Yum, tasty mutations...

MutationTaster - study a chromosomal position

MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 7 transcript(s)...
Querying Taster for transcript #1: ENST00000296794
Querying Taster for transcript #2: ENST00000437974
Querying Taster for transcript #3: ENST00000426542
Querying Taster for transcript #4: ENST00000296799
Querying Taster for transcript #5: ENST00000545377
Querying Taster for transcript #6: ENST00000513042
Querying Taster for transcript #7: ENST00000287898
MT speed 9.48 s - this script 9.137975 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ARHGEF28polymorphism_automatic4.72955008490317e-13simple_aaeaffectedH780Nsingle base exchangers2973558show file
ARHGEF28polymorphism_automatic4.72955008490317e-13simple_aaeaffectedH780Nsingle base exchangers2973558show file
ARHGEF28polymorphism_automatic4.72955008490317e-13simple_aaeaffectedH780Nsingle base exchangers2973558show file
ARHGEF28polymorphism_automatic4.72955008490317e-13simple_aaeaffectedH780Nsingle base exchangers2973558show file
ARHGEF28polymorphism_automatic4.72955008490317e-13simple_aaeaffectedH467Nsingle base exchangers2973558show file
ARHGEF28polymorphism_automatic4.72955008490317e-13simple_aaeaffectedH780Nsingle base exchangers2973558show file
ARHGEF28polymorphism_automatic4.72955008490317e-13simple_aaeaffectedH780Nsingle base exchangers2973558show file

Taster files

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 ENST00000296794
Genbank transcript ID N/A
UniProt peptide Q8N1W1
alteration type single base exchange
alteration region CDS
DNA changes c.2338C>A
cDNA.2514C>A
g.241983C>A
AA changes H780N Score: 68 explain score(s)
position(s) of altered AA
if AA alteration in CDS
780
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      780RSATSLESESDHNSCRSRSHSDEL
mutated  all conserved    780RSATSLESESDNNSCRSRSHSDE
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  no alignment  ENSFCAG00000013540  n/a
Mmusculus  not conserved  ENSMUSG00000021662  779--SWRSRSHSDE
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000060415  844RLSESPEADSDSNLWRNHIQSEE
Dmelanogaster  no alignment  FBgn0032796  n/a
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
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 4956 / 4956
position (AA) of stopcodon in wt / mu AA sequence 1652 / 1652
position of stopcodon in wt / mu cDNA 5132 / 5132
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 177 / 177
chromosome 5
strand 1
last intron/exon boundary 4824
theoretical NMD boundary in CDS 4597
length of CDS 4956
coding sequence (CDS) position 2338
cDNA position
(for ins/del: last normal base / first normal base)
2514
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 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 N*
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 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 ATSLESESDN
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 N*
speed 1.10 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
back to results table
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 ENST00000437974
Genbank transcript ID N/A
UniProt peptide Q8N1W1
alteration type single base exchange
alteration region CDS
DNA changes c.2338C>A
cDNA.2358C>A
g.241983C>A
AA changes H780N Score: 68 explain score(s)
position(s) of altered AA
if AA alteration in CDS
780
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      780RSATSLESESDHNSCRSRSHSDEL
mutated  all conserved    780RSATSLESESDNNSCRSRSHSDE
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  no alignment  ENSFCAG00000013540  n/a
Mmusculus  not conserved  ENSMUSG00000021662  779--SWRSRSHSDE
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000060415  844RLSESPEADSDSNLWRNHIQSEE
Dmelanogaster  no alignment  FBgn0032796  n/a
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
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 2338
cDNA position
(for ins/del: last normal base / first normal base)
2358
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 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 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 ATSLESESDN
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 1.54 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
back to results table
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 ENST00000426542
Genbank transcript ID NM_001244364
UniProt peptide Q8N1W1
alteration type single base exchange
alteration region CDS
DNA changes c.2338C>A
cDNA.2358C>A
g.241983C>A
AA changes H780N Score: 68 explain score(s)
position(s) of altered AA
if AA alteration in CDS
780
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      780RSATSLESESDHNSCRSRSHSDEL
mutated  all conserved    780RSATSLESESDNNSCRSRSHSDE
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  no alignment  ENSFCAG00000013540  n/a
Mmusculus  not conserved  ENSMUSG00000021662  779--SWRSRSHSDE
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000060415  844RLSESPEADSDSNLWRNHIQSEE
Dmelanogaster  no alignment  FBgn0032796  n/a
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
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 5118 / 5118
position (AA) of stopcodon in wt / mu AA sequence 1706 / 1706
position of stopcodon in wt / mu cDNA 5138 / 5138
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 4969
theoretical NMD boundary in CDS 4898
length of CDS 5118
coding sequence (CDS) position 2338
cDNA position
(for ins/del: last normal base / first normal base)
2358
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 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 ESSKDSCKND LDTSHTESPT PHDSNSHRPQ LQAFITEAKL
NLPTRTMTRQ DGETGDGAKE NIVYL*
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 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 ATSLESESDN
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 ESSKDSCKND LDTSHTESPT PHDSNSHRPQ LQAFITEAKL
NLPTRTMTRQ DGETGDGAKE NIVYL*
speed 1.48 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
back to results table
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 ENST00000545377
Genbank transcript ID NM_001080479
UniProt peptide Q8N1W1
alteration type single base exchange
alteration region CDS
DNA changes c.2338C>A
cDNA.2514C>A
g.241983C>A
AA changes H780N Score: 68 explain score(s)
position(s) of altered AA
if AA alteration in CDS
780
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      780RSATSLESESDHNSCRSRSHSDEL
mutated  all conserved    780RSATSLESESDNNSCRSRSHSDE
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  no alignment  ENSFCAG00000013540  n/a
Mmusculus  not conserved  ENSMUSG00000021662  779--SWRSRSHSDE
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000060415  844RLSESPEADSDSNLWRNHIQSEE
Dmelanogaster  no alignment  FBgn0032796  n/a
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
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 5372 / 5372
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 177 / 177
chromosome 5
strand 1
last intron/exon boundary 5203
theoretical NMD boundary in CDS 4976
length of CDS 5196
coding sequence (CDS) position 2338
cDNA position
(for ins/del: last normal base / first normal base)
2514
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 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 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 ATSLESESDN
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 1.53 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
back to results table
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 1.62 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
back to results table
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 ENST00000513042
Genbank transcript ID NM_001177693
UniProt peptide Q8N1W1
alteration type single base exchange
alteration region CDS
DNA changes c.2338C>A
cDNA.2514C>A
g.241983C>A
AA changes H780N Score: 68 explain score(s)
position(s) of altered AA
if AA alteration in CDS
780
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      780RSATSLESESDHNSCRSRSHSDEL
mutated  all conserved    780RSATSLESESDNNSCRSRSHSDE
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  no alignment  ENSFCAG00000013540  n/a
Mmusculus  not conserved  ENSMUSG00000021662  779--SWRSRSHSDE
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000060415  844RLSESPEADSDSNLWRNHIQSEE
Dmelanogaster  no alignment  FBgn0032796  n/a
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
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 5118 / 5118
position (AA) of stopcodon in wt / mu AA sequence 1706 / 1706
position of stopcodon in wt / mu cDNA 5294 / 5294
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 177 / 177
chromosome 5
strand 1
last intron/exon boundary 5125
theoretical NMD boundary in CDS 4898
length of CDS 5118
coding sequence (CDS) position 2338
cDNA position
(for ins/del: last normal base / first normal base)
2514
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 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 ESSKDSCKND LDTSHTESPT PHDSNSHRPQ LQAFITEAKL
NLPTRTMTRQ DGETGDGAKE NIVYL*
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 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 ATSLESESDN
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 ESSKDSCKND LDTSHTESPT PHDSNSHRPQ LQAFITEAKL
NLPTRTMTRQ DGETGDGAKE NIVYL*
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
back to results table
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 ENST00000287898
Genbank transcript ID N/A
UniProt peptide Q8N1W1
alteration type single base exchange
alteration region CDS
DNA changes c.2338C>A
cDNA.2514C>A
g.241983C>A
AA changes H780N Score: 68 explain score(s)
position(s) of altered AA
if AA alteration in CDS
780
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      780RSATSLESESDHNSCRSRSHSDEL
mutated  all conserved    780RSATSLESESDNNSCRSRSHSDE
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  no alignment  ENSFCAG00000013540  n/a
Mmusculus  not conserved  ENSMUSG00000021662  779--SWRSRSHSDE
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000060415  844RLSESPEADSDSNLWRNHIQSEE
Dmelanogaster  no alignment  FBgn0032796  n/a
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
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 5064 / 5064
position (AA) of stopcodon in wt / mu AA sequence 1688 / 1688
position of stopcodon in wt / mu cDNA 5240 / 5240
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 177 / 177
chromosome 5
strand 1
last intron/exon boundary 5071
theoretical NMD boundary in CDS 4844
length of CDS 5064
coding sequence (CDS) position 2338
cDNA position
(for ins/del: last normal base / first normal base)
2514
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 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 ALVTGGREGR GCSDVDPGIQ GVVTDLAVSD AGEKVECRNF
PGSSQSEIIQ AIQNLTRLLY SLQAALTIQD SHIEIHRLVL QQQEGLSLGH SILRGGPLQD
QKSRDADRQH EELANVHQLQ HQLQQEQRRW LRRCEQQQRA QATRESWLQE RERECQSQEE
LLLRSRGELD LQLQEYQHSL ERLREGQRLV EREQARMRAQ QSLLGHWKHG RQRSLPAVLL
PGGPEVMELN RSESLCHENS FFINEALVQM SFNTFNKLNP SVIHQDATYP TTQSHSDLVR
TSEHQVDLKV DPSQPSNVSH KLWTAAGSGH QILPFHESSK DSCKNGSSMT KCSCTLTSPP
GLWTGTTSTL KDLDTSHTES PTPHDSNSHR PQLQAFITEA KLNLPTRTMT RQDGETGDGA
KENIVYL*
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 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 ATSLESESDN
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 ALVTGGREGR GCSDVDPGIQ GVVTDLAVSD AGEKVECRNF
PGSSQSEIIQ AIQNLTRLLY SLQAALTIQD SHIEIHRLVL QQQEGLSLGH SILRGGPLQD
QKSRDADRQH EELANVHQLQ HQLQQEQRRW LRRCEQQQRA QATRESWLQE RERECQSQEE
LLLRSRGELD LQLQEYQHSL ERLREGQRLV EREQARMRAQ QSLLGHWKHG RQRSLPAVLL
PGGPEVMELN RSESLCHENS FFINEALVQM SFNTFNKLNP SVIHQDATYP TTQSHSDLVR
TSEHQVDLKV DPSQPSNVSH KLWTAAGSGH QILPFHESSK DSCKNGSSMT KCSCTLTSPP
GLWTGTTSTL KDLDTSHTES PTPHDSNSHR PQLQAFITEA KLNLPTRTMT RQDGETGDGA
KENIVYL*
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
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Problems