Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999996907727476 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM042704)
  • known disease mutation: rs5487 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:86662774T>CN/A show variant in all transcripts   IGV
HGNC symbol FZD4
Ensembl transcript ID ENST00000531380
Genbank transcript ID NM_012193
UniProt peptide Q9ULV1
alteration type single base exchange
alteration region CDS
DNA changes c.1024A>G
cDNA.1330A>G
g.3660A>G
AA changes M342V Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 342
frameshift no
known variant Reference ID: rs80358293
databasehomozygous (C/C)heterozygousallele carriers
1000G011
ExAC---

known disease mutation: rs5487 (pathogenic for Exudative vitreoretinopathy 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM042704)

known disease mutation at this position, please check HGMD for details (HGMD ID CM042704)
known disease mutation at this position, please check HGMD for details (HGMD ID CM042704)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.571
3.4631
(flanking)0.5470.998
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased3654wt: 0.9421 / mu: 0.9931 (marginal change - not scored)wt: AAGCCATTGAAATGC
mu: AAGCCATTGAAGTGC		 GCCA|ttga
distance from splice site 739
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      342AGLKWGHEAIEMHSSYFHIAAWAI
mutated  all conserved    342AGLKWGHEAIEVHSSYFHIAAWA
Ptroglodytes  all identical  ENSPTRG00000004148  342AGLKWGHEAIEMHSSYFHIAAWA
Mmulatta  all identical  ENSMMUG00000004048  342AGLKWGHEAIEMHSSYFHIAAWA
Fcatus  all identical  ENSFCAG00000011826  345AGLKWGHEAIEMHSSYFHIAAWA
Mmusculus  all identical  ENSMUSG00000049791  342AGLKWGHEAIEMHSSYFHIAAWA
Ggallus  all identical  ENSGALG00000017242  330AGLKWGHEAIEMHSSYFHIAAWA
Trubripes  all identical  ENSTRUG00000006345  334AGLKWGHEAIEMHSSYFHIAAWA
Drerio  all identical  ENSDARG00000077111  329AGLKWGHEAIEMHSSYFHIAAWA
Dmelanogaster  not conserved  FBgn0016797  435AGLKWGNEAITKHSQYFHLAAWL
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000010434  328AGLKWGHEAIEMHSSYFHIAAWA
protein features
start (aa)end (aa)featuredetails 
324344TOPO_DOMCytoplasmic (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1614 / 1614
position (AA) of stopcodon in wt / mu AA sequence 538 / 538
position of stopcodon in wt / mu cDNA 1920 / 1920
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 307 / 307
chromosome 11
strand -1
last intron/exon boundary 592
theoretical NMD boundary in CDS 235
length of CDS 1614
coding sequence (CDS) position 1024
cDNA position
(for ins/del: last normal base / first normal base)		 1330
gDNA position
(for ins/del: last normal base / first normal base)		 3660
chromosomal position
(for ins/del: last normal base / first normal base)		 86662774
original gDNA sequence snippet GGGGTCATGAAGCCATTGAAATGCACAGCTCTTATTTCCAC
altered gDNA sequence snippet GGGGTCATGAAGCCATTGAAGTGCACAGCTCTTATTTCCAC
original cDNA sequence snippet GGGGTCATGAAGCCATTGAAATGCACAGCTCTTATTTCCAC
altered cDNA sequence snippet GGGGTCATGAAGCCATTGAAGTGCACAGCTCTTATTTCCAC
wildtype AA sequence MAWRGAGPSV PGAPGGVGLS LGLLLQLLLL LGPARGFGDE EERRCDPIRI SMCQNLGYNV
TKMPNLVGHE LQTDAELQLT TFTPLIQYGC SSQLQFFLCS VYVPMCTEKI NIPIGPCGGM
CLSVKRRCEP VLKEFGFAWP ESLNCSKFPP QNDHNHMCME GPGDEEVPLP HKTPIQPGEE
CHSVGTNSDQ YIWVKRSLNC VLKCGYDAGL YSRSAKEFTD IWMAVWASLC FISTAFTVLT
FLIDSSRFSY PERPIIFLSM CYNIYSIAYI VRLTVGRERI SCDFEEAAEP VLIQEGLKNT
GCAIIFLLMY FFGMASSIWW VILTLTWFLA AGLKWGHEAI EMHSSYFHIA AWAIPAVKTI
VILIMRLVDA DELTGLCYVG NQNLDALTGF VVAPLFTYLV IGTLFIAAGL VALFKIRSNL
QKDGTKTDKL ERLMVKIGVF SVLYTVPATC VIACYFYEIS NWALFRYSAD DSNMAVEMLK
IFMSLLVGIT SGMWIWSAKT LHTWQKCSNR LVNSGKVKRE KRGNGWVKPG KGSETVV*
mutated AA sequence MAWRGAGPSV PGAPGGVGLS LGLLLQLLLL LGPARGFGDE EERRCDPIRI SMCQNLGYNV
TKMPNLVGHE LQTDAELQLT TFTPLIQYGC SSQLQFFLCS VYVPMCTEKI NIPIGPCGGM
CLSVKRRCEP VLKEFGFAWP ESLNCSKFPP QNDHNHMCME GPGDEEVPLP HKTPIQPGEE
CHSVGTNSDQ YIWVKRSLNC VLKCGYDAGL YSRSAKEFTD IWMAVWASLC FISTAFTVLT
FLIDSSRFSY PERPIIFLSM CYNIYSIAYI VRLTVGRERI SCDFEEAAEP VLIQEGLKNT
GCAIIFLLMY FFGMASSIWW VILTLTWFLA AGLKWGHEAI EVHSSYFHIA AWAIPAVKTI
VILIMRLVDA DELTGLCYVG NQNLDALTGF VVAPLFTYLV IGTLFIAAGL VALFKIRSNL
QKDGTKTDKL ERLMVKIGVF SVLYTVPATC VIACYFYEIS NWALFRYSAD DSNMAVEMLK
IFMSLLVGIT SGMWIWSAKT LHTWQKCSNR LVNSGKVKRE KRGNGWVKPG KGSETVV*
speed 0.75 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