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 10 transcript(s)...
Querying Taster for transcript #1: ENST00000449771
Querying Taster for transcript #2: ENST00000549151
Querying Taster for transcript #3: ENST00000389212
Querying Taster for transcript #4: ENST00000548919
Querying Taster for transcript #5: ENST00000395358
Querying Taster for transcript #6: ENST00000397089
Querying Taster for transcript #7: ENST00000405493
Querying Taster for transcript #8: ENST00000171000
Querying Taster for transcript #9: ENST00000389211
Querying Taster for transcript #10: ENST00000541821
MT speed 0 s - this script 7.369233 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
RAPGEF3	polymorphism_automatic	0.00367329916619397	simple_aae				A16P	single base exchange	rs11168230		show file
RAPGEF3	polymorphism_automatic	0.00367329916619397	simple_aae				A16P	single base exchange	rs11168230		show file
RAPGEF3	polymorphism_automatic	0.00367329916619397	simple_aae				A16P	single base exchange	rs11168230		show file
RAPGEF3	polymorphism_automatic	0.00367329916619397	simple_aae				A28P	single base exchange	rs11168230		show file
RAPGEF3	polymorphism_automatic	0.999955986646695	without_aae					single base exchange	rs11168230		show file
RAPGEF3	polymorphism_automatic	0.999955986646695	without_aae					single base exchange	rs11168230		show file
RAPGEF3	polymorphism_automatic	0.999955986646695	without_aae					single base exchange	rs11168230		show file
RAPGEF3	polymorphism_automatic	0.999955986646695	without_aae					single base exchange	rs11168230		show file
RAPGEF3	polymorphism_automatic	0.999955986646695	without_aae					single base exchange	rs11168230		show file
RAPGEF3	polymorphism_automatic	0.999955986646695	without_aae					single base exchange	rs11168230		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.996326700833806 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:48151822C>GN/A show variant in all transcripts IGV

HGNC symbol

RAPGEF3

Ensembl transcript ID

ENST00000449771

Genbank transcript ID

N/A

UniProt peptide

O95398

alteration type

single base exchange

alteration region

CDS

DNA changes

c.46G>C
cDNA.135G>C
g.13002G>C

AA changes

A16P Score: 27 explain score(s)

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

frameshift

known variant

Reference ID: rs11168230

database	homozygous (G/G)	heterozygous	allele carriers
1000G	242	1003	1245
ExAC	2414	10976	13390

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
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
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.028	0.758
	0.462	0.676
(flanking)	-0.335	0.603

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	13004	wt: 0.9799 / mu: 0.9902 (marginal change - not scored)	wt: CTGGCTGTGGAGGAT mu: CTGCCTGTGGAGGAT	GGCT\|gtgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000004866

Mmulatta

no alignment

ENSMMUG00000000477

n/a

Fcatus

all identical

ENSFCAG00000013996

Mmusculus

all identical

ENSMUSG00000022469

Ggallus

no homologue

Trubripes

no alignment

ENSTRUG00000014445

n/a

Drerio

no alignment

ENSDARG00000079291

n/a

Dmelanogaster

no alignment

FBgn0085421

n/a

Celegans

no alignment

T20G5.5

n/a

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2772 / 2772

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

924 / 924

position of stopcodon in wt / mu cDNA

2861 / 2861

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

90 / 90

chromosome

strand

-1

last intron/exon boundary

2743

theoretical NMD boundary in CDS

2603

length of CDS

2772

coding sequence (CDS) position

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

135

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

13002

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

48151822

original gDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGGCTGTGGAGGATAGCCCAGCT

altered gDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGCCTGTGGAGGATAGCCCAGCT

original cDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGGCTGTGGAGGATAGCCCAGCT

altered cDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGCCTGTGGAGGATAGCCCAGCT

