mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 1.83266877624817e-36 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:20905250C>TN/A show variant in all transcripts IGV

HGNC symbol

SLCO1C1

Ensembl transcript ID

ENST00000540354

Genbank transcript ID

NM_001145945

UniProt peptide

N/A

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1780C>T
cDNA.2028C>T
g.56962C>T

AA changes

no AA changes

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

N/A

frameshift

known variant

Reference ID: rs6487138

database	homozygous (T/T)	heterozygous	allele carriers
1000G	627	1097	1724
ExAC	17515	-2263	15252

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.011	0.997
	4.059	1
(flanking)	3.374	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
Acc marginally increased	56953	wt: 0.6612 / mu: 0.6965 (marginal change - not scored)	wt: AGATTCTCTCTTCTTCTAGACATATATATCTGGGACTAACT mu: AGATTCTCTCTTCTTCTAGACATATATATTTGGGACTAACT	agac\|ATAT
Acc marginally increased	56959	wt: 0.3579 / mu: 0.3846 (marginal change - not scored)	wt: TCTCTTCTTCTAGACATATATATCTGGGACTAACTGTGATA mu: TCTCTTCTTCTAGACATATATATTTGGGACTAACTGTGATA	atat\|ATCT
Acc marginally increased	56955	wt: 0.9031 / mu: 0.9324 (marginal change - not scored)	wt: ATTCTCTCTTCTTCTAGACATATATATCTGGGACTAACTGT mu: ATTCTCTCTTCTTCTAGACATATATATTTGGGACTAACTGT	acat\|ATAT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

normal

AA sequence altered

position of stopcodon in wt / mu CDS

1992 / 1992

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

664 / 664

position of stopcodon in wt / mu cDNA

2240 / 2240

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

249 / 249

chromosome

strand

last intron/exon boundary

2018

theoretical NMD boundary in CDS

1719

length of CDS

1992

coding sequence (CDS) position

1780

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

2028

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

56962

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

20905250

original gDNA sequence snippet

CTTCTTCTAGACATATATATCTGGGACTAACTGTGATACTG

altered gDNA sequence snippet

CTTCTTCTAGACATATATATTTGGGACTAACTGTGATACTG

original cDNA sequence snippet

ATGTCTTCAGACATATATATCTGGGACTAACTGTGATACTG

altered cDNA sequence snippet

ATGTCTTCAGACATATATATTTGGGACTAACTGTGATACTG

wildtype AA sequence

MDTSSKENIQ LFCKTSVQPV GRPSFKTEYP SSEEKQPCCG ELKVFLCALS FVYFAKALAE
GYLKSTITQI ERRFDIPSSL VGVIDGSFEI GNLLVITFVS YFGAKLHRPK IIGAGCVIMG
VGTLLIAMPQ FFMEQYKYER YSPSSNSTLS ISPCLLESSS QLPVSVMEKS KSKISNGCVQ
TVAIIGPIFG FLLGSLCAKL YVDIGFVNLD HITITPKDPQ WVGAWWLGYL IAGIISLLAA
VPFWYLPKSL PRSQSREDSN SSSEKSKFII DDHTDYQTPQ GENAKIMEMA RDFLPSLKNL
FGNPVYFLYL CTSTVQFNSL FGMVTYKPKY IEQQYGQSSS RANFVIGLIN IPAVALGIFS
GGIVMKKFRI SVCGAAKLYL GSSVFGYLLF LSLFALGCEN SDVAGLTVSY QGTKPVSYHE
RALFSDCNSR CKCSETKWEP MCGENGITYV SACLAGCQTS NRSGKNIIFY NCTCVGIAAS
KSGNSSGIVG RCQKDNGCPQ MFLYFLVISV ITSYTLSLGG IPGYILLLRC IKPQLKSFAL
GIYTLAIRVL AGIPAPVYFG VLIDTSCLKW GFKRCGSRGS CRLYDSNVFR HIYLGLTVIL
GTVSILLSIA VLFILKKNYV SKHRSFITKR ERTMVSTRFQ KENYTTSDHL LQPNYWPGKE
TQL*

mutated AA sequence

speed

0.37 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