mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999648550258 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM032833)
known disease mutation: rs2526 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr8:1830835C>TN/A show variant in all transcripts IGV

HGNC symbol

ARHGEF10

Ensembl transcript ID

ENST00000520359

Genbank transcript ID

N/A

UniProt peptide

O15013

alteration type

single base exchange

alteration region

CDS

DNA changes

c.881C>T
cDNA.1054C>T
g.58694C>T

AA changes

T294I Score: 89 explain score(s)

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

294

frameshift

known variant

Reference ID: rs28940281
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs2526 (pathogenic for Slowed nerve conduction velocity, autosomal dominant) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM032833)

known disease mutation at this position, please check HGMD for details (HGMD ID CM032833)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032833)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.609	0.998
	5.566	1
(flanking)	0.11	0.995

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	58692	wt: 0.6345 / mu: 0.6937 (marginal change - not scored)	wt: GACGGCACCAAGGAC mu: GACGGCATCAAGGAC	CGGC\|acca
Donor marginally increased	58697	wt: 0.6117 / mu: 0.6221 (marginal change - not scored)	wt: CACCAAGGACGGGCT mu: CATCAAGGACGGGCT	CCAA\|ggac
Donor gained	58698	0.33	mu: ATCAAGGACGGGCTG	CAAG\|gacg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

294

mutated

not conserved

294

Ptroglodytes

all identical

ENSPTRG00000019942

336

Mmulatta

all identical

ENSMMUG00000009472

311

Fcatus

all identical

ENSFCAG00000012553

245

Mmusculus

all identical

ENSMUSG00000071176

308

Ggallus

all identical

ENSGALG00000016350

321

Trubripes

no homologue

Drerio

all identical

ENSDARG00000077788

414

Dmelanogaster

no homologue

Celegans

no alignment

R02F2.2

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
304	355	COILED	Potential.	might get lost (downstream of altered splice site)
379	379	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
395	395	CONFLICT	L -> F (in Ref. 5; AAI12927).	might get lost (downstream of altered splice site)
421	608	DOMAIN	DH.	might get lost (downstream of altered splice site)
500	500	CONFLICT	D -> V (in Ref. 5; AAH40474).	might get lost (downstream of altered splice site)
1024	1024	CONFLICT	T -> S (in Ref. 6; AAB71662).	might get lost (downstream of altered splice site)
1046	1046	CONFLICT	S -> T (in Ref. 6; AAB71662).	might get lost (downstream of altered splice site)
1271	1304	COMPBIAS	Ser-rich.	might get lost (downstream of altered splice site)
1284	1284	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1287	1287	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3921 / 3921

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

1307 / 1307

position of stopcodon in wt / mu cDNA

4094 / 4094

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

174 / 174

chromosome

strand

last intron/exon boundary

3580

theoretical NMD boundary in CDS

3356

length of CDS

3921

coding sequence (CDS) position

881

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

1054

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

58694

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

1830835

original gDNA sequence snippet

GAAGGCCGCGAAGGACGGCACCAAGGACGGGCTGGAGAGGA

altered gDNA sequence snippet

GAAGGCCGCGAAGGACGGCATCAAGGACGGGCTGGAGAGGA

original cDNA sequence snippet

GAAGGCCGCGAAGGACGGCACCAAGGACGGGCTGGAGAGGA

altered cDNA sequence snippet

GAAGGCCGCGAAGGACGGCATCAAGGACGGGCTGGAGAGGA

wildtype AA sequence

MDQREPLPPA PAENEMKYDT NNNEEEEGEQ FDFDSGDEIP EADRQAPSAP ETGGAGASEA
PAPTGGEDGA GAETTPVAEP TKLVLPMKVN PYSVIDITPF QEDQPPTPVP SAEEENVGLH
VPCGYLVPVP CGYAVPSNLP LLLPAYSSPV IICATSLDEE AETPEVTEDR QPNSLSSEEP
PTSEDQVGRE DSALARWAAD PANTAWMENP EEAIYDDVPR ENSDSEPDEM IYDDVENGDE
GGNSSLEYGW SSSEFESYEE QSDSECKNGI PRSFLRSNHK KQMQKLVKAA KDGTKDGLER
TRAAVKRGRS FIRTKSLIAQ DHRSSLEEEQ NLFIDVDCKH PEAILTPMPE GLSQQQVVRR
YILGSVVDSE KNYVDALKRI LEQYEKPLSE MEPKVLSERK LKTVFYRVKE ILQCHSLFQI
ALASRVSEWD SVEMIGDVFV ASFSKSMVLD AYSEYVNNFS TAVAVLKKTC ATKPAFLEFL
KQEQEASPDR TTLYSLMMKP IQRFPQFILL LQDMLKNTSK GHPDRLPLQM ALTELETLAE
KLNERKRDAD QRCEVKQIAK AINERYLNKL LSSGSRYLIR SDDMIETVYN DRGEIVKTKE
RRVFMLNDVL MCATVSSRPS HDSRVMSSQR YLLKWSVPLG HVDAIEYGSS AGTGEHSRHL
AVHPPESLAV VANAKPNKVY MGPGQLYQDL QNLLHDLNVI GQITQLIGNL KGNYQNLNQS
VAHDWTSGLQ RLILKKEDEI RAADCCRIQL QLPGKQDKSG RPTFFTAVFN TFTPAIKESW
VNSLQMAKLA LEEENHMGWF CVEDDGNHIK KEKHPLLVGH MPVMVAKQQE FKIECAAYNP
EPYLNNESQP DSFSTAHGFL WIGSCTHQMG QIAIVSFQNS TPKVIECFNV ESRILCMLYV
PVEEKRREPG APPDPETPAV RASDVPTICV GTEEGSISIY KSSQGSKKVR LQHFFTPEKS
TVMSLACTSQ SLYAGLVNGA VASYARAPDG SWDSEPQKVI KLGVLPVRSL LMMEDTLWAA
SGGQVFIISV ETHAVEGQLE AHQEEGMVIS HMAVSGVGIW IAFTSGSTLR LFHTETLKHL
QDINIATPVH NMLPGHQRLS VTSLLVCHGL LMVGTSLGVL VALPVPRLQG IPKVTGRGMV
SYHAHNSPVK FIVLATALHE KDKDKSRDSL APGPEPQDED QKDALPSGGA GSSLSQGDPD
AAIWLGDSLG SMTQKSDLSS SSGSLSLSHG SSSLEHRSED STIYDLLKDP VSLRSKARRA
KKAKASSALV VCGGQGHRRV HRKARQPHQE ELAPTVMVWQ IPLLNI*

mutated AA sequence

MDQREPLPPA PAENEMKYDT NNNEEEEGEQ FDFDSGDEIP EADRQAPSAP ETGGAGASEA
PAPTGGEDGA GAETTPVAEP TKLVLPMKVN PYSVIDITPF QEDQPPTPVP SAEEENVGLH
VPCGYLVPVP CGYAVPSNLP LLLPAYSSPV IICATSLDEE AETPEVTEDR QPNSLSSEEP
PTSEDQVGRE DSALARWAAD PANTAWMENP EEAIYDDVPR ENSDSEPDEM IYDDVENGDE
GGNSSLEYGW SSSEFESYEE QSDSECKNGI PRSFLRSNHK KQMQKLVKAA KDGIKDGLER
TRAAVKRGRS FIRTKSLIAQ DHRSSLEEEQ NLFIDVDCKH PEAILTPMPE GLSQQQVVRR
YILGSVVDSE KNYVDALKRI LEQYEKPLSE MEPKVLSERK LKTVFYRVKE ILQCHSLFQI
ALASRVSEWD SVEMIGDVFV ASFSKSMVLD AYSEYVNNFS TAVAVLKKTC ATKPAFLEFL
KQEQEASPDR TTLYSLMMKP IQRFPQFILL LQDMLKNTSK GHPDRLPLQM ALTELETLAE
KLNERKRDAD QRCEVKQIAK AINERYLNKL LSSGSRYLIR SDDMIETVYN DRGEIVKTKE
RRVFMLNDVL MCATVSSRPS HDSRVMSSQR YLLKWSVPLG HVDAIEYGSS AGTGEHSRHL
AVHPPESLAV VANAKPNKVY MGPGQLYQDL QNLLHDLNVI GQITQLIGNL KGNYQNLNQS
VAHDWTSGLQ RLILKKEDEI RAADCCRIQL QLPGKQDKSG RPTFFTAVFN TFTPAIKESW
VNSLQMAKLA LEEENHMGWF CVEDDGNHIK KEKHPLLVGH MPVMVAKQQE FKIECAAYNP
EPYLNNESQP DSFSTAHGFL WIGSCTHQMG QIAIVSFQNS TPKVIECFNV ESRILCMLYV
PVEEKRREPG APPDPETPAV RASDVPTICV GTEEGSISIY KSSQGSKKVR LQHFFTPEKS
TVMSLACTSQ SLYAGLVNGA VASYARAPDG SWDSEPQKVI KLGVLPVRSL LMMEDTLWAA
SGGQVFIISV ETHAVEGQLE AHQEEGMVIS HMAVSGVGIW IAFTSGSTLR LFHTETLKHL
QDINIATPVH NMLPGHQRLS VTSLLVCHGL LMVGTSLGVL VALPVPRLQG IPKVTGRGMV
SYHAHNSPVK FIVLATALHE KDKDKSRDSL APGPEPQDED QKDALPSGGA GSSLSQGDPD
AAIWLGDSLG SMTQKSDLSS SSGSLSLSHG SSSLEHRSED STIYDLLKDP VSLRSKARRA
KKAKASSALV VCGGQGHRRV HRKARQPHQE ELAPTVMVWQ IPLLNI*

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