wildtype AA sequence

MKVGWPGESC WQVGLAVEDS PALGAPRVGA LPDVVPEGTL LNMVLRRMHR PRSCSYQLLL
EHQRPSCIQG LRWTPLTNSE ESLDFSESLE QASTERVLRA GRQLHRHLLA TCPNLIRDRK
YHLRLYRQCC SGRELVDGIL ALGLGVHSRS QVVGICQVLL DEGALCHVKH DWAFQDRDAQ
FYRFPGPEPE PVRTHEMEEE LAEAVALLSQ RGPDALLTVA LRKPPGQRTD EELDLIFEEL
LHIKAVAHLS NSVKRELAAV LLFEPHSKAG TVLFSQGDKG TSWYIIWKGS VNVVTHGKGL
VTTLHEGDDF GQLALVNDAP RAATIILRED NCHFLRVDKQ DFNRIIKDVE AKTMRLEEHG
KVVLVLERAS QGAGPSRPPT PGRNRYTVMS GTPEKILELL LEAMGPDSSA HDPTETFLSD
FLLTHRVFMP SAQLCAALLH HFHVEPAGGS EQERSTYVCN KRQQILRLVS QWVALYGSML
HTDPVATSFL QKLSDLVGRD TRLSNLLREQ WPERRRCHRL ENGCGNASPQ MKARNLPVWL
PNQDEPLPGS SCAIQVGDKV PYDICRPDHS VLTLQLPVTA SVREVMAALA QEDGWTKGQV
LVKVNSAGDA IGLQPDARGV ATSLGLNERL FVVNPQEVHE LIPHPDQLGP TVGSAEGLDL
VSAKDLAGQL TDHDWSLFNS IHQVELIHYV LGPQHLRDVT TANLERFMRR FNELQYWVAT
ELCLCPVPGP RAQLLRKFIK LAAHLKEQKN LNSFFAVMFG LSNSAISRLA HTWERLPHKV
RKLYSALERL LDPSWNHRVY RLALAKLSPP VIPFMPLLLK DMTFIHEGNH TLVENLINFE
KMRMMARAAR MLHHCRSHNP VPLSPLRSRV SHLHEDSQVA RISTCSEQSL STRSPASTWA
YVQQLKVIDN QRELSRLSRE LEP*

mutated AA sequence

MKVGWPGESC WQVGLPVEDS PALGAPRVGA LPDVVPEGTL LNMVLRRMHR PRSCSYQLLL
EHQRPSCIQG LRWTPLTNSE ESLDFSESLE QASTERVLRA GRQLHRHLLA TCPNLIRDRK
YHLRLYRQCC SGRELVDGIL ALGLGVHSRS QVVGICQVLL DEGALCHVKH DWAFQDRDAQ
FYRFPGPEPE PVRTHEMEEE LAEAVALLSQ RGPDALLTVA LRKPPGQRTD EELDLIFEEL
LHIKAVAHLS NSVKRELAAV LLFEPHSKAG TVLFSQGDKG TSWYIIWKGS VNVVTHGKGL
VTTLHEGDDF GQLALVNDAP RAATIILRED NCHFLRVDKQ DFNRIIKDVE AKTMRLEEHG
KVVLVLERAS QGAGPSRPPT PGRNRYTVMS GTPEKILELL LEAMGPDSSA HDPTETFLSD
FLLTHRVFMP SAQLCAALLH HFHVEPAGGS EQERSTYVCN KRQQILRLVS QWVALYGSML
HTDPVATSFL QKLSDLVGRD TRLSNLLREQ WPERRRCHRL ENGCGNASPQ MKARNLPVWL
PNQDEPLPGS SCAIQVGDKV PYDICRPDHS VLTLQLPVTA SVREVMAALA QEDGWTKGQV
LVKVNSAGDA IGLQPDARGV ATSLGLNERL FVVNPQEVHE LIPHPDQLGP TVGSAEGLDL
VSAKDLAGQL TDHDWSLFNS IHQVELIHYV LGPQHLRDVT TANLERFMRR FNELQYWVAT
ELCLCPVPGP RAQLLRKFIK LAAHLKEQKN LNSFFAVMFG LSNSAISRLA HTWERLPHKV
RKLYSALERL LDPSWNHRVY RLALAKLSPP VIPFMPLLLK DMTFIHEGNH TLVENLINFE
KMRMMARAAR MLHHCRSHNP VPLSPLRSRV SHLHEDSQVA RISTCSEQSL STRSPASTWA
YVQQLKVIDN QRELSRLSRE LEP*

speed

1.18 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: 0.996326700833806 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:48151822C>GN/A show variant in all transcripts IGV

HGNC symbol

RAPGEF3

Ensembl transcript ID

ENST00000389212

Genbank transcript ID

N/A

UniProt peptide

O95398

alteration type

single base exchange

alteration region

CDS

DNA changes

c.46G>C
cDNA.258G>C
g.13002G>C

AA changes

A16P Score: 27 explain score(s)

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

frameshift

known variant

Reference ID: rs11168230

database	homozygous (G/G)	heterozygous	allele carriers
1000G	242	1003	1245
ExAC	2414	10976	13390

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.028	0.758
	0.462	0.676
(flanking)	-0.335	0.603

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	13004	wt: 0.9799 / mu: 0.9902 (marginal change - not scored)	wt: CTGGCTGTGGAGGAT mu: CTGCCTGTGGAGGAT	GGCT\|gtgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000004866

Mmulatta

no alignment

ENSMMUG00000000477

n/a

Fcatus

all identical

ENSFCAG00000013996

Mmusculus

all identical

ENSMUSG00000022469

Ggallus

no homologue

Trubripes

no alignment

ENSTRUG00000014445

n/a

Drerio

no alignment

ENSDARG00000079291

n/a

Dmelanogaster

no alignment

FBgn0085421

n/a

Celegans

no alignment

T20G5.5

n/a

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2772 / 2772

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

924 / 924

position of stopcodon in wt / mu cDNA

2984 / 2984

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

213 / 213

chromosome

strand

-1

last intron/exon boundary

2866

theoretical NMD boundary in CDS

2603

length of CDS

2772

coding sequence (CDS) position

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

258

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

13002

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

48151822

original gDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGGCTGTGGAGGATAGCCCAGCT

altered gDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGCCTGTGGAGGATAGCCCAGCT

original cDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGGCTGTGGAGGATAGCCCAGCT

altered cDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGCCTGTGGAGGATAGCCCAGCT

wildtype AA sequence

mutated AA sequence

speed

1.19 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.996326700833806 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:48151822C>GN/A show variant in all transcripts IGV

HGNC symbol

RAPGEF3

Ensembl transcript ID

ENST00000395358

Genbank transcript ID

N/A

UniProt peptide

O95398

alteration type

single base exchange

alteration region

CDS

DNA changes

c.46G>C
cDNA.135G>C
g.13002G>C

AA changes

A16P Score: 27 explain score(s)

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

frameshift

known variant

Reference ID: rs11168230

database	homozygous (G/G)	heterozygous	allele carriers
1000G	242	1003	1245
ExAC	2414	10976	13390

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.028	0.758
	0.462	0.676
(flanking)	-0.335	0.603

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	13004	wt: 0.9799 / mu: 0.9902 (marginal change - not scored)	wt: CTGGCTGTGGAGGAT mu: CTGCCTGTGGAGGAT	GGCT\|gtgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000004866

Mmulatta

no alignment

ENSMMUG00000000477

n/a

Fcatus

all identical

ENSFCAG00000013996

Mmusculus

all identical

ENSMUSG00000022469

Ggallus

no homologue

Trubripes

no alignment

ENSTRUG00000014445

n/a

Drerio

no alignment

ENSDARG00000079291

n/a

Dmelanogaster

no alignment

FBgn0085421

n/a

Celegans

no alignment

T20G5.5

n/a

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1797 / 1797

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

599 / 599

position of stopcodon in wt / mu cDNA

1886 / 1886

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

90 / 90

chromosome

strand

-1

last intron/exon boundary

1646

theoretical NMD boundary in CDS

1506

length of CDS

1797

coding sequence (CDS) position

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

135

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

13002

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

48151822

original gDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGGCTGTGGAGGATAGCCCAGCT

altered gDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGCCTGTGGAGGATAGCCCAGCT

original cDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGGCTGTGGAGGATAGCCCAGCT

altered cDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGCCTGTGGAGGATAGCCCAGCT

wildtype AA sequence

mutated AA sequence

speed

1.23 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.996326700833806 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:48151822C>GN/A show variant in all transcripts IGV

