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 4 transcript(s)...
Querying Taster for transcript #1: ENST00000287598
Querying Taster for transcript #2: ENST00000412359
Querying Taster for transcript #3: ENST00000441369
Querying Taster for transcript #4: ENST00000453867
MT speed 0 s - this script 3.155382 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
BUB1B	disease_causing	0.999999990325385	simple_aae		affected		L1012P	single base exchange	rs28989185		show file
BUB1B	disease_causing	0.999999990325385	simple_aae		affected		L1026P	single base exchange	rs28989185		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999990325385 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM042948)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr15:40512842T>CN/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.3035T>C
cDNA.3230T>C
g.59619T>C

AA changes

L1012P Score: 98 explain score(s)

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

1012

frameshift

known variant

Reference ID: rs28989185

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

known disease mutation at this position, please check HGMD for details (HGMD ID CM042948)

known disease mutation at this position, please check HGMD for details (HGMD ID CM042948)
known disease mutation at this position, please check HGMD for details (HGMD ID CM042948)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.513	1
	3.409	1
(flanking)	0.584	0.996

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 increased	59620	wt: 0.86 / mu: 0.97	wt: GTTCTTGGGGAGCTT mu: GTTCCTGGGGAGCTT	TCTT\|gggg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1012

mutated

not conserved

1012

Ptroglodytes

all identical

ENSPTRG00000006913

1012

Mmulatta

all identical

ENSMMUG00000016686

1010

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000040084

1002

Ggallus

all identical

ENSGALG00000004838

1052

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000074927

n/a

Dmelanogaster

all identical

FBgn0025458

1429

Celegans

no alignment

R06C7.8

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
766	1050	DOMAIN	Protein kinase.	lost
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

3035

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

3230

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

59619

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

40512842

original gDNA sequence snippet

TGAGGCCACAGTGTCTGTTCTTGGGGAGCTTGCAGCAGAAA

altered gDNA sequence snippet

TGAGGCCACAGTGTCTGTTCCTGGGGAGCTTGCAGCAGAAA

original cDNA sequence snippet

TGAGGCCACAGTGTCTGTTCTTGGGGAGCTTGCAGCAGAAA

altered cDNA sequence snippet

TGAGGCCACAGTGTCTGTTCCTGGGGAGCTTGCAGCAGAAA

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

speed

0.22 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: 0.999999990325385 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM042948)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr15:40512842T>CN/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.3077T>C
cDNA.3231T>C
g.59619T>C

AA changes

L1026P Score: 98 explain score(s)

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

1026

frameshift

known variant

Reference ID: rs28989185

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.513	1
	3.409	1
(flanking)	0.584	0.996

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 increased	59620	wt: 0.86 / mu: 0.97	wt: GTTCTTGGGGAGCTT mu: GTTCCTGGGGAGCTT	TCTT\|gggg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1026

mutated

not conserved

1026

Ptroglodytes

all identical

ENSPTRG00000006913

1012

Mmulatta

all identical

ENSMMUG00000016686

1010

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000040084

1002

Ggallus

all identical

ENSGALG00000004838

1052

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000074927

n/a

Dmelanogaster

all identical

FBgn0025458

1429

Celegans

no alignment

R06C7.8

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
766	1050	DOMAIN	Protein kinase.	lost
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

3077

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

3231

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

59619

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

40512842

original gDNA sequence snippet

TGAGGCCACAGTGTCTGTTCTTGGGGAGCTTGCAGCAGAAA

altered gDNA sequence snippet

TGAGGCCACAGTGTCTGTTCCTGGGGAGCTTGCAGCAGAAA

original cDNA sequence snippet

TGAGGCCACAGTGTCTGTTCTTGGGGAGCTTGCAGCAGAAA

altered cDNA sequence snippet

TGAGGCCACAGTGTCTGTTCCTGGGGAGCTTGCAGCAGAAA

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

speed

1.15 s

Problems

data problem

Too many NCBI gene IDs found
56924
106821730

back to results table

data problem

Too many NCBI gene IDs found
56924
106821730

back to results table