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: ENST00000374765
Querying Taster for transcript #2: ENST00000374763
Querying Taster for transcript #3: ENST00000374757
Querying Taster for transcript #4: ENST00000290101
Querying Taster for transcript #5: ENST00000374761
Querying Taster for transcript #6: ENST00000542643
MT speed 0 s - this script 4.326977 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
RAP1GAP	polymorphism_automatic	6.07159600374274e-09	simple_aae				A171T	single base exchange	rs2275363		show file
RAP1GAP	polymorphism_automatic	1.00824819604384e-08	simple_aae				A249T	single base exchange	rs2275363		show file
RAP1GAP	polymorphism_automatic	2.74987530524129e-08	simple_aae				A138T	single base exchange	rs2275363		show file
RAP1GAP	polymorphism_automatic	2.74987530524129e-08	simple_aae				A138T	single base exchange	rs2275363		show file
RAP1GAP	polymorphism_automatic	3.06896109636412e-08	simple_aae				A107T	single base exchange	rs2275363		show file
RAP1GAP	polymorphism_automatic	3.06896109636412e-08	simple_aae				A107T	single base exchange	rs2275363		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999993928404 (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)

chr1:21940555C>TN/A show variant in all transcripts IGV

HGNC symbol

RAP1GAP

Ensembl transcript ID

ENST00000290101

Genbank transcript ID

NM_001145658

UniProt peptide

P47736

alteration type

single base exchange

alteration region

CDS

DNA changes

c.511G>A
cDNA.544G>A
g.55302G>A

AA changes

A171T Score: 58 explain score(s)

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

171

frameshift

known variant

Reference ID: rs2275363

database	homozygous (T/T)	heterozygous	allele carriers
1000G	398	1172	1570
ExAC	9681	13405	23086

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.841	0.163
	-0.613	0.143
(flanking)	1.078	0.808