HGNC symbol

RAPGEF3

Ensembl transcript ID

ENST00000397089

Genbank transcript ID

N/A

UniProt peptide

O95398

alteration type

single base exchange

alteration region

CDS

DNA changes

c.82G>C
cDNA.224G>C
g.13002G>C

AA changes

A28P Score: 27 explain score(s)

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

frameshift

known variant

Reference ID: rs11168230

database	homozygous (G/G)	heterozygous	allele carriers
1000G	242	1003	1245
ExAC	2414	10976	13390

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.028	0.758
	0.462	0.676
(flanking)	-0.335	0.603

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	13004	wt: 0.9799 / mu: 0.9902 (marginal change - not scored)	wt: CTGGCTGTGGAGGAT mu: CTGCCTGTGGAGGAT	GGCT\|gtgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000004866

Mmulatta

no alignment

ENSMMUG00000000477

n/a

Fcatus

all identical

ENSFCAG00000013996

Mmusculus

all identical

ENSMUSG00000022469

Ggallus

no homologue

Trubripes

no alignment

ENSTRUG00000014445

n/a

Drerio

no alignment

ENSDARG00000079291

n/a

Dmelanogaster

no alignment

FBgn0085421

n/a

Celegans

no alignment

T20G5.5

n/a

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2607 / 2607

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

869 / 869

position of stopcodon in wt / mu cDNA

2749 / 2749

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

143 / 143

chromosome

strand

-1

last intron/exon boundary

2631

theoretical NMD boundary in CDS

2438

length of CDS

2607

coding sequence (CDS) position

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

224

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

13002

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

48151822

original gDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGGCTGTGGAGGATAGCCCAGCT

altered gDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGCCTGTGGAGGATAGCCCAGCT

original cDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGGCTGTGGAGGATAGCCCAGCT

altered cDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGCCTGTGGAGGATAGCCCAGCT

wildtype AA sequence

MAQREEIKRP LWETVGWPGE SCWQVGLAVE DSPALGAPRV GALPDVVPEG TLLNMVLRRM
HRPRSCSYQL LLEHQRPSCI QGLRWTPLTN SEESLDFSES LEQASTERVL RAGRQLHRHL
LATCPNLIRD RKYHLRLYRQ CCSGRELVDG ILALGLGVHS RSQVVGICQV LLDEGALCHV
KHDWAFQDRD AQFYRFPGPE PEPVRTHEME EELAEAVALL SQRGPDALLT VALRKPPGQR
TDEELDLIFE ELLHIKAVAH LSNSVKRELA AVLLFEPHSK AGTVLFSQGD KGTSWYIIWK
GSVNVVTHGK GLVTTLHEGD DFGQLALVND APRAATIILR EDNCHFLRVD KQDFNRIIKD
VEAKTMRLEE HGKVVLVLER ASQGAGPSRP PTPGRNRYTV MSGTPEKILE LLLEAMGPDS
SAHDPTETFL SDFLLTHRVF MPSAQLCAAL LHHFHVEPAG GSEQERSTYV CNKRQQILRL
VSQWVALYGS MLHTDPVATS FLQKLSDLVG RDTRLSNLLR EQWPERRRCH RLENGCGNAS
PQMKARNLPV WLPNQDEPLP GSSCAIQVGD KDAIGLQPDA RGVATSLGLN ERLFVVNPQE
VHELIPHPDQ LGPTVGSAEG LDLVSAKDLA GQLTDHDWSL FNSIHQVELI HYVLGPQHLR
DVTTANLERF MRRFNELQYW VATELCLCPV PGPRAQLLRK FIKLAAHNSA ISRLAHTWER
LPHKVRKLYS ALERLLDPSW NHRVYRLALA KLSPPVIPFM PLLLKDMTFI HEGNHTLVEN
LINFEKMRMM ARAARMLHHC RSHNPVPLSP LRSRVSHLHE DSQVARISTC SEQSLSTRSP
ASTWAYVQQL KVIDNQRELS RLSRELEP*

