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 5 transcript(s)...
Querying Taster for transcript #1: ENST00000306052
Querying Taster for transcript #2: ENST00000371454
Querying Taster for transcript #3: ENST00000465675
Querying Taster for transcript #4: ENST00000354412
Querying Taster for transcript #5: ENST00000347547
MT speed 0 s - this script 6.942222 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
LRP8	polymorphism_automatic	0.909802971408288	simple_aae		affected		R689Q	single base exchange	rs5174		show file
LRP8	polymorphism_automatic	0.948265334353836	simple_aae		affected		R893Q	single base exchange	rs5174		show file
LRP8	polymorphism_automatic	0.948265334353836	simple_aae		affected		R446Q	single base exchange	rs5174		show file
LRP8	polymorphism_automatic	0.999993988082974	simple_aae		affected		R952Q	single base exchange	rs5174		show file
LRP8	polymorphism_automatic	0.999995382841845	simple_aae		affected		R782Q	single base exchange	rs5174		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.0901970285917115 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM074332)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:53712727C>TN/A show variant in all transcripts IGV

HGNC symbol

LRP8

Ensembl transcript ID

ENST00000354412

Genbank transcript ID

NM_017522

UniProt peptide

Q14114

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2066G>A
cDNA.2066G>A
g.81016G>A

AA changes

R689Q Score: 43 explain score(s)

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

689

frameshift

known variant

Reference ID: rs5174

database	homozygous (T/T)	heterozygous	allele carriers
1000G	102	519	621
ExAC	6541	19685	26226

known disease mutation at this position, please check HGMD for details (HGMD ID CM074332)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.644	1
	5.038	1
(flanking)	5.038	1

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Acceptor lost	81014.5	sequence motif lost	-	wt: ccca\|GCGA mu: ccca.GCAA
Acc marginally increased	81010	wt: 0.9640 / mu: 0.9640 (marginal change - not scored)	wt: TGAATTCTTTGGTTTGTCTCCCCAGCGAGTGGCATTAAGCC mu: TGAATTCTTTGGTTTGTCTCCCCAGCAAGTGGCATTAAGCC	ctcc\|CCAG
Donor marginally increased	81013	wt: 0.8369 / mu: 0.8562 (marginal change - not scored)	wt: TCCCCAGCGAGTGGC mu: TCCCCAGCAAGTGGC	CCCA\|gcga
Donor marginally increased	81012	wt: 0.8669 / mu: 0.9363 (marginal change - not scored)	wt: CTCCCCAGCGAGTGG mu: CTCCCCAGCAAGTGG	CCCC\|agcg
Donor increased	81017	wt: 0.50 / mu: 0.66	wt: CAGCGAGTGGCATTA mu: CAGCAAGTGGCATTA	GCGA\|gtgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

689

mutated

all conserved

689

Ptroglodytes

no alignment

ENSPTRG00000000754

n/a

Mmulatta

no alignment

ENSMMUG00000007612

n/a

Fcatus

no alignment

ENSFCAG00000005931

n/a

Mmusculus

no alignment

ENSMUSG00000028613

n/a

Ggallus

no alignment

ENSGALG00000010692

n/a

Trubripes

no alignment

ENSTRUG00000018485

n/a

Drerio

no alignment

ENSDARG00000070074

n/a

Dmelanogaster

no homologue

Celegans

no alignment

T13C2.6

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
42	826	TOPO_DOM	Extracellular (Potential).	lost
740	798	REGION	Clustered O-linked oligosaccharides.	might get lost (downstream of altered splice site)
772	772	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
807	807	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
827	847	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
848	963	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2103 / 2103