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

171

mutated

not conserved

171

Ptroglodytes

not conserved

ENSPTRG00000000303

103

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000041351

171

Ggallus

not conserved

ENSGALG00000014701

107

Trubripes

all conserved

ENSTRUG00000014029

110

Drerio

all conserved

ENSDARG00000056554

107

Dmelanogaster

not conserved

FBgn0085403

330

Celegans

not conserved

F53A10.2

278

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2184 / 2184

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

728 / 728

position of stopcodon in wt / mu cDNA

2217 / 2217

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

34 / 34

chromosome

strand

-1

last intron/exon boundary

2252

theoretical NMD boundary in CDS

2168

length of CDS

2184

coding sequence (CDS) position

511

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

544

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

55302

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

21940555

original gDNA sequence snippet

TCAATTACTACTCACTGGACGCTGCCCTCGGCCACCTTGTC

altered gDNA sequence snippet

TCAATTACTACTCACTGGACACTGCCCTCGGCCACCTTGTC

original cDNA sequence snippet

TCAATTACTACTCACTGGACGCTGCCCTCGGCCACCTTGTC

altered cDNA sequence snippet

TCAATTACTACTCACTGGACACTGCCCTCGGCCACCTTGTC

wildtype AA sequence

MSGRKRSFTF GAYGGVDKSF TSRRSVWRSD GQNQHFPQAL DLSRVNLVPS YTPSLYPKNT
DLFEMIEKMQ GSRMDEQRCS FPPPLKTEED YIPYPSVHEV LGREGPFPLI LLPQFGGYWI
EGTNHEITSI PETEPLQSPT TKVKLECNPT ARIYRKHFLG KEHFNYYSLD AALGHLVFSL
KYDVIGDQEH LRLLLRTKCR TYHDVIPISC LTEFPNVVQM AKLVCEDVNV DRFYPVLYPK
ASRLIVTFDE HVISNNFKFG VIYQKLGQTS EEELFSTNEE SPAFVEFLEF LGQKVKLQDF
KGFRGGLDVT HGQTGTESVY CNFRNKEIMF HVSTKLPYTE GDAQQLQRKR HIGNDIVAVV
FQDENTPFVP DMIASNFLHA YVVVQAEGGG PDGPLYKVSV TARDDVPFFG PPLPDPAVFR
KGPEFQEFLL TKLINAEYAC YKAEKFAKLE ERTRAALLET LYEELHIHSQ SMMGLGGDED
KMENGSGGGG FFESFKRVIR SRSQSMDAMG LSNKKPNTVS TSHSGSFAPN NPDLAKAAGI
SLIVPGKSPT RKKSGPFGSR RSSAIGIENI QEVQEKRESP PAGQKTPDSG HVSQEPKSEN
SSTQSSPEMP TTKNRAETAA QRAEALKDFS RSSSSASSFA SVVEETEGVD GEDTGLESVS
SSGTPHKRDS FIYSTWLEDS VSTTSGGSSP GPSRSPHPDA GKLGDPACPE IKIQLEASEQ
HMPQLGC*

mutated AA sequence

MSGRKRSFTF GAYGGVDKSF TSRRSVWRSD GQNQHFPQAL DLSRVNLVPS YTPSLYPKNT
DLFEMIEKMQ GSRMDEQRCS FPPPLKTEED YIPYPSVHEV LGREGPFPLI LLPQFGGYWI
EGTNHEITSI PETEPLQSPT TKVKLECNPT ARIYRKHFLG KEHFNYYSLD TALGHLVFSL
KYDVIGDQEH LRLLLRTKCR TYHDVIPISC LTEFPNVVQM AKLVCEDVNV DRFYPVLYPK
ASRLIVTFDE HVISNNFKFG VIYQKLGQTS EEELFSTNEE SPAFVEFLEF LGQKVKLQDF
KGFRGGLDVT HGQTGTESVY CNFRNKEIMF HVSTKLPYTE GDAQQLQRKR HIGNDIVAVV
FQDENTPFVP DMIASNFLHA YVVVQAEGGG PDGPLYKVSV TARDDVPFFG PPLPDPAVFR
KGPEFQEFLL TKLINAEYAC YKAEKFAKLE ERTRAALLET LYEELHIHSQ SMMGLGGDED
KMENGSGGGG FFESFKRVIR SRSQSMDAMG LSNKKPNTVS TSHSGSFAPN NPDLAKAAGI
SLIVPGKSPT RKKSGPFGSR RSSAIGIENI QEVQEKRESP PAGQKTPDSG HVSQEPKSEN
SSTQSSPEMP TTKNRAETAA QRAEALKDFS RSSSSASSFA SVVEETEGVD GEDTGLESVS
SSGTPHKRDS FIYSTWLEDS VSTTSGGSSP GPSRSPHPDA GKLGDPACPE IKIQLEASEQ
HMPQLGC*

speed

0.74 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: 0.999999989917518 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:21940555C>TN/A show variant in all transcripts IGV

HGNC symbol

RAP1GAP

Ensembl transcript ID

ENST00000374757

Genbank transcript ID

N/A

UniProt peptide

P47736

alteration type

single base exchange

alteration region

CDS

DNA changes

c.745G>A
cDNA.979G>A
g.55302G>A

AA changes

A249T Score: 58 explain score(s)

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

249

frameshift

known variant

Reference ID: rs2275363

database	homozygous (T/T)	heterozygous	allele carriers
1000G	398	1172	1570
ExAC	9681	13405	23086

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.841	0.163
	-0.613	0.143
(flanking)	1.078	0.808

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

249

mutated

not conserved

249

Ptroglodytes

not conserved

ENSPTRG00000000303

103

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000041351

171

Ggallus

not conserved

ENSGALG00000014701

107

Trubripes

all conserved

ENSTRUG00000014029

110

Drerio

all conserved

ENSDARG00000056554

107

Dmelanogaster

not conserved

FBgn0085403

330

Celegans

not conserved

F53A10.2

278

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
181	397	DOMAIN	Rap-GAP.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

