mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999999999988 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM950458)
known disease mutation at this position (HGMD CM970526)
known disease mutation: rs13272 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:123279677G>CN/A show variant in all transcripts IGV

HGNC symbol

FGFR2

Ensembl transcript ID

ENST00000369056

Genbank transcript ID

NM_001144913

UniProt peptide

P21802

alteration type

single base exchange

alteration region

CDS

DNA changes

c.755C>G
cDNA.779C>G
g.78296C>G

AA changes

S252W Score: 177 explain score(s)

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

252

frameshift

known variant

Reference ID: rs79184941

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

known disease mutation: rs13272 (pathogenic for Crouzon syndrome|Neoplasm of stomach|Endometrial carcinoma|Adenocarcinoma of stomach|Uterine Carcinosarcoma|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|Acrocephalosyndactyly|Antley-Bixler syndrome without genital anomalies or disordered steroidogenesis|Endometrial neoplasm|Malignant neoplasm of body of uterus|Endometrial Endometrioid Adenocarcinoma, Variant with Squamous Differentiation|FGFR2 related craniosynostosis|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950458)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950458)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970526)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950458)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970526)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950458)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950458)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970526)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950458)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970526)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-4.323	0
	6.235	1
(flanking)	5.149	0.999

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
Acc marginally increased	78289	wt: 0.9383 / mu: 0.9525 (marginal change - not scored)	wt: TTTCTTCCCTCTCTCCACCAGAGCGATCGCCTCACCGGCCC mu: TTTCTTCCCTCTCTCCACCAGAGCGATGGCCTCACCGGCCC	ccag\|AGCG
Acc marginally increased	78286	wt: 0.9844 / mu: 0.9866 (marginal change - not scored)	wt: TCCTTTCTTCCCTCTCTCCACCAGAGCGATCGCCTCACCGG mu: TCCTTTCTTCCCTCTCTCCACCAGAGCGATGGCCTCACCGG	ccac\|CAGA
Donor increased	78290	wt: 0.84 / mu: 1.00	wt: ACCAGAGCGATCGCC mu: ACCAGAGCGATGGCC	CAGA\|gcga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

252

mutated

not conserved

252

Ptroglodytes

all identical

ENSPTRG00000003003

252

Mmulatta

all identical

ENSMMUG00000009594

101

Fcatus

all identical

ENSFCAG00000003692

215

Mmusculus

all identical

ENSMUSG00000030849

271

Ggallus

all identical

ENSGALG00000009495

257

VGT

Trubripes

all identical

ENSTRUG00000017610

252

Drerio

all identical

ENSDARG00000058115

275

Dmelanogaster

not conserved

FBgn0010389

195

Celegans

not conserved

F58A3.2

388

Xtropicalis

all identical

ENSXETG00000015592

264

protein features

start (aa)	end (aa)	feature	details
22	377	TOPO_DOM	Extracellular (Potential).	lost
256	358	DOMAIN	Ig-like C2-type 3.	might get lost (downstream of altered splice site)
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

2310 / 2310

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

770 / 770

position of stopcodon in wt / mu cDNA

2334 / 2334

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

25 / 25

chromosome

strand

-1

last intron/exon boundary

2329

theoretical NMD boundary in CDS

2254

length of CDS

2310

coding sequence (CDS) position

755

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

779

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

78296

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

123279677

original gDNA sequence snippet

CCTCTCTCCACCAGAGCGATCGCCTCACCGGCCCATCCTCC

altered gDNA sequence snippet

CCTCTCTCCACCAGAGCGATGGCCTCACCGGCCCATCCTCC

original cDNA sequence snippet

CCTGGATGTTGTGGAGCGATCGCCTCACCGGCCCATCCTCC

altered cDNA sequence snippet

CCTGGATGTTGTGGAGCGATGGCCTCACCGGCCCATCCTCC

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 VLKHSGINSS NAEVLALFNV TEADAGEYIC KVSNYIGQAN QSAWLTVLPK
QQAPGREKEI TASPDYLEIA IYCIGVFLIA CMVVTVILCR MKNTTKKPDF SSQPAVHKLT
KRIPLRRQVT VSAESSSSMN SNTPLVRITT RLSSTADTPM LAGVSEYELP EDPKWEFPRD
KLTLGKPLGE GCFGQVVMAE AVGIDKDKPK EAVTVAVKML KDDATEKDLS DLVSEMEMMK
MIGKHKNIIN LLGACTQDGP LYVIVEYASK GNLREYLRAR RPPGMEYSYD INRVPEEQMT
FKDLVSCTYQ LARGMEYLAS QKCIHRDLAA RNVLVTENNV MKIADFGLAR DINNIDYYKK
TTNGRLPVKW MAPEALFDRV YTHQSDVWSF GVLMWEIFTL GGSPYPGIPV EELFKLLKEG
HRMDKPANCT NELYMMMRDC WHAVPSQRPT FKQLVEDLDR ILTLTTNEI*

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 RWPHRPILQA GLPANASTVV GGDVEFVCKV YSDAQPHIQW IKHVEKNGSK
YGPDGLPYLK VLKHSGINSS NAEVLALFNV TEADAGEYIC KVSNYIGQAN QSAWLTVLPK
QQAPGREKEI TASPDYLEIA IYCIGVFLIA CMVVTVILCR MKNTTKKPDF SSQPAVHKLT
KRIPLRRQVT VSAESSSSMN SNTPLVRITT RLSSTADTPM LAGVSEYELP EDPKWEFPRD
KLTLGKPLGE GCFGQVVMAE AVGIDKDKPK EAVTVAVKML KDDATEKDLS DLVSEMEMMK
MIGKHKNIIN LLGACTQDGP LYVIVEYASK GNLREYLRAR RPPGMEYSYD INRVPEEQMT
FKDLVSCTYQ LARGMEYLAS QKCIHRDLAA RNVLVTENNV MKIADFGLAR DINNIDYYKK
TTNGRLPVKW MAPEALFDRV YTHQSDVWSF GVLMWEIFTL GGSPYPGIPV EELFKLLKEG
HRMDKPANCT NELYMMMRDC WHAVPSQRPT FKQLVEDLDR ILTLTTNEI*

speed

1.09 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