Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999998370595 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM074175)
  • known disease mutation at this position (HGMD CM990596)
  • known disease mutation at this position (HGMD CX140380)
  • known disease mutation: rs16341 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr4:1807890A>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 CDS
DNA changes c.1613A>T
cDNA.1652A>T
g.12857A>T
AA changes K538M Score: 95 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 538
frameshift no
known variant Reference ID: rs121913105
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs16341 (pathogenic for SEVERE ACHONDRODYSPLASIA WITH DEVELOPMENTAL DELAY AND ACANTHOSIS NIGRICANS|Thanatophoric dysplasia type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM990596)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990596)
known disease mutation at this position, please check HGMD for details (HGMD ID CX140380)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990596)
known disease mutation at this position, please check HGMD for details (HGMD ID CX140380)
known disease mutation at this position, please check HGMD for details (HGMD ID CM074175)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990596)
known disease mutation at this position, please check HGMD for details (HGMD ID CX140380)
known disease mutation at this position, please check HGMD for details (HGMD ID CM074175)
known disease mutation at this position, please check HGMD for details (HGMD ID CM074175)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990596)
known disease mutation at this position, please check HGMD for details (HGMD ID CX140380)
known disease mutation at this position, please check HGMD for details (HGMD ID CM074175)
known disease mutation at this position, please check HGMD for details (HGMD ID CM074175)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990596)
regulatory features PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.6221
3.0711
(flanking)1.8771
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 increased12854wt: 0.6747 / mu: 0.7157 (marginal change - not scored)wt: GCACAACCTCGACTACTACAAGAAGACGACCAACGTGAGCC
mu: GCACAACCTCGACTACTACAAGATGACGACCAACGTGAGCC		 acaa|GAAG
Donor marginally increased12849wt: 0.8895 / mu: 0.9157 (marginal change - not scored)wt: GACTACTACAAGAAG
mu: GACTACTACAAGATG		 CTAC|taca
Donor marginally increased12855wt: 0.8322 / mu: 0.8757 (marginal change - not scored)wt: TACAAGAAGACGACC
mu: TACAAGATGACGACC		 CAAG|aaga
Donor marginally increased12862wt: 0.9798 / mu: 0.9799 (marginal change - not scored)wt: AGACGACCAACGTGA
mu: TGACGACCAACGTGA		 ACGA|ccaa
distance from splice site 11
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      538ARDVHNLDYYKKTTNGRLPVKWMA
mutated  not conserved    538ARDVHNLDYYKMTT
Ptroglodytes  all identical  ENSPTRG00000015836  649ARDVHNLDYYKKTTNGRLPVKWM
Mmulatta  all identical  ENSMMUG00000019945  652ARDVHNLDYYKKTTNGRLPVKWM
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000054252  646ARDVHNLDYYKKTTNGRLPVKWM
Ggallus  all identical  ENSGALG00000015708  649ARDVHNIDYYKKTTNGRLPVKWM
Trubripes  all identical  ENSTRUG00000003670  609ARDVHNIDYYKKTTNGRLPVKWM
Drerio  all identical  ENSDARG00000004782  642ARDVHNIDYYKKTTNGRLPVKWM
Dmelanogaster  all identical  FBgn0010389  589ARDIQSTDYYRKNTNGRLPIKWM
Celegans  all identical  F58A3.2  830SRDVHCNDYYRLKRGNGRLPIKWM
Xtropicalis  all identical  ENSXETG00000002396  666ARDIHNIDYYKKTTNGRLPVKWM
protein features
start (aa)end (aa)featuredetails 
397806TOPO_DOMCytoplasmic (Potential).lost
472761DOMAINProtein kinase.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2085 / 2085
position (AA) of stopcodon in wt / mu AA sequence 695 / 695
position of stopcodon in wt / mu cDNA 2124 / 2124
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 1613
cDNA position
(for ins/del: last normal base / first normal base)		 1652
gDNA position
(for ins/del: last normal base / first normal base)		 12857
chromosomal position
(for ins/del: last normal base / first normal base)		 1807890
original gDNA sequence snippet CAACCTCGACTACTACAAGAAGACGACCAACGTGAGCCCGG
altered gDNA sequence snippet CAACCTCGACTACTACAAGATGACGACCAACGTGAGCCCGG
original cDNA sequence snippet CAACCTCGACTACTACAAGAAGACGACCAACGGCCGGCTGC
altered cDNA sequence snippet CAACCTCGACTACTACAAGATGACGACCAACGGCCGGCTGC
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 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 HNLDYYKMTT
NGRLPVKWMA PEALFDRVYT HQSDVWSFGV LLWEIFTLGG SPYPGIPVEE LFKLLKEGHR
MDKPANCTHD LYMIMRECWH AAPSQRPTFK QLVEDLDRVL TVTSTDEYLD LSAPFEQYSP
GGQDTPSSSS SGDDSVFAHD LLPPAPPSSG GSRT*
speed 0.94 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