MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000272286
MT speed 0.59 s - this script 2.648333 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ABCG8	disease_causing_automatic	0.999995514468789	simple_aae		affected	0	L596R	single base exchange	rs137852992		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999995514468789 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM003585)
known disease mutation: rs4973 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:44104730T>GN/A show variant in all transcripts IGV

HGNC symbol

ABCG8

Ensembl transcript ID

ENST00000272286

Genbank transcript ID

NM_022437

UniProt peptide

Q9H221

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1787T>G
cDNA.1877T>G
g.38628T>G

AA changes

L596R Score: 102 explain score(s)

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

596

frameshift

known variant

Reference ID: rs137852992
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs4973 (pathogenic for Sitosterolemia 1) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM003585)

known disease mutation at this position, please check HGMD for details (HGMD ID CM003585)
known disease mutation at this position, please check HGMD for details (HGMD ID CM003585)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.075	1
	4.515	1
(flanking)	0.484	1

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	38628	wt: 0.29 / mu: 0.44	wt: CTTCCTGCGGTGGTG mu: CTTCCGGCGGTGGTG	TCCT\|gcgg
Acc gained	38627	0.62	mu: GGATTTCCAAAGTGTCCTTCCGGCGGTGGTGTTTTGAAGGG	ttcc\|GGCG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

596

mutated

not conserved

596

Ptroglodytes

all identical

ENSPTRG00000011879

596

Mmulatta

all identical

ENSMMUG00000008081

596

Fcatus

all identical

ENSFCAG00000013467

595

Mmusculus

all identical

ENSMUSG00000024254

596

Ggallus

all identical

ENSGALG00000009958

566

Trubripes

all conserved

ENSTRUG00000009126

569

Drerio

all conserved

ENSDARG00000063059

575

Dmelanogaster

not conserved

FBgn0051121

805

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000009293

582

protein features

start (aa)	end (aa)	feature	details
411	665	DOMAIN	ABC transmembrane type-2.	lost
591	639	TOPO_DOM	Extracellular (Potential).	lost
619	619	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
640	660	TRANSMEM	Helical; Name=6; (Potential).	might get lost (downstream of altered splice site)
661	673	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2022 / 2022

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

674 / 674

position of stopcodon in wt / mu cDNA

2112 / 2112

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

91 / 91

chromosome

strand

last intron/exon boundary

1975

theoretical NMD boundary in CDS

1834

length of CDS

2022

coding sequence (CDS) position

1787

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

1877

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

38628

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

44104730

original gDNA sequence snippet

GATTTCCAAAGTGTCCTTCCTGCGGTGGTGTTTTGAAGGGC

altered gDNA sequence snippet

GATTTCCAAAGTGTCCTTCCGGCGGTGGTGTTTTGAAGGGC

original cDNA sequence snippet

GATTTCCAAAGTGTCCTTCCTGCGGTGGTGTTTTGAAGGGC

altered cDNA sequence snippet

GATTTCCAAAGTGTCCTTCCGGCGGTGGTGTTTTGAAGGGC

wildtype AA sequence

MAGKAAEERG LPKGATPQDT SGLQDRLFSS ESDNSLYFTY SGQPNTLEVR DLNYQVDLAS
QVPWFEQLAQ FKMPWTSPSC QNSCELGIQN LSFKVRSGQM LAIIGSSGCG RASLLDVITG
RGHGGKIKSG QIWINGQPSS PQLVRKCVAH VRQHNQLLPN LTVRETLAFI AQMRLPRTFS
QAQRDKRVED VIAELRLRQC ADTRVGNMYV RGLSGGERRR VSIGVQLLWN PGILILDEPT
SGLDSFTAHN LVKTLSRLAK GNRLVLISLH QPRSDIFRLF DLVLLMTSGT PIYLGAAQHM
VQYFTAIGYP CPRYSNPADF YVDLTSIDRR SREQELATRE KAQSLAALFL EKVRDLDDFL
WKAETKDLDE DTCVESSVTP LDTNCLPSPT KMPGAVQQFT TLIRRQISND FRDLPTLLIH
GAEACLMSMT IGFLYFGHGS IQLSFMDTAA LLFMIGALIP FNVILDVISK CYSERAMLYY
ELEDGLYTTG PYFFAKILGE LPEHCAYIII YGMPTYWLAN LRPGLQPFLL HFLLVWLVVF
CCRIMALAAA ALLPTFHMAS FFSNALYNSF YLAGGFMINL SSLWTVPAWI SKVSFLRWCF
EGLMKIQFSR RTYKMPLGNL TIAVSGDKIL SVMELDSYPL YAIYLIVIGL SGGFMVLYYV
SLRFIKQKPS QDW*

mutated AA sequence

MAGKAAEERG LPKGATPQDT SGLQDRLFSS ESDNSLYFTY SGQPNTLEVR DLNYQVDLAS
QVPWFEQLAQ FKMPWTSPSC QNSCELGIQN LSFKVRSGQM LAIIGSSGCG RASLLDVITG
RGHGGKIKSG QIWINGQPSS PQLVRKCVAH VRQHNQLLPN LTVRETLAFI AQMRLPRTFS
QAQRDKRVED VIAELRLRQC ADTRVGNMYV RGLSGGERRR VSIGVQLLWN PGILILDEPT
SGLDSFTAHN LVKTLSRLAK GNRLVLISLH QPRSDIFRLF DLVLLMTSGT PIYLGAAQHM
VQYFTAIGYP CPRYSNPADF YVDLTSIDRR SREQELATRE KAQSLAALFL EKVRDLDDFL
WKAETKDLDE DTCVESSVTP LDTNCLPSPT KMPGAVQQFT TLIRRQISND FRDLPTLLIH
GAEACLMSMT IGFLYFGHGS IQLSFMDTAA LLFMIGALIP FNVILDVISK CYSERAMLYY
ELEDGLYTTG PYFFAKILGE LPEHCAYIII YGMPTYWLAN LRPGLQPFLL HFLLVWLVVF
CCRIMALAAA ALLPTFHMAS FFSNALYNSF YLAGGFMINL SSLWTVPAWI SKVSFRRWCF
EGLMKIQFSR RTYKMPLGNL TIAVSGDKIL SVMELDSYPL YAIYLIVIGL SGGFMVLYYV
SLRFIKQKPS QDW*

speed

0.59 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