Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999908918748 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM970530)
  • known disease mutation: rs16345 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr4:1807363A>GN/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.1615A>G
cDNA.1876A>G
g.12330A>G
AA changes I539V Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 539
frameshift no
known variant Reference ID: rs80053154
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs16345 (pathogenic for Hypochondroplasia|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970530)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970530)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970530)
regulatory features PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.1831
3.31
(flanking)4.8391
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased12324wt: 0.67 / mu: 0.99wt: AACACAAAAACATCA
mu: AACACAAAAACGTCA		 CACA|aaaa
Donor gained123290.66mu: AAAAACGTCATCAAC AAAC|gtca
distance from splice site 34
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      539EMMKMIGKHKNIINLLGACTQGGP
mutated  all conserved    539EMMKMIGKHKNVINLLGACTQGG
Ptroglodytes  all identical  ENSPTRG00000015836  537EMMKMIGKHKNIINLLGACTQGG
Mmulatta  all identical  ENSMMUG00000019945  540NIINLLGACTQGG
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000054252  534NIINLLGACTQGG
Ggallus  all identical  ENSGALG00000015708  537EMMKMIGKHKNIINLLGAC
Trubripes  all identical  ENSTRUG00000003670  497EMMKMIGKHKNIINLLGACTQDG
Drerio  all identical  ENSDARG00000004782  530EMMKMIGKHKNIINLLGACTQDG
Dmelanogaster  all identical  FBgn0010389  473IGRHINIINLLGCCSQNG
Celegans  all conserved  F58A3.2  706ETFKVIGEHENVLRLIGCC
Xtropicalis  all identical  ENSXETG00000002396  554EMMKMIGKHKNIIN
protein features
start (aa)end (aa)featuredetails 
397806TOPO_DOMCytoplasmic (Potential).lost
472761DOMAINProtein kinase.lost
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 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 1615
cDNA position
(for ins/del: last normal base / first normal base)		 1876
gDNA position
(for ins/del: last normal base / first normal base)		 12330
chromosomal position
(for ins/del: last normal base / first normal base)		 1807363
original gDNA sequence snippet TGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCC
altered gDNA sequence snippet TGATCGGGAAACACAAAAACGTCATCAACCTGCTGGGCGCC
original cDNA sequence snippet TGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCC
altered cDNA sequence snippet TGATCGGGAAACACAAAAACGTCATCAACCTGCTGGGCGCC
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
EELVEADEAG SVYAGILSYG VGFFLFILVV AAVTLCRLRS PPKKGLGSPT VHKISRFPLK
RQQVSLESNA SMSSNTPLVR IARLSSGEGP TLANVSELEL PADPKWELSR ARLTLGKPLG
EGCFGQVVMA EAIGIDKDRA AKPVTVAVKM LKDDATDKDL SDLVSEMEMM KMIGKHKNVI
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 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