Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.997068024136131 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • 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 ENST00000481110
Genbank transcript ID N/A
UniProt peptide P22607
alteration type single base exchange
alteration region CDS
DNA changes c.1108G>T
cDNA.1369G>T
g.11056G>T
AA changes G370C Score: 159 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 370
frameshift no
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 33
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      370AEEELVEADEAGSVYAGILSYGVG
mutated  not conserved    370EELVEADEACSVYAGILSYGV
Ptroglodytes  all identical  ENSPTRG00000015836  369EELVEADEAGSVYAGILSYGV
Mmulatta  all identical  ENSMMUG00000019945  372AEEELVEADEAGSVYAGILSYGV
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000054252  366AEEELMETDEAGSVYAGVLSYGV
Ggallus  all identical  ENSGALG00000015708  368DDSGSVYAGILSYGT
Trubripes  not conserved  ENSTRUG00000003670  327QKPALPVLSPGTADINTTDILIYVT
Drerio  not conserved  ENSDARG00000004782  365AVEMEREDD-----YADILIYVT
Dmelanogaster  all identical  FBgn0010389  303AGVASGSLHSTSFVYIFVF
Celegans  not conserved  F58A3.2  516GDEPKIDRWTTSDYIFTTIL----
Xtropicalis  not conserved  ENSXETG00000002396  388KPTTTSSSSTTVLIVVSVIT
protein features
start (aa)end (aa)featuredetails 
23375TOPO_DOMExtracellular (Potential).lost
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)
508508MUTAGENK->A: Loss of kinase activity. Abolishes ubiquitination.might get lost (downstream of altered splice site)
508508BINDINGATP (By similarity).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)
724724MUTAGENY->F: Strongly reduced kinase activity. Strongly reduced mitogen activity.might get lost (downstream of altered splice site)
724724MOD_RESPhosphotyrosine; by autocatalysis.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 normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2379 / 2379
position (AA) of stopcodon in wt / mu AA sequence 793 / 793
position of stopcodon in wt / mu cDNA 2640 / 2640
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 262 / 262
chromosome 4
strand 1
last intron/exon boundary 2468
theoretical NMD boundary in CDS 2156
length of CDS 2379
coding sequence (CDS) position 1108
cDNA position
(for ins/del: last normal base / first normal base)		 1369
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 TGGTGGAGGCTGACGAGGCGGGCAGTGTGTATGCAGGCATC
altered cDNA sequence snippet TGGTGGAGGCTGACGAGGCGTGCAGTGTGTATGCAGGCATC
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 TAGANTTDKE LEVLSLHNVT FEDAGEYTCL AGNSIGFSHH SAWLVVLPAE
EELVEADEAG SVYAGILSYG VGFFLFILVV AAVTLCRLRS PPKKGLGSPT VHKISRFPLK
RQQVSLESNA SMSSNTPLVR IARLSSGEGP TLANVSELEL PADPKWELSR ARLTLGKPLG
EGCFGQVVMA EAIGIDKDRA AKPVTVAVKM LKDDATDKDL SDLVSEMEMM KMIGKHKNII
NLLGACTQGG PLYVLVEYAA KGNLREFLRA RRPPGLDYSF DTCKPPEEQL TFKDLVSCAY
QVARGMEYLA SQKCIHRDLA ARNVLVTEDN VMKIADFGLA RDVHNLDYYK KTTNLVLWGP
ALGDLHAGGL PVPRHPCGGA LQAAEGGPPH GQARQLHTRP VHDHAGVLAC RALPEAHLQA
AGGGPGPCPY RDVHRRVPGP VGAFRAVLPG WPGHPQLQLL RGRLRVCPRP AAPGPTQQWG
LADVKGHWSP TM*
mutated 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 TAGANTTDKE LEVLSLHNVT FEDAGEYTCL AGNSIGFSHH SAWLVVLPAE
EELVEADEAC SVYAGILSYG VGFFLFILVV AAVTLCRLRS PPKKGLGSPT VHKISRFPLK
RQQVSLESNA SMSSNTPLVR IARLSSGEGP TLANVSELEL PADPKWELSR ARLTLGKPLG
EGCFGQVVMA EAIGIDKDRA AKPVTVAVKM LKDDATDKDL SDLVSEMEMM KMIGKHKNII
NLLGACTQGG PLYVLVEYAA KGNLREFLRA RRPPGLDYSF DTCKPPEEQL TFKDLVSCAY
QVARGMEYLA SQKCIHRDLA ARNVLVTEDN VMKIADFGLA RDVHNLDYYK KTTNLVLWGP
ALGDLHAGGL PVPRHPCGGA LQAAEGGPPH GQARQLHTRP VHDHAGVLAC RALPEAHLQA
AGGGPGPCPY RDVHRRVPGP VGAFRAVLPG WPGHPQLQLL RGRLRVCPRP AAPGPTQQWG
LADVKGHWSP TM*
speed 0.32 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