Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999997235956533 (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 ENST00000347978
Genbank transcript ID NM_006119
UniProt peptide P55075
alteration type single base exchange
alteration region CDS
DNA changes c.211A>G
cDNA.381A>G
g.1300A>G
AA changes K71E Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 71
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      71TSGKHVQVLANKRINAMAEDGDPF
mutated  all conserved    71SGKHVQVLANERINAMAEDGDP
Ptroglodytes  all identical  ENSPTRG00000002874  100TSGKHVQVLANKRINAMAEDGDP
Mmulatta  no alignment  ENSMMUG00000015771  n/a
Fcatus  not conserved  ENSFCAG00000007177  57QGVSQQEKPLQFSTHRFNLTGEV--P
Mmusculus  all identical  ENSMUSG00000025219  124LANKRINAMAEDGDP
Ggallus  all identical  ENSGALG00000007706  74QILDNKKINAMAEDGDV
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000003399  71QVLANKKINAMAEDGDV
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 
6976STRANDlost
7779TURNmight get lost (downstream of altered splice site)
8085STRANDmight get lost (downstream of altered splice site)
9195STRANDmight get lost (downstream of altered splice site)
100102HELIXmight get lost (downstream of altered splice site)
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 648 / 648
position (AA) of stopcodon in wt / mu AA sequence 216 / 216
position of stopcodon in wt / mu cDNA 818 / 818
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 171 / 171
chromosome 10
strand -1
last intron/exon boundary 528
theoretical NMD boundary in CDS 307
length of CDS 648
coding sequence (CDS) position 211
cDNA position
(for ins/del: last normal base / first normal base)		 381
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 QAQVTVQSSP NFTQHVREQS LVTDQLSRRL IRTYQLYSRT
SGKHVQVLAN KRINAMAEDG DPFAKLIVET DTFGSRVRVR GAETGLYICM NKKGKLIAKS
NGKGKDCVFT EIVLENNYTA LQNAKYEGWY MAFTRKGRPR KGSKTRQHQR EVHFMKRLPR
GHHTTEQSLR FEFLNYPPFT RSLRGSQRTW APEPR*
mutated AA sequence MGSPRSALSC LLLHLLVLCL QAQVTVQSSP NFTQHVREQS LVTDQLSRRL IRTYQLYSRT
SGKHVQVLAN ERINAMAEDG DPFAKLIVET DTFGSRVRVR GAETGLYICM NKKGKLIAKS
NGKGKDCVFT EIVLENNYTA LQNAKYEGWY MAFTRKGRPR KGSKTRQHQR EVHFMKRLPR
GHHTTEQSLR FEFLNYPPFT RSLRGSQRTW APEPR*
speed 1.25 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