Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999998268 (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) chr5:73072354T>CN/A show variant in all transcripts   IGV
HGNC symbol ARHGEF28
Ensembl transcript ID ENST00000437974
Genbank transcript ID N/A
UniProt peptide Q8N1W1
alteration type single base exchange
alteration region CDS
DNA changes c.673T>C
cDNA.693T>C
g.150372T>C
AA changes W225R Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 225
frameshift no
known variant Reference ID: rs7714670
databasehomozygous (C/C)heterozygousallele carriers
1000G36911171486
ExAC112681023121499
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-2.1580
0.4180
(flanking)-0.2210
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased150366wt: 0.56 / mu: 0.66wt: TGTGTTGTTTCAGTTTTCAGGGCAGATGGTCCCCAAGCTTC
mu: TGTGTTGTTTCAGTTTTCAGGGCAGACGGTCCCCAAGCTTC		 cagg|GCAG
Acc marginally increased150365wt: 0.9159 / mu: 0.9350 (marginal change - not scored)wt: TTGTGTTGTTTCAGTTTTCAGGGCAGATGGTCCCCAAGCTT
mu: TTGTGTTGTTTCAGTTTTCAGGGCAGACGGTCCCCAAGCTT		 tcag|GGCA
Acc marginally increased150363wt: 0.7735 / mu: 0.7831 (marginal change - not scored)wt: ATTTGTGTTGTTTCAGTTTTCAGGGCAGATGGTCCCCAAGC
mu: ATTTGTGTTGTTTCAGTTTTCAGGGCAGACGGTCCCCAAGC		 tttc|AGGG
Acc marginally increased150364wt: 0.8653 / mu: 0.8971 (marginal change - not scored)wt: TTTGTGTTGTTTCAGTTTTCAGGGCAGATGGTCCCCAAGCT
mu: TTTGTGTTGTTTCAGTTTTCAGGGCAGACGGTCCCCAAGCT		 ttca|GGGC
Donor marginally increased150376wt: 0.7997 / mu: 0.8136 (marginal change - not scored)wt: ATGGTCCCCAAGCTT
mu: ACGGTCCCCAAGCTT		 GGTC|ccca
Donor increased150364wt: 0.76 / mu: 0.90wt: TTTTCAGGGCAGATG
mu: TTTTCAGGGCAGACG		 TTCA|gggc
distance from splice site 14
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      225LVEDVTNFQGRWSPSFSRVQLSEE
mutated  not conserved    225LVEDVTNFQGRRSPSFSRVQLSE
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  all identical  ENSFCAG00000013540  419LQDEFQQDQRRWHRRCDQQQREQ
Mmusculus  not conserved  ENSMUSG00000021662  225LVEDITNFQGSHSPGFSRLRLNE
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000060415  290LITALTHGSALRPVWMCQIWTDC
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 5196 / 5196
position (AA) of stopcodon in wt / mu AA sequence 1732 / 1732
position of stopcodon in wt / mu cDNA 5216 / 5216
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 21 / 21
chromosome 5
strand 1
last intron/exon boundary 5047
theoretical NMD boundary in CDS 4976
length of CDS 5196
coding sequence (CDS) position 673
cDNA position
(for ins/del: last normal base / first normal base)		 693
gDNA position
(for ins/del: last normal base / first normal base)		 150372
chromosomal position
(for ins/del: last normal base / first normal base)		 73072354
original gDNA sequence snippet GTTTCAGTTTTCAGGGCAGATGGTCCCCAAGCTTCTCCCGA
altered gDNA sequence snippet GTTTCAGTTTTCAGGGCAGACGGTCCCCAAGCTTCTCCCGA
original cDNA sequence snippet TCACAAATTTTCAGGGCAGATGGTCCCCAAGCTTCTCCCGA
altered cDNA sequence snippet TCACAAATTTTCAGGGCAGACGGTCCCCAAGCTTCTCCCGA
wildtype AA sequence MELSCSEAPL YGQMMIYAKF DKNVYLPEDA EFYFTYDGSH QRHVMIAERI EDNVLQSSVP
GHGLQETVTV SVCLCSEGYS PVTMGSGSVT YVDNMACRLA RLLVTQANRL TACSHQTLLT
PFALTAGALP ALDEELVLAL THLELPLEWT VLGSSSLEVS SHRESLLHLA MRWGLAKLSQ
FFLCLPGGVQ ALALPNEEGA TPLDLALREG HSKLVEDVTN FQGRWSPSFS RVQLSEEASL
HYIHSSETLT LTLNHTAEHL LEADIKLFRK YFWDRAFLVK AFEPEARPEE RTAMPSSGAE
TEEEIKNSVS SRSAAEKEDI KRVKSLVVQH NEHEDQHSLD LDRSFDILKK SKPPSTLLAA
GRLSDMLNGG DEVYANCMVI DQVGDLDISY INIEGITATT SPESRGCTLW PQSSKHTLPT
ETSPSVYPLS ENVEGTAHTE AQQSFMSPSS SCASNLNLSF GWHGFEKEQS HLKKRSSSLD
ALDADSEGEG HSEPSHICYT PGSQSSSRTG IPSGDELDSF ETNTEPDFNI SRAESLPLSS
NLQSKESLLS GVRSRSYSCS SPKISLGKTR LVRELTVCSS SEEQRAYSLS EPPRENRIQE
EEWDKYIIPA KSESEKYKVS RTFSFLMNRM TSPRNKSKTK SKDAKDKEKL NRHQFAPGTF
SGVLQCLVCD KTLLGKESLQ CSNCNANVHK GCKDAAPACT KKFQEKYNKN KPQTILGNSS
FRDIPQPGLS LHPSSSVPVG LPTGRRETVG QVHPLSRSVP GTTLESFRRS ATSLESESDH
NSCRSRSHSD ELLQSMGSSP STESFIMEDV VDSSLWSDLS SDAQEFEAES WSLVVDPSFC
NRQEKDVIKR QDVIFELMQT EMHHIQTLFI MSEIFRKGMK EELQLDHSTV DKIFPCLDEL
LEIHRHFFYS MKERRQESCA GSDRNFVIDR IGDILVQQFS EENASKMKKI YGEFCCHHKE
AVNLFKELQQ NKKFQNFIKL RNSNLLARRR GIPECILLVT QRITKYPVLV ERILQYTKER
TEEHKDLRKA LCLIKDMIAT VDLKVNEYEK NQKWLEILNK IENKTYTKLK NGHVFRKQAL
MSEERTLLYD GLVYWKTATG RFKDILALLL TDVLLFLQEK DQKYIFAAVD QKPSVISLQK
LIAREVANEE RGMFLISASS AGPEMYEIHT NSKEERNNWM RRIQQAVESC PEEKGGRTSE
SDEDKRKAEA RVAKIQQCQE ILTNQDQQIC AYLEEKLHIY AELGELSGFE DVHLEPHLLI
KPDPGEPPQA ASLLAAALKE AESLQVAVKA SQMGAVSQSC EDSCGDSVLA DTLSSHDVPG
SPTASLVTGG REGRGCSDVD PGIQGVVTDL AVSDAGEKVE CRNFPGSSQS EIIQAIQNLT
RLLYSLQAAL TIQDSHIEIH RLVLQQQEGL SLGHSILRGG PLQDQKSRDA DRQHEELANV
HQLQHQLQQE QRRWLRRCEQ QQRAQATRES WLQERERECQ SQEELLLRSR GELDLQLQEY
QHSLERLREG QRLVEREQAR MRAQQSLLGH WKHGRQRSLP AVLLPGGPEV MELNRSESLC
HENSFFINEA LVQMSFNTFN KLNPSVIHQD ATYPTTQSHS DLVRTSEHQV DLKVDPSQPS
NVSHKLWTAA GSGHQILPFH ESSKDSCKNG SSMTKCSCTL TSPPGLWTGT TSTLKDLDTS
HTESPTPHDS NSHRPQLQAF ITEAKLNLPT RTMTRQDGET GDGAKENIVY L*
mutated AA sequence MELSCSEAPL YGQMMIYAKF DKNVYLPEDA EFYFTYDGSH QRHVMIAERI EDNVLQSSVP
GHGLQETVTV SVCLCSEGYS PVTMGSGSVT YVDNMACRLA RLLVTQANRL TACSHQTLLT
PFALTAGALP ALDEELVLAL THLELPLEWT VLGSSSLEVS SHRESLLHLA MRWGLAKLSQ
FFLCLPGGVQ ALALPNEEGA TPLDLALREG HSKLVEDVTN FQGRRSPSFS RVQLSEEASL
HYIHSSETLT LTLNHTAEHL LEADIKLFRK YFWDRAFLVK AFEPEARPEE RTAMPSSGAE
TEEEIKNSVS SRSAAEKEDI KRVKSLVVQH NEHEDQHSLD LDRSFDILKK SKPPSTLLAA
GRLSDMLNGG DEVYANCMVI DQVGDLDISY INIEGITATT SPESRGCTLW PQSSKHTLPT
ETSPSVYPLS ENVEGTAHTE AQQSFMSPSS SCASNLNLSF GWHGFEKEQS HLKKRSSSLD
ALDADSEGEG HSEPSHICYT PGSQSSSRTG IPSGDELDSF ETNTEPDFNI SRAESLPLSS
NLQSKESLLS GVRSRSYSCS SPKISLGKTR LVRELTVCSS SEEQRAYSLS EPPRENRIQE
EEWDKYIIPA KSESEKYKVS RTFSFLMNRM TSPRNKSKTK SKDAKDKEKL NRHQFAPGTF
SGVLQCLVCD KTLLGKESLQ CSNCNANVHK GCKDAAPACT KKFQEKYNKN KPQTILGNSS
FRDIPQPGLS LHPSSSVPVG LPTGRRETVG QVHPLSRSVP GTTLESFRRS ATSLESESDH
NSCRSRSHSD ELLQSMGSSP STESFIMEDV VDSSLWSDLS SDAQEFEAES WSLVVDPSFC
NRQEKDVIKR QDVIFELMQT EMHHIQTLFI MSEIFRKGMK EELQLDHSTV DKIFPCLDEL
LEIHRHFFYS MKERRQESCA GSDRNFVIDR IGDILVQQFS EENASKMKKI YGEFCCHHKE
AVNLFKELQQ NKKFQNFIKL RNSNLLARRR GIPECILLVT QRITKYPVLV ERILQYTKER
TEEHKDLRKA LCLIKDMIAT VDLKVNEYEK NQKWLEILNK IENKTYTKLK NGHVFRKQAL
MSEERTLLYD GLVYWKTATG RFKDILALLL TDVLLFLQEK DQKYIFAAVD QKPSVISLQK
LIAREVANEE RGMFLISASS AGPEMYEIHT NSKEERNNWM RRIQQAVESC PEEKGGRTSE
SDEDKRKAEA RVAKIQQCQE ILTNQDQQIC AYLEEKLHIY AELGELSGFE DVHLEPHLLI
KPDPGEPPQA ASLLAAALKE AESLQVAVKA SQMGAVSQSC EDSCGDSVLA DTLSSHDVPG
SPTASLVTGG REGRGCSDVD PGIQGVVTDL AVSDAGEKVE CRNFPGSSQS EIIQAIQNLT
RLLYSLQAAL TIQDSHIEIH RLVLQQQEGL SLGHSILRGG PLQDQKSRDA DRQHEELANV
HQLQHQLQQE QRRWLRRCEQ QQRAQATRES WLQERERECQ SQEELLLRSR GELDLQLQEY
QHSLERLREG QRLVEREQAR MRAQQSLLGH WKHGRQRSLP AVLLPGGPEV MELNRSESLC
HENSFFINEA LVQMSFNTFN KLNPSVIHQD ATYPTTQSHS DLVRTSEHQV DLKVDPSQPS
NVSHKLWTAA GSGHQILPFH ESSKDSCKNG SSMTKCSCTL TSPPGLWTGT TSTLKDLDTS
HTESPTPHDS NSHRPQLQAF ITEAKLNLPT RTMTRQDGET GDGAKENIVY L*
speed 1.00 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