mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999999954146 (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

ENST00000457416

Genbank transcript ID

NM_022970

UniProt peptide

P21802

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1127A>G
cDNA.1719A>G
g.83179A>G

AA changes

Y376C Score: 194 explain score(s)

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

376

frameshift

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

	PhyloP	PhastCons
(flanking)	1.522	1
	5.165	1
(flanking)	5.165	1

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

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

376

mutated

not conserved

376

Ptroglodytes

all identical

ENSPTRG00000003003

376

Mmulatta

all identical

ENSMMUG00000009594

225

Fcatus

no alignment

ENSFCAG00000003692

n/a

Mmusculus

all identical

ENSMUSG00000030849

397

Ggallus

all identical

ENSGALG00000009495

385

Trubripes

all identical

ENSTRUG00000017610

376

Drerio

all identical

ENSDARG00000058115

398

Dmelanogaster

all conserved

FBgn0010389

308

Celegans

all identical

F58A3.2

521

DRW

Xtropicalis

all identical

ENSXETG00000015592

390

protein features

start (aa)	end (aa)	feature	details
22	377	TOPO_DOM	Extracellular (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2469 / 2469

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

823 / 823

position of stopcodon in wt / mu cDNA

3061 / 3061

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

593 / 593

chromosome

strand

-1

last intron/exon boundary

2897

theoretical NMD boundary in CDS

2254

length of CDS

2469

coding sequence (CDS) position

1127

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

1719

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 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 ILTLTTNEEY LDLSQPLEQY
SPSYPDTRSS CSSGDDSVFS PDPMPYEPCL PQYPHINGSV KT*

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 VLKHSGINSS NAEVLALFNV TEADAGEYIC KVSNYIGQAN QSAWLTVLPK
QQAPGREKEI TASPDCLEIA 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 ILTLTTNEEY LDLSQPLEQY
SPSYPDTRSS CSSGDDSVFS PDPMPYEPCL PQYPHINGSV KT*

speed

1.12 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