984 / 984

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

328 / 328

position of stopcodon in wt / mu cDNA

1218 / 1218

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

235 / 235

chromosome

strand

-1

last intron/exon boundary

1135

theoretical NMD boundary in CDS

850

length of CDS

984

coding sequence (CDS) position

745

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

979

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

55302

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

21940555

original gDNA sequence snippet

TCAATTACTACTCACTGGACGCTGCCCTCGGCCACCTTGTC

altered gDNA sequence snippet

TCAATTACTACTCACTGGACACTGCCCTCGGCCACCTTGTC

original cDNA sequence snippet

TCAATTACTACTCACTGGACGCTGCCCTCGGCCACCTTGTC

altered cDNA sequence snippet

TCAATTACTACTCACTGGACACTGCCCTCGGCCACCTTGTC

wildtype AA sequence

MTAVGAERLT SVRAWLSCCG ACVCVFLFLC LCVFPLRVHV HVWGGECRVD IAVFVSKHMI
VALMHVTGAA GLLRLCVRAC VCMRVCATAH MYRVDKSFTS RRSVWRSDGQ NQHFPQALDL
SRVNLVPSYT PSLYPKNTDL FEMIEKMQGS RMDEQRCSFP PPLKTEEDYI PYPSVHEVLG
REGPFPLILL PQFGGYWIEG TNHEITSIPE TEPLQSPTTK VKLECNPTAR IYRKHFLGKE
HFNYYSLDAA LGHLVFSLKY DVIGDQEHLR LLLRTKCRTY HDVIPISCLT EFPNVVQMAK
LVCEDVNVDR FYPVLYPKVW LDLGTAH*

mutated AA sequence

MTAVGAERLT SVRAWLSCCG ACVCVFLFLC LCVFPLRVHV HVWGGECRVD IAVFVSKHMI
VALMHVTGAA GLLRLCVRAC VCMRVCATAH MYRVDKSFTS RRSVWRSDGQ NQHFPQALDL
SRVNLVPSYT PSLYPKNTDL FEMIEKMQGS RMDEQRCSFP PPLKTEEDYI PYPSVHEVLG
REGPFPLILL PQFGGYWIEG TNHEITSIPE TEPLQSPTTK VKLECNPTAR IYRKHFLGKE
HFNYYSLDTA LGHLVFSLKY DVIGDQEHLR LLLRTKCRTY HDVIPISCLT EFPNVVQMAK
LVCEDVNVDR FYPVLYPKVW LDLGTAH*

speed

0.81 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999972501247 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:21940555C>TN/A show variant in all transcripts IGV

HGNC symbol

RAP1GAP

Ensembl transcript ID

ENST00000374763

Genbank transcript ID

N/A

UniProt peptide

P47736

alteration type

single base exchange

alteration region

CDS

DNA changes

c.412G>A
cDNA.517G>A
g.55302G>A

AA changes

A138T Score: 58 explain score(s)

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

138

frameshift

known variant

Reference ID: rs2275363

database	homozygous (T/T)	heterozygous	allele carriers
1000G	398	1172	1570
ExAC	9681	13405	23086

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.841	0.163
	-0.613	0.143
(flanking)	1.078	0.808

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

138

mutated

not conserved

138

Ptroglodytes

not conserved

ENSPTRG00000000303

103

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000041351

171

Ggallus

not conserved

ENSGALG00000014701

107

Trubripes

all conserved

ENSTRUG00000014029

110

Drerio

all conserved

ENSDARG00000056554

107

Dmelanogaster

not conserved

FBgn0085403

330

Celegans

not conserved

F53A10.2

278

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
137	143	STRAND		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2082 / 2082

