Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999999997 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM940779)
  • known disease mutation at this position (HGMD CM960647)
  • known disease mutation at this position (HGMD CM960648)
  • known disease mutation: rs13263 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:123276892C>TN/A show variant in all transcripts   IGV
HGNC symbol FGFR2
Ensembl transcript ID ENST00000346997
Genbank transcript ID N/A
UniProt peptide P21802
alteration type single base exchange
alteration region CDS
DNA changes c.1025G>A
cDNA.1037G>A
g.81081G>A
AA changes C342Y Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 342
frameshift no
known variant Reference ID: rs121918487
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs13263 (pathogenic for Crouzon syndrome|Neoplasm of stomach|Acrocephalosyndactyly type I|Saethre-Chotzen syndrome|Pfeiffer syndrome|Jackson-Weiss syndrome|Beare-Stevenson cutis gyrata syndrome|Levy-Hollister syndrome|Scaphocephaly, maxillary retrusion, and mental retardation|Bent bone dysplasia syndrome|Antley-Bixler syndrome without genital anomalies or disordered steroidogenesis|FGFR2 related craniosynostosis|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM940779)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940779)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960647)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940779)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960647)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960648)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940779)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960647)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960648)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940779)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940779)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960647)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960648)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940779)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960647)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940779)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960647)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960648)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940779)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960647)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960648)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.5051
6.2681
(flanking)5.1771
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased81073wt: 0.9605 / mu: 0.9630 (marginal change - not scored)wt: GGGGAATATACGTGC
mu: GGGGAATATACGTAC		 GGAA|tata
Donor increased81084wt: 0.36 / mu: 0.62wt: GTGCTTGGCGGGTAA
mu: GTACTTGGCGGGTAA		 GCTT|ggcg
distance from splice site 60
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      342NVTFEDAGEYTCLAGNSIGISFHS
mutated  not conserved    342NVTFEDAGEYTYLAGNSIGISFH
Ptroglodytes  all identical  ENSPTRG00000003003  342NVTEADAGEYICKVSNYIGQANQ
Mmulatta  all identical  ENSMMUG00000009594  189TEADAGEYICKVSNYIGQANQ
Fcatus  no alignment  ENSFCAG00000003692  n/a
Mmusculus  all identical  ENSMUSG00000030849  361NVTFEDAGEYTCLAGNSIGISFH
Ggallus  all identical  ENSGALG00000009495  349NVTFEDAGEYTCLAGNSIGISF
Trubripes  all identical  ENSTRUG00000017610  342NVTEEDAGEYICKVSNYIGEASQ
Drerio  all identical  ENSDARG00000058115  365NVTFEDAGEYTCLAGNSIGISYH
Dmelanogaster  all identical  FBgn0010389  283NVRMEQEGWYTCVESNSLGQSN
Celegans  all identical  F58A3.2  478NVSLDDQGIYAC
Xtropicalis  all identical  ENSXETG00000015592  354NVSFEDAGEYTCIAGNSIGISQH
protein features
start (aa)end (aa)featuredetails 
22377TOPO_DOMExtracellular (Potential).lost
256358DOMAINIg-like C2-type 3.lost
338346STRANDlost
342342DISULFIDlost
349360STRANDmight get lost (downstream of altered splice site)
378398TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
399821TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
448448MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
449449MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
466466MOD_RESPhosphotyrosine; by autocatalysis.might get lost (downstream of altered splice site)
472474HELIXmight get lost (downstream of altered splice site)
478480HELIXmight get lost (downstream of altered splice site)
481489STRANDmight get lost (downstream of altered splice site)
481770DOMAINProtein kinase.might get lost (downstream of altered splice site)
487495NP_BINDATP.might get lost (downstream of altered splice site)
494501STRANDmight get lost (downstream of altered splice site)
504506STRANDmight get lost (downstream of altered splice site)
511518STRANDmight get lost (downstream of altered splice site)
517517BINDINGATP.might get lost (downstream of altered splice site)
525541HELIXmight get lost (downstream of altered splice site)
549549MUTAGENN->T: Constitutive kinase activity.might get lost (downstream of altered splice site)
550554STRANDmight get lost (downstream of altered splice site)
556558STRANDmight get lost (downstream of altered splice site)
561565STRANDmight get lost (downstream of altered splice site)
565565MUTAGENE->A: Constitutive kinase activity.might get lost (downstream of altered splice site)
565567NP_BINDATP.might get lost (downstream of altered splice site)
568571STRANDmight get lost (downstream of altered splice site)
571571BINDINGATP.might get lost (downstream of altered splice site)
572577HELIXmight get lost (downstream of altered splice site)
586586MOD_RESPhosphotyrosine; by autocatalysis.might get lost (downstream of altered splice site)
588588MOD_RESPhosphotyrosine; by autocatalysis.might get lost (downstream of altered splice site)
594596HELIXmight get lost (downstream of altered splice site)
600619HELIXmight get lost (downstream of altered splice site)
626626ACT_SITEProton acceptor.might get lost (downstream of altered splice site)
629631HELIXmight get lost (downstream of altered splice site)
632634STRANDmight get lost (downstream of altered splice site)
636638TURNmight get lost (downstream of altered splice site)
640642STRANDmight get lost (downstream of altered splice site)
652654TURNmight get lost (downstream of altered splice site)
656656MOD_RESPhosphotyrosine; by autocatalysis.might get lost (downstream of altered splice site)
656657MUTAGENMissing: Loss of kinase activity.might get lost (downstream of altered splice site)
657657MOD_RESPhosphotyrosine; by autocatalysis.might get lost (downstream of altered splice site)
657659TURNmight get lost (downstream of altered splice site)
664666STRANDmight get lost (downstream of altered splice site)
667669HELIXmight get lost (downstream of altered splice site)
672676HELIXmight get lost (downstream of altered splice site)
682697HELIXmight get lost (downstream of altered splice site)
709717HELIXmight get lost (downstream of altered splice site)
726728STRANDmight get lost (downstream of altered splice site)
730739HELIXmight get lost (downstream of altered splice site)
744746HELIXmight get lost (downstream of altered splice site)
750764HELIXmight get lost (downstream of altered splice site)
769769MOD_RESPhosphotyrosine; by autocatalysis.might get lost (downstream of altered splice site)
769769MUTAGENY->F: Increases fibroblast proliferation. Decreases phosphorylation of PLCG1 and FRS2. Decreases activation of MAP kinases.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2460 / 2460
position (AA) of stopcodon in wt / mu AA sequence 820 / 820
position of stopcodon in wt / mu cDNA 2472 / 2472
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 13 / 13
chromosome 10
strand -1
last intron/exon boundary 2308
theoretical NMD boundary in CDS 2245
length of CDS 2460
coding sequence (CDS) position 1025
cDNA position
(for ins/del: last normal base / first normal base)		 1037
gDNA position
(for ins/del: last normal base / first normal base)		 81081
chromosomal position
(for ins/del: last normal base / first normal base)		 123276892
original gDNA sequence snippet GGACGCTGGGGAATATACGTGCTTGGCGGGTAATTCTATTG
altered gDNA sequence snippet GGACGCTGGGGAATATACGTACTTGGCGGGTAATTCTATTG
original cDNA sequence snippet GGACGCTGGGGAATATACGTGCTTGGCGGGTAATTCTATTG
altered cDNA sequence snippet GGACGCTGGGGAATATACGTACTTGGCGGGTAATTCTATTG
wildtype AA sequence MVSWGRFICL VVVTMATLSL ARPSFSLVED TTLEPEEPPT KYQISQPEVY VAAPGESLEV
RCLLKDAAVI SWTKDGVHLG PNNRTVLIGE YLQIKGATPR DSGLYACTAS RTVDSETWYF
MVNVTDAISS GDDEDDTDGA EDFVSENSNN KRAPYWTNTE KMEKRLHAVP AANTVKFRCP
AGGNPMPTMR WLKNGKEFKQ EHRIGGYKVR NQHWSLIMES VVPSDKGNYT CVVENEYGSI
NHTYHLDVVE RSPHRPILQA GLPANASTVV GGDVEFVCKV YSDAQPHIQW IKHVEKNGSK
YGPDGLPYLK VLKAAGVNTT DKEIEVLYIR NVTFEDAGEY TCLAGNSIGI SFHSAWLTVL
PAPGREKEIT ASPDYLEIAI YCIGVFLIAC MVVTVILCRM KNTTKKPDFS SQPAVHKLTK
RIPLRRQVSA ESSSSMNSNT PLVRITTRLS STADTPMLAG VSEYELPEDP KWEFPRDKLT
LGKPLGEGCF GQVVMAEAVG IDKDKPKEAV TVAVKMLKDD ATEKDLSDLV SEMEMMKMIG
KHKNIINLLG ACTQDGPLYV IVEYASKGNL REYLRARRPP GMEYSYDINR VPEEQMTFKD
LVSCTYQLAR GMEYLASQKC IHRDLAARNV LVTENNVMKI ADFGLARDIN NIDYYKKTTN
GRLPVKWMAP EALFDRVYTH QSDVWSFGVL MWEIFTLGGS PYPGIPVEEL FKLLKEGHRM
DKPANCTNEL YMMMRDCWHA VPSQRPTFKQ LVEDLDRILT LTTNEEYLDL SQPLEQYSPS
YPDTRSSCSS GDDSVFSPDP MPYEPCLPQY PHINGSVKT*
mutated AA sequence MVSWGRFICL VVVTMATLSL ARPSFSLVED TTLEPEEPPT KYQISQPEVY VAAPGESLEV
RCLLKDAAVI SWTKDGVHLG PNNRTVLIGE YLQIKGATPR DSGLYACTAS RTVDSETWYF
MVNVTDAISS GDDEDDTDGA EDFVSENSNN KRAPYWTNTE KMEKRLHAVP AANTVKFRCP
AGGNPMPTMR WLKNGKEFKQ EHRIGGYKVR NQHWSLIMES VVPSDKGNYT CVVENEYGSI
NHTYHLDVVE RSPHRPILQA GLPANASTVV GGDVEFVCKV YSDAQPHIQW IKHVEKNGSK
YGPDGLPYLK VLKAAGVNTT DKEIEVLYIR NVTFEDAGEY TYLAGNSIGI SFHSAWLTVL
PAPGREKEIT ASPDYLEIAI YCIGVFLIAC MVVTVILCRM KNTTKKPDFS SQPAVHKLTK
RIPLRRQVSA ESSSSMNSNT PLVRITTRLS STADTPMLAG VSEYELPEDP KWEFPRDKLT
LGKPLGEGCF GQVVMAEAVG IDKDKPKEAV TVAVKMLKDD ATEKDLSDLV SEMEMMKMIG
KHKNIINLLG ACTQDGPLYV IVEYASKGNL REYLRARRPP GMEYSYDINR VPEEQMTFKD
LVSCTYQLAR GMEYLASQKC IHRDLAARNV LVTENNVMKI ADFGLARDIN NIDYYKKTTN
GRLPVKWMAP EALFDRVYTH QSDVWSFGVL MWEIFTLGGS PYPGIPVEEL FKLLKEGHRM
DKPANCTNEL YMMMRDCWHA VPSQRPTFKQ LVEDLDRILT LTTNEEYLDL SQPLEQYSPS
YPDTRSSCSS GDDSVFSPDP MPYEPCLPQY PHINGSVKT*
speed 0.74 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