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 5 transcript(s)...
Querying Taster for transcript #1: ENST00000393791
Querying Taster for transcript #2: ENST00000424809
Querying Taster for transcript #3: ENST00000393797
Querying Taster for transcript #4: ENST00000430041
Querying Taster for transcript #5: ENST00000356411
MT speed 0 s - this script 2.928737 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ARHGAP9	polymorphism_automatic	1.19930199105056e-09	simple_aae		affected		S441A	single base exchange	rs11544238		show file
ARHGAP9	polymorphism_automatic	1.19930199105056e-09	simple_aae		affected		S186A	single base exchange	rs11544238		show file
ARHGAP9	polymorphism_automatic	1.21375589579031e-08	simple_aae		affected		S370A	single base exchange	rs11544238		show file
ARHGAP9	polymorphism_automatic	1.21375589579031e-08	simple_aae		affected		S370A	single base exchange	rs11544238		show file
ARHGAP9	polymorphism_automatic	1.21375589579031e-08	simple_aae		affected		S370A	single base exchange	rs11544238		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999998800698 (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 CM100499)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:57870155A>CN/A show variant in all transcripts IGV

HGNC symbol

ARHGAP9

Ensembl transcript ID

ENST00000393797

Genbank transcript ID

N/A

UniProt peptide

Q9BRR9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1321T>G
cDNA.1514T>G
g.12443T>G

AA changes

S441A Score: 99 explain score(s)

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

441

frameshift

known variant

Reference ID: rs11544238

database	homozygous (C/C)	heterozygous	allele carriers
1000G	434	986	1420
ExAC	16976	-1185	15791

known disease mutation at this position, please check HGMD for details (HGMD ID CM100499)

regulatory features

CTCF, Transcription Factor, CCCTC-binding factor
CTCF, Transcription Factor, CCCTC-binding factor (1)
DNase1, Open Chromatin, DNase1 Hypersensitive Site
EBF, Transcription Factor, EBF Transcription Factor Binding
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.214	0.118
	-0.381	0.001
(flanking)	-0.284	0

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 lost	12451	0.20	wt: ACAGCGCCCTCCTCAGGCTGGGTGAGTGTGAGCGAGAGGCG	ctgg\|GTGA
Donor increased	12445	wt: 0.53 / mu: 0.60	wt: TCCTCAGGCTGGGTG mu: TCCGCAGGCTGGGTG	CTCA\|ggct

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

441

mutated

all conserved

441

Ptroglodytes

all identical

ENSPTRG00000005134

370

Mmulatta

all identical

ENSMMUG00000022060

449

Fcatus

no alignment

ENSFCAG00000002082

n/a

Mmusculus

not conserved

ENSMUSG00000040345

107

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000013390

147

Dmelanogaster

no homologue

Celegans

not conserved

C38D4.5

438

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
475	475	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
542	749	DOMAIN	Rho-GAP.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2466 / 2466

