Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.259219624255252 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
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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 ENST00000545102
Genbank transcript ID NM_001145944
UniProt peptide Q9NYB5
alteration type single base exchange
alteration region CDS
DNA changes c.1676C>T
cDNA.1970C>T
g.56962C>T
AA changes S559F Score: 155 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 559
frameshift no
known variant Reference ID: rs6487138
databasehomozygous (T/T)heterozygousallele carriers
1000G62710971724
ExAC17515-226315252
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0110.997
4.0591
(flanking)3.3741
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased56953wt: 0.6612 / mu: 0.6965 (marginal change - not scored)wt: AGATTCTCTCTTCTTCTAGACATATATATCTGGGACTAACT
mu: AGATTCTCTCTTCTTCTAGACATATATATTTGGGACTAACT		 agac|ATAT
Acc marginally increased56959wt: 0.3579 / mu: 0.3846 (marginal change - not scored)wt: TCTCTTCTTCTAGACATATATATCTGGGACTAACTGTGATA
mu: TCTCTTCTTCTAGACATATATATTTGGGACTAACTGTGATA		 atat|ATCT
Acc marginally increased56955wt: 0.9031 / mu: 0.9324 (marginal change - not scored)wt: ATTCTCTCTTCTTCTAGACATATATATCTGGGACTAACTGT
mu: ATTCTCTCTTCTTCTAGACATATATATTTGGGACTAACTGT		 acat|ATAT
distance from splice site 11
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      559SCHFTACKTYISGTNCDTGHSVNS
mutated  not conserved    559SCHFTACKTYIFGTNCDTGHSVN
Ptroglodytes  all identical  ENSPTRG00000004749  677SCHFTACKTYISGTNCDTGHSVN
Mmulatta  no alignment  ENSMMUG00000008271  n/a
Fcatus  no homologue    
Mmusculus  no alignment  ENSMUSG00000030235  n/a
Ggallus  no alignment  ENSGALG00000013154  n/a
Trubripes  no homologue    
Drerio  no alignment  ENSDARG00000016749  n/a
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no alignment  ENSXETG00000030963  n/a
protein features
start (aa)end (aa)featuredetails 
555577TRANSMEMHelical; Name=10; (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1839 / 1839
position (AA) of stopcodon in wt / mu AA sequence 613 / 613
position of stopcodon in wt / mu cDNA 2133 / 2133
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 295 / 295
chromosome 12
strand 1
last intron/exon boundary 1960
theoretical NMD boundary in CDS 1615
length of CDS 1839
coding sequence (CDS) position 1676
cDNA position
(for ins/del: last normal base / first normal base)		 1970
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 TGCTTGTAAGACATATATATCTGGGACTAACTGTGATACTG
altered cDNA sequence snippet TGCTTGTAAGACATATATATTTGGGACTAACTGTGATACTG
wildtype AA sequence MGVGTLLIAM PQFFMEQYKY ERYSPSSNST LSISPCLLES SSQLPVSVME KSKSKISNEC
EVDTSSSMWI YVFLGNLLRG IGETPIQPLG IAYLDDFASE DNAAFYIGCV QTVAIIGPIF
GFLLGSLCAK LYVDIGFVNL DHITITPKDP QWVGAWWLGY LIAGIISLLA AVPFWYLPKS
LPRSQSREDS NSSSEKSKFI IDDHTDYQTP QGENAKIMEM ARDFLPSLKN LFGNPVYFLY
LCTSTVQFNS LFGMVTYKPK YIEQQYGQSS SRANFVIGLI NIPAVALGIF SGGIVMKKFR
ISVCGAAKLY LGSSVFGYLL FLSLFALGCE NSDVAGLTVS YQGTKPVSYH ERALFSDCNS
RCKCSETKWE PMCGENGITY VSACLAGCQT SNRSGKNIIF YNCTCVGIAA SKSGNSSGIV
GRCQKDNGCP QMFLYFLVIS VITSYTLSLG GIPGYILLLR CIKPQLKSFA LGIYTLAIRV
LAGIPAPVYF GVLIDTSCLK WGFKRCGSRG SCRLYDSNVF RYQIKSIPAS HCYSIPDLHN
ATDTNKFSCH FTACKTYISG TNCDTGHSVN SPKHCSTFHF KEKLCFKTQK FYNQERKNNG
VYKIPKGKLH YK*
mutated AA sequence MGVGTLLIAM PQFFMEQYKY ERYSPSSNST LSISPCLLES SSQLPVSVME KSKSKISNEC
EVDTSSSMWI YVFLGNLLRG IGETPIQPLG IAYLDDFASE DNAAFYIGCV QTVAIIGPIF
GFLLGSLCAK LYVDIGFVNL DHITITPKDP QWVGAWWLGY LIAGIISLLA AVPFWYLPKS
LPRSQSREDS NSSSEKSKFI IDDHTDYQTP QGENAKIMEM ARDFLPSLKN LFGNPVYFLY
LCTSTVQFNS LFGMVTYKPK YIEQQYGQSS SRANFVIGLI NIPAVALGIF SGGIVMKKFR
ISVCGAAKLY LGSSVFGYLL FLSLFALGCE NSDVAGLTVS YQGTKPVSYH ERALFSDCNS
RCKCSETKWE PMCGENGITY VSACLAGCQT SNRSGKNIIF YNCTCVGIAA SKSGNSSGIV
GRCQKDNGCP QMFLYFLVIS VITSYTLSLG GIPGYILLLR CIKPQLKSFA LGIYTLAIRV
LAGIPAPVYF GVLIDTSCLK WGFKRCGSRG SCRLYDSNVF RYQIKSIPAS HCYSIPDLHN
ATDTNKFSCH FTACKTYIFG TNCDTGHSVN SPKHCSTFHF KEKLCFKTQK FYNQERKNNG
VYKIPKGKLH YK*
speed 0.54 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