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 3.108368 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ABCB11	disease_causing_automatic	0.999999999858434	simple_aae			0	E297G	single base exchange	rs11568372		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999858434 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM980245)
known disease mutation: rs6590 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:169847329T>CN/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.890A>G
cDNA.1015A>G
g.40504A>G

AA changes

E297G Score: 98 explain score(s)

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

297

frameshift

known variant

Reference ID: rs11568372

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	37	37

known disease mutation: rs6590 (pathogenic for Progressive familial intrahepatic cholestasis 2|Benign recurrent intrahepatic cholestasis type 2|Cholestasis, intrahepatic, of pregnancy 3|Progressive familial intrahepatic cholestasis|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980245)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980245)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980245)

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.763	0.924
	5.108	1
(flanking)	6.186	1

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

297

mutated

not conserved

297

Ptroglodytes

all identical

ENSPTRG00000012609

297

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000006114

283

Mmusculus

all identical

ENSMUSG00000027048

297

Ggallus

all identical

ENSGALG00000010891

298

Trubripes

all identical

ENSTRUG00000010768

324

Drerio

all identical

ENSDARG00000070078

312

Dmelanogaster

all identical

FBgn0010241

302

Celegans

not conserved

C34G6.4

276

Xtropicalis

all identical

ENSXETG00000016210

262

protein features

start (aa)	end (aa)	feature	details
62	385	DOMAIN	ABC transmembrane type-1 1.	lost
262	319	TOPO_DOM	Cytoplasmic (Potential).	lost

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

890

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

1015

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

40504

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

169847329

original gDNA sequence snippet

AGTGGCTGCTTTTGGTGGTGAGAAAAGAGAGGTTGAAAGGT

altered gDNA sequence snippet

AGTGGCTGCTTTTGGTGGTGGGAAAAGAGAGGTTGAAAGGT

original cDNA sequence snippet

AGTGGCTGCTTTTGGTGGTGAGAAAAGAGAGGTTGAAAGGT

altered cDNA sequence snippet

AGTGGCTGCTTTTGGTGGTGGGAAAAGAGAGGTTGAAAGGT

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 VAAFGGGKRE
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*

speed

1.09 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