mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999998940565496 (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

ENST00000398560

Genbank transcript ID

N/A

UniProt peptide

O15013

alteration type

single base exchange

alteration region

CDS

DNA changes

c.953C>T
cDNA.1116C>T
g.58694C>T

AA changes

T318I Score: 89 explain score(s)

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

318

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

318

mutated

not conserved

318

Ptroglodytes

all identical

ENSPTRG00000019942

318

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.	lost
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

1833 / 1833

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

611 / 611

position of stopcodon in wt / mu cDNA

1996 / 1996

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

164 / 164

chromosome

strand

last intron/exon boundary

1772

theoretical NMD boundary in CDS

1558

length of CDS

1833

coding sequence (CDS) position

953

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

1116

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

MRPPGFLSRA PSLNRAERGI WSCSMDQREP LPPAPAENEM KYDTNNNEEE EGEQFDFDSG
DEIPEADRQA PSAPETGGAG ASEAPAPTGG EDGAGAETTP VAEPTKLVLP MKVNPYSVID
ITPFQEDQPP TPVPSAEEEN VGLHVPCGYL VPVPCGYAVP SNLPLLLPAY SSPVIICATS
LDEEAETPEV TEDRQPNSLS SEEPPTSEDQ VGREDSALAR WAADPANTAW MENPEEAIYD
DVPRENSDSE PDEMIYDDVE NGDEGGNSSL EYGWSSSEFE SYEEQSDSEC KNGIPRSFLR
SNHKKQMQKL VKAAKDGTKD GLERTRAAVK RGRSFIRTKS LIAQDHRSSL EEEQNLFIDV
DCKHPEAILT PMPEGLSQQQ VVRRYILGSV VDSEKNYVDA LKRILEQYEK PLSEMEPKVL
SERKLKTVFY RVKEILQCHS LFQIALASRV SEWDSVEMIG DVFVASFSKS MVLDAYSEYV
NNFSTAVAVL KKTCATKPAF LEFLKQEQEA SPDRTTLYSL MMKPIQRFPQ FILLLQDMLK
NTSKGHPDRL PLQMALTELE TLAEKLNERK RDADQRCEVK QIAKAINERY LNKVERGFLQ
LYSKIIFALC *

mutated AA sequence

MRPPGFLSRA PSLNRAERGI WSCSMDQREP LPPAPAENEM KYDTNNNEEE EGEQFDFDSG
DEIPEADRQA PSAPETGGAG ASEAPAPTGG EDGAGAETTP VAEPTKLVLP MKVNPYSVID
ITPFQEDQPP TPVPSAEEEN VGLHVPCGYL VPVPCGYAVP SNLPLLLPAY SSPVIICATS
LDEEAETPEV TEDRQPNSLS SEEPPTSEDQ VGREDSALAR WAADPANTAW MENPEEAIYD
DVPRENSDSE PDEMIYDDVE NGDEGGNSSL EYGWSSSEFE SYEEQSDSEC KNGIPRSFLR
SNHKKQMQKL VKAAKDGIKD GLERTRAAVK RGRSFIRTKS LIAQDHRSSL EEEQNLFIDV
DCKHPEAILT PMPEGLSQQQ VVRRYILGSV VDSEKNYVDA LKRILEQYEK PLSEMEPKVL
SERKLKTVFY RVKEILQCHS LFQIALASRV SEWDSVEMIG DVFVASFSKS MVLDAYSEYV
NNFSTAVAVL KKTCATKPAF LEFLKQEQEA SPDRTTLYSL MMKPIQRFPQ FILLLQDMLK
NTSKGHPDRL PLQMALTELE TLAEKLNERK RDADQRCEVK QIAKAINERY LNKVERGFLQ
LYSKIIFALC *

speed

0.57 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