Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.0517346656461637 (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 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      446RTAQIGHVYPARVALSLEDDGLP*
mutated  all conserved    446RTAQIGHVYPAQVALSLEDDGLP
Ptroglodytes  not conserved  ENSPTRG00000000754  890RTAQIGHVYPAAIS
Mmulatta  not conserved  ENSMMUG00000007612  889RTAQIGHVYPAAIS
Fcatus  no alignment  ENSFCAG00000005931  n/a
Mmusculus  not conserved  ENSMUSG00000028613  926RTAQIGHVYPAAIS
Ggallus  all identical  ENSGALG00000010692  883RTAQIGHVYPARVALSLEDDGLP
Trubripes  no alignment  ENSTRUG00000018485  n/a
Drerio  all identical  ENSDARG00000070074  974RSEQIGHVYPPRVALSPDDDGFP
Dmelanogaster  no homologue    
Celegans  no alignment  T13C2.6  n/a
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
42826TOPO_DOMExtracellular (Potential).lost
462508REPEATLDL-receptor class B 1.might get lost (downstream of altered splice site)
488488CONFLICTQ -> R (in Ref. 3; CAA99509).might get lost (downstream of altered splice site)
509551REPEATLDL-receptor class B 2.might get lost (downstream of altered splice site)
518518CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
538538CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
552595REPEATLDL-receptor class B 3.might get lost (downstream of altered splice site)
596639REPEATLDL-receptor class B 4.might get lost (downstream of altered splice site)
640681REPEATLDL-receptor class B 5.might get lost (downstream of altered splice site)
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 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 1
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 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 HVYPAQVALS LEDDGLP*
speed 1.10 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