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

694 / 694

position of stopcodon in wt / mu cDNA

2187 / 2187

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

106 / 106

chromosome

strand

-1

last intron/exon boundary

2222

theoretical NMD boundary in CDS

2066

length of CDS

2082

coding sequence (CDS) position

412

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

517

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

55302

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

21940555

original gDNA sequence snippet

TCAATTACTACTCACTGGACGCTGCCCTCGGCCACCTTGTC

altered gDNA sequence snippet

TCAATTACTACTCACTGGACACTGCCCTCGGCCACCTTGTC

original cDNA sequence snippet

TCAATTACTACTCACTGGACGCTGCCCTCGGCCACCTTGTC

altered cDNA sequence snippet

TCAATTACTACTCACTGGACACTGCCCTCGGCCACCTTGTC

wildtype AA sequence

MAQLRPAVPP GRPRRGSLPA GASWQNTDLF EMIEKMQGSR MDEQRCSFPP PLKTEEDYIP
YPSVHEVLGR EGPFPLILLP QFGGYWIEGT NHEITSIPET EPLQSPTTKV KLECNPTARI
YRKHFLGKEH FNYYSLDAAL GHLVFSLKYD VIGDQEHLRL LLRTKCRTYH DVIPISCLTE
FPNVVQMAKL VCEDVNVDRF YPVLYPKASR LIVTFDEHVI SNNFKFGVIY QKLGQTSEEE
LFSTNEESPA FVEFLEFLGQ KVKLQDFKGF RGGLDVTHGQ TGTESVYCNF RNKEIMFHVS
TKLPYTEGDA QLQRKRHIGN DIVAVVFQDE NTPFVPDMIA SNFLHAYVVV QAEGGGPDGP
LYKVSVTARD DVPFFGPPLP DPAVFRKGPE FQEFLLTKLI NAEYACYKAE KFAKLEERTR
AALLETLYEE LHIHSQSMMG LGGDEDKMEN GSGGGGFFES FKRVIRSRSQ SMDAMGLSNK
KPNTVSTSHS GSFAPNNPDL AKAAGISLIV PGKSPTRKKS GPFGSRRSSA IGIENIQEVQ
EKRESPPAGQ KTPDSGHVSQ EPKSENSSTQ SSPEMPTTKN RAETAAQRAE ALKDFSRSSS
SASSFASVVE ETEGVDGEDT GLESVSSSGT PHKRDSFIYS TWLEDSVSTT SGGSSPGPSR
SPHPDAGKLG DPACPEIKIQ LEASEQHMPQ LGC*

mutated AA sequence

MAQLRPAVPP GRPRRGSLPA GASWQNTDLF EMIEKMQGSR MDEQRCSFPP PLKTEEDYIP
YPSVHEVLGR EGPFPLILLP QFGGYWIEGT NHEITSIPET EPLQSPTTKV KLECNPTARI
YRKHFLGKEH FNYYSLDTAL GHLVFSLKYD VIGDQEHLRL LLRTKCRTYH DVIPISCLTE
FPNVVQMAKL VCEDVNVDRF YPVLYPKASR LIVTFDEHVI SNNFKFGVIY QKLGQTSEEE
LFSTNEESPA FVEFLEFLGQ KVKLQDFKGF RGGLDVTHGQ TGTESVYCNF RNKEIMFHVS
TKLPYTEGDA QLQRKRHIGN DIVAVVFQDE NTPFVPDMIA SNFLHAYVVV QAEGGGPDGP
LYKVSVTARD DVPFFGPPLP DPAVFRKGPE FQEFLLTKLI NAEYACYKAE KFAKLEERTR
AALLETLYEE LHIHSQSMMG LGGDEDKMEN GSGGGGFFES FKRVIRSRSQ SMDAMGLSNK
KPNTVSTSHS GSFAPNNPDL AKAAGISLIV PGKSPTRKKS GPFGSRRSSA IGIENIQEVQ
EKRESPPAGQ KTPDSGHVSQ EPKSENSSTQ SSPEMPTTKN RAETAAQRAE ALKDFSRSSS
SASSFASVVE ETEGVDGEDT GLESVSSSGT PHKRDSFIYS TWLEDSVSTT SGGSSPGPSR
SPHPDAGKLG DPACPEIKIQ LEASEQHMPQ LGC*

speed

0.78 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999972501247 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:21940555C>TN/A show variant in all transcripts IGV

HGNC symbol

RAP1GAP

Ensembl transcript ID

ENST00000374761

Genbank transcript ID

N/A

UniProt peptide

P47736

alteration type

single base exchange

alteration region

CDS

DNA changes

c.412G>A
cDNA.412G>A
g.55302G>A

AA changes

A138T Score: 58 explain score(s)

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

138

frameshift

known variant

Reference ID: rs2275363

database	homozygous (T/T)	heterozygous	allele carriers
1000G	398	1172	1570
ExAC	9681	13405	23086

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.841	0.163
	-0.613	0.143
(flanking)	1.078	0.808

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

138

mutated

not conserved

138

Ptroglodytes

not conserved

ENSPTRG00000000303

103

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000041351

171

Ggallus

not conserved

ENSGALG00000014701

107

Trubripes

all conserved

ENSTRUG00000014029

110

Drerio

all conserved

ENSDARG00000056554

107

Dmelanogaster

not conserved

FBgn0085403

330

Celegans

not conserved

F53A10.2

278

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
137	143	STRAND		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2085 / 2085

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

695 / 695

position of stopcodon in wt / mu cDNA

2085 / 2085

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

1 / 1

chromosome

strand

-1

last intron/exon boundary

2120

theoretical NMD boundary in CDS

2069

length of CDS

2085

coding sequence (CDS) position

412

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

412

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

55302

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

21940555

original gDNA sequence snippet

TCAATTACTACTCACTGGACGCTGCCCTCGGCCACCTTGTC

altered gDNA sequence snippet

TCAATTACTACTCACTGGACACTGCCCTCGGCCACCTTGTC

original cDNA sequence snippet

TCAATTACTACTCACTGGACGCTGCCCTCGGCCACCTTGTC

altered cDNA sequence snippet

TCAATTACTACTCACTGGACACTGCCCTCGGCCACCTTGTC

wildtype AA sequence

MAQLRPAVPP GRPRRGSLPA GASWQNTDLF EMIEKMQGSR MDEQRCSFPP PLKTEEDYIP
YPSVHEVLGR EGPFPLILLP QFGGYWIEGT NHEITSIPET EPLQSPTTKV KLECNPTARI
YRKHFLGKEH FNYYSLDAAL GHLVFSLKYD VIGDQEHLRL LLRTKCRTYH DVIPISCLTE
FPNVVQMAKL VCEDVNVDRF YPVLYPKASR LIVTFDEHVI SNNFKFGVIY QKLGQTSEEE
LFSTNEESPA FVEFLEFLGQ KVKLQDFKGF RGGLDVTHGQ TGTESVYCNF RNKEIMFHVS
TKLPYTEGDA QQLQRKRHIG NDIVAVVFQD ENTPFVPDMI ASNFLHAYVV VQAEGGGPDG
PLYKVSVTAR DDVPFFGPPL PDPAVFRKGP EFQEFLLTKL INAEYACYKA EKFAKLEERT
RAALLETLYE ELHIHSQSMM GLGGDEDKME NGSGGGGFFE SFKRVIRSRS QSMDAMGLSN
KKPNTVSTSH SGSFAPNNPD LAKAAGISLI VPGKSPTRKK SGPFGSRRSS AIGIENIQEV
QEKRESPPAG QKTPDSGHVS QEPKSENSST QSSPEMPTTK NRAETAAQRA EALKDFSRSS
SSASSFASVV EETEGVDGED TGLESVSSSG TPHKRDSFIY STWLEDSVST TSGGSSPGPS
RSPHPDAGKL GDPACPEIKI QLEASEQHMP QLGC*

mutated AA sequence

MAQLRPAVPP GRPRRGSLPA GASWQNTDLF EMIEKMQGSR MDEQRCSFPP PLKTEEDYIP
YPSVHEVLGR EGPFPLILLP QFGGYWIEGT NHEITSIPET EPLQSPTTKV KLECNPTARI
YRKHFLGKEH FNYYSLDTAL GHLVFSLKYD VIGDQEHLRL LLRTKCRTYH DVIPISCLTE
FPNVVQMAKL VCEDVNVDRF YPVLYPKASR LIVTFDEHVI SNNFKFGVIY QKLGQTSEEE
LFSTNEESPA FVEFLEFLGQ KVKLQDFKGF RGGLDVTHGQ TGTESVYCNF RNKEIMFHVS
TKLPYTEGDA QQLQRKRHIG NDIVAVVFQD ENTPFVPDMI ASNFLHAYVV VQAEGGGPDG
PLYKVSVTAR DDVPFFGPPL PDPAVFRKGP EFQEFLLTKL INAEYACYKA EKFAKLEERT
RAALLETLYE ELHIHSQSMM GLGGDEDKME NGSGGGGFFE SFKRVIRSRS QSMDAMGLSN
KKPNTVSTSH SGSFAPNNPD LAKAAGISLI VPGKSPTRKK SGPFGSRRSS AIGIENIQEV
QEKRESPPAG QKTPDSGHVS QEPKSENSST QSSPEMPTTK NRAETAAQRA EALKDFSRSS
SSASSFASVV EETEGVDGED TGLESVSSSG TPHKRDSFIY STWLEDSVST TSGGSSPGPS
RSPHPDAGKL GDPACPEIKI QLEASEQHMP QLGC*

speed

0.56 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999969310389 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:21940555C>TN/A show variant in all transcripts IGV

HGNC symbol

RAP1GAP

Ensembl transcript ID

ENST00000374765

Genbank transcript ID

NM_002885

UniProt peptide

P47736

alteration type

single base exchange

alteration region

CDS

DNA changes

c.319G>A
cDNA.520G>A
g.55302G>A

AA changes

A107T Score: 58 explain score(s)

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

107

frameshift

known variant

Reference ID: rs2275363

database	homozygous (T/T)	heterozygous	allele carriers
1000G	398	1172	1570
ExAC	9681	13405	23086

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.841	0.163
	-0.613	0.143
(flanking)	1.078	0.808

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

107

mutated

not conserved

107

Ptroglodytes

not conserved

ENSPTRG00000000303

103

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000041351

171

Ggallus

not conserved

ENSGALG00000014701

107

Trubripes

all conserved

ENSTRUG00000014029

110

Drerio

all conserved

ENSDARG00000056554

107

Dmelanogaster

not conserved

FBgn0085403

330

Celegans

not conserved

F53A10.2

278

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
107	109	TURN		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1992 / 1992

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

664 / 664

position of stopcodon in wt / mu cDNA

2193 / 2193

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

202 / 202

chromosome

strand

-1

last intron/exon boundary

2228

theoretical NMD boundary in CDS

1976

length of CDS

1992

coding sequence (CDS) position

319

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

520

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

55302

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

21940555

original gDNA sequence snippet

TCAATTACTACTCACTGGACGCTGCCCTCGGCCACCTTGTC

altered gDNA sequence snippet

TCAATTACTACTCACTGGACACTGCCCTCGGCCACCTTGTC

original cDNA sequence snippet

TCAATTACTACTCACTGGACGCTGCCCTCGGCCACCTTGTC

altered cDNA sequence snippet

TCAATTACTACTCACTGGACACTGCCCTCGGCCACCTTGTC

wildtype AA sequence

MIEKMQGSRM DEQRCSFPPP LKTEEDYIPY PSVHEVLGRE GPFPLILLPQ FGGYWIEGTN
HEITSIPETE PLQSPTTKVK LECNPTARIY RKHFLGKEHF NYYSLDAALG HLVFSLKYDV
IGDQEHLRLL LRTKCRTYHD VIPISCLTEF PNVVQMAKLV CEDVNVDRFY PVLYPKASRL
IVTFDEHVIS NNFKFGVIYQ KLGQTSEEEL FSTNEESPAF VEFLEFLGQK VKLQDFKGFR
GGLDVTHGQT GTESVYCNFR NKEIMFHVST KLPYTEGDAQ QLQRKRHIGN DIVAVVFQDE
NTPFVPDMIA SNFLHAYVVV QAEGGGPDGP LYKVSVTARD DVPFFGPPLP DPAVFRKGPE
FQEFLLTKLI NAEYACYKAE KFAKLEERTR AALLETLYEE LHIHSQSMMG LGGDEDKMEN
GSGGGGFFES FKRVIRSRSQ SMDAMGLSNK KPNTVSTSHS GSFAPNNPDL AKAAGISLIV
PGKSPTRKKS GPFGSRRSSA IGIENIQEVQ EKRESPPAGQ KTPDSGHVSQ EPKSENSSTQ
SSPEMPTTKN RAETAAQRAE ALKDFSRSSS SASSFASVVE ETEGVDGEDT GLESVSSSGT
PHKRDSFIYS TWLEDSVSTT SGGSSPGPSR SPHPDAGKLG DPACPEIKIQ LEASEQHMPQ
LGC*

mutated AA sequence

MIEKMQGSRM DEQRCSFPPP LKTEEDYIPY PSVHEVLGRE GPFPLILLPQ FGGYWIEGTN
HEITSIPETE PLQSPTTKVK LECNPTARIY RKHFLGKEHF NYYSLDTALG HLVFSLKYDV
IGDQEHLRLL LRTKCRTYHD VIPISCLTEF PNVVQMAKLV CEDVNVDRFY PVLYPKASRL
IVTFDEHVIS NNFKFGVIYQ KLGQTSEEEL FSTNEESPAF VEFLEFLGQK VKLQDFKGFR
GGLDVTHGQT GTESVYCNFR NKEIMFHVST KLPYTEGDAQ QLQRKRHIGN DIVAVVFQDE
NTPFVPDMIA SNFLHAYVVV QAEGGGPDGP LYKVSVTARD DVPFFGPPLP DPAVFRKGPE
FQEFLLTKLI NAEYACYKAE KFAKLEERTR AALLETLYEE LHIHSQSMMG LGGDEDKMEN
GSGGGGFFES FKRVIRSRSQ SMDAMGLSNK KPNTVSTSHS GSFAPNNPDL AKAAGISLIV
PGKSPTRKKS GPFGSRRSSA IGIENIQEVQ EKRESPPAGQ KTPDSGHVSQ EPKSENSSTQ
SSPEMPTTKN RAETAAQRAE ALKDFSRSSS SASSFASVVE ETEGVDGEDT GLESVSSSGT
PHKRDSFIYS TWLEDSVSTT SGGSSPGPSR SPHPDAGKLG DPACPEIKIQ LEASEQHMPQ
LGC*

speed

0.79 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999969310389 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:21940555C>TN/A show variant in all transcripts IGV

HGNC symbol

RAP1GAP

Ensembl transcript ID

ENST00000542643

Genbank transcript ID

NM_001145657

UniProt peptide

P47736

alteration type

single base exchange

alteration region

CDS

DNA changes

c.319G>A
cDNA.684G>A
g.55302G>A

AA changes

A107T Score: 58 explain score(s)

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

107

frameshift

known variant

Reference ID: rs2275363

database	homozygous (T/T)	heterozygous	allele carriers
1000G	398	1172	1570
ExAC	9681	13405	23086

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.841	0.163
	-0.613	0.143
(flanking)	1.078	0.808

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

107

mutated

not conserved

107

Ptroglodytes

not conserved

ENSPTRG00000000303

103

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000041351

171

Ggallus

not conserved

ENSGALG00000014701

107

Trubripes

all conserved

ENSTRUG00000014029

110

Drerio

all conserved

ENSDARG00000056554

107

Dmelanogaster

not conserved

FBgn0085403

330

Celegans

not conserved

F53A10.2

278

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
107	109	TURN		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2046 / 2046

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

682 / 682

position of stopcodon in wt / mu cDNA

2411 / 2411

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

366 / 366

chromosome

strand

-1

last intron/exon boundary

2446

theoretical NMD boundary in CDS

2030

length of CDS

2046

coding sequence (CDS) position

319

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

684

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

55302

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

21940555

original gDNA sequence snippet

TCAATTACTACTCACTGGACGCTGCCCTCGGCCACCTTGTC

altered gDNA sequence snippet

TCAATTACTACTCACTGGACACTGCCCTCGGCCACCTTGTC

original cDNA sequence snippet

TCAATTACTACTCACTGGACGCTGCCCTCGGCCACCTTGTC

altered cDNA sequence snippet

TCAATTACTACTCACTGGACACTGCCCTCGGCCACCTTGTC

wildtype AA sequence

MIEKMQGSRM DEQRCSFPPP LKTEEDYIPY PSVHEVLGRE GPFPLILLPQ FGGYWIEGTN
HEITSIPETE PLQSPTTKVK LECNPTARIY RKHFLGKEHF NYYSLDAALG HLVFSLKYDV
IGDQEHLRLL LRTKCRTYHD VIPISCLTEF PNVVQMAKLV CEDVNVDRFY PVLYPKASRL
IVTFDEHVIS NNFKFGVIYQ KLGQTSEEEL FSTNEESPAF VEFLEFLGQK VKLQDFKGFR
GGLDVTHGQT GTESVYCNFR NKEIMFHVST KLPYTEGDAQ QLQRKRHIGN DIVAVVFQDE
NTPFVPDMIA SNFLHAYVVV QAEGGGPDGP LYKVSVTARD DVPFFGPPLP DPAVFRKGPE
FQEFLLTKLI NAEYACYKAE KFAKLEERTR AALLETLYEE LHIHSQSMMG LGGDEDKMEN
GSGGGGFFES FKRVIRSRSQ SMDAMGLSNK KPNTVSTSHS GSFAPNNPDL AKAAGISLLI
PGKSASRFGR RGSAIGIGTV EESLIVPGKS PTRKKSGPFG SRRSSAIGIE NIQEVQEKRE
SPPAGQKTPD SGHVSQEPKS ENSSTQSSPE MPTTKNRAET AAQRAEALKD FSRSSSSASS
FASVVEETEG VDGEDTGLES VSSSGTPHKR DSFIYSTWLE DSVSTTSGGS SPDAGKLGDP
ACPEIKIQLE ASEQHMPQLG C*

mutated AA sequence

MIEKMQGSRM DEQRCSFPPP LKTEEDYIPY PSVHEVLGRE GPFPLILLPQ FGGYWIEGTN
HEITSIPETE PLQSPTTKVK LECNPTARIY RKHFLGKEHF NYYSLDTALG HLVFSLKYDV
IGDQEHLRLL LRTKCRTYHD VIPISCLTEF PNVVQMAKLV CEDVNVDRFY PVLYPKASRL
IVTFDEHVIS NNFKFGVIYQ KLGQTSEEEL FSTNEESPAF VEFLEFLGQK VKLQDFKGFR
GGLDVTHGQT GTESVYCNFR NKEIMFHVST KLPYTEGDAQ QLQRKRHIGN DIVAVVFQDE
NTPFVPDMIA SNFLHAYVVV QAEGGGPDGP LYKVSVTARD DVPFFGPPLP DPAVFRKGPE
FQEFLLTKLI NAEYACYKAE KFAKLEERTR AALLETLYEE LHIHSQSMMG LGGDEDKMEN
GSGGGGFFES FKRVIRSRSQ SMDAMGLSNK KPNTVSTSHS GSFAPNNPDL AKAAGISLLI
PGKSASRFGR RGSAIGIGTV EESLIVPGKS PTRKKSGPFG SRRSSAIGIE NIQEVQEKRE
SPPAGQKTPD SGHVSQEPKS ENSSTQSSPE MPTTKNRAET AAQRAEALKD FSRSSSSASS
FASVVEETEG VDGEDTGLES VSSSGTPHKR DSFIYSTWLE DSVSTTSGGS SPDAGKLGDP
ACPEIKIQLE ASEQHMPQLG C*

speed

0.71 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