Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.96807216922313 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM950473)
  • known disease mutation: rs16329 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr4:1806153C>AN/A show variant in all transcripts   IGV
HGNC symbol FGFR3
Ensembl transcript ID ENST00000340107
Genbank transcript ID NM_001163213
UniProt peptide P22607
alteration type single base exchange
alteration region CDS
DNA changes c.1178C>A
cDNA.1434C>A
g.11120C>A
AA changes A393E Score: 107 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 393
frameshift no
known variant Reference ID: rs28931615
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs16329 (pathogenic for Craniosynostosis syndrome|Carcinoma|Crouzon syndrome with acanthosis nigricans|Inborn genetic diseases|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950473)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950473)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950473)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.6111
2.0830.992
(flanking)-1.2130.023
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased11111wt: 0.9099 / mu: 0.9190 (marginal change - not scored)wt: GGGCTTCTTCCTGTTCATCCTGGTGGTGGCGGCTGTGACGC
mu: GGGCTTCTTCCTGTTCATCCTGGTGGTGGAGGCTGTGACGC		 tcct|GGTG
Acc marginally increased11110wt: 0.9510 / mu: 0.9568 (marginal change - not scored)wt: TGGGCTTCTTCCTGTTCATCCTGGTGGTGGCGGCTGTGACG
mu: TGGGCTTCTTCCTGTTCATCCTGGTGGTGGAGGCTGTGACG		 atcc|TGGT
Donor increased11112wt: 0.31 / mu: 0.42wt: ATCCTGGTGGTGGCG
mu: ATCCTGGTGGTGGAG		 CCTG|gtgg
Donor marginally increased11124wt: 0.9330 / mu: 0.9727 (marginal change - not scored)wt: GCGGCTGTGACGCTC
mu: GAGGCTGTGACGCTC		 GGCT|gtga
Donor gained111150.67mu: CTGGTGGTGGAGGCT GGTG|gtgg
distance from splice site 95
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      393GVGFFLFILVVAAVTLCRLRSPPK
mutated  not conserved    393GVGFFLFILVVEAVTLCRLRSPP
Ptroglodytes  all identical  ENSPTRG00000015836  390GVGFFLFILVVAAVTLCRLRSPP
Mmulatta  all identical  ENSMMUG00000019945  393GVGFFLFILVVAAVTLCRLRSTP
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000054252  387GVVFFLFILVVAAVILCRLRSPP
Ggallus  not conserved  ENSGALG00000015708  389GTGLVLFILVLVIVIICRMKMPN
Trubripes  not conserved  ENSTRUG00000003670  351VTGCVLFILAVVIIVLCRMRMTT
Drerio  not conserved  ENSDARG00000004782  389VTSCVLFILTMVIIILCRMWI
Dmelanogaster  not conserved  FBgn0010389  328GGLIFIFMTTLFVFYAIRKMKHEKVL
Celegans  all identical  F58A3.2  540IFTTILLFLLLAATLFGILFMVC
Xtropicalis  not conserved  ENSXETG00000002396  410ITGFILLVIIFVTY---RVKVPS
protein features
start (aa)end (aa)featuredetails 
376396TRANSMEMHelical; (Potential).lost
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 2427 / 2427
position (AA) of stopcodon in wt / mu AA sequence 809 / 809
position of stopcodon in wt / mu cDNA 2683 / 2683
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 257 / 257
chromosome 4
strand 1
last intron/exon boundary 2537
theoretical NMD boundary in CDS 2230
length of CDS 2427
coding sequence (CDS) position 1178
cDNA position
(for ins/del: last normal base / first normal base)		 1434
gDNA position
(for ins/del: last normal base / first normal base)		 11120
chromosomal position
(for ins/del: last normal base / first normal base)		 1806153
original gDNA sequence snippet CCTGTTCATCCTGGTGGTGGCGGCTGTGACGCTCTGCCGCC
altered gDNA sequence snippet CCTGTTCATCCTGGTGGTGGAGGCTGTGACGCTCTGCCGCC
original cDNA sequence snippet CCTGTTCATCCTGGTGGTGGCGGCTGTGACGCTCTGCCGCC
altered cDNA sequence snippet CCTGTTCATCCTGGTGGTGGAGGCTGTGACGCTCTGCCGCC
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 SWISESVEAD VRLRLANVSE RDGGEYLCRA TNFIGVAEKA FWLSVHGPRA
AEEELVEADE AGSVYAGILS YGVGFFLFIL VVAAVTLCRL RSPPKKGLGS PTVHKISRFP
LKRQVSLESN ASMSSNTPLV RIARLSSGEG PTLANVSELE LPADPKWELS RARLTLGKPL
GEGCFGQVVM AEAIGIDKDR AAKPVTVAVK MLKDDATDKD LSDLVSEMEM MKMIGKHKNI
INLLGACTQG GPLYVLVEYA AKGNLREFLR ARRPPGLDYS FDTCKPPEEQ LTFKDLVSCA
YQVARGMEYL ASQKCIHRDL AARNVLVTED NVMKIADFGL ARDVHNLDYY KKTTNGRLPV
KWMAPEALFD RVYTHQSDVW SFGVLLWEIF TLGGSPYPGI PVEELFKLLK EGHRMDKPAN
CTHDLYMIMR ECWHAAPSQR PTFKQLVEDL DRVLTVTSTD EYLDLSAPFE QYSPGGQDTP
SSSSSGDDSV FAHDLLPPAP PSSGGSRT*
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 SWISESVEAD VRLRLANVSE RDGGEYLCRA TNFIGVAEKA FWLSVHGPRA
AEEELVEADE AGSVYAGILS YGVGFFLFIL VVEAVTLCRL RSPPKKGLGS PTVHKISRFP
LKRQVSLESN ASMSSNTPLV RIARLSSGEG PTLANVSELE LPADPKWELS RARLTLGKPL
GEGCFGQVVM AEAIGIDKDR AAKPVTVAVK MLKDDATDKD LSDLVSEMEM MKMIGKHKNI
INLLGACTQG GPLYVLVEYA AKGNLREFLR ARRPPGLDYS FDTCKPPEEQ LTFKDLVSCA
YQVARGMEYL ASQKCIHRDL AARNVLVTED NVMKIADFGL ARDVHNLDYY KKTTNGRLPV
KWMAPEALFD RVYTHQSDVW SFGVLLWEIF TLGGSPYPGI PVEELFKLLK EGHRMDKPAN
CTHDLYMIMR ECWHAAPSQR PTFKQLVEDL DRVLTVTSTD EYLDLSAPFE QYSPGGQDTP
SSSSSGDDSV FAHDLLPPAP PSSGGSRT*
speed 1.55 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