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

822 / 822

position of stopcodon in wt / mu cDNA

2659 / 2659

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

194 / 194

chromosome

strand

-1

last intron/exon boundary

2488

theoretical NMD boundary in CDS

2244

length of CDS

2466

coding sequence (CDS) position

1321

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

1514

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

12443

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

57870155

original gDNA sequence snippet

CACCGCCGACAGCGCCCTCCTCAGGCTGGGTGAGTGTGAGC

altered gDNA sequence snippet

CACCGCCGACAGCGCCCTCCGCAGGCTGGGTGAGTGTGAGC

original cDNA sequence snippet

CACCGCCGACAGCGCCCTCCTCAGGCTGGGGACCAGCGGGT

altered cDNA sequence snippet

CACCGCCGACAGCGCCCTCCGCAGGCTGGGGACCAGCGGGT

wildtype AA sequence

MRRGSSDSCA SGSQVAGTTV AGPAHPESLT LCSGEAERRG KEEWPDSHHY PGPTPAPESS
DGPHKVTVLA TMLSSRWWPS SWGILGLGPR SPPRGSQLCA LYAFTYTGAD GQQVSLAEGD
RFLLLRKTNS DWWLARRLEA PSTSRPIFVP AAYMIEESIP SQSPTTVIPG QLLWTPGPKL
FHGSLEELSQ ALPSRAQASS EQPPPLPRKM CRSVSTDNLS PSLLKPFQEG PSGRSLSQED
LPSEASASTA GPQPLMSEPP VYCNLVDLRR CPRSPPPGPA CPLLQRLDAW EQHLDPNSGR
CFYINSLTGC KSWKPPRRSR SETNPGSMEG TQTLKRNNDV LQPQAKGFRS DTGTPEPLDP
QGSLSLSQRT SQLDPPALQA PRPLPQLLDD PHEVEKSGLL NMTKIAQGGR KLRKNWGPSW
VVLTGNSLVF YREPPPTAPS SGWGPAGSRP ESSVDLRGAA LAHGRHLSSR RNVLHIRTIP
GHEFLLQSDH ETELRAWHRA LRTVIERLVR WVEARREAPT GRDQGSGDRE NPLELRLSGS
GPAELSAGED EEEESELVSK PLLRLSSRRS SIRGPEGTEQ NRVRNKLKRL IAKRPPLQSL
QERGLLRDQV FGCQLESLCQ REGDTVPSFL RLCIAAVDKR GLDVDGIYRV SGNLAVVQKL
RFLVDRERAV TSDGRYVFPE QPGQEGRLDL DSTEWDDIHV VTGALKLFLR ELPQPLVPPL
LLPHFRAALA LSESEQCLSQ IQELIGSMPK PNHDTLRYLL EHLCRVIAHS DKNRMTPHNL
GIVFGPTLFR PEQETSDPAA HALYPGQLVQ LMLTNFTSLF P*

mutated AA sequence

MRRGSSDSCA SGSQVAGTTV AGPAHPESLT LCSGEAERRG KEEWPDSHHY PGPTPAPESS
DGPHKVTVLA TMLSSRWWPS SWGILGLGPR SPPRGSQLCA LYAFTYTGAD GQQVSLAEGD
RFLLLRKTNS DWWLARRLEA PSTSRPIFVP AAYMIEESIP SQSPTTVIPG QLLWTPGPKL
FHGSLEELSQ ALPSRAQASS EQPPPLPRKM CRSVSTDNLS PSLLKPFQEG PSGRSLSQED
LPSEASASTA GPQPLMSEPP VYCNLVDLRR CPRSPPPGPA CPLLQRLDAW EQHLDPNSGR
CFYINSLTGC KSWKPPRRSR SETNPGSMEG TQTLKRNNDV LQPQAKGFRS DTGTPEPLDP
QGSLSLSQRT SQLDPPALQA PRPLPQLLDD PHEVEKSGLL NMTKIAQGGR KLRKNWGPSW
VVLTGNSLVF YREPPPTAPS AGWGPAGSRP ESSVDLRGAA LAHGRHLSSR RNVLHIRTIP
GHEFLLQSDH ETELRAWHRA LRTVIERLVR WVEARREAPT GRDQGSGDRE NPLELRLSGS
GPAELSAGED EEEESELVSK PLLRLSSRRS SIRGPEGTEQ NRVRNKLKRL IAKRPPLQSL
QERGLLRDQV FGCQLESLCQ REGDTVPSFL RLCIAAVDKR GLDVDGIYRV SGNLAVVQKL
RFLVDRERAV TSDGRYVFPE QPGQEGRLDL DSTEWDDIHV VTGALKLFLR ELPQPLVPPL
LLPHFRAALA LSESEQCLSQ IQELIGSMPK PNHDTLRYLL EHLCRVIAHS DKNRMTPHNL
GIVFGPTLFR PEQETSDPAA HALYPGQLVQ LMLTNFTSLF P*

speed

0.30 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: 0.999999998800698 (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 CM100499)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:57870155A>CN/A show variant in all transcripts IGV

HGNC symbol

ARHGAP9

Ensembl transcript ID

ENST00000430041

Genbank transcript ID

NM_001080156

UniProt peptide

Q9BRR9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.556T>G
cDNA.988T>G
g.12443T>G

AA changes

S186A Score: 99 explain score(s)

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

186

frameshift

known variant

Reference ID: rs11544238

database	homozygous (C/C)	heterozygous	allele carriers
1000G	434	986	1420
ExAC	16976	-1185	15791

known disease mutation at this position, please check HGMD for details (HGMD ID CM100499)

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.214	0.118
	-0.381	0.001
(flanking)	-0.284	0

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 lost	12451	0.20	wt: ACAGCGCCCTCCTCAGGCTGGGTGAGTGTGAGCGAGAGGCG	ctgg\|GTGA
Donor increased	12445	wt: 0.53 / mu: 0.60	wt: TCCTCAGGCTGGGTG mu: TCCGCAGGCTGGGTG	CTCA\|ggct

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

186

mutated

all conserved

186

Ptroglodytes

all identical

ENSPTRG00000005134

370

Mmulatta

all identical

ENSMMUG00000022060

449

Fcatus

no alignment

ENSFCAG00000002082

n/a

Mmusculus

not conserved

ENSMUSG00000040345

107

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000013390

147

Dmelanogaster

no homologue

Celegans

not conserved

C38D4.5

438

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
213	247	DOMAIN	WW.	might get lost (downstream of altered splice site)
322	336	STRAND		might get lost (downstream of altered splice site)
322	435	DOMAIN	PH.	might get lost (downstream of altered splice site)
346	361	STRAND		might get lost (downstream of altered splice site)
368	370	HELIX		might get lost (downstream of altered splice site)
380	384	STRAND		might get lost (downstream of altered splice site)
389	392	STRAND		might get lost (downstream of altered splice site)
394	396	TURN		might get lost (downstream of altered splice site)
398	406	STRAND		might get lost (downstream of altered splice site)
412	416	STRAND		might get lost (downstream of altered splice site)
420	439	HELIX		might get lost (downstream of altered splice site)
475	475	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
542	749	DOMAIN	Rho-GAP.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1644 / 1644

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

548 / 548

position of stopcodon in wt / mu cDNA

2076 / 2076

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

433 / 433

chromosome

strand

-1

last intron/exon boundary

1905

theoretical NMD boundary in CDS

1422

length of CDS

1644

coding sequence (CDS) position

556

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

988

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

12443

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

57870155

original gDNA sequence snippet

CACCGCCGACAGCGCCCTCCTCAGGCTGGGTGAGTGTGAGC

altered gDNA sequence snippet

CACCGCCGACAGCGCCCTCCGCAGGCTGGGTGAGTGTGAGC

original cDNA sequence snippet

CACCGCCGACAGCGCCCTCCTCAGGCTGGGGACCAGCGGGT

altered cDNA sequence snippet

CACCGCCGACAGCGCCCTCCGCAGGCTGGGGACCAGCGGGT

wildtype AA sequence

MSEPPVYCNL VDLRRCPRSP PPGPACPLLQ RLDAWEQHLD PNSGRCFYIN SLTGCKSWKP
PRRSRSETNP GSMEGTQTLK RNNDVLQPQA KGFRSDTGTP EPLDPQGSLS LSQRTSQLDP
PALQAPRPLP QLLDDPHEVE KSGLLNMTKI AQGGRKLRKN WGPSWVVLTG NSLVFYREPP
PTAPSSGWGP AGSRPESSVD LRGAALAHGR HLSSRRNVLH IRTIPGHEFL LQSDHETELR
AWHRALRTVI ERLDRENPLE LRLSGSGPAE LSAGEDEEEE SELVSKPLLR LSSRRSSIRG
PEGTEQNRVR NKLKRLIAKR PPLQSLQERG LLRDQVFGCQ LESLCQREGD TVPSFLRLCI
AAVDKRGLDV DGIYRVSGNL AVVQKLRFLV DRERAVTSDG RYVFPEQPGQ EGRLDLDSTE
WDDIHVVTGA LKLFLRELPQ PLVPPLLLPH FRAALALSES EQCLSQIQEL IGSMPKPNHD
TLRYLLEHLC RVIAHSDKNR MTPHNLGIVF GPTLFRPEQE TSDPAAHALY PGQLVQLMLT
NFTSLFP*

mutated AA sequence

MSEPPVYCNL VDLRRCPRSP PPGPACPLLQ RLDAWEQHLD PNSGRCFYIN SLTGCKSWKP
PRRSRSETNP GSMEGTQTLK RNNDVLQPQA KGFRSDTGTP EPLDPQGSLS LSQRTSQLDP
PALQAPRPLP QLLDDPHEVE KSGLLNMTKI AQGGRKLRKN WGPSWVVLTG NSLVFYREPP
PTAPSAGWGP AGSRPESSVD LRGAALAHGR HLSSRRNVLH IRTIPGHEFL LQSDHETELR
AWHRALRTVI ERLDRENPLE LRLSGSGPAE LSAGEDEEEE SELVSKPLLR LSSRRSSIRG
PEGTEQNRVR NKLKRLIAKR PPLQSLQERG LLRDQVFGCQ LESLCQREGD TVPSFLRLCI
AAVDKRGLDV DGIYRVSGNL AVVQKLRFLV DRERAVTSDG RYVFPEQPGQ EGRLDLDSTE
WDDIHVVTGA LKLFLRELPQ PLVPPLLLPH FRAALALSES EQCLSQIQEL IGSMPKPNHD
TLRYLLEHLC RVIAHSDKNR MTPHNLGIVF GPTLFRPEQE TSDPAAHALY PGQLVQLMLT
NFTSLFP*

speed

0.18 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999987862441 (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 CM100499)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:57870155A>CN/A show variant in all transcripts IGV

HGNC symbol

ARHGAP9

Ensembl transcript ID

ENST00000393791

Genbank transcript ID

NM_032496

UniProt peptide

Q9BRR9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1108T>G
cDNA.1247T>G
g.12443T>G

AA changes

S370A Score: 99 explain score(s)

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

370

frameshift

known variant

Reference ID: rs11544238

database	homozygous (C/C)	heterozygous	allele carriers
1000G	434	986	1420
ExAC	16976	-1185	15791

known disease mutation at this position, please check HGMD for details (HGMD ID CM100499)

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.214	0.118
	-0.381	0.001
(flanking)	-0.284	0

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 lost	12451	0.20	wt: ACAGCGCCCTCCTCAGGCTGGGTGAGTGTGAGCGAGAGGCG	ctgg\|GTGA
Donor increased	12445	wt: 0.53 / mu: 0.60	wt: TCCTCAGGCTGGGTG mu: TCCGCAGGCTGGGTG	CTCA\|ggct

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

370

mutated

all conserved

370

Ptroglodytes

all identical

ENSPTRG00000005134

370

Mmulatta

all identical

ENSMMUG00000022060

449

Fcatus

no alignment

ENSFCAG00000002082

n/a

Mmusculus

not conserved

ENSMUSG00000040345

107

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000013390

147

Dmelanogaster

no homologue

Celegans

not conserved

C38D4.5

438

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
322	435	DOMAIN	PH.	lost
368	370	HELIX		lost
380	384	STRAND		might get lost (downstream of altered splice site)
389	392	STRAND		might get lost (downstream of altered splice site)
394	396	TURN		might get lost (downstream of altered splice site)
398	406	STRAND		might get lost (downstream of altered splice site)
412	416	STRAND		might get lost (downstream of altered splice site)
420	439	HELIX		might get lost (downstream of altered splice site)
475	475	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
542	749	DOMAIN	Rho-GAP.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2196 / 2196

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

732 / 732

position of stopcodon in wt / mu cDNA

2335 / 2335

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

140 / 140

chromosome

strand

-1

last intron/exon boundary

2164

theoretical NMD boundary in CDS

1974

length of CDS

2196

coding sequence (CDS) position

1108

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

1247

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

12443

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

57870155

original gDNA sequence snippet

CACCGCCGACAGCGCCCTCCTCAGGCTGGGTGAGTGTGAGC

altered gDNA sequence snippet

CACCGCCGACAGCGCCCTCCGCAGGCTGGGTGAGTGTGAGC

original cDNA sequence snippet

CACCGCCGACAGCGCCCTCCTCAGGCTGGGGACCAGCGGGT

altered cDNA sequence snippet

CACCGCCGACAGCGCCCTCCGCAGGCTGGGGACCAGCGGGT

wildtype AA sequence

MLSSRWWPSS WGILGLGPRS PPRGSQLCAL YAFTYTGADG QQVSLAEGDR FLLLRKTNSD
WWLARRLEAP STSRPIFVPA AYMIEESIPS QSPTTVIPGQ LLWTPGPKLF HGSLEELSQA
LPSRAQASSE QPPPLPRKMC RSVSTDNLSP SLLKPFQEGP SGRSLSQEDL PSEASASTAG
PQPLMSEPPV YCNLVDLRRC PRSPPPGPAC PLLQRLDAWE QHLDPNSGRC FYINSLTGCK
SWKPPRRSRS ETNPGSMEGT QTLKRNNDVL QPQAKGFRSD TGTPEPLDPQ GSLSLSQRTS
QLDPPALQAP RPLPQLLDDP HEVEKSGLLN MTKIAQGGRK LRKNWGPSWV VLTGNSLVFY
REPPPTAPSS GWGPAGSRPE SSVDLRGAAL AHGRHLSSRR NVLHIRTIPG HEFLLQSDHE
TELRAWHRAL RTVIERLDRE NPLELRLSGS GPAELSAGED EEEESELVSK PLLRLSSRRS
SIRGPEGTEQ NRVRNKLKRL IAKRPPLQSL QERGLLRDQV FGCQLESLCQ REGDTVPSFL
RLCIAAVDKR GLDVDGIYRV SGNLAVVQKL RFLVDRERAV TSDGRYVFPE QPGQEGRLDL
DSTEWDDIHV VTGALKLFLR ELPQPLVPPL LLPHFRAALA LSESEQCLSQ IQELIGSMPK
PNHDTLRYLL EHLCRVIAHS DKNRMTPHNL GIVFGPTLFR PEQETSDPAA HALYPGQLVQ
LMLTNFTSLF P*

mutated AA sequence

MLSSRWWPSS WGILGLGPRS PPRGSQLCAL YAFTYTGADG QQVSLAEGDR FLLLRKTNSD
WWLARRLEAP STSRPIFVPA AYMIEESIPS QSPTTVIPGQ LLWTPGPKLF HGSLEELSQA
LPSRAQASSE QPPPLPRKMC RSVSTDNLSP SLLKPFQEGP SGRSLSQEDL PSEASASTAG
PQPLMSEPPV YCNLVDLRRC PRSPPPGPAC PLLQRLDAWE QHLDPNSGRC FYINSLTGCK
SWKPPRRSRS ETNPGSMEGT QTLKRNNDVL QPQAKGFRSD TGTPEPLDPQ GSLSLSQRTS
QLDPPALQAP RPLPQLLDDP HEVEKSGLLN MTKIAQGGRK LRKNWGPSWV VLTGNSLVFY
REPPPTAPSA GWGPAGSRPE SSVDLRGAAL AHGRHLSSRR NVLHIRTIPG HEFLLQSDHE
TELRAWHRAL RTVIERLDRE NPLELRLSGS GPAELSAGED EEEESELVSK PLLRLSSRRS
SIRGPEGTEQ NRVRNKLKRL IAKRPPLQSL QERGLLRDQV FGCQLESLCQ REGDTVPSFL
RLCIAAVDKR GLDVDGIYRV SGNLAVVQKL RFLVDRERAV TSDGRYVFPE QPGQEGRLDL
DSTEWDDIHV VTGALKLFLR ELPQPLVPPL LLPHFRAALA LSESEQCLSQ IQELIGSMPK
PNHDTLRYLL EHLCRVIAHS DKNRMTPHNL GIVFGPTLFR PEQETSDPAA HALYPGQLVQ
LMLTNFTSLF P*

speed

0.38 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999987862441 (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 CM100499)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:57870155A>CN/A show variant in all transcripts IGV

HGNC symbol

ARHGAP9

Ensembl transcript ID

ENST00000424809

Genbank transcript ID

NM_001080157

UniProt peptide

Q9BRR9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1108T>G
cDNA.1334T>G
g.12443T>G

AA changes

S370A Score: 99 explain score(s)

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

370

frameshift

known variant

Reference ID: rs11544238

database	homozygous (C/C)	heterozygous	allele carriers
1000G	434	986	1420
ExAC	16976	-1185	15791

known disease mutation at this position, please check HGMD for details (HGMD ID CM100499)

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.214	0.118
	-0.381	0.001
(flanking)	-0.284	0

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 lost	12451	0.20	wt: ACAGCGCCCTCCTCAGGCTGGGTGAGTGTGAGCGAGAGGCG	ctgg\|GTGA
Donor increased	12445	wt: 0.53 / mu: 0.60	wt: TCCTCAGGCTGGGTG mu: TCCGCAGGCTGGGTG	CTCA\|ggct

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

370

mutated

all conserved

370

Ptroglodytes

all identical

ENSPTRG00000005134

370

Mmulatta

all identical

ENSMMUG00000022060

449

Fcatus

no alignment

ENSFCAG00000002082

n/a

Mmusculus

not conserved

ENSMUSG00000040345

107

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000013390

147

Dmelanogaster

no homologue

Celegans

not conserved

C38D4.5

438

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
322	435	DOMAIN	PH.	lost
368	370	HELIX		lost
380	384	STRAND		might get lost (downstream of altered splice site)
389	392	STRAND		might get lost (downstream of altered splice site)
394	396	TURN		might get lost (downstream of altered splice site)
398	406	STRAND		might get lost (downstream of altered splice site)
412	416	STRAND		might get lost (downstream of altered splice site)
420	439	HELIX		might get lost (downstream of altered splice site)
475	475	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
542	749	DOMAIN	Rho-GAP.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1923 / 1923

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

641 / 641

position of stopcodon in wt / mu cDNA

2149 / 2149

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

227 / 227

chromosome

strand

-1

last intron/exon boundary

2145

theoretical NMD boundary in CDS

1868

length of CDS

1923

coding sequence (CDS) position

1108

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

1334

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

12443

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

57870155

original gDNA sequence snippet

CACCGCCGACAGCGCCCTCCTCAGGCTGGGTGAGTGTGAGC

altered gDNA sequence snippet

CACCGCCGACAGCGCCCTCCGCAGGCTGGGTGAGTGTGAGC

original cDNA sequence snippet

CACCGCCGACAGCGCCCTCCTCAGGCTGGGGACCAGCGGGT

altered cDNA sequence snippet

CACCGCCGACAGCGCCCTCCGCAGGCTGGGGACCAGCGGGT

wildtype AA sequence

mutated AA sequence

MLSSRWWPSS WGILGLGPRS PPRGSQLCAL YAFTYTGADG QQVSLAEGDR FLLLRKTNSD
WWLARRLEAP STSRPIFVPA AYMIEESIPS QSPTTVIPGQ LLWTPGPKLF HGSLEELSQA
LPSRAQASSE QPPPLPRKMC RSVSTDNLSP SLLKPFQEGP SGRSLSQEDL PSEASASTAG
PQPLMSEPPV YCNLVDLRRC PRSPPPGPAC PLLQRLDAWE QHLDPNSGRC FYINSLTGCK
SWKPPRRSRS ETNPGSMEGT QTLKRNNDVL QPQAKGFRSD TGTPEPLDPQ GSLSLSQRTS
QLDPPALQAP RPLPQLLDDP HEVEKSGLLN MTKIAQGGRK LRKNWGPSWV VLTGNSLVFY
REPPPTAPSA GWGPAGSRPE SSVDLRGAAL AHGRHLSSRR NVLHIRTIPG HEFLLQSDHE
TELRAWHRAL RTVIERLDRE NPLELRLSGS GPAELSAGED EEEESELVSK PLLRLSSRRS
SIRGPEGTEQ NRVRNKLKRL IAKRPPLQSL QERGLLRDQV FGCQLESLCQ REGDTVPSFL
RLCIAAVDKR GLDVDGIYRV SGNLAVVQKL RFLVDRERAV TSDGRYVFPE QPGQEGRLDL
DSTEWDDIHV VTGALKLFLR ELPQPLVPPL LLPHFRAALG *

speed

0.40 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999987862441 (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 CM100499)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:57870155A>CN/A show variant in all transcripts IGV

HGNC symbol

ARHGAP9

Ensembl transcript ID

ENST00000356411

Genbank transcript ID

N/A

UniProt peptide

Q9BRR9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1108T>G
cDNA.1247T>G
g.12443T>G

AA changes

S370A Score: 99 explain score(s)

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

370

frameshift

known variant

Reference ID: rs11544238

database	homozygous (C/C)	heterozygous	allele carriers
1000G	434	986	1420
ExAC	16976	-1185	15791

known disease mutation at this position, please check HGMD for details (HGMD ID CM100499)

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.214	0.118
	-0.381	0.001
(flanking)	-0.284	0

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 lost	12451	0.20	wt: ACAGCGCCCTCCTCAGGCTGGGTGAGTGTGAGCGAGAGGCG	ctgg\|GTGA
Donor increased	12445	wt: 0.53 / mu: 0.60	wt: TCCTCAGGCTGGGTG mu: TCCGCAGGCTGGGTG	CTCA\|ggct

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

370

mutated

all conserved

370

Ptroglodytes

all identical

ENSPTRG00000005134

370

Mmulatta

all identical

ENSMMUG00000022060

449

Fcatus

no alignment

ENSFCAG00000002082

n/a

Mmusculus

not conserved

ENSMUSG00000040345

107

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000013390

147

Dmelanogaster

no homologue

Celegans

not conserved

C38D4.5

438

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
322	435	DOMAIN	PH.	lost
368	370	HELIX		lost
380	384	STRAND		might get lost (downstream of altered splice site)
389	392	STRAND		might get lost (downstream of altered splice site)
394	396	TURN		might get lost (downstream of altered splice site)
398	406	STRAND		might get lost (downstream of altered splice site)
412	416	STRAND		might get lost (downstream of altered splice site)
420	439	HELIX		might get lost (downstream of altered splice site)
475	475	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
542	749	DOMAIN	Rho-GAP.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2253 / 2253

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

751 / 751

position of stopcodon in wt / mu cDNA

2392 / 2392

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

140 / 140

chromosome

strand

-1

last intron/exon boundary

2221

theoretical NMD boundary in CDS

2031

length of CDS

2253

coding sequence (CDS) position

1108

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

1247

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

12443

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

57870155

original gDNA sequence snippet

CACCGCCGACAGCGCCCTCCTCAGGCTGGGTGAGTGTGAGC

altered gDNA sequence snippet

CACCGCCGACAGCGCCCTCCGCAGGCTGGGTGAGTGTGAGC

original cDNA sequence snippet

CACCGCCGACAGCGCCCTCCTCAGGCTGGGGACCAGCGGGT

altered cDNA sequence snippet

CACCGCCGACAGCGCCCTCCGCAGGCTGGGGACCAGCGGGT

wildtype AA sequence

MLSSRWWPSS WGILGLGPRS PPRGSQLCAL YAFTYTGADG QQVSLAEGDR FLLLRKTNSD
WWLARRLEAP STSRPIFVPA AYMIEESIPS QSPTTVIPGQ LLWTPGPKLF HGSLEELSQA
LPSRAQASSE QPPPLPRKMC RSVSTDNLSP SLLKPFQEGP SGRSLSQEDL PSEASASTAG
PQPLMSEPPV YCNLVDLRRC PRSPPPGPAC PLLQRLDAWE QHLDPNSGRC FYINSLTGCK
SWKPPRRSRS ETNPGSMEGT QTLKRNNDVL QPQAKGFRSD TGTPEPLDPQ GSLSLSQRTS
QLDPPALQAP RPLPQLLDDP HEVEKSGLLN MTKIAQGGRK LRKNWGPSWV VLTGNSLVFY
REPPPTAPSS GWGPAGSRPE SSVDLRGAAL AHGRHLSSRR NVLHIRTIPG HEFLLQSDHE
TELRAWHRAL RTVIERLVRW VEARREAPTG RDQGSGDREN PLELRLSGSG PAELSAGEDE
EEESELVSKP LLRLSSRRSS IRGPEGTEQN RVRNKLKRLI AKRPPLQSLQ ERGLLRDQVF
GCQLESLCQR EGDTVPSFLR LCIAAVDKRG LDVDGIYRVS GNLAVVQKLR FLVDRERAVT
SDGRYVFPEQ PGQEGRLDLD STEWDDIHVV TGALKLFLRE LPQPLVPPLL LPHFRAALAL
SESEQCLSQI QELIGSMPKP NHDTLRYLLE HLCRVIAHSD KNRMTPHNLG IVFGPTLFRP
EQETSDPAAH ALYPGQLVQL MLTNFTSLFP *

mutated AA sequence

MLSSRWWPSS WGILGLGPRS PPRGSQLCAL YAFTYTGADG QQVSLAEGDR FLLLRKTNSD
WWLARRLEAP STSRPIFVPA AYMIEESIPS QSPTTVIPGQ LLWTPGPKLF HGSLEELSQA
LPSRAQASSE QPPPLPRKMC RSVSTDNLSP SLLKPFQEGP SGRSLSQEDL PSEASASTAG
PQPLMSEPPV YCNLVDLRRC PRSPPPGPAC PLLQRLDAWE QHLDPNSGRC FYINSLTGCK
SWKPPRRSRS ETNPGSMEGT QTLKRNNDVL QPQAKGFRSD TGTPEPLDPQ GSLSLSQRTS
QLDPPALQAP RPLPQLLDDP HEVEKSGLLN MTKIAQGGRK LRKNWGPSWV VLTGNSLVFY
REPPPTAPSA GWGPAGSRPE SSVDLRGAAL AHGRHLSSRR NVLHIRTIPG HEFLLQSDHE
TELRAWHRAL RTVIERLVRW VEARREAPTG RDQGSGDREN PLELRLSGSG PAELSAGEDE
EEESELVSKP LLRLSSRRSS IRGPEGTEQN RVRNKLKRLI AKRPPLQSLQ ERGLLRDQVF
GCQLESLCQR EGDTVPSFLR LCIAAVDKRG LDVDGIYRVS GNLAVVQKLR FLVDRERAVT
SDGRYVFPEQ PGQEGRLDLD STEWDDIHVV TGALKLFLRE LPQPLVPPLL LPHFRAALAL
SESEQCLSQI QELIGSMPKP NHDTLRYLLE HLCRVIAHSD KNRMTPHNLG IVFGPTLFRP
EQETSDPAAH ALYPGQLVQL MLTNFTSLFP *

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

Problems