Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999997945921173 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM082675)
  • known disease mutation: rs9124 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:103534528T>CN/A show variant in all transcripts   IGV
HGNC symbol FGF8
Ensembl transcript ID ENST00000320185
Genbank transcript ID NM_033163
UniProt peptide P55075
alteration type single base exchange
alteration region CDS
DNA changes c.298A>G
cDNA.357A>G
g.1300A>G
AA changes K100E Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 100
frameshift no
known variant Reference ID: rs137852662
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs9124 (pathogenic for Hypogonadotropic hypogonadism 6 with or without anosmia) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM082675)

known disease mutation at this position, please check HGMD for details (HGMD ID CM082675)
known disease mutation at this position, please check HGMD for details (HGMD ID CM082675)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.0731
4.6771
(flanking)5.6621
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 increased1293wt: 0.9010 / mu: 0.9127 (marginal change - not scored)wt: GTCCTGGCCAACAAG
mu: GTCCTGGCCAACGAG		 CCTG|gcca
Donor gained12940.44mu: TCCTGGCCAACGAGC CTGG|ccaa
distance from splice site 40
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      100TSGKHVQVLANKRINAMAEDGDPF
mutated  all conserved    100TSGKHVQVLANERINAMAEDGDP
Ptroglodytes  all identical  ENSPTRG00000002874  100TSGKHVQVLANKRINAMAEDGDP
Mmulatta  no alignment  ENSMMUG00000015771  n/a
Fcatus  not conserved  ENSFCAG00000007177  97------------RFNLTGEV--P
Mmusculus  all identical  ENSMUSG00000025219  124LANKRINAMAEDGDP
Ggallus  all identical  ENSGALG00000007706  74TSGKHVQILDNKKINAMAEDGDV
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000003399  71TSGKHVQVLANKKINAMAEDGDV
Dmelanogaster  not conserved  FBgn0014135  268N--RILQILRDGVVNGTQDENSE
Celegans  no alignment  C05D11.4  n/a
Xtropicalis  all identical  ENSXETG00000014474  100TSGKHVQILGNKKINAMAEDGDP
protein features
start (aa)end (aa)featuredetails 
100102HELIXlost
104110STRANDmight get lost (downstream of altered splice site)
111113TURNmight get lost (downstream of altered splice site)
114119STRANDmight get lost (downstream of altered splice site)
120122TURNmight get lost (downstream of altered splice site)
125128STRANDmight get lost (downstream of altered splice site)
134138STRANDmight get lost (downstream of altered splice site)
143145HELIXmight get lost (downstream of altered splice site)
146151STRANDmight get lost (downstream of altered splice site)
155155CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
157164STRANDmight get lost (downstream of altered splice site)
180182HELIXmight get lost (downstream of altered splice site)
188190HELIXmight get lost (downstream of altered splice site)
192195STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 735 / 735
position (AA) of stopcodon in wt / mu AA sequence 245 / 245
position of stopcodon in wt / mu cDNA 794 / 794
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 60 / 60
chromosome 10
strand -1
last intron/exon boundary 504
theoretical NMD boundary in CDS 394
length of CDS 735
coding sequence (CDS) position 298
cDNA position
(for ins/del: last normal base / first normal base)		 357
gDNA position
(for ins/del: last normal base / first normal base)		 1300
chromosomal position
(for ins/del: last normal base / first normal base)		 103534528
original gDNA sequence snippet ACGTGCAGGTCCTGGCCAACAAGCGCATCAACGCCATGGCA
altered gDNA sequence snippet ACGTGCAGGTCCTGGCCAACGAGCGCATCAACGCCATGGCA
original cDNA sequence snippet ACGTGCAGGTCCTGGCCAACAAGCGCATCAACGCCATGGCA
altered cDNA sequence snippet ACGTGCAGGTCCTGGCCAACGAGCGCATCAACGCCATGGCA
wildtype AA sequence MGSPRSALSC LLLHLLVLCL QAQEGPGRGP ALGRELASLF RAGREPQGVS QQVTVQSSPN
FTQHVREQSL VTDQLSRRLI RTYQLYSRTS GKHVQVLANK RINAMAEDGD PFAKLIVETD
TFGSRVRVRG AETGLYICMN KKGKLIAKSN GKGKDCVFTE IVLENNYTAL QNAKYEGWYM
AFTRKGRPRK GSKTRQHQRE VHFMKRLPRG HHTTEQSLRF EFLNYPPFTR SLRGSQRTWA
PEPR*
mutated AA sequence MGSPRSALSC LLLHLLVLCL QAQEGPGRGP ALGRELASLF RAGREPQGVS QQVTVQSSPN
FTQHVREQSL VTDQLSRRLI RTYQLYSRTS GKHVQVLANE RINAMAEDGD PFAKLIVETD
TFGSRVRVRG AETGLYICMN KKGKLIAKSN GKGKDCVFTE IVLENNYTAL QNAKYEGWYM
AFTRKGRPRK GSKTRQHQRE VHFMKRLPRG HHTTEQSLRF EFLNYPPFTR SLRGSQRTWA
PEPR*
speed 0.95 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