Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999832945004784 (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 CM094608)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:89450587G>TN/A show variant in all transcripts   IGV
HGNC symbol MFGE8
Ensembl transcript ID ENST00000566497
Genbank transcript ID N/A
UniProt peptide Q08431
alteration type single base exchange
alteration region CDS
DNA changes c.226C>A
cDNA.288C>A
g.6056C>A
AA changes L76M Score: 15 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 76
frameshift no
known variant Reference ID: rs1878326
databasehomozygous (T/T)heterozygousallele carriers
1000G105610852141
ExAC23799-148318968

known disease mutation at this position, please check HGMD for details (HGMD ID CM094608)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.771
0.9871
(flanking)1.4891
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 increased6058wt: 0.4449 / mu: 0.4452 (marginal change - not scored)wt: GGCCTGGAGAATGGG
mu: GGCATGGAGAATGGG		 CCTG|gaga
Donor increased6057wt: 0.30 / mu: 0.44wt: GGGCCTGGAGAATGG
mu: GGGCATGGAGAATGG		 GCCT|ggag
Donor gained60520.87mu: CCACTGGGCATGGAG ACTG|ggca
distance from splice site 21
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      76HCETKCVEPLGLENGNIANSQIAA
mutated  all conserved    76HCETKCVEPLGMENGNIANSQIA
Ptroglodytes  all conserved  ENSPTRG00000007426  76HCETKCVEPLGMENGNIANSQIA
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000030605  132AVPNTAVPTPAPTPDLSNNLASRCSTQLGMEGGAIADSQIS
Ggallus  all conserved  ENSGALG00000006702  134MDGDYACKCPSPFFGKTCHARCAIPLGMEGGAISDAQLS
Trubripes  all conserved  ENSTRUG00000016888  169QCQQRCTSLLGMEGGAIVESQI
Drerio  all conserved  ENSDARG00000045803  147HCNLRCISLLGMEGGGIAESQIS
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all conserved  ENSXETG00000017772  137LGDDFSCKCASPYIGKVCNIRCANALGMEGRAISDAQIT
protein features
start (aa)end (aa)featuredetails 
70225DOMAINF5/8 type C 1.lost
212212DISULFIDBy similarity.might get lost (downstream of altered splice site)
216216DISULFIDBy similarity.might get lost (downstream of altered splice site)
225225DISULFIDBy similarity.might get lost (downstream of altered splice site)
228228CARBOHYDN-linked (GlcNAc...); atypical.might get lost (downstream of altered splice site)
230230DISULFIDBy similarity.might get lost (downstream of altered splice site)
230387DOMAINF5/8 type C 2.might get lost (downstream of altered splice site)
238238CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
268268CONFLICTR -> W (in Ref. 5; CAD97938).might get lost (downstream of altered splice site)
325325CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
329329CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
350350CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
352352CONFLICTS -> T (in Ref. 5; CAD97938).might get lost (downstream of altered splice site)
387387DISULFIDBy similarity.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1164 / 1164
position (AA) of stopcodon in wt / mu AA sequence 388 / 388
position of stopcodon in wt / mu cDNA 1226 / 1226
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 63 / 63
chromosome 15
strand -1
last intron/exon boundary 1247
theoretical NMD boundary in CDS 1134
length of CDS 1164
coding sequence (CDS) position 226
cDNA position
(for ins/del: last normal base / first normal base)		 288
gDNA position
(for ins/del: last normal base / first normal base)		 6056
chromosomal position
(for ins/del: last normal base / first normal base)		 89450587
original gDNA sequence snippet AATGTGTCGAGCCACTGGGCCTGGAGAATGGGAACATTGCC
altered gDNA sequence snippet AATGTGTCGAGCCACTGGGCATGGAGAATGGGAACATTGCC
original cDNA sequence snippet AATGTGTCGAGCCACTGGGCCTGGAGAATGGGAACATTGCC
altered cDNA sequence snippet AATGTGTCGAGCCACTGGGCATGGAGAATGGGAACATTGCC
wildtype AA sequence MPRPRLLAAL CGALLCAPSL LVALDICSKN PCHNGGLCEE ISQEVRGDVF PSYTCTCLKG
YAGNHCETKC VEPLGLENGN IANSQIAASS VRVTFLGLQH WVPELARLNR AGMVNAWTPS
SNDDNPWIQV NLLRRMWVTG VVTQGASRLA SHEYLKAFKV AYSLNGHEFD FIHDVNKKHK
EFVGNWNKNA VHVNLFETPV EAQYVRLYPT SCHTACTLRF ELLGCELNGC ANPLGLKNNS
IPDKQITASS SYKTWGLHLF SWNPSYARLD KQGNFNAWVA GSYGNDQWLQ VDLGSSKEVT
GIITQGARNF GSVQFVASYK VAYSNDSANW TEYQDPRTGS SKIFPGNWDN HSHKKNLFET
PILARYVRIL PVAWHNRIAL RLELLGC*
mutated AA sequence MPRPRLLAAL CGALLCAPSL LVALDICSKN PCHNGGLCEE ISQEVRGDVF PSYTCTCLKG
YAGNHCETKC VEPLGMENGN IANSQIAASS VRVTFLGLQH WVPELARLNR AGMVNAWTPS
SNDDNPWIQV NLLRRMWVTG VVTQGASRLA SHEYLKAFKV AYSLNGHEFD FIHDVNKKHK
EFVGNWNKNA VHVNLFETPV EAQYVRLYPT SCHTACTLRF ELLGCELNGC ANPLGLKNNS
IPDKQITASS SYKTWGLHLF SWNPSYARLD KQGNFNAWVA GSYGNDQWLQ VDLGSSKEVT
GIITQGARNF GSVQFVASYK VAYSNDSANW TEYQDPRTGS SKIFPGNWDN HSHKKNLFET
PILARYVRIL PVAWHNRIAL RLELLGC*
speed 1.17 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