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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000561603
Querying Taster for transcript #2: ENST00000304330
MT speed 0 s - this script 3.48159 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
RPAP1	polymorphism_automatic	4.04698496936362e-12	simple_aae				K165M	single base exchange	rs2297382		show file
RPAP1	polymorphism_automatic	4.04698496936362e-12	simple_aae				K165M	single base exchange	rs2297382		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999995953 (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)

chr15:41827757T>AN/A show variant in all transcripts IGV

HGNC symbol

RPAP1

Ensembl transcript ID

ENST00000561603

Genbank transcript ID

N/A

UniProt peptide

Q9BWH6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.494A>T
cDNA.609A>T
g.8711A>T

AA changes

K165M Score: 95 explain score(s)

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

165

frameshift

known variant

Reference ID: rs2297382

database	homozygous (A/A)	heterozygous	allele carriers
1000G	135	442	577
ExAC	905	8423	9328

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.563	0.001
	-0.504	0
(flanking)	0.532	0.003

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

165

mutated

not conserved

165

Ptroglodytes

all identical

ENSPTRG00000006949

165

Mmulatta

all conserved

ENSMMUG00000008175

165

Fcatus

all conserved

ENSFCAG00000012619

165

Mmusculus

all conserved

ENSMUSG00000034032

165

Ggallus

not conserved

ENSGALG00000008624

164

EKP

SAECTQ

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000075072

181

Dmelanogaster

all identical

FBgn0052104

169

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000000054

168

SPQMLS

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3387 / 3387

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

1129 / 1129

position of stopcodon in wt / mu cDNA

3502 / 3502

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

116 / 116

chromosome

strand

-1

last intron/exon boundary

3391

theoretical NMD boundary in CDS

3225

length of CDS

3387

coding sequence (CDS) position

494

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

609

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

8711

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

41827757

original gDNA sequence snippet

AAGGAGGATAGCTGAAGCCAAGGGCCCATCAGTTGGGGAAG

altered gDNA sequence snippet

AAGGAGGATAGCTGAAGCCATGGGCCCATCAGTTGGGGAAG

original cDNA sequence snippet

AAGGAGGATAGCTGAAGCCAAGGGCCCATCAGTTGGGGAAG

altered cDNA sequence snippet

AAGGAGGATAGCTGAAGCCATGGGCCCATCAGTTGGGGAAG

wildtype AA sequence

MLSRPKPGES EVDLLHFQSQ FLAAGAAPAV QLVKKGNRGG GDANSDRPPL QDHRDVVMLD
NLPDLPPALV PSPPKRARPS PGHCLPEDED PEERLRRHDQ HITAVLTKII ERDTSSVAVN
LPVPSGVAFP AVFLRSRDTQ GKSATSGKRS IFAQEIAARR IAEAKGPSVG EVVPNVGPPE
GAVTCETPTP RNQGCQLPGS SHSFQGPNLV TGKGLRDQEA EQEAQTIHEE NIARLQAMAP
EEILQEQQRL LAQLDPSLVA FLRSHSHTQE QTGETASEEQ RPGGPSANVT KEEPLMSAFA
SEPRKRDKLE PEAPALALPV TPQKEWLHMD TVELEKLHWT QDLPPVRRQQ TQERMQARFS
LQGELLAPDV DLPTHLGLHH HGEEAERAGY SLQELFHLTR SQVSQQRALA LHVLAQVISR
AQAGEFGDRL AGSVLSLLLD AGFLFLLRFS LDDRVDGVIA TAIRALRALL VAPGDEELLD
STFSWYHGAL TFPLMPSQED KEDEDEDEEC PAGKAKRKSP EEESRPPPDL ARHDVIKGLL
ATSLLPRLRY VLEVTYPGPA VVLDILAVLI RLARHSLESA TRVLECPRLI ETIVREFLPT
SWSPVGAGPT PSLYKVPCAT AMKLLRVLAS AGRNIAARLL SSFDLRSRLC RIIAEAPQEL
ALPPEEAEML STEALRLWAV AASYGQGGYL YRELYPVLMR ALQVVPRELS THPPQPLSMQ
RIASLLTLLT QLTLAAGSTP AETISDSAEA SLSATPSLVT WTQVSGLQPL VEPCLRQTLK
LLSRPEMWRA VGPVPVACLL FLGAYYQAWS QQPSSCPEDW LQDMQRLSEE LLLPLLSQPT
LGSLWDSLRH CSLLCNPLSC VPALEAPPSL VSLGCSGGCP RLSLAGSASP FPFLTALLSL
LNTLAQIHKG LCGQLAAILA APGLQNYFLQ CVAPGAAPHL TPFSAWALRH EYHLQYLALA
LAQKAAALQP LPATHAALYH GMALALLSRL LPGSEYLTHE LLLSCVFRLE FLPCLCPWSV
TQCLLKTTWP SFSSTSGPWL LVRSAHVGAP CSMLWLWLMS IASSSLRTHR AQMRSKLPAG
VCCRKHGCWQ MRVSGSTSCT ISFPIPRSQR ALSSILSCPL CVSTTSRD*

mutated AA sequence

MLSRPKPGES EVDLLHFQSQ FLAAGAAPAV QLVKKGNRGG GDANSDRPPL QDHRDVVMLD
NLPDLPPALV PSPPKRARPS PGHCLPEDED PEERLRRHDQ HITAVLTKII ERDTSSVAVN
LPVPSGVAFP AVFLRSRDTQ GKSATSGKRS IFAQEIAARR IAEAMGPSVG EVVPNVGPPE
GAVTCETPTP RNQGCQLPGS SHSFQGPNLV TGKGLRDQEA EQEAQTIHEE NIARLQAMAP
EEILQEQQRL LAQLDPSLVA FLRSHSHTQE QTGETASEEQ RPGGPSANVT KEEPLMSAFA
SEPRKRDKLE PEAPALALPV TPQKEWLHMD TVELEKLHWT QDLPPVRRQQ TQERMQARFS
LQGELLAPDV DLPTHLGLHH HGEEAERAGY SLQELFHLTR SQVSQQRALA LHVLAQVISR
AQAGEFGDRL AGSVLSLLLD AGFLFLLRFS LDDRVDGVIA TAIRALRALL VAPGDEELLD
STFSWYHGAL TFPLMPSQED KEDEDEDEEC PAGKAKRKSP EEESRPPPDL ARHDVIKGLL
ATSLLPRLRY VLEVTYPGPA VVLDILAVLI RLARHSLESA TRVLECPRLI ETIVREFLPT
SWSPVGAGPT PSLYKVPCAT AMKLLRVLAS AGRNIAARLL SSFDLRSRLC RIIAEAPQEL
ALPPEEAEML STEALRLWAV AASYGQGGYL YRELYPVLMR ALQVVPRELS THPPQPLSMQ
RIASLLTLLT QLTLAAGSTP AETISDSAEA SLSATPSLVT WTQVSGLQPL VEPCLRQTLK
LLSRPEMWRA VGPVPVACLL FLGAYYQAWS QQPSSCPEDW LQDMQRLSEE LLLPLLSQPT
LGSLWDSLRH CSLLCNPLSC VPALEAPPSL VSLGCSGGCP RLSLAGSASP FPFLTALLSL
LNTLAQIHKG LCGQLAAILA APGLQNYFLQ CVAPGAAPHL TPFSAWALRH EYHLQYLALA
LAQKAAALQP LPATHAALYH GMALALLSRL LPGSEYLTHE LLLSCVFRLE FLPCLCPWSV
TQCLLKTTWP SFSSTSGPWL LVRSAHVGAP CSMLWLWLMS IASSSLRTHR AQMRSKLPAG
VCCRKHGCWQ MRVSGSTSCT ISFPIPRSQR ALSSILSCPL CVSTTSRD*

speed

0.79 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: 0.999999999995953 (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)

chr15:41827757T>AN/A show variant in all transcripts IGV

HGNC symbol

RPAP1

Ensembl transcript ID

ENST00000304330

Genbank transcript ID

NM_015540

UniProt peptide

Q9BWH6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.494A>T
cDNA.611A>T
g.8711A>T

AA changes

K165M Score: 95 explain score(s)

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

165

frameshift

known variant

Reference ID: rs2297382

database	homozygous (A/A)	heterozygous	allele carriers
1000G	135	442	577
ExAC	905	8423	9328

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.563	0.001
	-0.504	0
(flanking)	0.532	0.003

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

165

mutated

not conserved

165

Ptroglodytes

all identical

ENSPTRG00000006949

165

Mmulatta

all conserved

ENSMMUG00000008175

165

Fcatus

all conserved

ENSFCAG00000012619

165

Mmusculus

all conserved

ENSMUSG00000034032

165

Ggallus

not conserved

ENSGALG00000008624

164

EKP

SAECTQ

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000075072

181

Dmelanogaster

all identical

FBgn0052104

169

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000000054

168

SPQMLS

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

4182 / 4182

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

1394 / 1394

position of stopcodon in wt / mu cDNA

4299 / 4299

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

118 / 118

chromosome

strand

-1

last intron/exon boundary

4150

theoretical NMD boundary in CDS

3982

length of CDS

4182

coding sequence (CDS) position

494

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

611

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

8711

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

41827757

original gDNA sequence snippet

AAGGAGGATAGCTGAAGCCAAGGGCCCATCAGTTGGGGAAG

altered gDNA sequence snippet

AAGGAGGATAGCTGAAGCCATGGGCCCATCAGTTGGGGAAG

original cDNA sequence snippet

AAGGAGGATAGCTGAAGCCAAGGGCCCATCAGTTGGGGAAG

altered cDNA sequence snippet

AAGGAGGATAGCTGAAGCCATGGGCCCATCAGTTGGGGAAG

wildtype AA sequence

MLSRPKPGES EVDLLHFQSQ FLAAGAAPAV QLVKKGNRGG GDANSDRPPL QDHRDVVMLD
NLPDLPPALV PSPPKRARPS PGHCLPEDED PEERLRRHDQ HITAVLTKII ERDTSSVAVN
LPVPSGVAFP AVFLRSRDTQ GKSATSGKRS IFAQEIAARR IAEAKGPSVG EVVPNVGPPE
GAVTCETPTP RNQGCQLPGS SHSFQGPNLV TGKGLRDQEA EQEAQTIHEE NIARLQAMAP
EEILQEQQRL LAQLDPSLVA FLRSHSHTQE QTGETASEEQ RPGGPSANVT KEEPLMSAFA
SEPRKRDKLE PEAPALALPV TPQKEWLHMD TVELEKLHWT QDLPPVRRQQ TQERMQARFS
LQGELLAPDV DLPTHLGLHH HGEEAERAGY SLQELFHLTR SQVSQQRALA LHVLAQVISR
AQAGEFGDRL AGSVLSLLLD AGFLFLLRFS LDDRVDGVIA TAIRALRALL VAPGDEELLD
STFSWYHGAL TFPLMPSQED KEDEDEDEEC PAGKAKRKSP EEESRPPPDL ARHDVIKGLL
ATSLLPRLRY VLEVTYPGPA VVLDILAVLI RLARHSLESA TRVLECPRLI ETIVREFLPT
SWSPVGAGPT PSLYKVPCAT AMKLLRVLAS AGRNIAARLL SSFDLRSRLC RIIAEAPQEL
ALPPEEAEML STEALRLWAV AASYGQGGYL YRELYPVLMR ALQVVPRELS THPPQPLSMQ
RIASLLTLLT QLTLAAGSTP AETISDSAEA SLSATPSLVT WTQVSGLQPL VEPCLRQTLK
LLSRPEMWRA VGPVPVACLL FLGAYYQAWS QQPSSCPEDW LQDMQRLSEE LLLPLLSQPT
LGSLWDSLRH CSLLCNPLSC VPALEAPPSL VSLGCSGGCP RLSLAGSASP FPFLTALLSL
LNTLAQIHKG LCGQLAAILA APGLQNYFLQ CVAPGAAPHL TPFSAWALRH EYHLQYLALA
LAQKAAALQP LPATHAALYH GMALALLSRL LPGSEYLTHE LLLSCVFRLE FLPERTSGGP
EAADFSDQLS LGSSRVPRCG QGTLLAQACQ DLPSIRNCYL THCSPARASL LASQALHRGE
LQRVPTLLLP MPTEPLLPTD WPFLPLIRLY HRASDTPSGL SPTDTMGTAM RVLQWVLVLE
SWRPQALWAV PPAARLARLM CVFLVDSELF RESPVQHLVA ALLAQLCQPQ VLPNLNLDCR
LPGLTSFPDL YANFLDHFEA VSFGDHLFGA LVLLPLQRRF SVTLRLALFG EHVGALRALS
LPLTQLPVSL ECYTVPPEDN LALLQLYFRT LVTGALRPRW CPVLYAVAVA HVNSFIFSQD
PQSSDEVKAA RRSMLQKTWL LADEGLRQHL LHYKLPNSTL PEGFELYSQL PPLRQHYLQR
LTSTVLQNGV SET*

mutated AA sequence

MLSRPKPGES EVDLLHFQSQ FLAAGAAPAV QLVKKGNRGG GDANSDRPPL QDHRDVVMLD
NLPDLPPALV PSPPKRARPS PGHCLPEDED PEERLRRHDQ HITAVLTKII ERDTSSVAVN
LPVPSGVAFP AVFLRSRDTQ GKSATSGKRS IFAQEIAARR IAEAMGPSVG EVVPNVGPPE
GAVTCETPTP RNQGCQLPGS SHSFQGPNLV TGKGLRDQEA EQEAQTIHEE NIARLQAMAP
EEILQEQQRL LAQLDPSLVA FLRSHSHTQE QTGETASEEQ RPGGPSANVT KEEPLMSAFA
SEPRKRDKLE PEAPALALPV TPQKEWLHMD TVELEKLHWT QDLPPVRRQQ TQERMQARFS
LQGELLAPDV DLPTHLGLHH HGEEAERAGY SLQELFHLTR SQVSQQRALA LHVLAQVISR
AQAGEFGDRL AGSVLSLLLD AGFLFLLRFS LDDRVDGVIA TAIRALRALL VAPGDEELLD
STFSWYHGAL TFPLMPSQED KEDEDEDEEC PAGKAKRKSP EEESRPPPDL ARHDVIKGLL
ATSLLPRLRY VLEVTYPGPA VVLDILAVLI RLARHSLESA TRVLECPRLI ETIVREFLPT
SWSPVGAGPT PSLYKVPCAT AMKLLRVLAS AGRNIAARLL SSFDLRSRLC RIIAEAPQEL
ALPPEEAEML STEALRLWAV AASYGQGGYL YRELYPVLMR ALQVVPRELS THPPQPLSMQ
RIASLLTLLT QLTLAAGSTP AETISDSAEA SLSATPSLVT WTQVSGLQPL VEPCLRQTLK
LLSRPEMWRA VGPVPVACLL FLGAYYQAWS QQPSSCPEDW LQDMQRLSEE LLLPLLSQPT
LGSLWDSLRH CSLLCNPLSC VPALEAPPSL VSLGCSGGCP RLSLAGSASP FPFLTALLSL
LNTLAQIHKG LCGQLAAILA APGLQNYFLQ CVAPGAAPHL TPFSAWALRH EYHLQYLALA
LAQKAAALQP LPATHAALYH GMALALLSRL LPGSEYLTHE LLLSCVFRLE FLPERTSGGP
EAADFSDQLS LGSSRVPRCG QGTLLAQACQ DLPSIRNCYL THCSPARASL LASQALHRGE
LQRVPTLLLP MPTEPLLPTD WPFLPLIRLY HRASDTPSGL SPTDTMGTAM RVLQWVLVLE
SWRPQALWAV PPAARLARLM CVFLVDSELF RESPVQHLVA ALLAQLCQPQ VLPNLNLDCR
LPGLTSFPDL YANFLDHFEA VSFGDHLFGA LVLLPLQRRF SVTLRLALFG EHVGALRALS
LPLTQLPVSL ECYTVPPEDN LALLQLYFRT LVTGALRPRW CPVLYAVAVA HVNSFIFSQD
PQSSDEVKAA RRSMLQKTWL LADEGLRQHL LHYKLPNSTL PEGFELYSQL PPLRQHYLQR
LTSTVLQNGV SET*

speed

0.76 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems