Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: without_aae, prob: 0.999999999999255 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM960656)
  • known disease mutation: rs16359 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr4:1806089G>TN/A show variant in all transcripts   IGV
HGNC symbol FGFR3
Ensembl transcript ID ENST00000352904
Genbank transcript ID N/A
UniProt peptide P22607
alteration type single base exchange
alteration region intron
DNA changes g.11056G>T
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs121913479
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs16359 (pathogenic for Bladder carcinoma|Epidermal nevus|Thanatophoric dysplasia type 1|none provided|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960656)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960656)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960656)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.0580.056
1.4060.872
(flanking)2.9620.974
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased11054wt: 0.74 / mu: 0.94wt: CGAGGCGGGCAGTGT
mu: CGAGGCGTGCAGTGT		 AGGC|gggc
Donor increased11049wt: 0.79 / mu: 0.97wt: GCTGACGAGGCGGGC
mu: GCTGACGAGGCGTGC		 TGAC|gagg
Donor increased11056wt: 0.55 / mu: 0.63wt: AGGCGGGCAGTGTGT
mu: AGGCGTGCAGTGTGT		 GCGG|gcag
Donor increased11051wt: 0.82 / mu: 0.95wt: TGACGAGGCGGGCAG
mu: TGACGAGGCGTGCAG		 ACGA|ggcg
distance from splice site 462
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
23375TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
253355DOMAINIg-like C2-type 3.might get lost (downstream of altered splice site)
315315CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
324326STRANDmight get lost (downstream of altered splice site)
328328CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
335345STRANDmight get lost (downstream of altered splice site)
339339DISULFIDBy similarity.might get lost (downstream of altered splice site)
348357STRANDmight get lost (downstream of altered splice site)
376396TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
395395CONFLICTL -> V (in Ref. 7; AAA58470).might get lost (downstream of altered splice site)
397806TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
421421CONFLICTR -> RQ (in Ref. 3; BAD92678).might get lost (downstream of altered splice site)
472761DOMAINProtein kinase.might get lost (downstream of altered splice site)
478486NP_BINDATP (By similarity).might get lost (downstream of altered splice site)
508508BINDINGATP (By similarity).might get lost (downstream of altered splice site)
508508MUTAGENK->A: Loss of kinase activity. Abolishes ubiquitination.might get lost (downstream of altered splice site)
577577MUTAGENY->F: Minor effect on kinase activity.might get lost (downstream of altered splice site)
617617ACT_SITEProton acceptor (By similarity).might get lost (downstream of altered splice site)
647647MOD_RESPhosphotyrosine; by autocatalysis.might get lost (downstream of altered splice site)
648648MOD_RESPhosphotyrosine; by autocatalysis.might get lost (downstream of altered splice site)
724724MOD_RESPhosphotyrosine; by autocatalysis.might get lost (downstream of altered splice site)
724724MUTAGENY->F: Strongly reduced kinase activity. Strongly reduced mitogen activity.might get lost (downstream of altered splice site)
760760MUTAGENY->F: Minor effect on kinase activity.might get lost (downstream of altered splice site)
760760MOD_RESPhosphotyrosine; by autocatalysis.might get lost (downstream of altered splice site)
770770MUTAGENY->F: Minor effect on kinase activity. Increased mitogen activity.might get lost (downstream of altered splice site)
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 40 / 40
chromosome 4
strand 1
last intron/exon boundary 1978
theoretical NMD boundary in CDS 1888
length of CDS 2085
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 11056
chromosomal position
(for ins/del: last normal base / first normal base)		 1806089
original gDNA sequence snippet TGGTGGAGGCTGACGAGGCGGGCAGTGTGTATGCAGGCATC
altered gDNA sequence snippet TGGTGGAGGCTGACGAGGCGTGCAGTGTGTATGCAGGCATC
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MGAPACALAL CVAVAIVAGA SSESLGTEQR VVGRAAEVPG PEPGQQEQLV FGSGDAVELS
CPPPGGGPMG PTVWVKDGTG LVPSERVLVG PQRLQVLNAS HEDSGAYSCR QRLTQRVLCH
FSVRVTDAPS SGDDEDGEDE AEDTGVDTGA PYWTRPERMD KKLLAVPAAN TVRFRCPAAG
NPTPSISWLK NGREFRGEHR IGGIKLRHQQ WSLVMESVVP SDRGNYTCVV ENKFGSIRQT
YTLDVLERSP HRPILQAGLP ANQTAVLGSD VEFHCKVYSD AQPHIQWLKH VEVNGSKVGP
DGTPYVTVLK VSLESNASMS SNTPLVRIAR LSSGEGPTLA NVSELELPAD PKWELSRARL
TLGKPLGEGC FGQVVMAEAI GIDKDRAAKP VTVAVKMLKD DATDKDLSDL VSEMEMMKMI
GKHKNIINLL GACTQGGPLY VLVEYAAKGN LREFLRARRP PGLDYSFDTC KPPEEQLTFK
DLVSCAYQVA RGMEYLASQK CIHRDLAARN VLVTEDNVMK IADFGLARDV HNLDYYKKTT
NGRLPVKWMA PEALFDRVYT HQSDVWSFGV LLWEIFTLGG SPYPGIPVEE LFKLLKEGHR
MDKPANCTHD LYMIMRECWH AAPSQRPTFK QLVEDLDRVL TVTSTDEYLD LSAPFEQYSP
GGQDTPSSSS SGDDSVFAHD LLPPAPPSSG GSRT*
mutated AA sequence N/A
speed 0.50 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