Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.0901970285917114 (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 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 increased81013wt: 0.8369 / mu: 0.8562 (marginal change - not scored)wt: TCCCCAGCGAGTGGC
mu: TCCCCAGCAAGTGGC		 CCCA|gcga
Donor increased81017wt: 0.50 / mu: 0.66wt: CAGCGAGTGGCATTA
mu: CAGCAAGTGGCATTA		 GCGA|gtgg
Donor marginally increased81012wt: 0.8669 / mu: 0.9363 (marginal change - not scored)wt: CTCCCCAGCGAGTGG
mu: CTCCCCAGCAAGTGG		 CCCC|agcg
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      689RTAQIGHVYPARVALSLEDDGLP*
mutated  all conserved    689RTAQIGHVYPAQVALSLEDDGLP
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)featuredetails 
42826TOPO_DOMExtracellular (Potential).lost
740798REGIONClustered O-linked oligosaccharides.might get lost (downstream of altered splice site)
772772CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
807807CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
827847TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
848963TOPO_DOMCytoplasmic (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 1
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 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 QIGHVYPAQV ALSLEDDGLP *
speed 1.37 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