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

701 / 701

position of stopcodon in wt / mu cDNA

2103 / 2103

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

1 / 1

chromosome

strand

-1

last intron/exon boundary

2065

theoretical NMD boundary in CDS

2014

length of CDS

2103

coding sequence (CDS) position

2066

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

2066

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

81016

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

53712727

original gDNA sequence snippet

CTTTGGTTTGTCTCCCCAGCGAGTGGCATTAAGCCTTGAAG

altered gDNA sequence snippet

CTTTGGTTTGTCTCCCCAGCAAGTGGCATTAAGCCTTGAAG

original cDNA sequence snippet

TGGCCATGTCTATCCTGCACGAGTGGCATTAAGCCTTGAAG

altered cDNA sequence snippet

TGGCCATGTCTATCCTGCACAAGTGGCATTAAGCCTTGAAG

wildtype AA sequence

MGLPEPGPLR LLALLLLLLL LLLLQLQHLA AAAADPLLGG QGPAKDCEKD QFQCRNERCI
PSVWRCDEDD DCLDHSDEDD CPKKTCADSD FTCDNGHCIH ERWKCDGEEE CPDGSDESEA
TCTKQVCPAE KLSCGPTSHK CVPASWRCDG EKDCEGGADE AGCATSLGTC RGDEFQCGDG
TCVLAIKHCN QEQDCPDGSD EAGCLQGLNE CLHNNGGCSH ICTDLKIGFE CTCPAGFQLL
DQKTCGDIDE CKDPDACSQI CVNYKGYFKC ECYPGYEMDL LTKNCKAAAG KSPSLIFTNR
HEVRRIDLVK RNYSRLIPML KNVVALDVEV ATNRIYWCDL SYRKIYSAYM DKASDPKEQE
VLIDEQLHSP EGLAVDWVHK HIYWTDSGNK TISVATVDGG RRRTLFSRNL SEPRAIAVDP
LRGFMYWSDW GDQAKIEKSG LNGVDRQTLV SDNIEWPNGI TLDLLSQRLY WVDSKLHQLS
SIDFSGGNRK TLISSTDFLS HPFGIAVFED KVFWTDLENE AIFSANRLNG LEISILAENL
NNPHDIVIFH ELKQPRAPDA CELSVQPNGG CEYLCLPAPQ ISSHSPKYTC ACPDTMWLGP
DMKRCYRDAN EDSKMGSTVT AAVIGIIVPI VVIALLCMSG YLIWRNWKRK NTKSMNFDNP
VYRKTTEEED EDELHIGRTA QIGHVYPARV ALSLEDDGLP *

mutated AA sequence

speed

1.13 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: 0.0517346656461638 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM074332)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:53712727C>TN/A show variant in all transcripts IGV

HGNC symbol

LRP8

Ensembl transcript ID

ENST00000371454

Genbank transcript ID

NM_001018054

UniProt peptide

Q14114

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2678G>A
cDNA.2820G>A
g.81016G>A

AA changes

R893Q Score: 43 explain score(s)

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

893

frameshift

known variant

Reference ID: rs5174

database	homozygous (T/T)	heterozygous	allele carriers
1000G	102	519	621
ExAC	6541	19685	26226

known disease mutation at this position, please check HGMD for details (HGMD ID CM074332)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.644	1
	5.038	1
(flanking)	5.038	1

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Acceptor lost	81014.5	sequence motif lost	-	wt: ccca\|GCGA mu: ccca.GCAA
Acc marginally increased	81010	wt: 0.9640 / mu: 0.9640 (marginal change - not scored)	wt: TGAATTCTTTGGTTTGTCTCCCCAGCGAGTGGCATTAAGCC mu: TGAATTCTTTGGTTTGTCTCCCCAGCAAGTGGCATTAAGCC	ctcc\|CCAG
Donor marginally increased	81013	wt: 0.8369 / mu: 0.8562 (marginal change - not scored)	wt: TCCCCAGCGAGTGGC mu: TCCCCAGCAAGTGGC	CCCA\|gcga
Donor marginally increased	81012	wt: 0.8669 / mu: 0.9363 (marginal change - not scored)	wt: CTCCCCAGCGAGTGG mu: CTCCCCAGCAAGTGG	CCCC\|agcg
Donor increased	81017	wt: 0.50 / mu: 0.66	wt: CAGCGAGTGGCATTA mu: CAGCAAGTGGCATTA	GCGA\|gtgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

893

mutated

all conserved

893

Ptroglodytes

not conserved

ENSPTRG00000000754

890

Mmulatta

not conserved

ENSMMUG00000007612

889

Fcatus

no alignment

ENSFCAG00000005931

n/a

Mmusculus

not conserved

ENSMUSG00000028613

926

Ggallus

all identical

ENSGALG00000010692

883

Trubripes

no alignment

ENSTRUG00000018485

n/a

Drerio

all identical

ENSDARG00000070074

972

Dmelanogaster

no homologue

Celegans

no alignment

T13C2.6

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
848	963	TOPO_DOM	Cytoplasmic (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2715 / 2715

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

905 / 905

position of stopcodon in wt / mu cDNA

2857 / 2857

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

143 / 143

chromosome

strand

-1

last intron/exon boundary

2819

theoretical NMD boundary in CDS

2626

length of CDS

2715

coding sequence (CDS) position

2678

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

2820

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

81016

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

53712727

original gDNA sequence snippet

CTTTGGTTTGTCTCCCCAGCGAGTGGCATTAAGCCTTGAAG

altered gDNA sequence snippet

CTTTGGTTTGTCTCCCCAGCAAGTGGCATTAAGCCTTGAAG

original cDNA sequence snippet

TGGCCATGTCTATCCTGCACGAGTGGCATTAAGCCTTGAAG

altered cDNA sequence snippet

TGGCCATGTCTATCCTGCACAAGTGGCATTAAGCCTTGAAG

wildtype AA sequence

MGLPEPGPLR LLALLLLLLL LLLLQLQHLA AAAADPLLGG QGPAKDCEKD QFQCRNERCI
PSVWRCDEDD DCLDHSDEDD CPKKTCADSD FTCDNGHCIH ERWKCDGEEE CPDGSDESEA
TCTKQVCPAE KLSCGPTSHK CVPASWRCDG EKDCEGGADE AGCATLCAPH EFQCGNRSCL
AAVFVCDGDD DCGDGSDERG CADPACGPRE FRCGGDGGGA CIPERWVCDR QFDCEDRSDE
AAELCGRPGP GATSAPAACA TASQFACRSG ECVHLGWRCD GDRDCKDKSD EADCPLGTCR
GDEFQCGDGT CVLAIKHCNQ EQDCPDGSDE AGCLQGLNEC LHNNGGCSHI CTDLKIGFEC
TCPAGFQLLD QKTCGDIDEC KDPDACSQIC VNYKGYFKCE CYPGYEMDLL TKNCKAAAGK
SPSLIFTNRH EVRRIDLVKR NYSRLIPMLK NVVALDVEVA TNRIYWCDLS YRKIYSAYMD
KASDPKEQEV LIDEQLHSPE GLAVDWVHKH IYWTDSGNKT ISVATVDGGR RRTLFSRNLS
EPRAIAVDPL RGFMYWSDWG DQAKIEKSGL NGVDRQTLVS DNIEWPNGIT LDLLSQRLYW
VDSKLHQLSS IDFSGGNRKT LISSTDFLSH PFGIAVFEDK VFWTDLENEA IFSANRLNGL
EISILAENLN NPHDIVIFHE LKQPRAPDAC ELSVQPNGGC EYLCLPAPQI SSHSPKYTCA
CPDTMWLGPD MKRCYRAPQS TSTTTLASTM TRTVPATTRA PGTTVHRSTY QNHSTETPSL
TAAVPSSVSV PRAPSISPST LSPATSNHSQ HYANEDSKMG STVTAAVIGI IVPIVVIALL
CMSGYLIWRN WKRKNTKSMN FDNPVYRKTT EEEDEDELHI GRTAQIGHVY PARVALSLED
DGLP*

mutated AA sequence

MGLPEPGPLR LLALLLLLLL LLLLQLQHLA AAAADPLLGG QGPAKDCEKD QFQCRNERCI
PSVWRCDEDD DCLDHSDEDD CPKKTCADSD FTCDNGHCIH ERWKCDGEEE CPDGSDESEA
TCTKQVCPAE KLSCGPTSHK CVPASWRCDG EKDCEGGADE AGCATLCAPH EFQCGNRSCL
AAVFVCDGDD DCGDGSDERG CADPACGPRE FRCGGDGGGA CIPERWVCDR QFDCEDRSDE
AAELCGRPGP GATSAPAACA TASQFACRSG ECVHLGWRCD GDRDCKDKSD EADCPLGTCR
GDEFQCGDGT CVLAIKHCNQ EQDCPDGSDE AGCLQGLNEC LHNNGGCSHI CTDLKIGFEC
TCPAGFQLLD QKTCGDIDEC KDPDACSQIC VNYKGYFKCE CYPGYEMDLL TKNCKAAAGK
SPSLIFTNRH EVRRIDLVKR NYSRLIPMLK NVVALDVEVA TNRIYWCDLS YRKIYSAYMD
KASDPKEQEV LIDEQLHSPE GLAVDWVHKH IYWTDSGNKT ISVATVDGGR RRTLFSRNLS
EPRAIAVDPL RGFMYWSDWG DQAKIEKSGL NGVDRQTLVS DNIEWPNGIT LDLLSQRLYW
VDSKLHQLSS IDFSGGNRKT LISSTDFLSH PFGIAVFEDK VFWTDLENEA IFSANRLNGL
EISILAENLN NPHDIVIFHE LKQPRAPDAC ELSVQPNGGC EYLCLPAPQI SSHSPKYTCA
CPDTMWLGPD MKRCYRAPQS TSTTTLASTM TRTVPATTRA PGTTVHRSTY QNHSTETPSL
TAAVPSSVSV PRAPSISPST LSPATSNHSQ HYANEDSKMG STVTAAVIGI IVPIVVIALL
CMSGYLIWRN WKRKNTKSMN FDNPVYRKTT EEEDEDELHI GRTAQIGHVY PAQVALSLED
DGLP*

speed

0.83 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.0517346656461638 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM074332)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:53712727C>TN/A show variant in all transcripts IGV

HGNC symbol

LRP8

Ensembl transcript ID

ENST00000465675

Genbank transcript ID

N/A

UniProt peptide

Q14114

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1337G>A
cDNA.2183G>A
g.81016G>A

AA changes

R446Q Score: 43 explain score(s)

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

446

frameshift

known variant

Reference ID: rs5174

database	homozygous (T/T)	heterozygous	allele carriers
1000G	102	519	621
ExAC	6541	19685	26226

known disease mutation at this position, please check HGMD for details (HGMD ID CM074332)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.644	1
	5.038	1
(flanking)	5.038	1

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Acceptor lost	81014.5	sequence motif lost	-	wt: ccca\|GCGA mu: ccca.GCAA
Acc marginally increased	81010	wt: 0.9640 / mu: 0.9640 (marginal change - not scored)	wt: TGAATTCTTTGGTTTGTCTCCCCAGCGAGTGGCATTAAGCC mu: TGAATTCTTTGGTTTGTCTCCCCAGCAAGTGGCATTAAGCC	ctcc\|CCAG
Donor marginally increased	81013	wt: 0.8369 / mu: 0.8562 (marginal change - not scored)	wt: TCCCCAGCGAGTGGC mu: TCCCCAGCAAGTGGC	CCCA\|gcga
Donor marginally increased	81012	wt: 0.8669 / mu: 0.9363 (marginal change - not scored)	wt: CTCCCCAGCGAGTGG mu: CTCCCCAGCAAGTGG	CCCC\|agcg
Donor increased	81017	wt: 0.50 / mu: 0.66	wt: CAGCGAGTGGCATTA mu: CAGCAAGTGGCATTA	GCGA\|gtgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

446

mutated

all conserved

446

Ptroglodytes

not conserved

ENSPTRG00000000754

890

Mmulatta

not conserved

ENSMMUG00000007612

889

Fcatus

no alignment

ENSFCAG00000005931

n/a

Mmusculus

not conserved

ENSMUSG00000028613

926

Ggallus

all identical

ENSGALG00000010692

883

Trubripes

no alignment

ENSTRUG00000018485

n/a

Drerio

all identical

ENSDARG00000070074

974

Dmelanogaster

no homologue

Celegans

no alignment

T13C2.6

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
42	826	TOPO_DOM	Extracellular (Potential).	lost
462	508	REPEAT	LDL-receptor class B 1.	might get lost (downstream of altered splice site)
488	488	CONFLICT	Q -> R (in Ref. 3; CAA99509).	might get lost (downstream of altered splice site)
509	551	REPEAT	LDL-receptor class B 2.	might get lost (downstream of altered splice site)
518	518	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
538	538	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
552	595	REPEAT	LDL-receptor class B 3.	might get lost (downstream of altered splice site)
596	639	REPEAT	LDL-receptor class B 4.	might get lost (downstream of altered splice site)
640	681	REPEAT	LDL-receptor class B 5.	might get lost (downstream of altered splice site)
740	798	REGION	Clustered O-linked oligosaccharides.	might get lost (downstream of altered splice site)
772	772	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
807	807	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
827	847	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
848	963	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1374 / 1374

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

458 / 458

position of stopcodon in wt / mu cDNA

2220 / 2220

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

847 / 847

chromosome

strand

-1

last intron/exon boundary

2182

theoretical NMD boundary in CDS

1285

length of CDS

1374

coding sequence (CDS) position

1337

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

2183

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

81016

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

53712727

original gDNA sequence snippet

CTTTGGTTTGTCTCCCCAGCGAGTGGCATTAAGCCTTGAAG

altered gDNA sequence snippet

CTTTGGTTTGTCTCCCCAGCAAGTGGCATTAAGCCTTGAAG

original cDNA sequence snippet

TGGCCATGTCTATCCTGCACGAGTGGCATTAAGCCTTGAAG

altered cDNA sequence snippet

TGGCCATGTCTATCCTGCACAAGTGGCATTAAGCCTTGAAG

wildtype AA sequence

MLKNVVALDV EVATNRIYWC DLSYRKIYSA YMDKASDPKE QEVLIDEQLH SPEGLAVDWV
HKHIYWTDSG NKTISVATVD GGRRRTLFSR NLSEPRAIAV DPLRGFMYWS DWGDQAKIEK
SGLNGVDRQT LVSDNIEWPN GITLDLLSQR LYWVDSKLHQ LSSIDFSGGN RKTLISSTDF
LSHPFGIAVF EDKVFWTDLE NEAIFSANRL NGLEISILAE NLNNPHDIVI FHELKQPRAP
DACELSVQPN GGCEYLCLPA PQISSHSPKY TCACPDTMWL GPDMKRCYRA PQSTSTTTLA
STMTRTVPAT TRAPGTTVHR STYQNHSTET PSLTAAVPSS VSVPRAPSIS PSTLSPATSN
HSQHYANEDS KMGSTVTAAV IGIIVPIVVI ALLCMSGYLI WRNWKRKNTK SMNFDNPVYR
KTTEEEDEDE LHIGRTAQIG HVYPARVALS LEDDGLP*

mutated AA sequence

speed

1.95 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 6.0119170264792e-06 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM074332)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:53712727C>TN/A show variant in all transcripts IGV

HGNC symbol

LRP8

Ensembl transcript ID

ENST00000306052

Genbank transcript ID

NM_004631

UniProt peptide

Q14114

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2855G>A
cDNA.2957G>A
g.81016G>A

AA changes

R952Q Score: 43 explain score(s)

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

952

frameshift

known variant

Reference ID: rs5174

database	homozygous (T/T)	heterozygous	allele carriers
1000G	102	519	621
ExAC	6541	19685	26226

known disease mutation at this position, please check HGMD for details (HGMD ID CM074332)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.644	1
	5.038	1
(flanking)	5.038	1

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Acceptor lost	81014.5	sequence motif lost	-	wt: ccca\|GCGA mu: ccca.GCAA
Acc marginally increased	81010	wt: 0.9640 / mu: 0.9640 (marginal change - not scored)	wt: TGAATTCTTTGGTTTGTCTCCCCAGCGAGTGGCATTAAGCC mu: TGAATTCTTTGGTTTGTCTCCCCAGCAAGTGGCATTAAGCC	ctcc\|CCAG
Donor marginally increased	81013	wt: 0.8369 / mu: 0.8562 (marginal change - not scored)	wt: TCCCCAGCGAGTGGC mu: TCCCCAGCAAGTGGC	CCCA\|gcga
Donor marginally increased	81012	wt: 0.8669 / mu: 0.9363 (marginal change - not scored)	wt: CTCCCCAGCGAGTGG mu: CTCCCCAGCAAGTGG	CCCC\|agcg
Donor increased	81017	wt: 0.50 / mu: 0.66	wt: CAGCGAGTGGCATTA mu: CAGCAAGTGGCATTA	GCGA\|gtgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

952

mutated

all conserved

952

Ptroglodytes

all identical

ENSPTRG00000000754

949

Mmulatta

all identical

ENSMMUG00000007612

948

Fcatus

all identical

ENSFCAG00000005931

913

Mmusculus

all identical

ENSMUSG00000028613

985

Ggallus

no alignment

ENSGALG00000010692

n/a

Trubripes

all identical

ENSTRUG00000018485

911

DCF

Drerio

no alignment

ENSDARG00000070074

n/a

Dmelanogaster

no homologue

Celegans

no alignment

T13C2.6

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
848	963	TOPO_DOM	Cytoplasmic (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2892 / 2892

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

964 / 964

position of stopcodon in wt / mu cDNA

2994 / 2994

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

103 / 103

chromosome

strand

-1

last intron/exon boundary

2956

theoretical NMD boundary in CDS

2803

length of CDS

2892

coding sequence (CDS) position

2855

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

2957

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

81016

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

53712727

original gDNA sequence snippet

CTTTGGTTTGTCTCCCCAGCGAGTGGCATTAAGCCTTGAAG

altered gDNA sequence snippet

CTTTGGTTTGTCTCCCCAGCAAGTGGCATTAAGCCTTGAAG

original cDNA sequence snippet

GCCTGTCGTCAAATCCAAGCGAGTGGCATTAAGCCTTGAAG

altered cDNA sequence snippet

GCCTGTCGTCAAATCCAAGCAAGTGGCATTAAGCCTTGAAG

wildtype AA sequence

MGLPEPGPLR LLALLLLLLL LLLLQLQHLA AAAADPLLGG QGPAKDCEKD QFQCRNERCI
PSVWRCDEDD DCLDHSDEDD CPKKTCADSD FTCDNGHCIH ERWKCDGEEE CPDGSDESEA
TCTKQVCPAE KLSCGPTSHK CVPASWRCDG EKDCEGGADE AGCATLCAPH EFQCGNRSCL
AAVFVCDGDD DCGDGSDERG CADPACGPRE FRCGGDGGGA CIPERWVCDR QFDCEDRSDE
AAELCGRPGP GATSAPAACA TASQFACRSG ECVHLGWRCD GDRDCKDKSD EADCPLGTCR
GDEFQCGDGT CVLAIKHCNQ EQDCPDGSDE AGCLQGLNEC LHNNGGCSHI CTDLKIGFEC
TCPAGFQLLD QKTCGDIDEC KDPDACSQIC VNYKGYFKCE CYPGYEMDLL TKNCKAAAGK
SPSLIFTNRH EVRRIDLVKR NYSRLIPMLK NVVALDVEVA TNRIYWCDLS YRKIYSAYMD
KASDPKEQEV LIDEQLHSPE GLAVDWVHKH IYWTDSGNKT ISVATVDGGR RRTLFSRNLS
EPRAIAVDPL RGFMYWSDWG DQAKIEKSGL NGVDRQTLVS DNIEWPNGIT LDLLSQRLYW
VDSKLHQLSS IDFSGGNRKT LISSTDFLSH PFGIAVFEDK VFWTDLENEA IFSANRLNGL
EISILAENLN NPHDIVIFHE LKQPRAPDAC ELSVQPNGGC EYLCLPAPQI SSHSPKYTCA
CPDTMWLGPD MKRCYRAPQS TSTTTLASTM TRTVPATTRA PGTTVHRSTY QNHSTETPSL
TAAVPSSVSV PRAPSISPST LSPATSNHSQ HYANEDSKMG STVTAAVIGI IVPIVVIALL
CMSGYLIWRN WKRKNTKSMN FDNPVYRKTT EEEDEDELHI GRTAQIGHVY PAAISSFDRP
LWAEPCLGET REPEDPAPAL KELFVLPGEP RSQLHQLPKN PLSELPVVKS KRVALSLEDD
GLP*

mutated AA sequence

MGLPEPGPLR LLALLLLLLL LLLLQLQHLA AAAADPLLGG QGPAKDCEKD QFQCRNERCI
PSVWRCDEDD DCLDHSDEDD CPKKTCADSD FTCDNGHCIH ERWKCDGEEE CPDGSDESEA
TCTKQVCPAE KLSCGPTSHK CVPASWRCDG EKDCEGGADE AGCATLCAPH EFQCGNRSCL
AAVFVCDGDD DCGDGSDERG CADPACGPRE FRCGGDGGGA CIPERWVCDR QFDCEDRSDE
AAELCGRPGP GATSAPAACA TASQFACRSG ECVHLGWRCD GDRDCKDKSD EADCPLGTCR
GDEFQCGDGT CVLAIKHCNQ EQDCPDGSDE AGCLQGLNEC LHNNGGCSHI CTDLKIGFEC
TCPAGFQLLD QKTCGDIDEC KDPDACSQIC VNYKGYFKCE CYPGYEMDLL TKNCKAAAGK
SPSLIFTNRH EVRRIDLVKR NYSRLIPMLK NVVALDVEVA TNRIYWCDLS YRKIYSAYMD
KASDPKEQEV LIDEQLHSPE GLAVDWVHKH IYWTDSGNKT ISVATVDGGR RRTLFSRNLS
EPRAIAVDPL RGFMYWSDWG DQAKIEKSGL NGVDRQTLVS DNIEWPNGIT LDLLSQRLYW
VDSKLHQLSS IDFSGGNRKT LISSTDFLSH PFGIAVFEDK VFWTDLENEA IFSANRLNGL
EISILAENLN NPHDIVIFHE LKQPRAPDAC ELSVQPNGGC EYLCLPAPQI SSHSPKYTCA
CPDTMWLGPD MKRCYRAPQS TSTTTLASTM TRTVPATTRA PGTTVHRSTY QNHSTETPSL
TAAVPSSVSV PRAPSISPST LSPATSNHSQ HYANEDSKMG STVTAAVIGI IVPIVVIALL
CMSGYLIWRN WKRKNTKSMN FDNPVYRKTT EEEDEDELHI GRTAQIGHVY PAAISSFDRP
LWAEPCLGET REPEDPAPAL KELFVLPGEP RSQLHQLPKN PLSELPVVKS KQVALSLEDD
GLP*

speed

1.50 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 4.61715815527211e-06 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM074332)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:53712727C>TN/A show variant in all transcripts IGV

HGNC symbol

LRP8

Ensembl transcript ID

ENST00000347547

Genbank transcript ID

NM_033300

UniProt peptide

Q14114

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2345G>A
cDNA.2345G>A
g.81016G>A

AA changes

R782Q Score: 43 explain score(s)

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

782

frameshift

known variant

Reference ID: rs5174

database	homozygous (T/T)	heterozygous	allele carriers
1000G	102	519	621
ExAC	6541	19685	26226

known disease mutation at this position, please check HGMD for details (HGMD ID CM074332)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.644	1
	5.038	1
(flanking)	5.038	1

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Acceptor lost	81014.5	sequence motif lost	-	wt: ccca\|GCGA mu: ccca.GCAA
Acc marginally increased	81010	wt: 0.9640 / mu: 0.9640 (marginal change - not scored)	wt: TGAATTCTTTGGTTTGTCTCCCCAGCGAGTGGCATTAAGCC mu: TGAATTCTTTGGTTTGTCTCCCCAGCAAGTGGCATTAAGCC	ctcc\|CCAG
Donor marginally increased	81013	wt: 0.8369 / mu: 0.8562 (marginal change - not scored)	wt: TCCCCAGCGAGTGGC mu: TCCCCAGCAAGTGGC	CCCA\|gcga
Donor marginally increased	81012	wt: 0.8669 / mu: 0.9363 (marginal change - not scored)	wt: CTCCCCAGCGAGTGG mu: CTCCCCAGCAAGTGG	CCCC\|agcg
Donor increased	81017	wt: 0.50 / mu: 0.66	wt: CAGCGAGTGGCATTA mu: CAGCAAGTGGCATTA	GCGA\|gtgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

782

mutated

all conserved

782

Ptroglodytes

all identical

ENSPTRG00000000754

949

Mmulatta

all identical

ENSMMUG00000007612

948

Fcatus

all identical

ENSFCAG00000005931

913

Mmusculus

all identical

ENSMUSG00000028613

985

Ggallus

no alignment

ENSGALG00000010692

n/a

Trubripes

all identical

ENSTRUG00000018485

911

DCF

Drerio

no alignment

ENSDARG00000070074

n/a

Dmelanogaster

no homologue

Celegans

no alignment

T13C2.6

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
42	826	TOPO_DOM	Extracellular (Potential).	lost
740	798	REGION	Clustered O-linked oligosaccharides.	lost
807	807	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
827	847	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
848	963	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2382 / 2382

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

794 / 794

position of stopcodon in wt / mu cDNA

2382 / 2382

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

1 / 1

chromosome

strand

-1

last intron/exon boundary

2344

theoretical NMD boundary in CDS

2293

length of CDS

2382

coding sequence (CDS) position

2345

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

2345

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

81016

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

53712727

original gDNA sequence snippet

CTTTGGTTTGTCTCCCCAGCGAGTGGCATTAAGCCTTGAAG

altered gDNA sequence snippet

CTTTGGTTTGTCTCCCCAGCAAGTGGCATTAAGCCTTGAAG

original cDNA sequence snippet

GCCTGTCGTCAAATCCAAGCGAGTGGCATTAAGCCTTGAAG

altered cDNA sequence snippet

GCCTGTCGTCAAATCCAAGCAAGTGGCATTAAGCCTTGAAG

wildtype AA sequence

MGLPEPGPLR LLALLLLLLL LLLLQLQHLA AAAADPLLGG QGPAKDCEKD QFQCRNERCI
PSVWRCDEDD DCLDHSDEDD CPKKTCADSD FTCDNGHCIH ERWKCDGEEE CPDGSDESEA
TCTKQVCPAE KLSCGPTSHK CVPASWRCDG EKDCEGGADE AGCATWLNEC LHNNGGCSHI
CTDLKIGFEC TCPAGFQLLD QKTCGDIDEC KDPDACSQIC VNYKGYFKCE CYPGYEMDLL
TKNCKAAAGK SPSLIFTNRH EVRRIDLVKR NYSRLIPMLK NVVALDVEVA TNRIYWCDLS
YRKIYSAYMD KASDPKEQEV LIDEQLHSPE GLAVDWVHKH IYWTDSGNKT ISVATVDGGR
RRTLFSRNLS EPRAIAVDPL RGFMYWSDWG DQAKIEKSGL NGVDRQTLVS DNIEWPNGIT
LDLLSQRLYW VDSKLHQLSS IDFSGGNRKT LISSTDFLSH PFGIAVFEDK VFWTDLENEA
IFSANRLNGL EISILAENLN NPHDIVIFHE LKQPRAPDAC ELSVQPNGGC EYLCLPAPQI
SSHSPKYTCA CPDTMWLGPD MKRCYRAPQS TSTTTLASTM TRTVPATTRA PGTTVHRSTY
QNHSTETPSL TAAVPSSVSV PRAPSISPST LSPATSNHSQ HYANEDSKMG STVTAAVIGI
IVPIVVIALL CMSGYLIWRN WKRKNTKSMN FDNPVYRKTT EEEDEDELHI GRTAQIGHVY
PAAISSFDRP LWAEPCLGET REPEDPAPAL KELFVLPGEP RSQLHQLPKN PLSELPVVKS
KRVALSLEDD GLP*

mutated AA sequence

MGLPEPGPLR LLALLLLLLL LLLLQLQHLA AAAADPLLGG QGPAKDCEKD QFQCRNERCI
PSVWRCDEDD DCLDHSDEDD CPKKTCADSD FTCDNGHCIH ERWKCDGEEE CPDGSDESEA
TCTKQVCPAE KLSCGPTSHK CVPASWRCDG EKDCEGGADE AGCATWLNEC LHNNGGCSHI
CTDLKIGFEC TCPAGFQLLD QKTCGDIDEC KDPDACSQIC VNYKGYFKCE CYPGYEMDLL
TKNCKAAAGK SPSLIFTNRH EVRRIDLVKR NYSRLIPMLK NVVALDVEVA TNRIYWCDLS
YRKIYSAYMD KASDPKEQEV LIDEQLHSPE GLAVDWVHKH IYWTDSGNKT ISVATVDGGR
RRTLFSRNLS EPRAIAVDPL RGFMYWSDWG DQAKIEKSGL NGVDRQTLVS DNIEWPNGIT
LDLLSQRLYW VDSKLHQLSS IDFSGGNRKT LISSTDFLSH PFGIAVFEDK VFWTDLENEA
IFSANRLNGL EISILAENLN NPHDIVIFHE LKQPRAPDAC ELSVQPNGGC EYLCLPAPQI
SSHSPKYTCA CPDTMWLGPD MKRCYRAPQS TSTTTLASTM TRTVPATTRA PGTTVHRSTY
QNHSTETPSL TAAVPSSVSV PRAPSISPST LSPATSNHSQ HYANEDSKMG STVTAAVIGI
IVPIVVIALL CMSGYLIWRN WKRKNTKSMN FDNPVYRKTT EEEDEDELHI GRTAQIGHVY
PAAISSFDRP LWAEPCLGET REPEDPAPAL KELFVLPGEP RSQLHQLPKN PLSELPVVKS
KQVALSLEDD GLP*

speed

0.77 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems