MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000287598
Querying Taster for transcript #2: ENST00000412359
MT speed 0 s - this script 2.643359 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
BUB1B	disease_causing	0.999530189733954	simple_aae		affected		L844F	single base exchange	rs28989181		show file
BUB1B	disease_causing	0.999530189733954	simple_aae		affected		L858F	single base exchange	rs28989181		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999530189733954 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM042945)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr15:40504844C>TN/A show variant in all transcripts IGV

HGNC symbol

BUB1B

Ensembl transcript ID

ENST00000287598

Genbank transcript ID

NM_001211

UniProt peptide

O60566

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2530C>T
cDNA.2725C>T
g.51621C>T

AA changes

L844F Score: 22 explain score(s)

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

844

frameshift

known variant

Reference ID: rs28989181

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

known disease mutation at this position, please check HGMD for details (HGMD ID CM042945)

known disease mutation at this position, please check HGMD for details (HGMD ID CM042945)
known disease mutation at this position, please check HGMD for details (HGMD ID CM042945)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.404	0.947
	1.515	0.993
(flanking)	3.386	0.997

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

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Acc marginally increased	51626	wt: 0.9268 / mu: 0.9513 (marginal change - not scored)	wt: ATAAACTGCTTCACCCTTCAGGTCTGTAATACTAAAAACAT mu: ATAAACTGCTTCACCTTTCAGGTCTGTAATACTAAAAACAT	tcag\|GTCT
Acc increased	51624	wt: 0.28 / mu: 0.41	wt: ATATAAACTGCTTCACCCTTCAGGTCTGTAATACTAAAAAC mu: ATATAAACTGCTTCACCTTTCAGGTCTGTAATACTAAAAAC	cttc\|AGGT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

844

mutated

not conserved

844

Ptroglodytes

all identical

ENSPTRG00000006913

844

Mmulatta

all identical

ENSMMUG00000016686

842

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000040084

833

Ggallus

all identical

ENSGALG00000004838

880

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000074927

n/a

Dmelanogaster

all identical

FBgn0025458

1251

NSSV

SDYGS

Celegans

all identical

R06C7.8

767

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
766	1050	DOMAIN	Protein kinase.	lost
882	882	ACT_SITE	Proton acceptor (By similarity).	might get lost (downstream of altered splice site)
1008	1008	MOD_RES	Phosphothreonine; by PLK1.	might get lost (downstream of altered splice site)
1018	1018	CONFLICT	E -> K (in Ref. 3; AAC33435).	might get lost (downstream of altered splice site)
1043	1043	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3153 / 3153

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

1051 / 1051

position of stopcodon in wt / mu cDNA

3348 / 3348

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

196 / 196

chromosome

strand

last intron/exon boundary

3153

theoretical NMD boundary in CDS

2907

length of CDS

3153

coding sequence (CDS) position

2530

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

2725

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

51621

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

40504844

original gDNA sequence snippet

AATATATAAACTGCTTCACCCTTCAGGTCTGTAATACTAAA

altered gDNA sequence snippet

AATATATAAACTGCTTCACCTTTCAGGTCTGTAATACTAAA

original cDNA sequence snippet

AATATATAAACTGCTTCACCCTTCAGGATCTTCTCCAACAC

altered cDNA sequence snippet

AATATATAAACTGCTTCACCTTTCAGGATCTTCTCCAACAC

wildtype AA sequence

MAAVKKEGGA LSEAMSLEGD EWELSKENVQ PLRQGRIMST LQGALAQESA CNNTLQQQKR
AFEYEIRFYT GNDPLDVWDR YISWTEQNYP QGGKESNMST LLERAVEALQ GEKRYYSDPR
FLNLWLKLGR LCNEPLDMYS YLHNQGIGVS LAQFYISWAE EYEARENFRK ADAIFQEGIQ
QKAEPLERLQ SQHRQFQARV SRQTLLALEK EEEEEVFESS VPQRSTLAEL KSKGKKTARA
PIIRVGGALK APSQNRGLQN PFPQQMQNNS RITVFDENAD EASTAELSKP TVQPWIAPPM
PRAKENELQA GPWNTGRSLE HRPRGNTASL IAVPAVLPSF TPYVEETARQ PVMTPCKIEP
SINHILSTRK PGKEEGDPLQ RVQSHQQASE EKKEKMMYCK EKIYAGVGEF SFEEIRAEVF
RKKLKEQREA ELLTSAEKRA EMQKQIEEME KKLKEIQTTQ QERTGDQQEE TMPTKETTKL
QIASESQKIP GMTLSSSVCQ VNCCARETSL AENIWQEQPH SKGPSVPFSI FDEFLLSEKK
NKSPPADPPR VLAQRRPLAV LKTSESITSN EDVSPDVCDE FTGIEPLSED AIITGFRNVT
ICPNPEDTCD FARAARFVST PFHEIMSLKD LPSDPERLLP EEDLDVKTSE DQQTACGTIY
SQTLSIKKLS PIIEDSREAT HSSGFSGSSA SVASTSSIKC LQIPEKLELT NETSENPTQS
PWCSQYRRQL LKSLPELSAS AELCIEDRPM PKLEIEKEIE LGNEDYCIKR EYLICEDYKL
FWVAPRNSAE LTVIKVSSQP VPWDFYINLK LKERLNEDFD HFCSCYQYQD GCIVWHQYIN
CFTLQDLLQH SEYITHEITV LIIYNLLTIV EMLHKAEIVH GDLSPRCLIL RNRIHDPYDC
NKNNQALKIV DFSYSVDLRV QLDVFTLSGF RTVQILEGQK ILANCSSPYQ VDLFGIADLA
HLLLFKEHLQ VFWDGSFWKL SQNISELKDG ELWNKFFVRI LNANDEATVS VLGELAAEMN
GVFDTTFQSH LNKALWKVGK LTSPGALLFQ *

mutated AA sequence

MAAVKKEGGA LSEAMSLEGD EWELSKENVQ PLRQGRIMST LQGALAQESA CNNTLQQQKR
AFEYEIRFYT GNDPLDVWDR YISWTEQNYP QGGKESNMST LLERAVEALQ GEKRYYSDPR
FLNLWLKLGR LCNEPLDMYS YLHNQGIGVS LAQFYISWAE EYEARENFRK ADAIFQEGIQ
QKAEPLERLQ SQHRQFQARV SRQTLLALEK EEEEEVFESS VPQRSTLAEL KSKGKKTARA
PIIRVGGALK APSQNRGLQN PFPQQMQNNS RITVFDENAD EASTAELSKP TVQPWIAPPM
PRAKENELQA GPWNTGRSLE HRPRGNTASL IAVPAVLPSF TPYVEETARQ PVMTPCKIEP
SINHILSTRK PGKEEGDPLQ RVQSHQQASE EKKEKMMYCK EKIYAGVGEF SFEEIRAEVF
RKKLKEQREA ELLTSAEKRA EMQKQIEEME KKLKEIQTTQ QERTGDQQEE TMPTKETTKL
QIASESQKIP GMTLSSSVCQ VNCCARETSL AENIWQEQPH SKGPSVPFSI FDEFLLSEKK
NKSPPADPPR VLAQRRPLAV LKTSESITSN EDVSPDVCDE FTGIEPLSED AIITGFRNVT
ICPNPEDTCD FARAARFVST PFHEIMSLKD LPSDPERLLP EEDLDVKTSE DQQTACGTIY
SQTLSIKKLS PIIEDSREAT HSSGFSGSSA SVASTSSIKC LQIPEKLELT NETSENPTQS
PWCSQYRRQL LKSLPELSAS AELCIEDRPM PKLEIEKEIE LGNEDYCIKR EYLICEDYKL
FWVAPRNSAE LTVIKVSSQP VPWDFYINLK LKERLNEDFD HFCSCYQYQD GCIVWHQYIN
CFTFQDLLQH SEYITHEITV LIIYNLLTIV EMLHKAEIVH GDLSPRCLIL RNRIHDPYDC
NKNNQALKIV DFSYSVDLRV QLDVFTLSGF RTVQILEGQK ILANCSSPYQ VDLFGIADLA
HLLLFKEHLQ VFWDGSFWKL SQNISELKDG ELWNKFFVRI LNANDEATVS VLGELAAEMN
GVFDTTFQSH LNKALWKVGK LTSPGALLFQ *

speed

0.31 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

disease causing

Model: simple_aae, prob: 0.999530189733954 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM042945)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr15:40504844C>TN/A show variant in all transcripts IGV

HGNC symbol

BUB1B

Ensembl transcript ID

ENST00000412359

Genbank transcript ID

N/A

UniProt peptide

O60566

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2572C>T
cDNA.2726C>T
g.51621C>T

AA changes

L858F Score: 22 explain score(s)

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

858

frameshift

known variant

Reference ID: rs28989181

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.404	0.947
	1.515	0.993
(flanking)	3.386	0.997

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

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Acc marginally increased	51626	wt: 0.9268 / mu: 0.9513 (marginal change - not scored)	wt: ATAAACTGCTTCACCCTTCAGGTCTGTAATACTAAAAACAT mu: ATAAACTGCTTCACCTTTCAGGTCTGTAATACTAAAAACAT	tcag\|GTCT
Acc increased	51624	wt: 0.28 / mu: 0.41	wt: ATATAAACTGCTTCACCCTTCAGGTCTGTAATACTAAAAAC mu: ATATAAACTGCTTCACCTTTCAGGTCTGTAATACTAAAAAC	cttc\|AGGT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

858

mutated

not conserved

858

Ptroglodytes

all identical

ENSPTRG00000006913

844

Mmulatta

all identical

ENSMMUG00000016686

842

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000040084

833

Ggallus

all identical

ENSGALG00000004838

884

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000074927

n/a

Dmelanogaster

all identical

FBgn0025458

1251

NSSV

SDYGS

Celegans

all identical

R06C7.8

767

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
766	1050	DOMAIN	Protein kinase.	lost
882	882	ACT_SITE	Proton acceptor (By similarity).	might get lost (downstream of altered splice site)
1008	1008	MOD_RES	Phosphothreonine; by PLK1.	might get lost (downstream of altered splice site)
1018	1018	CONFLICT	E -> K (in Ref. 3; AAC33435).	might get lost (downstream of altered splice site)
1043	1043	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3195 / 3195

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

1065 / 1065

position of stopcodon in wt / mu cDNA

3349 / 3349

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

155 / 155

chromosome

strand

last intron/exon boundary

3154

theoretical NMD boundary in CDS

2949

length of CDS

3195

coding sequence (CDS) position

2572

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

2726

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

51621

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

40504844

original gDNA sequence snippet

AATATATAAACTGCTTCACCCTTCAGGTCTGTAATACTAAA

altered gDNA sequence snippet

AATATATAAACTGCTTCACCTTTCAGGTCTGTAATACTAAA

original cDNA sequence snippet

AATATATAAACTGCTTCACCCTTCAGGATCTTCTCCAACAC

altered cDNA sequence snippet

AATATATAAACTGCTTCACCTTTCAGGATCTTCTCCAACAC

wildtype AA sequence

MAAVKKEGGA LSEAMSLEGD EWELSKENVQ PLRQGRIMST LQGALAQESA CNNTLQQQKR
AFEYEIRFYT GNDPLDVWDR WVFLFHKDNR NINRYISWTE QNYPQGGKES NMSTLLERAV
EALQGEKRYY SDPRFLNLWL KLGRLCNEPL DMYSYLHNQG IGVSLAQFYI SWAEEYEARE
NFRKADAIFQ EGIQQKAEPL ERLQSQHRQF QARVSRQTLL ALEKEEEEEV FESSVPQRST
LAELKSKGKK TARAPIIRVG GALKAPSQNR GLQNPFPQQM QNNSRITVFD ENADEASTAE
LSKPTVQPWI APPMPRAKEN ELQAGPWNTG RSLEHRPRGN TASLIAVPAV LPSFTPYVEE
TARQPVMTPC KIEPSINHIL STRKPGKEEG DPLQRVQSHQ QASEEKKEKM MYCKEKIYAG
VGEFSFEEIR AEVFRKKLKE QREAELLTSA EKRAEMQKQI EEMEKKLKEI QTTQQERTGD
QQEETMPTKE TTKLQIASES QKIPGMTLSS SVCQVNCCAR ETSLAENIWQ EQPHSKGPSV
PFSIFDEFLL SEKKNKSPPA DPPRVLAQRR PLAVLKTSES ITSNEDVSPD VCDEFTGIEP
LSEDAIITGF RNVTICPNPE DTCDFARAAR FVSTPFHEIM SLKDLPSDPE RLLPEEDLDV
KTSEDQQTAC GTIYSQTLSI KKLSPIIEDS REATHSSGFS GSSASVASTS SIKCLQIPEK
LELTNETSEN PTQSPWCSQY RRQLLKSLPE LSASAELCIE DRPMPKLEIE KEIELGNEDY
CIKREYLICE DYKLFWVAPR NSAELTVIKV SSQPVPWDFY INLKLKERLN EDFDHFCSCY
QYQDGCIVWH QYINCFTLQD LLQHSEYITH EITVLIIYNL LTIVEMLHKA EIVHGDLSPR
CLILRNRIHD PYDCNKNNQA LKIVDFSYSV DLRVQLDVFT LSGFRTVQIL EGQKILANCS
SPYQVDLFGI ADLAHLLLFK EHLQVFWDGS FWKLSQNISE LKDGELWNKF FVRILNANDE
ATVSVLGELA AEMNGVFDTT FQSHLNKALW KVGKLTSPGA LLFQ*

mutated AA sequence

MAAVKKEGGA LSEAMSLEGD EWELSKENVQ PLRQGRIMST LQGALAQESA CNNTLQQQKR
AFEYEIRFYT GNDPLDVWDR WVFLFHKDNR NINRYISWTE QNYPQGGKES NMSTLLERAV
EALQGEKRYY SDPRFLNLWL KLGRLCNEPL DMYSYLHNQG IGVSLAQFYI SWAEEYEARE
NFRKADAIFQ EGIQQKAEPL ERLQSQHRQF QARVSRQTLL ALEKEEEEEV FESSVPQRST
LAELKSKGKK TARAPIIRVG GALKAPSQNR GLQNPFPQQM QNNSRITVFD ENADEASTAE
LSKPTVQPWI APPMPRAKEN ELQAGPWNTG RSLEHRPRGN TASLIAVPAV LPSFTPYVEE
TARQPVMTPC KIEPSINHIL STRKPGKEEG DPLQRVQSHQ QASEEKKEKM MYCKEKIYAG
VGEFSFEEIR AEVFRKKLKE QREAELLTSA EKRAEMQKQI EEMEKKLKEI QTTQQERTGD
QQEETMPTKE TTKLQIASES QKIPGMTLSS SVCQVNCCAR ETSLAENIWQ EQPHSKGPSV
PFSIFDEFLL SEKKNKSPPA DPPRVLAQRR PLAVLKTSES ITSNEDVSPD VCDEFTGIEP
LSEDAIITGF RNVTICPNPE DTCDFARAAR FVSTPFHEIM SLKDLPSDPE RLLPEEDLDV
KTSEDQQTAC GTIYSQTLSI KKLSPIIEDS REATHSSGFS GSSASVASTS SIKCLQIPEK
LELTNETSEN PTQSPWCSQY RRQLLKSLPE LSASAELCIE DRPMPKLEIE KEIELGNEDY
CIKREYLICE DYKLFWVAPR NSAELTVIKV SSQPVPWDFY INLKLKERLN EDFDHFCSCY
QYQDGCIVWH QYINCFTFQD LLQHSEYITH EITVLIIYNL LTIVEMLHKA EIVHGDLSPR
CLILRNRIHD PYDCNKNNQA LKIVDFSYSV DLRVQLDVFT LSGFRTVQIL EGQKILANCS
SPYQVDLFGI ADLAHLLLFK EHLQVFWDGS FWKLSQNISE LKDGELWNKF FVRILNANDE
ATVSVLGELA AEMNGVFDTT FQSHLNKALW KVGKLTSPGA LLFQ*

speed

0.34 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems