mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.99999999927981 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM0911238)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:74883577G>AN/A show variant in all transcripts IGV

HGNC symbol

SLCO2B1

Ensembl transcript ID

ENST00000341411

Genbank transcript ID

N/A

UniProt peptide

O94956

alteration type

single base exchange

alteration region

CDS

DNA changes

c.254G>A
cDNA.989G>A
g.71970G>A

AA changes

R85Q Score: 43 explain score(s)

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

frameshift

known variant

Reference ID: rs12422149

database	homozygous (A/A)	heterozygous	allele carriers
1000G	160	731	891
ExAC	2692	15639	18331

known disease mutation at this position, please check HGMD for details (HGMD ID CM0911238)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.01	0
	-0.334	0
(flanking)	0.029	0.001

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 marginally increased	71967	wt: 0.9567 / mu: 0.9589 (marginal change - not scored)	wt: GTTTCGGCGAAAGGT mu: GTTTCGGCAAAAGGT	TTCG\|gcga
Donor marginally increased	71968	wt: 0.9646 / mu: 0.9783 (marginal change - not scored)	wt: TTTCGGCGAAAGGTC mu: TTTCGGCAAAAGGTC	TCGG\|cgaa
Donor gained	71966	0.69	mu: AGTTTCGGCAAAAGG	TTTC\|ggca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all identical

ENSPTRG00000004078

312

Mmulatta

all identical

ENSMMUG00000009126

312

Fcatus

all identical

ENSFCAG00000011940

314

Mmusculus

all identical

ENSMUSG00000030737

314

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000054609

281

Dmelanogaster

all conserved

FBgn0036732

456

Celegans

not conserved

Y32F6B.1

348

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
70	88	TOPO_DOM	Extracellular (Potential).	lost
89	109	TRANSMEM	Helical; Name=2; (Potential).	might get lost (downstream of altered splice site)
110	115	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
116	140	TRANSMEM	Helical; Name=3; (Potential).	might get lost (downstream of altered splice site)
141	185	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
176	176	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
186	215	TRANSMEM	Helical; Name=4; (Potential).	might get lost (downstream of altered splice site)
215	215	CONFLICT	D -> V (in Ref. 6).	might get lost (downstream of altered splice site)
216	234	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
235	255	TRANSMEM	Helical; Name=5; (Potential).	might get lost (downstream of altered splice site)
256	273	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
274	298	TRANSMEM	Helical; Name=6; (Potential).	might get lost (downstream of altered splice site)
299	366	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
367	388	TRANSMEM	Helical; Name=7; (Potential).	might get lost (downstream of altered splice site)
389	408	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
409	432	TRANSMEM	Helical; Name=8; (Potential).	might get lost (downstream of altered splice site)
433	436	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
437	460	TRANSMEM	Helical; Name=9; (Potential).	might get lost (downstream of altered splice site)
461	564	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
483	543	DOMAIN	Kazal-like.	might get lost (downstream of altered splice site)
489	489	DISULFID	By similarity.	might get lost (downstream of altered splice site)
493	493	DISULFID	By similarity.	might get lost (downstream of altered splice site)
495	495	DISULFID	By similarity.	might get lost (downstream of altered splice site)
504	504	DISULFID	By similarity.	might get lost (downstream of altered splice site)
516	516	DISULFID	By similarity.	might get lost (downstream of altered splice site)
520	520	DISULFID	By similarity.	might get lost (downstream of altered splice site)
538	538	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
565	587	TRANSMEM	Helical; Name=10; (Potential).	might get lost (downstream of altered splice site)
588	596	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
597	622	TRANSMEM	Helical; Name=11; (Potential).	might get lost (downstream of altered splice site)
623	655	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
656	673	TRANSMEM	Helical; Name=12; (Potential).	might get lost (downstream of altered splice site)
674	709	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

1449 / 1449

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

483 / 483

position of stopcodon in wt / mu cDNA

2184 / 2184

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

736 / 736

chromosome

strand

last intron/exon boundary

2004

theoretical NMD boundary in CDS

1218

length of CDS

1449

coding sequence (CDS) position

254

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

989

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

71970

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

74883577

original gDNA sequence snippet

ACGTGAGCTTCAGTTTCGGCGAAAGGTCTTAGCAGTCACAG

altered gDNA sequence snippet

ACGTGAGCTTCAGTTTCGGCAAAAGGTCTTAGCAGTCACAG

original cDNA sequence snippet

ACGTGAGCTTCAGTTTCGGCGAAAGGTCTTAGCAGTCACAG

altered cDNA sequence snippet

ACGTGAGCTTCAGTTTCGGCAAAAGGTCTTAGCAGTCACAG

wildtype AA sequence

MIGYGAILVA LAGLLMTLPH FISEPYRYDN TSPGGISLTI KDPRWVGAWW LGFLIAAGAV
ALAAIPYFFF PKEMPKEKRE LQFRRKVLAV TDSPARKGKD SPSKQSPGES TKKQDGLVQI
APNLTVIQFI KVFPRVLLQT LRHPIFLLVV LSQVCLSSMA AGMAIFLPKF LERQFSITAS
YANLLIGCLS FPSVIVGIVV GGVLVKRLHL GPVGCGALCL LGMLLCLFFS LPLFFIGCSS
HQIAGITHQT SAHPGLELSP SCMEACSCPL DGFNPVCDPS TRVEYITPCH AGCSSWVVQD
ALDNSQVFYT NCSCVVEGNP VLAGSCDSTC SHLVVPFLLL VSLGSALACL THTPSFMLIL
RGVKKEDKTL AVGIQFMFLR ILAWMPSPVI HGSAIDTTCV HWALSCGRRA VCRYYNNDLL
RNRFIGLQFF FKTGSVICFA LVLAVLRQQD KEARTKESRS SPAVEQQLLV SGPGKKPEDS
RV*

mutated AA sequence

MIGYGAILVA LAGLLMTLPH FISEPYRYDN TSPGGISLTI KDPRWVGAWW LGFLIAAGAV
ALAAIPYFFF PKEMPKEKRE LQFRQKVLAV TDSPARKGKD SPSKQSPGES TKKQDGLVQI
APNLTVIQFI KVFPRVLLQT LRHPIFLLVV LSQVCLSSMA AGMAIFLPKF LERQFSITAS
YANLLIGCLS FPSVIVGIVV GGVLVKRLHL GPVGCGALCL LGMLLCLFFS LPLFFIGCSS
HQIAGITHQT SAHPGLELSP SCMEACSCPL DGFNPVCDPS TRVEYITPCH AGCSSWVVQD
ALDNSQVFYT NCSCVVEGNP VLAGSCDSTC SHLVVPFLLL VSLGSALACL THTPSFMLIL
RGVKKEDKTL AVGIQFMFLR ILAWMPSPVI HGSAIDTTCV HWALSCGRRA VCRYYNNDLL
RNRFIGLQFF FKTGSVICFA LVLAVLRQQD KEARTKESRS SPAVEQQLLV SGPGKKPEDS
RV*

speed

0.93 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