Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999876434738 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM090142)
  • known disease mutation: rs13840 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:69633506C>AN/A show variant in all transcripts   IGV
HGNC symbol FGF3
Ensembl transcript ID ENST00000334134
Genbank transcript ID NM_005247
UniProt peptide P11487
alteration type single base exchange
alteration region CDS
DNA changes c.196G>T
cDNA.287G>T
g.287G>T
AA changes G66C Score: 159 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 66
frameshift no
known variant Reference ID: rs121917705
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs13840 (pathogenic for Deafness with labyrinthine aplasia microtia and microdontia (LAMM)) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM090142)

known disease mutation at this position, please check HGMD for details (HGMD ID CM090142)
known disease mutation at this position, please check HGMD for details (HGMD ID CM090142)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.4811
4.4811
(flanking)1.3171
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased292wt: 0.62 / mu: 0.74wt: GGCAGCCTGGAGAAC
mu: TGCAGCCTGGAGAAC		 CAGC|ctgg
Donor marginally increased280wt: 0.9074 / mu: 0.9737 (marginal change - not scored)wt: GGCCGCGTCAACGGC
mu: GGCCGCGTCAACTGC		 CCGC|gtca
Donor increased285wt: 0.36 / mu: 0.78wt: CGTCAACGGCAGCCT
mu: CGTCAACTGCAGCCT		 TCAA|cggc
Donor increased290wt: 0.34 / mu: 0.65wt: ACGGCAGCCTGGAGA
mu: ACTGCAGCCTGGAGA		 GGCA|gcct
distance from splice site 25
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      66HLQLHPSGRVNGSLENSAYSILEI
mutated  not conserved    66SGRVNCSLENSAYSILE
Ptroglodytes  all identical  ENSPTRG00000004001  66SGRVNGSLENSAYSILE
Mmulatta  all identical  ENSMMUG00000002969  66SGRVNGSLENSAYSILE
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000031074  66SGRVNGSLENSAYSILE
Ggallus  all identical  ENSGALG00000007563  89PGGKINGTLEKNSVFSILE
Trubripes  all identical  ENSTRUG00000015735  73TNGRIGGSLEDNNPFSIME
Drerio  all identical  ENSDARG00000068094  84HLQIHPNGKIDGSLEENNPLSILE
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no alignment  ENSXETG00000002761  n/a
protein features
start (aa)end (aa)featuredetails 
6565CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 720 / 720
position (AA) of stopcodon in wt / mu AA sequence 240 / 240
position of stopcodon in wt / mu cDNA 811 / 811
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 92 / 92
chromosome 11
strand -1
last intron/exon boundary 416
theoretical NMD boundary in CDS 274
length of CDS 720
coding sequence (CDS) position 196
cDNA position
(for ins/del: last normal base / first normal base)		 287
gDNA position
(for ins/del: last normal base / first normal base)		 287
chromosomal position
(for ins/del: last normal base / first normal base)		 69633506
original gDNA sequence snippet ACCCGAGCGGCCGCGTCAACGGCAGCCTGGAGAACAGCGCC
altered gDNA sequence snippet ACCCGAGCGGCCGCGTCAACTGCAGCCTGGAGAACAGCGCC
original cDNA sequence snippet ACCCGAGCGGCCGCGTCAACGGCAGCCTGGAGAACAGCGCC
altered cDNA sequence snippet ACCCGAGCGGCCGCGTCAACTGCAGCCTGGAGAACAGCGCC
wildtype AA sequence MGLIWLLLLS LLEPGWPAAG PGARLRRDAG GRGGVYEHLG GAPRRRKLYC ATKYHLQLHP
SGRVNGSLEN SAYSILEITA VEVGIVAIRG LFSGRYLAMN KRGRLYASEH YSAECEFVER
IHELGYNTYA SRLYRTVSST PGARRQPSAE RLWYVSVNGK GRPRRGFKTR RTQKSSLFLP
RVLDHRDHEM VRQLQSGLPR PPGKGVQPRR RRQKQSPDNL EPSHVQASRL GSQLEASAH*
mutated AA sequence MGLIWLLLLS LLEPGWPAAG PGARLRRDAG GRGGVYEHLG GAPRRRKLYC ATKYHLQLHP
SGRVNCSLEN SAYSILEITA VEVGIVAIRG LFSGRYLAMN KRGRLYASEH YSAECEFVER
IHELGYNTYA SRLYRTVSST PGARRQPSAE RLWYVSVNGK GRPRRGFKTR RTQKSSLFLP
RVLDHRDHEM VRQLQSGLPR PPGKGVQPRR RRQKQSPDNL EPSHVQASRL GSQLEASAH*
speed 1.11 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