Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999527 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr5:73163965C>AN/A show variant in all transcripts   IGV
HGNC symbol ARHGEF28
Ensembl transcript ID ENST00000296799
Genbank transcript ID N/A
UniProt peptide Q8N1W1
alteration type single base exchange
alteration region CDS
DNA changes c.1399C>A
cDNA.1470C>A
g.241983C>A
AA changes H467N Score: 68 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 467
frameshift no
known variant Reference ID: rs2973558
databasehomozygous (A/A)heterozygousallele carriers
1000G140835975
ExAC46922239927091
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0450.028
-0.4550.001
(flanking)1.3390.002
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 increased241977wt: 0.8678 / mu: 0.8801 (marginal change - not scored)wt: CTGAGAGTGACCATA
mu: CTGAGAGTGACAATA		 GAGA|gtga
Donor gained2419790.91mu: GAGAGTGACAATAAC GAGT|gaca
distance from splice site 41
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      467RSATSLESESDHNSCRSRSHSDEL
mutated  all conserved    467RSATSLESESDNNSCRSRSHSDE
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  no alignment  ENSFCAG00000013540  n/a
Mmusculus  not conserved  ENSMUSG00000021662  779RAVTSLESEGD--SWRSRSHSDE
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000060415  840PEADSDSNLWRNHIQSEE
Dmelanogaster  no alignment  FBgn0032796  n/a
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
624624MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
652699ZN_FINGPhorbol-ester/DAG-type.might get lost (downstream of altered splice site)
8491044DOMAINDH.might get lost (downstream of altered splice site)
10861188DOMAINPH.might get lost (downstream of altered splice site)
12951304REGIONInteraction with PTK2/FAK1; required for regulation of axonal branching and synapse formation (By similarity).might get lost (downstream of altered splice site)
13721383REGIONMediates cytoplasmic retention and interaction with YWHAH (By similarity).might get lost (downstream of altered splice site)
14251705REGIONInteraction with microtubules (By similarity).might get lost (downstream of altered splice site)
14501450CONFLICTE -> G (in Ref. 3; BAB15141).might get lost (downstream of altered splice site)
14881525COILEDPotential.might get lost (downstream of altered splice site)
14961527REGIONRNA-binding (By similarity).might get lost (downstream of altered splice site)
15401540CONFLICTP -> S (in Ref. 3; BAB15141).might get lost (downstream of altered splice site)
15661579REGIONMediates cytoplasmic retention and interaction with MAPK8IP1 (By similarity).might get lost (downstream of altered splice site)
15981598CONFLICTS -> F (in Ref. 4; AAH12946).might get lost (downstream of altered splice site)
16131613CONFLICTK -> L (in Ref. 4; AAH12946).might get lost (downstream of altered splice site)
16201620CONFLICTS -> L (in Ref. 4; AAH12946).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 4179 / 4179
position (AA) of stopcodon in wt / mu AA sequence 1393 / 1393
position of stopcodon in wt / mu cDNA 4250 / 4250
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 72 / 72
chromosome 5
strand 1
last intron/exon boundary 4081
theoretical NMD boundary in CDS 3959
length of CDS 4179
coding sequence (CDS) position 1399
cDNA position
(for ins/del: last normal base / first normal base)		 1470
gDNA position
(for ins/del: last normal base / first normal base)		 241983
chromosomal position
(for ins/del: last normal base / first normal base)		 73163965
original gDNA sequence snippet CCTTGGAGTCTGAGAGTGACCATAACAGCTGCAGAAGCAGG
altered gDNA sequence snippet CCTTGGAGTCTGAGAGTGACAATAACAGCTGCAGAAGCAGG
original cDNA sequence snippet CCTTGGAGTCTGAGAGTGACCATAACAGCTGCAGAAGCAGG
altered cDNA sequence snippet CCTTGGAGTCTGAGAGTGACAATAACAGCTGCAGAAGCAGG
wildtype AA sequence MDSDSDSPFN YSWPSFPKMK IRRRTSKQDR SFDILKKSKP PSTLLAAGRL SDMLNGGDEV
YANCMVIDQV GDLDISYINI EGITATTSPE SRGCTLWPQS SKHTLPTETS PSVYPLSENV
EGTAHTEAQQ SFMSPSSSCA SNLNLSFGWH GFEKEQSHLK KRSSSLDALD ADSEGEGHSE
PSHICYTPGS QSSSRTGIPS GDELDSFETN TEPDFNISRA ESLPLSSNLQ SKESLLSGVR
SRSYSCSSPK ISLGKTRLVR ELTVCSSSEE QRAYSLSEPP RENRIQEEEW DKYIIPAKSE
SEKYKVSRTF SFLMNRMTSP RNKSKTKSKD AKDKEKLNRH QFAPGTFSGV LQCLVCDKTL
LGKESLQCSN CNANVHKGCK DAAPACTKKF QEKYNKNKPQ TILGNSSFRD IPQPGLSLHP
SSSVPVGLPT GRRETVGQVH PLSRSVPGTT LESFRRSATS LESESDHNSC RSRSHSDELL
QSMGSSPSTE SFIMEDVVDS SLWSDLSSDA QEFEAESWSL VVDPSFCNRQ EKDVIKRQDV
IFELMQTEMH HIQTLFIMSE IFRKGMKEEL QLDHSTVDKI FPCLDELLEI HRHFFYSMKE
RRQESCAGSD RNFVIDRIGD ILVQQFSEEN ASKMKKIYGE FCCHHKEAVN LFKELQQNKK
FQNFIKLRNS NLLARRRGIP ECILLVTQRI TKYPVLVERI LQYTKERTEE HKDLRKALCL
IKDMIATVDL KVNEYEKNQK WLEILNKIEN KTYTKLKNGH VFRKQALMSE ERTLLYDGLV
YWKTATGRFK DILALLLTDV LLFLQEKDQK YIFAAVDQKP SVISLQKLIA REVANEERGM
FLISASSAGP EMYEIHTNSK EERNNWMRRI QQAVESCPEE KGGRTSESDE DKRKAEARVA
KIQQCQEILT NQDQQICAYL EEKLHIYAEL GELSGFEDVH LEPHLLIKPD PGEPPQAASL
LAAALKEAES LQVAVKASQM GAVSQSCEDS CGDSVLADTL SSHDVPGSPT ASLVTGGREG
RGCSDVDPGI QGVVTDLAVS DAGEKVECRN FPGSSQSEII QAIQNLTRLL YSLQAALTIQ
DSHIEIHRLV LQQQEGLSLG HSILRGGPLQ DQKSRDADRQ HEELANVHQL QHQLQQEQRR
WLRRCEQQQR AQATRESWLQ ERERECQSQE ELLLRSRGEL DLQLQEYQHS LERLREGQRL
VEREQARMRA QQSLLGHWKH GRQRSLPAVL LPGGPEVMEL NRSESLCHEN SFFINEALVQ
MSFNTFNKLN PSVIHQDATY PTTQSHSDLV RTSEHQVDLK VDPSQPSNVS HKLWTAAGSG
HQILPFHESS KDSCKNDLDT SHTESPTPHD SNSHRPQLQA FITEAKLNLP TRTMTRQDGE
TGDGAKENIV YL*
mutated AA sequence MDSDSDSPFN YSWPSFPKMK IRRRTSKQDR SFDILKKSKP PSTLLAAGRL SDMLNGGDEV
YANCMVIDQV GDLDISYINI EGITATTSPE SRGCTLWPQS SKHTLPTETS PSVYPLSENV
EGTAHTEAQQ SFMSPSSSCA SNLNLSFGWH GFEKEQSHLK KRSSSLDALD ADSEGEGHSE
PSHICYTPGS QSSSRTGIPS GDELDSFETN TEPDFNISRA ESLPLSSNLQ SKESLLSGVR
SRSYSCSSPK ISLGKTRLVR ELTVCSSSEE QRAYSLSEPP RENRIQEEEW DKYIIPAKSE
SEKYKVSRTF SFLMNRMTSP RNKSKTKSKD AKDKEKLNRH QFAPGTFSGV LQCLVCDKTL
LGKESLQCSN CNANVHKGCK DAAPACTKKF QEKYNKNKPQ TILGNSSFRD IPQPGLSLHP
SSSVPVGLPT GRRETVGQVH PLSRSVPGTT LESFRRSATS LESESDNNSC RSRSHSDELL
QSMGSSPSTE SFIMEDVVDS SLWSDLSSDA QEFEAESWSL VVDPSFCNRQ EKDVIKRQDV
IFELMQTEMH HIQTLFIMSE IFRKGMKEEL QLDHSTVDKI FPCLDELLEI HRHFFYSMKE
RRQESCAGSD RNFVIDRIGD ILVQQFSEEN ASKMKKIYGE FCCHHKEAVN LFKELQQNKK
FQNFIKLRNS NLLARRRGIP ECILLVTQRI TKYPVLVERI LQYTKERTEE HKDLRKALCL
IKDMIATVDL KVNEYEKNQK WLEILNKIEN KTYTKLKNGH VFRKQALMSE ERTLLYDGLV
YWKTATGRFK DILALLLTDV LLFLQEKDQK YIFAAVDQKP SVISLQKLIA REVANEERGM
FLISASSAGP EMYEIHTNSK EERNNWMRRI QQAVESCPEE KGGRTSESDE DKRKAEARVA
KIQQCQEILT NQDQQICAYL EEKLHIYAEL GELSGFEDVH LEPHLLIKPD PGEPPQAASL
LAAALKEAES LQVAVKASQM GAVSQSCEDS CGDSVLADTL SSHDVPGSPT ASLVTGGREG
RGCSDVDPGI QGVVTDLAVS DAGEKVECRN FPGSSQSEII QAIQNLTRLL YSLQAALTIQ
DSHIEIHRLV LQQQEGLSLG HSILRGGPLQ DQKSRDADRQ HEELANVHQL QHQLQQEQRR
WLRRCEQQQR AQATRESWLQ ERERECQSQE ELLLRSRGEL DLQLQEYQHS LERLREGQRL
VEREQARMRA QQSLLGHWKH GRQRSLPAVL LPGGPEVMEL NRSESLCHEN SFFINEALVQ
MSFNTFNKLN PSVIHQDATY PTTQSHSDLV RTSEHQVDLK VDPSQPSNVS HKLWTAAGSG
HQILPFHESS KDSCKNDLDT SHTESPTPHD SNSHRPQLQA FITEAKLNLP TRTMTRQDGE
TGDGAKENIV YL*
speed 0.11 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