mutated AA sequence

MAQREEIKRP LWETVGWPGE SCWQVGLPVE DSPALGAPRV GALPDVVPEG TLLNMVLRRM
HRPRSCSYQL LLEHQRPSCI QGLRWTPLTN SEESLDFSES LEQASTERVL RAGRQLHRHL
LATCPNLIRD RKYHLRLYRQ CCSGRELVDG ILALGLGVHS RSQVVGICQV LLDEGALCHV
KHDWAFQDRD AQFYRFPGPE PEPVRTHEME EELAEAVALL SQRGPDALLT VALRKPPGQR
TDEELDLIFE ELLHIKAVAH LSNSVKRELA AVLLFEPHSK AGTVLFSQGD KGTSWYIIWK
GSVNVVTHGK GLVTTLHEGD DFGQLALVND APRAATIILR EDNCHFLRVD KQDFNRIIKD
VEAKTMRLEE HGKVVLVLER ASQGAGPSRP PTPGRNRYTV MSGTPEKILE LLLEAMGPDS
SAHDPTETFL SDFLLTHRVF MPSAQLCAAL LHHFHVEPAG GSEQERSTYV CNKRQQILRL
VSQWVALYGS MLHTDPVATS FLQKLSDLVG RDTRLSNLLR EQWPERRRCH RLENGCGNAS
PQMKARNLPV WLPNQDEPLP GSSCAIQVGD KDAIGLQPDA RGVATSLGLN ERLFVVNPQE
VHELIPHPDQ LGPTVGSAEG LDLVSAKDLA GQLTDHDWSL FNSIHQVELI HYVLGPQHLR
DVTTANLERF MRRFNELQYW VATELCLCPV PGPRAQLLRK FIKLAAHNSA ISRLAHTWER
LPHKVRKLYS ALERLLDPSW NHRVYRLALA KLSPPVIPFM PLLLKDMTFI HEGNHTLVEN
LINFEKMRMM ARAARMLHHC RSHNPVPLSP LRSRVSHLHE DSQVARISTC SEQSLSTRSP
ASTWAYVQQL KVIDNQRELS RLSRELEP*

speed

1.22 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 4.40133533044631e-05 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:48151822C>GN/A show variant in all transcripts IGV

HGNC symbol

RAPGEF3

Ensembl transcript ID

ENST00000549151

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.218G>C
g.13002G>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs11168230

database	homozygous (G/G)	heterozygous	allele carriers
1000G	242	1003	1245
ExAC	2414	10976	13390

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.028	0.758
	0.462	0.676
(flanking)	-0.335	0.603

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	13004	wt: 0.9799 / mu: 0.9902 (marginal change - not scored)	wt: CTGGCTGTGGAGGAT mu: CTGCCTGTGGAGGAT	GGCT\|gtgg

distance from splice site

Kozak consensus sequence altered?

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

299 / 299

chromosome

strand

-1

last intron/exon boundary

2826

theoretical NMD boundary in CDS

2477

length of CDS

2646

coding sequence (CDS) position

N/A

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

218

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

13002

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

48151822

original gDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGGCTGTGGAGGATAGCCCAGCT

altered gDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGCCTGTGGAGGATAGCCCAGCT

original cDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGGCTGTGGAGGATAGCCCAGCT

altered cDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGCCTGTGGAGGATAGCCCAGCT

