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 1 transcript(s)...
Querying Taster for transcript #1: ENST00000263817
MT speed 0 s - this script 2.820066 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ABCB11	disease_causing_automatic	0.999999999886653	simple_aae		affected	0	R432T	single base exchange	rs121908935		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999886653 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM056278)
known disease mutation: rs6595 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:169833100C>GN/A show variant in all transcripts IGV

HGNC symbol

ABCB11

Ensembl transcript ID

ENST00000263817

Genbank transcript ID

NM_003742

UniProt peptide

O95342

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1295G>C
cDNA.1420G>C
g.54733G>C

AA changes

R432T Score: 71 explain score(s)

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

432

frameshift

known variant

Reference ID: rs121908935
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs6595 (pathogenic for Benign recurrent intrahepatic cholestasis type 2) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM056278)

known disease mutation at this position, please check HGMD for details (HGMD ID CM056278)
known disease mutation at this position, please check HGMD for details (HGMD ID CM056278)

regulatory features

H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
PolII, Polymerase, RNA Polymerase II
Gata2, Transcription Factor, Gata2 Transcription Factor Binding
Jund, Transcription Factor, Jund TF binding
Cjun, Transcription Factor, Cjun TF binding
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.077	0.994
	6.189	1
(flanking)	1.823	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
Acc marginally increased	54724	wt: 0.7081 / mu: 0.7269 (marginal change - not scored)	wt: CCATAATGTGACCTTCCATTATCCTTCCAGACCAGAGGTGA mu: CCATAATGTGACCTTCCATTATCCTTCCACACCAGAGGTGA	atta\|TCCT
Acc marginally increased	54734	wt: 0.4398 / mu: 0.4676 (marginal change - not scored)	wt: ACCTTCCATTATCCTTCCAGACCAGAGGTGAAGGTGAGTGC mu: ACCTTCCATTATCCTTCCACACCAGAGGTGAAGGTGAGTGC	caga\|CCAG
Acc increased	54730	wt: 0.71 / mu: 0.83	wt: TGTGACCTTCCATTATCCTTCCAGACCAGAGGTGAAGGTGA mu: TGTGACCTTCCATTATCCTTCCACACCAGAGGTGAAGGTGA	cttc\|CAGA
Acc increased	54731	wt: 0.54 / mu: 0.63	wt: GTGACCTTCCATTATCCTTCCAGACCAGAGGTGAAGGTGAG mu: GTGACCTTCCATTATCCTTCCACACCAGAGGTGAAGGTGAG	ttcc\|AGAC
Acc increased	54737	wt: 0.67 / mu: 0.95	wt: TTCCATTATCCTTCCAGACCAGAGGTGAAGGTGAGTGCTGG mu: TTCCATTATCCTTCCACACCAGAGGTGAAGGTGAGTGCTGG	acca\|GAGG
Acc marginally increased	54727	wt: 0.9029 / mu: 0.9139 (marginal change - not scored)	wt: TAATGTGACCTTCCATTATCCTTCCAGACCAGAGGTGAAGG mu: TAATGTGACCTTCCATTATCCTTCCACACCAGAGGTGAAGG	atcc\|TTCC
Acc marginally increased	54733	wt: 0.9724 / mu: 0.9778 (marginal change - not scored)	wt: GACCTTCCATTATCCTTCCAGACCAGAGGTGAAGGTGAGTG mu: GACCTTCCATTATCCTTCCACACCAGAGGTGAAGGTGAGTG	ccag\|ACCA
Acc marginally increased	54728	wt: 0.3184 / mu: 0.3450 (marginal change - not scored)	wt: AATGTGACCTTCCATTATCCTTCCAGACCAGAGGTGAAGGT mu: AATGTGACCTTCCATTATCCTTCCACACCAGAGGTGAAGGT	tcct\|TCCA
Donor marginally increased	54734	wt: 0.9328 / mu: 0.9471 (marginal change - not scored)	wt: TCCAGACCAGAGGTG mu: TCCACACCAGAGGTG	CAGA\|ccag
Donor marginally increased	54737	wt: 0.9849 / mu: 0.9857 (marginal change - not scored)	wt: AGACCAGAGGTGAAG mu: ACACCAGAGGTGAAG	ACCA\|gagg
Donor marginally increased	54735	wt: 0.6686 / mu: 0.6734 (marginal change - not scored)	wt: CCAGACCAGAGGTGA mu: CCACACCAGAGGTGA	AGAC\|caga
Acc gained	54735	0.82	mu: CCTTCCATTATCCTTCCACACCAGAGGTGAAGGTGAGTGCT	acac\|CAGA

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

432

mutated

not conserved

432

Ptroglodytes

all identical

ENSPTRG00000012609

432

Mmulatta

no homologue

Fcatus

no alignment

ENSFCAG00000006114

n/a

Mmusculus

all identical

ENSMUSG00000027048

432

Ggallus

all identical

ENSGALG00000010891

433

Trubripes

all identical

ENSTRUG00000010768

459

Drerio

all identical

ENSDARG00000070078

447

Dmelanogaster

all identical

FBgn0010241

443

Celegans

all identical

C34G6.4

411

Xtropicalis

all identical

ENSXETG00000016210

397

protein features

start (aa)	end (aa)	feature	details
375	755	TOPO_DOM	Cytoplasmic (Potential).	lost
420	656	DOMAIN	ABC transporter 1.	lost
455	462	NP_BIND	ATP 1 (Potential).	might get lost (downstream of altered splice site)
651	672	REGION	Interaction with HAX1 (By similarity).	might get lost (downstream of altered splice site)
690	690	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
694	694	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
701	701	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
755	1043	DOMAIN	ABC transmembrane type-1 2.	might get lost (downstream of altered splice site)
756	776	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
777	794	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
795	815	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
816	869	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
870	890	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
891	911	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
912	979	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
980	1000	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1001	1011	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
1012	1032	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1033	1321	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1078	1316	DOMAIN	ABC transporter 2.	might get lost (downstream of altered splice site)
1113	1120	NP_BIND	ATP 2 (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3966 / 3966

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

1322 / 1322

position of stopcodon in wt / mu cDNA

4091 / 4091

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

126 / 126

chromosome

strand

-1

last intron/exon boundary

3891

theoretical NMD boundary in CDS

3715

length of CDS

3966

coding sequence (CDS) position

1295

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

1420

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

54733

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

169833100

original gDNA sequence snippet

GACCTTCCATTATCCTTCCAGACCAGAGGTGAAGGTGAGTG

altered gDNA sequence snippet

GACCTTCCATTATCCTTCCACACCAGAGGTGAAGGTGAGTG

original cDNA sequence snippet

GACCTTCCATTATCCTTCCAGACCAGAGGTGAAGATTCTAA

altered cDNA sequence snippet

GACCTTCCATTATCCTTCCACACCAGAGGTGAAGATTCTAA

wildtype AA sequence

MSDSVILRSI KKFGEENDGF ESDKSYNNDK KSRLQDEKKG DGVRVGFFQL FRFSSSTDIW
LMFVGSLCAF LHGIAQPGVL LIFGTMTDVF IDYDVELQEL QIPGKACVNN TIVWTNSSLN
QNMTNGTRCG LLNIESEMIK FASYYAGIAV AVLITGYIQI CFWVIAAARQ IQKMRKFYFR
RIMRMEIGWF DCNSVGELNT RFSDDINKIN DAIADQMALF IQRMTSTICG FLLGFFRGWK
LTLVIISVSP LIGIGAATIG LSVSKFTDYE LKAYAKAGVV ADEVISSMRT VAAFGGEKRE
VERYEKNLVF AQRWGIRKGI VMGFFTGFVW CLIFLCYALA FWYGSTLVLD EGEYTPGTLV
QIFLSVIVGA LNLGNASPCL EAFATGRAAA TSIFETIDRK PIIDCMSEDG YKLDRIKGEI
EFHNVTFHYP SRPEVKILND LNMVIKPGEM TALVGPSGAG KSTALQLIQR FYDPCEGMVT
VDGHDIRSLN IQWLRDQIGI VEQEPVLFST TIAENIRYGR EDATMEDIVQ AAKEANAYNF
IMDLPQQFDT LVGEGGGQMS GGQKQRVAIA RALIRNPKIL LLDMATSALD NESEAMVQEV
LSKIQHGHTI ISVAHRLSTV RAADTIIGFE HGTAVERGTH EELLERKGVY FTLVTLQSQG
NQALNEEDIK DATEDDMLAR TFSRGSYQDS LRASIRQRSK SQLSYLVHEP PLAVVDHKST
YEEDRKDKDI PVQEEVEPAP VRRILKFSAP EWPYMLVGSV GAAVNGTVTP LYAFLFSQIL
GTFSIPDKEE QRSQINGVCL LFVAMGCVSL FTQFLQGYAF AKSGELLTKR LRKFGFRAML
GQDIAWFDDL RNSPGALTTR LATDASQVQG AAGSQIGMIV NSFTNVTVAM IIAFSFSWKL
SLVILCFFPF LALSGATQTR MLTGFASRDK QALEMVGQIT NEALSNIRTV AGIGKERRFI
EALETELEKP FKTAIQKANI YGFCFAFAQC IMFIANSASY RYGGYLISNE GLHFSYVFRV
ISAVVLSATA LGRAFSYTPS YAKAKISAAR FFQLLDRQPP ISVYNTAGEK WDNFQGKIDF
VDCKFTYPSR PDSQVLNGLS VSISPGQTLA FVGSSGCGKS TSIQLLERFY DPDQGKVMID
GHDSKKVNVQ FLRSNIGIVS QEPVLFACSI MDNIKYGDNT KEIPMERVIA AAKQAQLHDF
VMSLPEKYET NVGSQGSQLS RGEKQRIAIA RAIVRDPKIL LLDEATSALD TESEKTVQVA
LDKAREGRTC IVIAHRLSTI QNADIIAVMA QGVVIEKGTH EELMAQKGAY YKLVTTGSPI
S*

mutated AA sequence

MSDSVILRSI KKFGEENDGF ESDKSYNNDK KSRLQDEKKG DGVRVGFFQL FRFSSSTDIW
LMFVGSLCAF LHGIAQPGVL LIFGTMTDVF IDYDVELQEL QIPGKACVNN TIVWTNSSLN
QNMTNGTRCG LLNIESEMIK FASYYAGIAV AVLITGYIQI CFWVIAAARQ IQKMRKFYFR
RIMRMEIGWF DCNSVGELNT RFSDDINKIN DAIADQMALF IQRMTSTICG FLLGFFRGWK
LTLVIISVSP LIGIGAATIG LSVSKFTDYE LKAYAKAGVV ADEVISSMRT VAAFGGEKRE
VERYEKNLVF AQRWGIRKGI VMGFFTGFVW CLIFLCYALA FWYGSTLVLD EGEYTPGTLV
QIFLSVIVGA LNLGNASPCL EAFATGRAAA TSIFETIDRK PIIDCMSEDG YKLDRIKGEI
EFHNVTFHYP STPEVKILND LNMVIKPGEM TALVGPSGAG KSTALQLIQR FYDPCEGMVT
VDGHDIRSLN IQWLRDQIGI VEQEPVLFST TIAENIRYGR EDATMEDIVQ AAKEANAYNF
IMDLPQQFDT LVGEGGGQMS GGQKQRVAIA RALIRNPKIL LLDMATSALD NESEAMVQEV
LSKIQHGHTI ISVAHRLSTV RAADTIIGFE HGTAVERGTH EELLERKGVY FTLVTLQSQG
NQALNEEDIK DATEDDMLAR TFSRGSYQDS LRASIRQRSK SQLSYLVHEP PLAVVDHKST
YEEDRKDKDI PVQEEVEPAP VRRILKFSAP EWPYMLVGSV GAAVNGTVTP LYAFLFSQIL
GTFSIPDKEE QRSQINGVCL LFVAMGCVSL FTQFLQGYAF AKSGELLTKR LRKFGFRAML
GQDIAWFDDL RNSPGALTTR LATDASQVQG AAGSQIGMIV NSFTNVTVAM IIAFSFSWKL
SLVILCFFPF LALSGATQTR MLTGFASRDK QALEMVGQIT NEALSNIRTV AGIGKERRFI
EALETELEKP FKTAIQKANI YGFCFAFAQC IMFIANSASY RYGGYLISNE GLHFSYVFRV
ISAVVLSATA LGRAFSYTPS YAKAKISAAR FFQLLDRQPP ISVYNTAGEK WDNFQGKIDF
VDCKFTYPSR PDSQVLNGLS VSISPGQTLA FVGSSGCGKS TSIQLLERFY DPDQGKVMID
GHDSKKVNVQ FLRSNIGIVS QEPVLFACSI MDNIKYGDNT KEIPMERVIA AAKQAQLHDF
VMSLPEKYET NVGSQGSQLS RGEKQRIAIA RAIVRDPKIL LLDEATSALD TESEKTVQVA
LDKAREGRTC IVIAHRLSTI QNADIIAVMA QGVVIEKGTH EELMAQKGAY YKLVTTGSPI
S*

speed

0.70 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

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

Problems