Yum, tasty mutations...

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 no
known variant Reference ID: rs5174
databasehomozygous (T/T)heterozygousallele carriers
1000G102519621
ExAC65411968526226

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
PhyloPPhastCons
(flanking)0.6441
5.0381
(flanking)5.0381
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
effectgDNA positionscoredetection sequence  exon-intron border
Acceptor lost81014.5sequence motif lost- wt: ccca|GCGA
 mu: ccca.GCAA
Acc marginally increased81010wt: 0.9640 / mu: 0.9640 (marginal change - not scored)wt: TGAATTCTTTGGTTTGTCTCCCCAGCGAGTGGCATTAAGCC
mu: TGAATTCTTTGGTTTGTCTCCCCAGCAAGTGGCATTAAGCC		 ctcc|CCAG
Donor marginally increased81012wt: 0.8669 / mu: 0.9363 (marginal change - not scored)wt: CTCCCCAGCGAGTGG
mu: CTCCCCAGCAAGTGG		 CCCC|agcg
Donor increased81017wt: 0.50 / mu: 0.66wt: CAGCGAGTGGCATTA
mu: CAGCAAGTGGCATTA		 GCGA|gtgg
Donor marginally increased81013wt: 0.8369 / mu: 0.8562 (marginal change - not scored)wt: TCCCCAGCGAGTGGC
mu: TCCCCAGCAAGTGGC		 CCCA|gcga
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      952PLSELPVVKSKRVALSLEDDGLP*
mutated  all conserved    952PLSELPVVKSKQVALSLEDD
Ptroglodytes  all identical  ENSPTRG00000000754  949PLSELPVVKSKRVALSLEDD
Mmulatta  all identical  ENSMMUG00000007612  948PLSELPVVKSKRVALSLEDD
Fcatus  all identical  ENSFCAG00000005931  913PLSELPVVKCKRVAL
Mmusculus  all identical  ENSMUSG00000028613  985PLSELPVVKCKRVALSLEDDGLP
Ggallus  no alignment  ENSGALG00000010692  n/a
Trubripes  all identical  ENSTRUG00000018485  911QNGSIHITADCFQRVALSLEDDGYP
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)featuredetails 
848963TOPO_DOMCytoplasmic (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 1
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 1.07 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