MutationTaster - study a chromosomal position

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 6 transcript(s)...
Querying Taster for transcript #1: ENST00000296315
Querying Taster for transcript #2: ENST00000338458
Querying Taster for transcript #3: ENST00000413728
Querying Taster for transcript #4: ENST00000496106
Querying Taster for transcript #5: ENST00000497267
Querying Taster for transcript #6: ENST00000495373
MT speed 0 s - this script 2.860527 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ARHGEF3	polymorphism_automatic	0.999890879920242	simple_aae		affected		L335V	single base exchange	rs3772219		show file
ARHGEF3	polymorphism_automatic	0.999890879920242	simple_aae		affected		L367V	single base exchange	rs3772219		show file
ARHGEF3	polymorphism_automatic	0.999890879920242	simple_aae		affected		L341V	single base exchange	rs3772219		show file
ARHGEF3	polymorphism_automatic	0.999890879920242	simple_aae		affected		L306V	single base exchange	rs3772219		show file
ARHGEF3	polymorphism_automatic	0.999890879920242	simple_aae		affected		L341V	single base exchange	rs3772219		show file
ARHGEF3	polymorphism_automatic	0.999890879920242	simple_aae		affected		L335V	single base exchange	rs3772219		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.000109120079758181 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM167853)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:56771251A>CN/A show variant in all transcripts IGV

HGNC symbol

ARHGEF3

Ensembl transcript ID

ENST00000296315

Genbank transcript ID

NM_019555

UniProt peptide

Q9NR81

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1003T>G
cDNA.1172T>G
g.342107T>G

AA changes

L335V Score: 32 explain score(s)

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

335

frameshift

known variant

Reference ID: rs3772219

database	homozygous (C/C)	heterozygous	allele carriers
1000G	485	1107	1592
ExAC	7740	17287	25027

known disease mutation at this position, please check HGMD for details (HGMD ID CM167853)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.206	1
	0.629	0.994
(flanking)	0.916	0.991

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
Acc marginally increased	342103	wt: 0.5047 / mu: 0.5337 (marginal change - not scored)	wt: TCCCTGATCGACAGCTCTCGAGTCTTGTGTTGTCATGGTGA mu: TCCCTGATCGACAGCTCTCGAGTCGTGTGTTGTCATGGTGA	tcga\|GTCT
Donor marginally increased	342103	wt: 0.9494 / mu: 0.9913 (marginal change - not scored)	wt: TCTCGAGTCTTGTGT mu: TCTCGAGTCGTGTGT	TCGA\|gtct
Donor marginally increased	342108	wt: 0.2383 / mu: 0.2609 (marginal change - not scored)	wt: AGTCTTGTGTTGTCA mu: AGTCGTGTGTTGTCA	TCTT\|gtgt
Donor gained	342101	0.46	mu: GCTCTCGAGTCGTGT	TCTC\|gagt

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

335

mutated

all conserved

335

Ptroglodytes

all identical

ENSPTRG00000015041

367

Mmulatta

all identical

ENSMMUG00000010163

367

Fcatus

all identical

ENSFCAG00000003569

367

Mmusculus

all identical

ENSMUSG00000021895

341

Ggallus

all identical

ENSGALG00000005481

335

Trubripes

no homologue

Drerio

all identical

ENSDARG00000013834

368

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000000921

303

protein features

start (aa)	end (aa)	feature	details
291	449	DOMAIN	PH.	lost
410	410	CONFLICT	I -> T (in Ref. 3; AAP97313).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1581 / 1581

