mutation t@sting

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	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
Donor marginally increased	81013	wt: 0.8369 / mu: 0.8562 (marginal change - not scored)	wt: TCCCCAGCGAGTGGC mu: TCCCCAGCAAGTGGC	CCCA\|gcga

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

speed

1.25 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