Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999950487 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM960653)
  • known disease mutation: rs13277 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:123274794T>CN/A show variant in all transcripts   IGV
HGNC symbol FGFR2
Ensembl transcript ID ENST00000356226
Genbank transcript ID NM_001144918
UniProt peptide P21802
alteration type single base exchange
alteration region CDS
DNA changes c.779A>G
cDNA.1426A>G
g.83179A>G
AA changes Y260C Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 260
frameshift no
known variant Reference ID: rs121913478
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs13277 (pathogenic for Crouzon syndrome|Neoplasm of stomach|Endometrial carcinoma|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|Endometrial neoplasm|FGFR2 related craniosynostosis|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960653)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960653)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960653)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.5221
5.1651
(flanking)5.1651
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 40
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      260GREKEITASPDYLEIAIYCIGVFL
mutated  not conserved    260GREKEITASPDCLEIAIYCIGVF
Ptroglodytes  all identical  ENSPTRG00000003003  373GREKEITASPDYLEIAIYCIGVF
Mmulatta  all identical  ENSMMUG00000009594  222GREKEITASPDYLEIAIYCIGVF
Fcatus  no alignment  ENSFCAG00000003692  n/a
Mmusculus  all identical  ENSMUSG00000030849  394VREKEITASPDYLEIAIYCIGVF
Ggallus  all identical  ENSGALG00000009495  382EKEKEFPTSPDYLEIAIYCIGVF
Trubripes  all identical  ENSTRUG00000017610  373-RETSIEESHGPLSPHYVEIAIYCAGVF
Drerio  all identical  ENSDARG00000058115  398TNPIETDYPPDYVEIAIYCIGVF
Dmelanogaster  not conserved  FBgn0010389  306HVLEAGVASGSLHSTSFVYIF
Celegans  all identical  F58A3.2  524IDRWTTSDYIFTTILLF--L
Xtropicalis  all identical  ENSXETG00000015592  387VSPGEDNPVPYYMEIGIYSAGIF
protein features
start (aa)end (aa)featuredetails 
22377TOPO_DOMExtracellular (Potential).lost
256358DOMAINIg-like C2-type 3.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2115 / 2115
position (AA) of stopcodon in wt / mu AA sequence 705 / 705
position of stopcodon in wt / mu cDNA 2762 / 2762
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 648 / 648
chromosome 10
strand -1
last intron/exon boundary 2598
theoretical NMD boundary in CDS 1900
length of CDS 2115
coding sequence (CDS) position 779
cDNA position
(for ins/del: last normal base / first normal base)		 1426
gDNA position
(for ins/del: last normal base / first normal base)		 83179
chromosomal position
(for ins/del: last normal base / first normal base)		 123274794
original gDNA sequence snippet GATTACAGCTTCCCCAGACTACCTGGAGATAGCCATTTACT
altered gDNA sequence snippet GATTACAGCTTCCCCAGACTGCCTGGAGATAGCCATTTACT
original cDNA sequence snippet GATTACAGCTTCCCCAGACTACCTGGAGATAGCCATTTACT
altered cDNA sequence snippet GATTACAGCTTCCCCAGACTGCCTGGAGATAGCCATTTACT
wildtype AA sequence MVSWGRFICL VVVTMATLSL ARPSFSLVED TTLEPEGAPY WTNTEKMEKR LHAVPAANTV
KFRCPAGGNP MPTMRWLKNG KEFKQEHRIG GYKVRNQHWS LIMESVVPSD KGNYTCVVEN
EYGSINHTYH LDVVERSPHR PILQAGLPAN ASTVVGGDVE FVCKVYSDAQ PHIQWIKHVE
KNGSKYGPDG LPYLKVLKAA GVNTTDKEIE VLYIRNVTFE DAGEYTCLAG NSIGISFHSA
WLTVLPAPGR EKEITASPDY LEIAIYCIGV FLIACMVVTV ILCRMKNTTK KPDFSSQPAV
HKLTKRIPLR RQVSAESSSS MNSNTPLVRI TTRLSSTADT PMLAGVSEYE LPEDPKWEFP
RDKLTLGKPL GEGCFGQVVM AEAVGIDKDK PKEAVTVAVK MLKDDATEKD LSDLVSEMEM
MKMIGKHKNI INLLGACTQD GPLYVIVEYA SKGNLREYLR ARRPPGMEYS YDINRVPEEQ
MTFKDLVSCT YQLARGMEYL ASQKCIHRDL AARNVLVTEN NVMKIADFGL ARDINNIDYY
KKTTNGRLPV KWMAPEALFD RVYTHQSDVW SFGVLMWEIF TLGGSPYPGI PVEELFKLLK
EGHRMDKPAN CTNELYMMMR DCWHAVPSQR PTFKQLVEDL DRILTLTTNE EYLDLSQPLE
QYSPSYPDTR SSCSSGDDSV FSPDPMPYEP CLPQYPHING SVKT*
mutated AA sequence MVSWGRFICL VVVTMATLSL ARPSFSLVED TTLEPEGAPY WTNTEKMEKR LHAVPAANTV
KFRCPAGGNP MPTMRWLKNG KEFKQEHRIG GYKVRNQHWS LIMESVVPSD KGNYTCVVEN
EYGSINHTYH LDVVERSPHR PILQAGLPAN ASTVVGGDVE FVCKVYSDAQ PHIQWIKHVE
KNGSKYGPDG LPYLKVLKAA GVNTTDKEIE VLYIRNVTFE DAGEYTCLAG NSIGISFHSA
WLTVLPAPGR EKEITASPDC LEIAIYCIGV FLIACMVVTV ILCRMKNTTK KPDFSSQPAV
HKLTKRIPLR RQVSAESSSS MNSNTPLVRI TTRLSSTADT PMLAGVSEYE LPEDPKWEFP
RDKLTLGKPL GEGCFGQVVM AEAVGIDKDK PKEAVTVAVK MLKDDATEKD LSDLVSEMEM
MKMIGKHKNI INLLGACTQD GPLYVIVEYA SKGNLREYLR ARRPPGMEYS YDINRVPEEQ
MTFKDLVSCT YQLARGMEYL ASQKCIHRDL AARNVLVTEN NVMKIADFGL ARDINNIDYY
KKTTNGRLPV KWMAPEALFD RVYTHQSDVW SFGVLMWEIF TLGGSPYPGI PVEELFKLLK
EGHRMDKPAN CTNELYMMMR DCWHAVPSQR PTFKQLVEDL DRILTLTTNE EYLDLSQPLE
QYSPSYPDTR SSCSSGDDSV FSPDPMPYEP CLPQYPHING SVKT*
speed 1.37 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