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

527 / 527

position of stopcodon in wt / mu cDNA

1750 / 1750

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

170 / 170

chromosome

strand

-1

last intron/exon boundary

1398

theoretical NMD boundary in CDS

1178

length of CDS

1581

coding sequence (CDS) position

1003

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

1172

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

342107

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

56771251

original gDNA sequence snippet

TGATCGACAGCTCTCGAGTCTTGTGTTGTCATGGTGAACTG

altered gDNA sequence snippet

TGATCGACAGCTCTCGAGTCGTGTGTTGTCATGGTGAACTG

original cDNA sequence snippet

TGATCGACAGCTCTCGAGTCTTGTGTTGTCATGGTGAACTG

altered cDNA sequence snippet

TGATCGACAGCTCTCGAGTCGTGTGTTGTCATGGTGAACTG

wildtype AA sequence

MVAKDYPFYL TVKRANCSLE LPPASGPAKD AEEPSNKRVK PLSRVTSLAN LIPPVKATPL
KRFSQTLQRS ISFRSESRPD ILAPRPWSRN AAPSSTKRRD SKLWSETFDV CVNQMLTSKE
IKRQEAIFEL SQGEEDLIED LKLAKKAYHD PMLKLSIMTE QELNQIFGTL DSLIPLHEEL
LSQLRDVRKP DGSTEHVGPI LVGWLPCLSS YDSYCSNQVA AKALLDHKKQ DHRVQDFLQR
CLESPFSRKL DLWNFLDIPR SRLVKYPLLL REILRHTPND NPDQQHLEEA INIIQGIVAE
INTKTGESEC RYYKERLLYL EEGQKDSLID SSRVLCCHGE LKNNRGVKLH VFLFQEVLVI
TRAVTHNEQL CYQLYRQPIP VKDLLLEDLQ DGEVRLGGSL RGAFSNNERI KNFFRVSFKN
GSQSQTHSLQ ANDTFNKQQW LNCIRQAKET VLCAAGQAGV LDSEGSFLNP TTGSRELQGE
TKLEQMDQSD SESDCSMDTS EVSLDCERME QTDSSCGNSR HGESNV*

mutated AA sequence

MVAKDYPFYL TVKRANCSLE LPPASGPAKD AEEPSNKRVK PLSRVTSLAN LIPPVKATPL
KRFSQTLQRS ISFRSESRPD ILAPRPWSRN AAPSSTKRRD SKLWSETFDV CVNQMLTSKE
IKRQEAIFEL SQGEEDLIED LKLAKKAYHD PMLKLSIMTE QELNQIFGTL DSLIPLHEEL
LSQLRDVRKP DGSTEHVGPI LVGWLPCLSS YDSYCSNQVA AKALLDHKKQ DHRVQDFLQR
CLESPFSRKL DLWNFLDIPR SRLVKYPLLL REILRHTPND NPDQQHLEEA INIIQGIVAE
INTKTGESEC RYYKERLLYL EEGQKDSLID SSRVVCCHGE LKNNRGVKLH VFLFQEVLVI
TRAVTHNEQL CYQLYRQPIP VKDLLLEDLQ DGEVRLGGSL RGAFSNNERI KNFFRVSFKN
GSQSQTHSLQ ANDTFNKQQW LNCIRQAKET VLCAAGQAGV LDSEGSFLNP TTGSRELQGE
TKLEQMDQSD SESDCSMDTS EVSLDCERME QTDSSCGNSR HGESNV*

speed

0.32 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

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.000109120079758181 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM167853)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:56771251A>CN/A show variant in all transcripts IGV

HGNC symbol

ARHGEF3

Ensembl transcript ID

ENST00000338458

Genbank transcript ID

NM_001128615

UniProt peptide

Q9NR81

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1099T>G
cDNA.1209T>G
g.342107T>G

AA changes

L367V Score: 32 explain score(s)

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

367

frameshift

known variant

Reference ID: rs3772219

database	homozygous (C/C)	heterozygous	allele carriers
1000G	485	1107	1592
ExAC	7740	17287	25027

known disease mutation at this position, please check HGMD for details (HGMD ID CM167853)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.206	1
	0.629	0.994
(flanking)	0.916	0.991

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
Acc marginally increased	342103	wt: 0.5047 / mu: 0.5337 (marginal change - not scored)	wt: TCCCTGATCGACAGCTCTCGAGTCTTGTGTTGTCATGGTGA mu: TCCCTGATCGACAGCTCTCGAGTCGTGTGTTGTCATGGTGA	tcga\|GTCT
Donor marginally increased	342103	wt: 0.9494 / mu: 0.9913 (marginal change - not scored)	wt: TCTCGAGTCTTGTGT mu: TCTCGAGTCGTGTGT	TCGA\|gtct
Donor marginally increased	342108	wt: 0.2383 / mu: 0.2609 (marginal change - not scored)	wt: AGTCTTGTGTTGTCA mu: AGTCGTGTGTTGTCA	TCTT\|gtgt
Donor gained	342101	0.46	mu: GCTCTCGAGTCGTGT	TCTC\|gagt

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

367

mutated

all conserved

367

Ptroglodytes

all identical

ENSPTRG00000015041

367

Mmulatta

all identical

ENSMMUG00000010163

367

Fcatus

all identical

ENSFCAG00000003569

367

Mmusculus

all identical

ENSMUSG00000021895

341

Ggallus

all identical

ENSGALG00000005481

335

Trubripes

no homologue

Drerio

all identical

ENSDARG00000013834

368

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000000921

303

protein features

start (aa)	end (aa)	feature	details
291	449	DOMAIN	PH.	lost
410	410	CONFLICT	I -> T (in Ref. 3; AAP97313).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1677 / 1677

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

559 / 559

position of stopcodon in wt / mu cDNA

1787 / 1787

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

111 / 111

chromosome

strand

-1

last intron/exon boundary

1435

theoretical NMD boundary in CDS

1274

length of CDS

1677

coding sequence (CDS) position

1099

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

1209

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

342107

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

56771251

original gDNA sequence snippet

TGATCGACAGCTCTCGAGTCTTGTGTTGTCATGGTGAACTG

altered gDNA sequence snippet

TGATCGACAGCTCTCGAGTCGTGTGTTGTCATGGTGAACTG

original cDNA sequence snippet

TGATCGACAGCTCTCGAGTCTTGTGTTGTCATGGTGAACTG

altered cDNA sequence snippet

TGATCGACAGCTCTCGAGTCGTGTGTTGTCATGGTGAACTG

wildtype AA sequence

MDSSTAMNQC SCRGMEENKE RPKRQRQNNF PMFPSPKAWN FRGRKRKQST QDEDAVSLCS
LDISEPSNKR VKPLSRVTSL ANLIPPVKAT PLKRFSQTLQ RSISFRSESR PDILAPRPWS
RNAAPSSTKR RDSKLWSETF DVCVNQMLTS KEIKRQEAIF ELSQGEEDLI EDLKLAKKAY
HDPMLKLSIM TEQELNQIFG TLDSLIPLHE ELLSQLRDVR KPDGSTEHVG PILVGWLPCL
SSYDSYCSNQ VAAKALLDHK KQDHRVQDFL QRCLESPFSR KLDLWNFLDI PRSRLVKYPL
LLREILRHTP NDNPDQQHLE EAINIIQGIV AEINTKTGES ECRYYKERLL YLEEGQKDSL
IDSSRVLCCH GELKNNRGVK LHVFLFQEVL VITRAVTHNE QLCYQLYRQP IPVKDLLLED
LQDGEVRLGG SLRGAFSNNE RIKNFFRVSF KNGSQSQTHS LQANDTFNKQ QWLNCIRQAK
ETVLCAAGQA GVLDSEGSFL NPTTGSRELQ GETKLEQMDQ SDSESDCSMD TSEVSLDCER
MEQTDSSCGN SRHGESNV*

mutated AA sequence

MDSSTAMNQC SCRGMEENKE RPKRQRQNNF PMFPSPKAWN FRGRKRKQST QDEDAVSLCS
LDISEPSNKR VKPLSRVTSL ANLIPPVKAT PLKRFSQTLQ RSISFRSESR PDILAPRPWS
RNAAPSSTKR RDSKLWSETF DVCVNQMLTS KEIKRQEAIF ELSQGEEDLI EDLKLAKKAY
HDPMLKLSIM TEQELNQIFG TLDSLIPLHE ELLSQLRDVR KPDGSTEHVG PILVGWLPCL
SSYDSYCSNQ VAAKALLDHK KQDHRVQDFL QRCLESPFSR KLDLWNFLDI PRSRLVKYPL
LLREILRHTP NDNPDQQHLE EAINIIQGIV AEINTKTGES ECRYYKERLL YLEEGQKDSL
IDSSRVVCCH GELKNNRGVK LHVFLFQEVL VITRAVTHNE QLCYQLYRQP IPVKDLLLED
LQDGEVRLGG SLRGAFSNNE RIKNFFRVSF KNGSQSQTHS LQANDTFNKQ QWLNCIRQAK
ETVLCAAGQA GVLDSEGSFL NPTTGSRELQ GETKLEQMDQ SDSESDCSMD TSEVSLDCER
MEQTDSSCGN SRHGESNV*

speed

0.38 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.000109120079758181 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM167853)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:56771251A>CN/A show variant in all transcripts IGV

HGNC symbol

ARHGEF3

Ensembl transcript ID

ENST00000413728

Genbank transcript ID

NM_001128616

UniProt peptide

Q9NR81

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1021T>G
cDNA.1565T>G
g.342107T>G

AA changes

L341V Score: 32 explain score(s)

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

341

frameshift

known variant

Reference ID: rs3772219

database	homozygous (C/C)	heterozygous	allele carriers
1000G	485	1107	1592
ExAC	7740	17287	25027

known disease mutation at this position, please check HGMD for details (HGMD ID CM167853)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.206	1
	0.629	0.994
(flanking)	0.916	0.991

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
Acc marginally increased	342103	wt: 0.5047 / mu: 0.5337 (marginal change - not scored)	wt: TCCCTGATCGACAGCTCTCGAGTCTTGTGTTGTCATGGTGA mu: TCCCTGATCGACAGCTCTCGAGTCGTGTGTTGTCATGGTGA	tcga\|GTCT
Donor marginally increased	342103	wt: 0.9494 / mu: 0.9913 (marginal change - not scored)	wt: TCTCGAGTCTTGTGT mu: TCTCGAGTCGTGTGT	TCGA\|gtct
Donor marginally increased	342108	wt: 0.2383 / mu: 0.2609 (marginal change - not scored)	wt: AGTCTTGTGTTGTCA mu: AGTCGTGTGTTGTCA	TCTT\|gtgt
Donor gained	342101	0.46	mu: GCTCTCGAGTCGTGT	TCTC\|gagt

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

341

mutated

all conserved

341

Ptroglodytes

all identical

ENSPTRG00000015041

367

Mmulatta

all identical

ENSMMUG00000010163

367

Fcatus

all identical

ENSFCAG00000003569

367

Mmusculus

all identical

ENSMUSG00000021895

341

Ggallus

all identical

ENSGALG00000005481

335

Trubripes

no homologue

Drerio

all identical

ENSDARG00000013834

368

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000000921

303

protein features

start (aa)	end (aa)	feature	details
291	449	DOMAIN	PH.	lost
410	410	CONFLICT	I -> T (in Ref. 3; AAP97313).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1599 / 1599

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

533 / 533

position of stopcodon in wt / mu cDNA

2143 / 2143

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

545 / 545

chromosome

strand

-1

last intron/exon boundary

1791

theoretical NMD boundary in CDS

1196

length of CDS

1599

coding sequence (CDS) position

1021

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

1565

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

342107

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

56771251

original gDNA sequence snippet

TGATCGACAGCTCTCGAGTCTTGTGTTGTCATGGTGAACTG

altered gDNA sequence snippet

TGATCGACAGCTCTCGAGTCGTGTGTTGTCATGGTGAACTG

original cDNA sequence snippet

TGATCGACAGCTCTCGAGTCTTGTGTTGTCATGGTGAACTG

altered cDNA sequence snippet

TGATCGACAGCTCTCGAGTCGTGTGTTGTCATGGTGAACTG

wildtype AA sequence

MIEVCHHNWL LWLCPSKFGI FMCCLASTTG QMELRRTREP SNKRVKPLSR VTSLANLIPP
VKATPLKRFS QTLQRSISFR SESRPDILAP RPWSRNAAPS STKRRDSKLW SETFDVCVNQ
MLTSKEIKRQ EAIFELSQGE EDLIEDLKLA KKAYHDPMLK LSIMTEQELN QIFGTLDSLI
PLHEELLSQL RDVRKPDGST EHVGPILVGW LPCLSSYDSY CSNQVAAKAL LDHKKQDHRV
QDFLQRCLES PFSRKLDLWN FLDIPRSRLV KYPLLLREIL RHTPNDNPDQ QHLEEAINII
QGIVAEINTK TGESECRYYK ERLLYLEEGQ KDSLIDSSRV LCCHGELKNN RGVKLHVFLF
QEVLVITRAV THNEQLCYQL YRQPIPVKDL LLEDLQDGEV RLGGSLRGAF SNNERIKNFF
RVSFKNGSQS QTHSLQANDT FNKQQWLNCI RQAKETVLCA AGQAGVLDSE GSFLNPTTGS
RELQGETKLE QMDQSDSESD CSMDTSEVSL DCERMEQTDS SCGNSRHGES NV*

mutated AA sequence

MIEVCHHNWL LWLCPSKFGI FMCCLASTTG QMELRRTREP SNKRVKPLSR VTSLANLIPP
VKATPLKRFS QTLQRSISFR SESRPDILAP RPWSRNAAPS STKRRDSKLW SETFDVCVNQ
MLTSKEIKRQ EAIFELSQGE EDLIEDLKLA KKAYHDPMLK LSIMTEQELN QIFGTLDSLI
PLHEELLSQL RDVRKPDGST EHVGPILVGW LPCLSSYDSY CSNQVAAKAL LDHKKQDHRV
QDFLQRCLES PFSRKLDLWN FLDIPRSRLV KYPLLLREIL RHTPNDNPDQ QHLEEAINII
QGIVAEINTK TGESECRYYK ERLLYLEEGQ KDSLIDSSRV VCCHGELKNN RGVKLHVFLF
QEVLVITRAV THNEQLCYQL YRQPIPVKDL LLEDLQDGEV RLGGSLRGAF SNNERIKNFF
RVSFKNGSQS QTHSLQANDT FNKQQWLNCI RQAKETVLCA AGQAGVLDSE GSFLNPTTGS
RELQGETKLE QMDQSDSESD CSMDTSEVSL DCERMEQTDS SCGNSRHGES NV*

speed

0.35 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.000109120079758181 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM167853)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:56771251A>CN/A show variant in all transcripts IGV

HGNC symbol

ARHGEF3

Ensembl transcript ID

ENST00000497267

Genbank transcript ID

N/A

UniProt peptide

Q9NR81

alteration type

single base exchange

alteration region

CDS

DNA changes

c.916T>G
cDNA.1370T>G
g.342107T>G

AA changes

L306V Score: 32 explain score(s)

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

306

frameshift

known variant

Reference ID: rs3772219

database	homozygous (C/C)	heterozygous	allele carriers
1000G	485	1107	1592
ExAC	7740	17287	25027

known disease mutation at this position, please check HGMD for details (HGMD ID CM167853)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.206	1
	0.629	0.994
(flanking)	0.916	0.991

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
Acc marginally increased	342103	wt: 0.5047 / mu: 0.5337 (marginal change - not scored)	wt: TCCCTGATCGACAGCTCTCGAGTCTTGTGTTGTCATGGTGA mu: TCCCTGATCGACAGCTCTCGAGTCGTGTGTTGTCATGGTGA	tcga\|GTCT
Donor marginally increased	342103	wt: 0.9494 / mu: 0.9913 (marginal change - not scored)	wt: TCTCGAGTCTTGTGT mu: TCTCGAGTCGTGTGT	TCGA\|gtct
Donor marginally increased	342108	wt: 0.2383 / mu: 0.2609 (marginal change - not scored)	wt: AGTCTTGTGTTGTCA mu: AGTCGTGTGTTGTCA	TCTT\|gtgt
Donor gained	342101	0.46	mu: GCTCTCGAGTCGTGT	TCTC\|gagt

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

306

mutated

all conserved

306

Ptroglodytes

all identical

ENSPTRG00000015041

367

Mmulatta

all identical

ENSMMUG00000010163

367

Fcatus

all identical

ENSFCAG00000003569

367

Mmusculus

all identical

ENSMUSG00000021895

341

Ggallus

all identical

ENSGALG00000005481

335

Trubripes

no homologue

Drerio

all identical

ENSDARG00000013834

368

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000000921

303

protein features

start (aa)	end (aa)	feature	details
122	304	DOMAIN	DH.	might get lost (downstream of altered splice site)
291	449	DOMAIN	PH.	lost
410	410	CONFLICT	I -> T (in Ref. 3; AAP97313).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1494 / 1494

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

498 / 498

position of stopcodon in wt / mu cDNA

1948 / 1948

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

455 / 455

chromosome

strand

-1

last intron/exon boundary

1596

theoretical NMD boundary in CDS

1091

length of CDS

1494

coding sequence (CDS) position

916

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

1370

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

342107

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

56771251

original gDNA sequence snippet

TGATCGACAGCTCTCGAGTCTTGTGTTGTCATGGTGAACTG

altered gDNA sequence snippet

TGATCGACAGCTCTCGAGTCGTGTGTTGTCATGGTGAACTG

original cDNA sequence snippet

TGATCGACAGCTCTCGAGTCTTGTGTTGTCATGGTGAACTG

altered cDNA sequence snippet

TGATCGACAGCTCTCGAGTCGTGTGTTGTCATGGTGAACTG

wildtype AA sequence

MIEEPSNKRV KPLSRVTSLA NLIPPVKATP LKRFSQTLQR SISFRSESRP DILAPRPWSR
NAAPSSTKRR DSKLWSETFD VCVNQMLTSK EIKRQEAIFE LSQGEEDLIE DLKLAKKAYH
DPMLKLSIMT EQELNQIFGT LDSLIPLHEE LLSQLRDVRK PDGSTEHVGP ILVGWLPCLS
SYDSYCSNQV AAKALLDHKK QDHRVQDFLQ RCLESPFSRK LDLWNFLDIP RSRLVKYPLL
LREILRHTPN DNPDQQHLEE AINIIQGIVA EINTKTGESE CRYYKERLLY LEEGQKDSLI
DSSRVLCCHG ELKNNRGVKL HVFLFQEVLV ITRAVTHNEQ LCYQLYRQPI PVKDLLLEDL
QDGEVRLGGS LRGAFSNNER IKNFFRVSFK NGSQSQTHSL QANDTFNKQQ WLNCIRQAKE
TVLCAAGQAG VLDSEGSFLN PTTGSRELQG ETKLEQMDQS DSESDCSMDT SEVSLDCERM
EQTDSSCGNS RHGESNV*

mutated AA sequence

MIEEPSNKRV KPLSRVTSLA NLIPPVKATP LKRFSQTLQR SISFRSESRP DILAPRPWSR
NAAPSSTKRR DSKLWSETFD VCVNQMLTSK EIKRQEAIFE LSQGEEDLIE DLKLAKKAYH
DPMLKLSIMT EQELNQIFGT LDSLIPLHEE LLSQLRDVRK PDGSTEHVGP ILVGWLPCLS
SYDSYCSNQV AAKALLDHKK QDHRVQDFLQ RCLESPFSRK LDLWNFLDIP RSRLVKYPLL
LREILRHTPN DNPDQQHLEE AINIIQGIVA EINTKTGESE CRYYKERLLY LEEGQKDSLI
DSSRVVCCHG ELKNNRGVKL HVFLFQEVLV ITRAVTHNEQ LCYQLYRQPI PVKDLLLEDL
QDGEVRLGGS LRGAFSNNER IKNFFRVSFK NGSQSQTHSL QANDTFNKQQ WLNCIRQAKE
TVLCAAGQAG VLDSEGSFLN PTTGSRELQG ETKLEQMDQS DSESDCSMDT SEVSLDCERM
EQTDSSCGNS RHGESNV*

speed

0.20 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.000109120079758181 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM167853)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:56771251A>CN/A show variant in all transcripts IGV

HGNC symbol

ARHGEF3

Ensembl transcript ID

ENST00000496106

Genbank transcript ID

N/A

UniProt peptide

Q9NR81

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1021T>G
cDNA.1133T>G
g.342107T>G

AA changes

L341V Score: 32 explain score(s)

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

341

frameshift

known variant

Reference ID: rs3772219

database	homozygous (C/C)	heterozygous	allele carriers
1000G	485	1107	1592
ExAC	7740	17287	25027

known disease mutation at this position, please check HGMD for details (HGMD ID CM167853)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.206	1
	0.629	0.994
(flanking)	0.916	0.991

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
Acc marginally increased	342103	wt: 0.5047 / mu: 0.5337 (marginal change - not scored)	wt: TCCCTGATCGACAGCTCTCGAGTCTTGTGTTGTCATGGTGA mu: TCCCTGATCGACAGCTCTCGAGTCGTGTGTTGTCATGGTGA	tcga\|GTCT
Donor marginally increased	342103	wt: 0.9494 / mu: 0.9913 (marginal change - not scored)	wt: TCTCGAGTCTTGTGT mu: TCTCGAGTCGTGTGT	TCGA\|gtct
Donor marginally increased	342108	wt: 0.2383 / mu: 0.2609 (marginal change - not scored)	wt: AGTCTTGTGTTGTCA mu: AGTCGTGTGTTGTCA	TCTT\|gtgt
Donor gained	342101	0.46	mu: GCTCTCGAGTCGTGT	TCTC\|gagt

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

341

mutated

all conserved

341

Ptroglodytes

all identical

ENSPTRG00000015041

367

Mmulatta

all identical

ENSMMUG00000010163

367

Fcatus

all identical

ENSFCAG00000003569

367

Mmusculus

all identical

ENSMUSG00000021895

341

Ggallus

all identical

ENSGALG00000005481

335

Trubripes

no homologue

Drerio

all identical

ENSDARG00000013834

368

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000000921

303

protein features

start (aa)	end (aa)	feature	details
291	449	DOMAIN	PH.	lost
410	410	CONFLICT	I -> T (in Ref. 3; AAP97313).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1599 / 1599

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

533 / 533

position of stopcodon in wt / mu cDNA

1711 / 1711

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

113 / 113

chromosome

strand

-1

last intron/exon boundary

1359

theoretical NMD boundary in CDS

1196

length of CDS

1599

coding sequence (CDS) position

1021

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

1133

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

342107

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

56771251

original gDNA sequence snippet

TGATCGACAGCTCTCGAGTCTTGTGTTGTCATGGTGAACTG

altered gDNA sequence snippet

TGATCGACAGCTCTCGAGTCGTGTGTTGTCATGGTGAACTG

original cDNA sequence snippet

TGATCGACAGCTCTCGAGTCTTGTGTTGTCATGGTGAACTG

altered cDNA sequence snippet

TGATCGACAGCTCTCGAGTCGTGTGTTGTCATGGTGAACTG

wildtype AA sequence

MRSERPMVWC CLFVRSQRKR KQSTQDEDAV SLCSLDISEP SNKRVKPLSR VTSLANLIPP
VKATPLKRFS QTLQRSISFR SESRPDILAP RPWSRNAAPS STKRRDSKLW SETFDVCVNQ
MLTSKEIKRQ EAIFELSQGE EDLIEDLKLA KKAYHDPMLK LSIMTEQELN QIFGTLDSLI
PLHEELLSQL RDVRKPDGST EHVGPILVGW LPCLSSYDSY CSNQVAAKAL LDHKKQDHRV
QDFLQRCLES PFSRKLDLWN FLDIPRSRLV KYPLLLREIL RHTPNDNPDQ QHLEEAINII
QGIVAEINTK TGESECRYYK ERLLYLEEGQ KDSLIDSSRV LCCHGELKNN RGVKLHVFLF
QEVLVITRAV THNEQLCYQL YRQPIPVKDL LLEDLQDGEV RLGGSLRGAF SNNERIKNFF
RVSFKNGSQS QTHSLQANDT FNKQQWLNCI RQAKETVLCA AGQAGVLDSE GSFLNPTTGS
RELQGETKLE QMDQSDSESD CSMDTSEVSL DCERMEQTDS SCGNSRHGES NV*

mutated AA sequence

MRSERPMVWC CLFVRSQRKR KQSTQDEDAV SLCSLDISEP SNKRVKPLSR VTSLANLIPP
VKATPLKRFS QTLQRSISFR SESRPDILAP RPWSRNAAPS STKRRDSKLW SETFDVCVNQ
MLTSKEIKRQ EAIFELSQGE EDLIEDLKLA KKAYHDPMLK LSIMTEQELN QIFGTLDSLI
PLHEELLSQL RDVRKPDGST EHVGPILVGW LPCLSSYDSY CSNQVAAKAL LDHKKQDHRV
QDFLQRCLES PFSRKLDLWN FLDIPRSRLV KYPLLLREIL RHTPNDNPDQ QHLEEAINII
QGIVAEINTK TGESECRYYK ERLLYLEEGQ KDSLIDSSRV VCCHGELKNN RGVKLHVFLF
QEVLVITRAV THNEQLCYQL YRQPIPVKDL LLEDLQDGEV RLGGSLRGAF SNNERIKNFF
RVSFKNGSQS QTHSLQANDT FNKQQWLNCI RQAKETVLCA AGQAGVLDSE GSFLNPTTGS
RELQGETKLE QMDQSDSESD CSMDTSEVSL DCERMEQTDS SCGNSRHGES NV*

speed

0.23 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.000109120079758181 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM167853)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:56771251A>CN/A show variant in all transcripts IGV

HGNC symbol

ARHGEF3

Ensembl transcript ID

ENST00000495373

Genbank transcript ID

N/A

UniProt peptide

Q9NR81

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1003T>G
cDNA.1154T>G
g.342107T>G

AA changes

L335V Score: 32 explain score(s)

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

335

frameshift

known variant

Reference ID: rs3772219

database	homozygous (C/C)	heterozygous	allele carriers
1000G	485	1107	1592
ExAC	7740	17287	25027

known disease mutation at this position, please check HGMD for details (HGMD ID CM167853)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.206	1
	0.629	0.994
(flanking)	0.916	0.991

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
Acc marginally increased	342103	wt: 0.5047 / mu: 0.5337 (marginal change - not scored)	wt: TCCCTGATCGACAGCTCTCGAGTCTTGTGTTGTCATGGTGA mu: TCCCTGATCGACAGCTCTCGAGTCGTGTGTTGTCATGGTGA	tcga\|GTCT
Donor marginally increased	342103	wt: 0.9494 / mu: 0.9913 (marginal change - not scored)	wt: TCTCGAGTCTTGTGT mu: TCTCGAGTCGTGTGT	TCGA\|gtct
Donor marginally increased	342108	wt: 0.2383 / mu: 0.2609 (marginal change - not scored)	wt: AGTCTTGTGTTGTCA mu: AGTCGTGTGTTGTCA	TCTT\|gtgt
Donor gained	342101	0.46	mu: GCTCTCGAGTCGTGT	TCTC\|gagt

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

335

mutated

all conserved

335

Ptroglodytes

all identical

ENSPTRG00000015041

367

Mmulatta

all identical

ENSMMUG00000010163

367

Fcatus

all identical

ENSFCAG00000003569

367

Mmusculus

all identical

ENSMUSG00000021895

341

Ggallus

all identical

ENSGALG00000005481

335

Trubripes

no homologue

Drerio

all identical

ENSDARG00000013834

368

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000000921

303

protein features

start (aa)	end (aa)	feature	details
291	449	DOMAIN	PH.	lost
410	410	CONFLICT	I -> T (in Ref. 3; AAP97313).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1251 / 1251

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

417 / 417

position of stopcodon in wt / mu cDNA

1402 / 1402

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

152 / 152

chromosome

strand

-1

last intron/exon boundary

1193

theoretical NMD boundary in CDS

991

length of CDS

1251

coding sequence (CDS) position

1003

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

1154

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

342107

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

56771251

original gDNA sequence snippet

TGATCGACAGCTCTCGAGTCTTGTGTTGTCATGGTGAACTG

altered gDNA sequence snippet

TGATCGACAGCTCTCGAGTCGTGTGTTGTCATGGTGAACTG

original cDNA sequence snippet

TGATCGACAGCTCTCGAGTCTTGTGTTGTCATGGTGAACTG

altered cDNA sequence snippet

TGATCGACAGCTCTCGAGTCGTGTGTTGTCATGGTGAACTG

wildtype AA sequence

mutated AA sequence

MVAKDYPFYL TVKRANCSLE LPPASGPAKD AEEPSNKRVK PLSRVTSLAN LIPPVKATPL
KRFSQTLQRS ISFRSESRPD ILAPRPWSRN AAPSSTKRRD SKLWSETFDV CVNQMLTSKE
IKRQEAIFEL SQGEEDLIED LKLAKKAYHD PMLKLSIMTE QELNQIFGTL DSLIPLHEEL
LSQLRDVRKP DGSTEHVGPI LVGWLPCLSS YDSYCSNQVA AKALLDHKKQ DHRVQDFLQR
CLESPFSRKL DLWNFLDIPR SRLVKYPLLL REILRHTPND NPDQQHLEEA INIIQGIVAE
INTKTGESEC RYYKERLLYL EEGQKDSLID SSRVVCCHGE LKNNRGVKLH VFLFQEVLVI
TRAVTHNEQL CYQLYRQPIP VKDLLLEDLQ DGEVRLGGSL RGAFSNNERS MDSSRG*

speed

0.12 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems