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

ENST00000349830

Genbank transcript ID

NM_014629

UniProt peptide

O15013

alteration type

single base exchange

alteration region

CDS

DNA changes

c.995C>T
cDNA.1180C>T
g.58694C>T

AA changes

T332I Score: 89 explain score(s)

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

332

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

332

mutated

not conserved

332

Ptroglodytes

all identical

ENSPTRG00000019942

357

Mmulatta

all identical

ENSMMUG00000009472

332

Fcatus

all identical

ENSFCAG00000012553

245

Mmusculus

all identical

ENSMUSG00000071176

333

Ggallus

all identical

ENSGALG00000016350

341

Trubripes

no homologue

Drerio

all identical

ENSDARG00000077788

411

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

4035 / 4035

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

1345 / 1345

position of stopcodon in wt / mu cDNA

4220 / 4220

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

186 / 186

chromosome

strand

last intron/exon boundary

3706

theoretical NMD boundary in CDS

3470

length of CDS

4035

coding sequence (CDS) position

995

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

1180

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 ETPEVTEDRQ PNSLSSEEPP
TSEDQVGRED SALARWAADP ANTAWMENPE EAIYDDVPRE NSDSEPDEMI YDDVENGDEG
GNSSLEYGWS SSEFESYEEQ SDSECKNGIP RSFLRSNHKK QLSHDLTRLK EHYEKKMRDL
MASTVGVVEI QQLRQKHELK MQKLVKAAKD GTKDGLERTR AAVKRGRSFI RTKSLIAQDH
RSSLEEEQNL FIDVDCKHPE AILTPMPEGL SQQQVVRRYI LGSVVDSEKN YVDALKRILE
QYEKPLSEME PKVLSERKLK TVFYRVKEIL QCHSLFQIAL ASRVSEWDSV EMIGDVFVAS
FSKSMVLDAY SEYVNNFSTA VAVLKKTCAT KPAFLEFLKQ EQEASPDRTT LYSLMMKPIQ
RFPQFILLLQ DMLKNTSKGH PDRLPLQMAL TELETLAEKL NERKRDADQR CEVKQIAKAI
NERYLNKLLS SGSRYLIRSD DMIETVYNDR GEIVKTKERR VFMLNDVLMC ATVSSRPSHD
SRVMSSQRYL LKWSVPLGHV DAIEYGSSAG TGEHSRHLAV HPPESLAVVA NAKPNKVYMG
PGQLYQDLQN LLHDLNVIGQ ITQLIGNLKG NYQNLNQSVA HDWTSGLQRL ILKKEDEIRA
ADCCRIQLQL PGKQDKSGRP TFFTAVFNTF TPAIKESWVN SLQMAKLALE EENHMGWFCV
EDDGNHIKKE KHPLLVGHMP VMVAKQQEFK IECAAYNPEP YLNNESQPDS FSTAHGFLWI
GSCTHQMGQI AIVSFQNSTP KVIECFNVES RILCMLYVPV EEKRREPGAP PDPETPAVRA
SDVPTICVGT EEGSISIYKS SQGSKKVRLQ HFFTPEKSTV MSLACTSQSL YAGLVNGAVA
SYARAPDGSW DSEPQKVIKL GVLPVRSLLM MEDTLWAASG GQVFIISVET HAVEGQLEAH
QEEGMVISHM AVSGVGIWIA FTSGSTLRLF HTETLKHLQD INIATPVHNM LPGHQRLSVT
SLLVCHGLLM VGTSLGVLVA LPVPRLQGIP KVTGRGMVSY HAHNSPVKFI VLATALHEKD
KDKSRDSLAP GPEPQDEDQK DALPSGGAGS SLSQGDPDAA IWLGDSLGSM TQKSDLSSSS
GSLSLSHGSS SLEHRSEDST IYDLLKDPVS LRSKARRAKK AKASSALVVC GGQGHRRVHR
KARQPHQEEL APTVMVWQIP LLNI*

mutated AA sequence

MDQREPLPPA PAENEMKYDT NNNEEEEGEQ FDFDSGDEIP EADRQAPSAP ETGGAGASEA
PAPTGGEDGA GAETTPVAEP TKLVLPMKVN PYSVIDITPF QEDQPPTPVP SAEEENVGLH
VPCGYLVPVP CGYAVPSNLP LLLPAYSSPV IICATSLDEE ETPEVTEDRQ PNSLSSEEPP
TSEDQVGRED SALARWAADP ANTAWMENPE EAIYDDVPRE NSDSEPDEMI YDDVENGDEG
GNSSLEYGWS SSEFESYEEQ SDSECKNGIP RSFLRSNHKK QLSHDLTRLK EHYEKKMRDL
MASTVGVVEI QQLRQKHELK MQKLVKAAKD GIKDGLERTR AAVKRGRSFI RTKSLIAQDH
RSSLEEEQNL FIDVDCKHPE AILTPMPEGL SQQQVVRRYI LGSVVDSEKN YVDALKRILE
QYEKPLSEME PKVLSERKLK TVFYRVKEIL QCHSLFQIAL ASRVSEWDSV EMIGDVFVAS
FSKSMVLDAY SEYVNNFSTA VAVLKKTCAT KPAFLEFLKQ EQEASPDRTT LYSLMMKPIQ
RFPQFILLLQ DMLKNTSKGH PDRLPLQMAL TELETLAEKL NERKRDADQR CEVKQIAKAI
NERYLNKLLS SGSRYLIRSD DMIETVYNDR GEIVKTKERR VFMLNDVLMC ATVSSRPSHD
SRVMSSQRYL LKWSVPLGHV DAIEYGSSAG TGEHSRHLAV HPPESLAVVA NAKPNKVYMG
PGQLYQDLQN LLHDLNVIGQ ITQLIGNLKG NYQNLNQSVA HDWTSGLQRL ILKKEDEIRA
ADCCRIQLQL PGKQDKSGRP TFFTAVFNTF TPAIKESWVN SLQMAKLALE EENHMGWFCV
EDDGNHIKKE KHPLLVGHMP VMVAKQQEFK IECAAYNPEP YLNNESQPDS FSTAHGFLWI
GSCTHQMGQI AIVSFQNSTP KVIECFNVES RILCMLYVPV EEKRREPGAP PDPETPAVRA
SDVPTICVGT EEGSISIYKS SQGSKKVRLQ HFFTPEKSTV MSLACTSQSL YAGLVNGAVA
SYARAPDGSW DSEPQKVIKL GVLPVRSLLM MEDTLWAASG GQVFIISVET HAVEGQLEAH
QEEGMVISHM AVSGVGIWIA FTSGSTLRLF HTETLKHLQD INIATPVHNM LPGHQRLSVT
SLLVCHGLLM VGTSLGVLVA LPVPRLQGIP KVTGRGMVSY HAHNSPVKFI VLATALHEKD
KDKSRDSLAP GPEPQDEDQK DALPSGGAGS SLSQGDPDAA IWLGDSLGSM TQKSDLSSSS
GSLSLSHGSS SLEHRSEDST IYDLLKDPVS LRSKARRAKK AKASSALVVC GGQGHRRVHR
KARQPHQEEL APTVMVWQIP LLNI*

speed

0.70 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