mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.997073945825125 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM960652)
known disease mutation: rs13278 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:123274803G>CN/A show variant in all transcripts IGV

HGNC symbol

FGFR2

Ensembl transcript ID

ENST00000369061

Genbank transcript ID

NM_001144914

UniProt peptide

P21802

alteration type

single base exchange

alteration region

CDS

DNA changes

c.779C>G
cDNA.929C>G
g.83170C>G

AA changes

S260C Score: 112 explain score(s)

position(s) of altered AA
if AA alteration in CDS

260

frameshift

known variant

Reference ID: rs121913477
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs13278 (pathogenic for Beare-Stevenson cutis gyrata syndrome|Endometrial neoplasm) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960652)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960652)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960652)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.196	1
	2.897	1
(flanking)	2.903	0.992

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Donor gained	83169	0.44	mu: CAGCTTGCCCAGACT	GCTT\|gccc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

260

mutated

not conserved

260

Ptroglodytes

all identical

ENSPTRG00000003003

369

LPKQQ

Mmulatta

all identical

ENSMMUG00000009594

218

LPKQQ

Fcatus

no alignment

ENSFCAG00000003692

n/a

Mmusculus

all identical

ENSMUSG00000030849

390

Ggallus

all identical

ENSGALG00000009495

377

Trubripes

not conserved

ENSTRUG00000017610

363

SHGPLS

Drerio

not conserved

ENSDARG00000058115

393

Dmelanogaster

all conserved

FBgn0010389

301

HSTSF

Celegans

all conserved

F58A3.2

521

DRW

Xtropicalis

not conserved

ENSXETG00000015592

383

protein features

start (aa)	end (aa)	feature	details
22	377	TOPO_DOM	Extracellular (Potential).	lost
256	358	DOMAIN	Ig-like C2-type 3.	lost
265	265	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
265	265	MUTAGEN	N->Q: Reduced N-glycosylation. Reduced expression at the cell surface.	might get lost (downstream of altered splice site)
266	269	STRAND		might get lost (downstream of altered splice site)
274	277	STRAND		might get lost (downstream of altered splice site)
278	278	DISULFID		might get lost (downstream of altered splice site)
287	293	STRAND		might get lost (downstream of altered splice site)
296	298	STRAND		might get lost (downstream of altered splice site)
297	297	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
299	301	STRAND		might get lost (downstream of altered splice site)
309	313	STRAND		might get lost (downstream of altered splice site)
310	310	CONFLICT	K -> N (in Ref. 16; BAG57383).	might get lost (downstream of altered splice site)
315	319	STRAND		might get lost (downstream of altered splice site)
318	318	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
321	325	TURN		might get lost (downstream of altered splice site)
326	329	STRAND		might get lost (downstream of altered splice site)
331	331	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
334	336	HELIX		might get lost (downstream of altered splice site)
338	346	STRAND		might get lost (downstream of altered splice site)
342	342	DISULFID		might get lost (downstream of altered splice site)
349	360	STRAND		might get lost (downstream of altered splice site)
378	398	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
399	821	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
448	448	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
449	449	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
466	466	MOD_RES	Phosphotyrosine; by autocatalysis.	might get lost (downstream of altered splice site)
472	474	HELIX		might get lost (downstream of altered splice site)
478	480	HELIX		might get lost (downstream of altered splice site)
481	489	STRAND		might get lost (downstream of altered splice site)
481	770	DOMAIN	Protein kinase.	might get lost (downstream of altered splice site)
487	495	NP_BIND	ATP.	might get lost (downstream of altered splice site)
494	501	STRAND		might get lost (downstream of altered splice site)
504	506	STRAND		might get lost (downstream of altered splice site)
511	518	STRAND		might get lost (downstream of altered splice site)
517	517	BINDING	ATP.	might get lost (downstream of altered splice site)
525	541	HELIX		might get lost (downstream of altered splice site)
549	549	MUTAGEN	N->T: Constitutive kinase activity.	might get lost (downstream of altered splice site)
550	554	STRAND		might get lost (downstream of altered splice site)
556	558	STRAND		might get lost (downstream of altered splice site)
561	565	STRAND		might get lost (downstream of altered splice site)
565	565	MUTAGEN	E->A: Constitutive kinase activity.	might get lost (downstream of altered splice site)
565	567	NP_BIND	ATP.	might get lost (downstream of altered splice site)
568	571	STRAND		might get lost (downstream of altered splice site)
571	571	BINDING	ATP.	might get lost (downstream of altered splice site)
572	577	HELIX		might get lost (downstream of altered splice site)
586	586	MOD_RES	Phosphotyrosine; by autocatalysis.	might get lost (downstream of altered splice site)
588	588	MOD_RES	Phosphotyrosine; by autocatalysis.	might get lost (downstream of altered splice site)
594	596	HELIX		might get lost (downstream of altered splice site)
600	619	HELIX		might get lost (downstream of altered splice site)
626	626	ACT_SITE	Proton acceptor.	might get lost (downstream of altered splice site)
629	631	HELIX		might get lost (downstream of altered splice site)
632	634	STRAND		might get lost (downstream of altered splice site)
636	638	TURN		might get lost (downstream of altered splice site)
640	642	STRAND		might get lost (downstream of altered splice site)
652	654	TURN		might get lost (downstream of altered splice site)
656	656	MOD_RES	Phosphotyrosine; by autocatalysis.	might get lost (downstream of altered splice site)
656	657	MUTAGEN	Missing: Loss of kinase activity.	might get lost (downstream of altered splice site)
657	657	MOD_RES	Phosphotyrosine; by autocatalysis.	might get lost (downstream of altered splice site)
657	659	TURN		might get lost (downstream of altered splice site)
664	666	STRAND		might get lost (downstream of altered splice site)
667	669	HELIX		might get lost (downstream of altered splice site)
672	676	HELIX		might get lost (downstream of altered splice site)
682	697	HELIX		might get lost (downstream of altered splice site)
709	717	HELIX		might get lost (downstream of altered splice site)
726	728	STRAND		might get lost (downstream of altered splice site)
730	739	HELIX		might get lost (downstream of altered splice site)
744	746	HELIX		might get lost (downstream of altered splice site)
750	764	HELIX		might get lost (downstream of altered splice site)
769	769	MOD_RES	Phosphotyrosine; by autocatalysis.	might get lost (downstream of altered splice site)
769	769	MUTAGEN	Y->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

2130 / 2130

position (AA) of stopcodon in wt / mu AA sequence

710 / 710

position of stopcodon in wt / mu cDNA

2280 / 2280

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

151 / 151

chromosome

strand

-1

last intron/exon boundary

2116

theoretical NMD boundary in CDS

1915

length of CDS

2130

coding sequence (CDS) position

779

cDNA position
(for ins/del: last normal base / first normal base)

929

gDNA position
(for ins/del: last normal base / first normal base)

83170

chromosomal position
(for ins/del: last normal base / first normal base)

123274803

original gDNA sequence snippet

AGAAAAGGAGATTACAGCTTCCCCAGACTACCTGGAGATAG

altered gDNA sequence snippet

AGAAAAGGAGATTACAGCTTGCCCAGACTACCTGGAGATAG

original cDNA sequence snippet

AGAAAAGGAGATTACAGCTTCCCCAGACTACCTGGAGATAG

altered cDNA sequence snippet

AGAAAAGGAGATTACAGCTTGCCCAGACTACCTGGAGATAG

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
NHTYHLDVVA PGREKEITAS PDYLEIAIYC IGVFLIACMV VTVILCRMKN TTKKPDFSSQ
PAVHKLTKRI PLRRQVTVSA 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
NHTYHLDVVA PGREKEITAC PDYLEIAIYC IGVFLIACMV VTVILCRMKN TTKKPDFSSQ
PAVHKLTKRI PLRRQVTVSA 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