wildtype AA sequence

MVLRRMHRPR SCSYQLLLEH QRPSCIQGLR WTPLTNSEES LDFSESLEQA STERVLRAGR
QLHRHLLATC PNLIRDRKYH LRLYRQCCSG RELVDGILAL GLGVHSRSQV VGICQVLLDE
GALCHVKHDW AFQDRDAQFY RFPGPEPEPV RTHEMEEELA EAVALLSQRG PDALLTVALR
KPPGQRTDEE LDLIFEELLH IKAVAHLSNS VKRELAAVLL FEPHSKAGTV LFSQGDKGTS
WYIIWKGSVN VVTHGKGLVT TLHEGDDFGQ LALVNDAPRA ATIILREDNC HFLRVDKQDF
NRIIKDVEAK TMRLEEHGKV VLVLERASQG AGPSRPPTPG RNRYTVMSGT PEKILELLLE
AMGPDSSAHD PTETFLSDFL LTHRVFMPSA QLCAALLHHF HVEPAGGSEQ ERSTYVCNKR
QQILRLVSQW VALYGSMLHT DPVATSFLQK LSDLVGRDTR LSNLLREQWP ERRRCHRLEN
GCGNASPQMK ARNLPVWLPN QDEPLPGSSC AIQVGDKVPY DICRPDHSVL TLQLPVTASV
REVMAALAQE DGWTKGQVLV KVNSAGDAIG LQPDARGVAT SLGLNERLFV VNPQEVHELI
PHPDQLGPTV GSAEGLDLVS AKDLAGQLTD HDWSLFNSIH QVELIHYVLG PQHLRDVTTA
NLERFMRRFN ELQYWVATEL CLCPVPGPRA QLLRKFIKLA AHLKEQKNLN SFFAVMFGLS
NSAISRLAHT WERLPHKVRK LYSALERLLD PSWNHRVYRL ALAKLSPPVI PFMPLLLKDM
TFIHEGNHTL VENLINFEKM RMMARAARML HHCRSHNPVP LSPLRSRVSH LHEDSQVARI
STCSEQSLST RSPASTWAYV QQLKVIDNQR ELSRLSRELE P*

mutated AA sequence

N/A

speed

0.80 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 4.40133533044631e-05 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:48151822C>GN/A show variant in all transcripts IGV

HGNC symbol

RAPGEF3

Ensembl transcript ID

ENST00000548919

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.224G>C
g.13002G>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs11168230

database	homozygous (G/G)	heterozygous	allele carriers
1000G	242	1003	1245
ExAC	2414	10976	13390

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.028	0.758
	0.462	0.676
(flanking)	-0.335	0.603

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	13004	wt: 0.9799 / mu: 0.9902 (marginal change - not scored)	wt: CTGGCTGTGGAGGAT mu: CTGCCTGTGGAGGAT	GGCT\|gtgg

distance from splice site

Kozak consensus sequence altered?

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

305 / 305

chromosome

strand

-1

last intron/exon boundary

2631

theoretical NMD boundary in CDS

2276

length of CDS

2445

coding sequence (CDS) position

N/A

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

224

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

13002

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

48151822

original gDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGGCTGTGGAGGATAGCCCAGCT

altered gDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGCCTGTGGAGGATAGCCCAGCT

original cDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGGCTGTGGAGGATAGCCCAGCT

altered cDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGCCTGTGGAGGATAGCCCAGCT

wildtype AA sequence

MVLRRMHRPR SCSYQLLLEH QRPSCIQGLR WTPLTNSEES LDFSESLEQA STERVLRAGR
QLHRHLLATC PNLIRDRKYH LRLYRQCCSG RELVDGILAL GLGVHSRSQV VGICQVLLDE
GALCHVKHDW AFQDRDAQFY RFPGPEPEPV RTHEMEEELA EAVALLSQRG PDALLTVALR
KPPGQRTDEE LDLIFEELLH IKAVAHLSNS VKRELAAVLL FEPHSKAGTV LFSQGDKGTS
WYIIWKGSVN VVTHGKGLVT TLHEGDDFGQ LALVNDAPRA ATIILREDNC HFLRVDKQDF
NRIIKDVEAK TMRLEEHGKV VLVLERASQG AGPSRPPTPG RNRYTVMSGT PEKILELLLE
AMGPDSSAHD PTETFLSDFL LTHRVFMPSA QLCAALLHHF HVEPAGGSEQ ERSTYVCNKR
QQILRLVSQW VALYGSMLHT DPVATSFLQK LSDLVGRDTR LSNLLREQWP ERRRCHRLEN
GCGNASPQMK ARNLPVWLPN QDEPLPGSSC AIQVGDKDAI GLQPDARGVA TSLGLNERLF
VVNPQEVHEL IPHPDQLGPT VGSAEGLDLV SAKDLAGQLT DHDWSLFNSI HQVELIHYVL
GPQHLRDVTT ANLERFMRRF NELQYWVATE LCLCPVPGPR AQLLRKFIKL AAHNSAISRL
AHTWERLPHK VRKLYSALER LLDPSWNHRV YRLALAKLSP PVIPFMPLLL KDMTFIHEGN
HTLVENLINF EKMRMMARAA RMLHHCRSHN PVPLSPLRSR VSHLHEDSQV ARISTCSEQS
LSTRSPASTW AYVQQLKVID NQRELSRLSR ELEP*

mutated AA sequence

N/A

speed

0.92 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 4.4013353304463e-05 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:48151822C>GN/A show variant in all transcripts IGV

HGNC symbol

RAPGEF3

Ensembl transcript ID

ENST00000171000

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.568G>C
g.13002G>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs11168230

database	homozygous (G/G)	heterozygous	allele carriers
1000G	242	1003	1245
ExAC	2414	10976	13390

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.028	0.758
	0.462	0.676
(flanking)	-0.335	0.603

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	13004	wt: 0.9799 / mu: 0.9902 (marginal change - not scored)	wt: CTGGCTGTGGAGGAT mu: CTGCCTGTGGAGGAT	GGCT\|gtgg

distance from splice site

Kozak consensus sequence altered?

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

649 / 649

chromosome

strand

-1

last intron/exon boundary

3176

theoretical NMD boundary in CDS

2477

length of CDS

2646

coding sequence (CDS) position

N/A

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

568

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

13002

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

48151822

original gDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGGCTGTGGAGGATAGCCCAGCT

altered gDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGCCTGTGGAGGATAGCCCAGCT

original cDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGGCTGTGGAGGATAGCCCAGCT

altered cDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGCCTGTGGAGGATAGCCCAGCT

wildtype AA sequence

mutated AA sequence

N/A

speed

0.30 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 4.4013353304463e-05 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:48151822C>GN/A show variant in all transcripts IGV

HGNC symbol

RAPGEF3

Ensembl transcript ID

ENST00000405493

Genbank transcript ID

NM_001098531

UniProt peptide

N/A

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.130G>C
g.13002G>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs11168230

database	homozygous (G/G)	heterozygous	allele carriers
1000G	242	1003	1245
ExAC	2414	10976	13390

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.028	0.758
	0.462	0.676
(flanking)	-0.335	0.603

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	13004	wt: 0.9799 / mu: 0.9902 (marginal change - not scored)	wt: CTGGCTGTGGAGGAT mu: CTGCCTGTGGAGGAT	GGCT\|gtgg

distance from splice site

Kozak consensus sequence altered?

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

211 / 211

chromosome

strand

-1

last intron/exon boundary

2738

theoretical NMD boundary in CDS

2477

length of CDS

2646

coding sequence (CDS) position

N/A

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

130

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

13002

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

48151822

original gDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGGCTGTGGAGGATAGCCCAGCT

altered gDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGCCTGTGGAGGATAGCCCAGCT

original cDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGGCTGTGGAGGATAGCCCAGCT

altered cDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGCCTGTGGAGGATAGCCCAGCT

wildtype AA sequence

mutated AA sequence

N/A

speed

0.84 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 4.40133533044631e-05 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:48151822C>GN/A show variant in all transcripts IGV

HGNC symbol

RAPGEF3

Ensembl transcript ID

ENST00000541821

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.66G>C
g.13002G>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs11168230

database	homozygous (G/G)	heterozygous	allele carriers
1000G	242	1003	1245
ExAC	2414	10976	13390

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.028	0.758
	0.462	0.676
(flanking)	-0.335	0.603

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	13004	wt: 0.9799 / mu: 0.9902 (marginal change - not scored)	wt: CTGGCTGTGGAGGAT mu: CTGCCTGTGGAGGAT	GGCT\|gtgg

distance from splice site

Kozak consensus sequence altered?

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

628 / 628

chromosome

strand

-1

last intron/exon boundary

2222

theoretical NMD boundary in CDS

1544

length of CDS

1713

coding sequence (CDS) position

N/A

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

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

13002

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

48151822

original gDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGGCTGTGGAGGATAGCCCAGCT

altered gDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGCCTGTGGAGGATAGCCCAGCT

original cDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGGCTGTGGAGGATAGCCCAGCT

altered cDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGCCTGTGGAGGATAGCCCAGCT

wildtype AA sequence

MRLEEHGKVV LVLERASQGA GPSRPPTPGR NRYTVMSGTP EKILELLLEA MGPDSSAHDP
TETFLSDFLL THRVFMPSAQ LCAALLHHFH VEPAGGSEQE RSTYVCNKRQ QILRLVSQWV
ALYGSMLHTD PVATSFLQKL SDLVGRDTRL SNLLREQWPE RRRCHRLENG CGNASPQMKA
RNLPVWLPNQ DEPLPGSSCA IQVGDKVPYD ICRPDHSVLT LQLPVTASVR EVMAALAQED
GWTKGQVLVK VNSAGDAIGL QPDARGVATS LGLNERLFVV NPQEVHELIP HPDQLGPTVG
SAEGLDLVSA KDLAGQLTDH DWSLFNSIHQ VELIHYVLGP QHLRDVTTAN LERFMRRFNE
LQYWVATELC LCPVPGPRAQ LLRKFIKLAA HLKEQKNLNS FFAVMFGLSN SAISRLAHTW
ERLPHKVRKL YSALERLLDP SWNHRVYRLA LAKLSPPVIP FMPLLLKDMT FIHEGNHTLV
ENLINFEKMR MMARAARMLH HCRSHNPVPL SPLRSRVSHL HEDSQVARIS TCSEQSLSTR
SPASTWAYVQ QLKVIDNQRE LSRLSRELEP *

mutated AA sequence

N/A

speed

0.82 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 4.40133533044631e-05 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:48151822C>GN/A show variant in all transcripts IGV

HGNC symbol

RAPGEF3

Ensembl transcript ID

ENST00000389211

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.258G>C
g.13002G>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs11168230

database	homozygous (G/G)	heterozygous	allele carriers
1000G	242	1003	1245
ExAC	2414	10976	13390

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.028	0.758
	0.462	0.676
(flanking)	-0.335	0.603

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	13004	wt: 0.9799 / mu: 0.9902 (marginal change - not scored)	wt: CTGGCTGTGGAGGAT mu: CTGCCTGTGGAGGAT	GGCT\|gtgg

distance from splice site

Kozak consensus sequence altered?

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

339 / 339

chromosome

strand

-1

last intron/exon boundary

2866

theoretical NMD boundary in CDS

2477

length of CDS

2646

coding sequence (CDS) position

N/A

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

258

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

13002

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

48151822

original gDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGGCTGTGGAGGATAGCCCAGCT

altered gDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGCCTGTGGAGGATAGCCCAGCT

original cDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGGCTGTGGAGGATAGCCCAGCT

altered cDNA sequence snippet

GCTGCTGGCAGGTGGGCCTGCCTGTGGAGGATAGCCCAGCT

wildtype AA sequence

mutated AA sequence

N/A

speed

1.00 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

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems