
cDNA.2379C>T
g.46686C>T

AA changes

P759S Score: 74 explain score(s)

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

759

frameshift

known variant

Reference ID: rs1661715

database	homozygous (T/T)	heterozygous	allele carriers
1000G	305	942	1247
ExAC	5176	22415	27591

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.229	0.994
	2.287	0.997
(flanking)	2.6	0.986

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	46679	wt: 0.87 / mu: 0.99	wt: AGAATGGATGAGCCT mu: AGAATGGATGAGTCT	AATG\|gatg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

759

mutated

not conserved

759

Ptroglodytes

all identical

ENSPTRG00000009647

759

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000020782

785

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000023920

756

Dmelanogaster

not conserved

FBgn0002121

754

TAATAVPSASGNAPP

Celegans

not conserved

F56F10.4

783

Xtropicalis

not conserved

ENSXETG00000012529

732

protein features

start (aa)	end (aa)	feature	details
713	769	REPEAT	WD 11.	lost
778	830	REPEAT	WD 12.	might get lost (downstream of altered splice site)
835	888	REPEAT	WD 13.	might get lost (downstream of altered splice site)
902	925	REPEAT	WD 14.	might get lost (downstream of altered splice site)
1015	1015	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3060 / 3060

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

1020 / 1020

position of stopcodon in wt / mu cDNA

3164 / 3164

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

105 / 105

chromosome

strand

last intron/exon boundary

3160

theoretical NMD boundary in CDS

3005

length of CDS

3060

coding sequence (CDS) position

2275

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

2379

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

46686

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

73567846

original gDNA sequence snippet

CCGAGCGGAGAATGGATGAGCCTGTGCGGGCAGAGCAGGGT

altered gDNA sequence snippet

CCGAGCGGAGAATGGATGAGTCTGTGCGGGCAGAGCAGGGT

original cDNA sequence snippet

CCGAGCGGAGAATGGATGAGCCTGTGCGGGCAGAGCAGGCC

altered cDNA sequence snippet

CCGAGCGGAGAATGGATGAGTCTGTGCGGGCAGAGCAGGCC

wildtype AA sequence

mutated AA sequence

MRRFLRPGHD PVRERLKRDL FQFNKTVEHG FPHQPSALGY SPSLRILAIG TRSGAIKLYG
APGVEFMGLH QENNAVTQIH LLPGQCQLVT LLDDNSLHLW SLKVKGGASE LQEDESFTLR
GPPGAAPSAT QITVVLPHSS CELLYLGTES GNVFVVQLPA FRALEDRTIS SDAVLQRLPE
EARHRRVFEM VEALQEHPRD PNQILIGYSR GLVVIWDLQG SRVLYHFLSS QQLENIWWQR
DGRLLVSCHS DGSYCQWPVS SEAQQPEPLR SLVPYGPFPC KAITRILWLT TRQGLPFTIF
QGGMPRASYG DRHCISVIHD GQQTAFDFTS RVIGFTVLTE ADPAATFDDP YALVVLAEEE
LVVIDLQTAG WPPVQLPYLA SLHCSAITCS HHVSNIPLKL WERIIAAGSR QNAHFSTMEW
PIDGGTSLTP APPQRDLLLT GHEDGTVRFW DASGVCLRLL YKLSTVRVFL TDTDPNENFS
AQGEDEWPPL RKVGSFDPYS DDPRLGIQKI FLCKYSGYLA VAGTAGQVLV LELNDEAAEQ
AVEQVEADLL QDQEGYRWKG HERLAARSGP VRFEPGFQPF VLVQCQPPAV VTSLALHSEW
RLVAFGTSHG FGLFDHQQRR QVFVKCTLHP SDQLALEGPL SRVKSLKKSL RQSFRRMRRS
RVSSRKRHPA GPPGEAQEGS AKAERPGLQN MELAPVQRKI EARSAEDSFT GFVRTLYFAD
TYLKDSSRHC PSLWAGTNGG TIYAFSLRVP PAERRMDESV RAEQAKEIQL MHRAPVVGIL
VLDGHSVPLP EPLEVAHDLS KSPDMQGSHQ LLVVSEEQFK VFTLPKVSAK LKLKLTALEG
SRVRRVSVAH FGSRRAEDYG EHHLAVLTNL GDIQVVSLPL LKPQVRYSCI RREDVSGIAS
CVFTKYGQGF YLISPSEFER FSLSTKWLVE PRCLVDSAET KNHRPGNGAG PKKAPSRARN
SGTQSDGEEK QPGLVMERAL LSDERVLKEI QSTLEGDRGS GNWRSHRAAV GCSLSNGGE*

speed

0.61 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