Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999999953 (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 ENST00000356226
Genbank transcript ID NM_001144918
UniProt peptide P21802
alteration type single base exchange
alteration region CDS
DNA changes c.680G>A
cDNA.1327G>A
g.81081G>A
AA changes C227Y Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 227
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      227NVTFEDAGEYTCLAGNSIGISFHS
mutated  not conserved    227NVTFEDAGEYTYLAGNSIGISFH
Ptroglodytes  all identical  ENSPTRG00000003003  340TEADAGEYICKVSNYIGQANQ
Mmulatta  all identical  ENSMMUG00000009594  189VTEADAGEYICKVSNYIGQANQ
Fcatus  no alignment  ENSFCAG00000003692  n/a
Mmusculus  all identical  ENSMUSG00000030849  361TFEDAGEYTCLAGNSIGISFH
Ggallus  all identical  ENSGALG00000009495  349NVTFEDAGEYTCLAGNSIGISFH
Trubripes  all identical  ENSTRUG00000017610  340VTEEDAGEYICKVSNYIGEASQ
Drerio  all identical  ENSDARG00000058115  365FEDAGEYTCLAGNSIGISYH
Dmelanogaster  all identical  FBgn0010389  273NVRMEQEGWYTCVESNSLGQSNS
Celegans  all identical  F58A3.2  478NVSLDDQGIYACLSGNSLGMSMA
Xtropicalis  all identical  ENSXETG00000015592  354SFEDAGEYTCIAGNSIGISQH
protein features
start (aa)end (aa)featuredetails 
22377TOPO_DOMExtracellular (Potential).lost
154247DOMAINIg-like C2-type 2.lost
227235STRANDlost
228228CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
231231DISULFIDmight get lost (downstream of altered splice site)
238249STRANDmight get lost (downstream of altered splice site)
241241CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
246246CONFLICTL -> P (in Ref. 16; BAG57383).might get lost (downstream of altered splice site)
256358DOMAINIg-like C2-type 3.might get lost (downstream of altered splice site)
265265MUTAGENN->Q: Reduced N-glycosylation. Reduced expression at the cell surface.might get lost (downstream of altered splice site)
265265CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
266269STRANDmight get lost (downstream of altered splice site)
274277STRANDmight get lost (downstream of altered splice site)
278278DISULFIDmight get lost (downstream of altered splice site)
287293STRANDmight get lost (downstream of altered splice site)
296298STRANDmight get lost (downstream of altered splice site)
297297CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
299301STRANDmight get lost (downstream of altered splice site)
309313STRANDmight get lost (downstream of altered splice site)
310310CONFLICTK -> N (in Ref. 16; BAG57383).might get lost (downstream of altered splice site)
315319STRANDmight get lost (downstream of altered splice site)
318318CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
321325TURNmight get lost (downstream of altered splice site)
326329STRANDmight get lost (downstream of altered splice site)
331331CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
334336HELIXmight get lost (downstream of altered splice site)
338346STRANDmight get lost (downstream of altered splice site)
342342DISULFIDmight get lost (downstream of altered splice site)
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 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 680
cDNA position
(for ins/del: last normal base / first normal base)		 1327
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 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 DAGEYTYLAG 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*
speed 0.99 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