mutation t@sting

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

known variant

Reference ID: rs2973558

database	homozygous (A/A)	heterozygous	allele carriers
1000G	140	835	975
ExAC	4692	22399	27091

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.045	0.028
	-0.455	0.001
(flanking)	1.339	0.002

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
Donor marginally increased	241977	wt: 0.8678 / mu: 0.8801 (marginal change - not scored)	wt: CTGAGAGTGACCATA mu: CTGAGAGTGACAATA	GAGA\|gtga
Donor gained	241979	0.91	mu: GAGAGTGACAATAAC	GAGT\|gaca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

780

mutated

all conserved

780

Ptroglodytes

no homologue

Mmulatta

no homologue

Fcatus

no alignment

ENSFCAG00000013540

n/a

Mmusculus

not conserved

ENSMUSG00000021662

779

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000060415

844

Dmelanogaster

no alignment

FBgn0032796

n/a

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
849	1044	DOMAIN	DH.	might get lost (downstream of altered splice site)
1086	1188	DOMAIN	PH.	might get lost (downstream of altered splice site)
1295	1304	REGION	Interaction with PTK2/FAK1; required for regulation of axonal branching and synapse formation (By similarity).	might get lost (downstream of altered splice site)
1372	1383	REGION	Mediates cytoplasmic retention and interaction with YWHAH (By similarity).	might get lost (downstream of altered splice site)
1425	1705	REGION	Interaction with microtubules (By similarity).	might get lost (downstream of altered splice site)
1450	1450	CONFLICT	E -> G (in Ref. 3; BAB15141).	might get lost (downstream of altered splice site)
1488	1525	COILED	Potential.	might get lost (downstream of altered splice site)
1496	1527	REGION	RNA-binding (By similarity).	might get lost (downstream of altered splice site)
1540	1540	CONFLICT	P -> S (in Ref. 3; BAB15141).	might get lost (downstream of altered splice site)
1566	1579	REGION	Mediates cytoplasmic retention and interaction with MAPK8IP1 (By similarity).	might get lost (downstream of altered splice site)
1598	1598	CONFLICT	S -> F (in Ref. 4; AAH12946).	might get lost (downstream of altered splice site)
1613	1613	CONFLICT	K -> L (in Ref. 4; AAH12946).	might get lost (downstream of altered splice site)
1620	1620	CONFLICT	S -> 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

strand

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

1.02 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