Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.0635187006315441 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM022207)
  • known disease mutation at this position (HGMD CM960655)
  • known disease mutation: rs16340 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr4:1803571C>GN/A show variant in all transcripts   IGV
HGNC symbol FGFR3
Ensembl transcript ID ENST00000412135
Genbank transcript ID NM_022965
UniProt peptide P22607
alteration type single base exchange
alteration region CDS
DNA changes c.749C>G
cDNA.1005C>G
g.8538C>G
AA changes P250R Score: 103 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 250
frameshift no
known variant Reference ID: rs4647924
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs16340 (pathogenic for Unilateral renal agenesis|Facial asymmetry|Seizures|Craniosynostosis syndrome|Absence seizures|Coronal craniosynostosis|Crouzon syndrome|Infantile axial hypotonia|Malignant tumor of testis|Epidermal nevus|Urinary bladder cancer|Carcinoma of colon|Cancer of cervix|Achondroplasia|Saethre-Chotzen syndrome|Hypochondroplasia|Levy-Hollister syndrome|Thanatophoric dysplasia type 1|Thanatophoric dysplasia, type 2|Muenke syndrome|Camptodactyly-tall stature-scoliosis-hearing loss syndrome|Crouzon syndrome with acanthosis nigricans|Severe achondroplasia with developmental delay and acanthosis nigricans|Inborn genetic diseases|not specified|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960655)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960655)
known disease mutation at this position, please check HGMD for details (HGMD ID CM022207)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960655)
known disease mutation at this position, please check HGMD for details (HGMD ID CM022207)
known disease mutation at this position, please check HGMD for details (HGMD ID CM022207)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960655)
known disease mutation at this position, please check HGMD for details (HGMD ID CM022207)
known disease mutation at this position, please check HGMD for details (HGMD ID CM022207)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960655)
regulatory features PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.7640.998
3.8120.999
(flanking)-0.6360.82
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 decreased8528wt: 0.9303 / mu: 0.9301 (marginal change - not scored)wt: GAGCGTCATCTGCCCCCACAGAGCGCTCCCCGCACCGGCCC
mu: GAGCGTCATCTGCCCCCACAGAGCGCTCCCGGCACCGGCCC		 acag|AGCG
distance from splice site 10
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      250QTYTLDVLERSPHRPILQAGLPAN
mutated  not conserved    250YTLDVLERSRHRPILQAGLPA
Ptroglodytes  not conserved  ENSPTRG00000015836  360HSAWLVVL--PAEEELVEADEAG
Mmulatta  not conserved  ENSMMUG00000019945  361KAFWLSVHRPRAAEEELVEADEAG
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000054252  354KAFWLRVHGPQAAEEELMETDEAG
Ggallus  not conserved  ENSGALG00000015708  359HSAWLTVLPAEELMEMDDSGSVYAGILS
Trubripes  all identical  ENSTRUG00000003670  318KVFWLKIHNQKPALPVLSPGTAD
Drerio  not conserved  ENSDARG00000004782  356HSAWLTVLPAVEMEREDDYADILIYVTS
Dmelanogaster  not conserved  FBgn0010389  294STAYLRVV-RSLH--VLEAGVAS
Celegans  not conserved  F58A3.2  389KYFHVIIVNRMRRPPIIVPNILA
Xtropicalis  not conserved  ENSXETG00000002396  377HTAWLTVLPAEPVEKPTTTSSSST
protein features
start (aa)end (aa)featuredetails 
23375TOPO_DOMExtracellular (Potential).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 2341 / 2341
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 2195
theoretical NMD boundary in CDS 1888
length of CDS 2085
coding sequence (CDS) position 749
cDNA position
(for ins/del: last normal base / first normal base)		 1005
gDNA position
(for ins/del: last normal base / first normal base)		 8538
chromosomal position
(for ins/del: last normal base / first normal base)		 1803571
original gDNA sequence snippet TGCCCCCACAGAGCGCTCCCCGCACCGGCCCATCCTGCAGG
altered gDNA sequence snippet TGCCCCCACAGAGCGCTCCCGGCACCGGCCCATCCTGCAGG
original cDNA sequence snippet GGACGTGCTGGAGCGCTCCCCGCACCGGCCCATCCTGCAGG
altered cDNA sequence snippet GGACGTGCTGGAGCGCTCCCGGCACCGGCCCATCCTGCAGG
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
YTLDVLERSR 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*
speed 0.72 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