Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999863302 (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
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:124802888C>TN/A show variant in all transcripts   IGV
HGNC symbol SLC12A8
Ensembl transcript ID ENST00000423114
Genbank transcript ID N/A
UniProt peptide A0AV02
alteration type single base exchange
alteration region CDS
DNA changes c.2078G>A
cDNA.2078G>A
g.195134G>A
AA changes R693Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 693
frameshift no
known variant Reference ID: rs2981482
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC1594687516821
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.120.001
0.1280
(flanking)0.5440.001
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 increased195125wt: 0.7882 / mu: 0.7976 (marginal change - not scored)wt: TCTGTGTCTCTCTCACTGCAGGAGCTTGCGGTCCCCTCAGG
mu: TCTGTGTCTCTCTCACTGCAGGAGCTTGCAGTCCCCTCAGG		 gcag|GAGC
Donor gained1951390.39mu: AGTCCCCTCAGGAGC TCCC|ctca
distance from splice site 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      693RSLLLPSCRSLRSPQEQIILAPSL
mutated  all conserved    693RSLLLPSCRSLQSPQEQIILAPS
Ptroglodytes  all identical  ENSPTRG00000015317  664RSLLLPSCRSLRSPQEQIILAPS
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000035506  655KSFLVPSCRSLRSAQEQIILAPS
Ggallus  not conserved  ENSGALG00000012045  679KSVLTTSCRRRPSPKEQIVVTPA
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000074384  655KTSLHNLGRQNGALQDQIVVTPS
Dmelanogaster  not conserved  FBgn0024365  663KSVIFRCFGKRMNEYEQIVVTPS
Celegans  all identical  F10E7.9  560KT-VFSSLDSLRSGATTILPETT
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
698698CONFLICTR -> H (in Ref. 2; AAO49174).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2232 / 2232
position (AA) of stopcodon in wt / mu AA sequence 744 / 744
position of stopcodon in wt / mu cDNA 2232 / 2232
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 1 / 1
chromosome 3
strand -1
last intron/exon boundary 2070
theoretical NMD boundary in CDS 2019
length of CDS 2232
coding sequence (CDS) position 2078
cDNA position
(for ins/del: last normal base / first normal base)		 2078
gDNA position
(for ins/del: last normal base / first normal base)		 195134
chromosomal position
(for ins/del: last normal base / first normal base)		 124802888
original gDNA sequence snippet CTCTCACTGCAGGAGCTTGCGGTCCCCTCAGGAGCAGATCA
altered gDNA sequence snippet CTCTCACTGCAGGAGCTTGCAGTCCCCTCAGGAGCAGATCA
original cDNA sequence snippet CCCCTCCTGCAGGAGCTTGCGGTCCCCTCAGGAGCAGATCA
altered cDNA sequence snippet CCCCTCCTGCAGGAGCTTGCAGTCCCCTCAGGAGCAGATCA
wildtype AA sequence MLPLERTITY RDMSSFIQVK NHFNVVNVTC VSYRSTCFRD MRRFILDALA QPQPWWKTQL
FMWEPVLFGT WDGVFTSCMI NIFGVVLFLR TGWLVGNTGV LLGMFLVSFV ILVALVTVLS
GIGVGERSSI GSGGVYSMIS SVLGGQTGGT IGLLYVFGQC VAGAMYITGF AESISDLLGL
GNIWAVRGIS VAVLLALLGI NLAGVKWIIR LQLLLLFLLA VSTLDFVVGS FTHLDPEHGF
IGYSPELLQN NTLPDYSPGE SFFTVFGVFF PAATGVMAGF NMGGDLREPA ASIPPGSLAA
VGISWFLYII FVFLLGAICT REALRYDFLI AEKVSLMGFL FLLGLYISSL ASCMGGLYGA
PRILQCIAQE KVIPALACLG QGKGPNKTPV AAICLTSLVT MAFVFVGQVN VLAPIVTINF
MLTYVAVDYS YFSLSMCSCS LTPVPEPVLR EGAEGLHCSE HLLLEKAPSY GSEGPAQRVL
EGTLLEFTKD MDQLLQLTRK LESSQPRQGE GNRTPESQKR KSKKATKQTL QDSFLLDLKS
PPSFPVEISD RLPAASWEGQ ESCWNKQTSK SEGTQPEGTY GEQLVPELCN QSESSGEDFF
LKSRLQEQDV WRRSTSFYTH MCNPWVSLLG AVGSLLIMFV IQWVYTLVNM GVAAIVYFYI
GRASPGLHLG SASNFSFFRW MRSLLLPSCR SLRSPQEQII LAPSLAKVDM EMTQLTQENA
DFATRDRYHH SSLVNREQLM PHY*
mutated AA sequence MLPLERTITY RDMSSFIQVK NHFNVVNVTC VSYRSTCFRD MRRFILDALA QPQPWWKTQL
FMWEPVLFGT WDGVFTSCMI NIFGVVLFLR TGWLVGNTGV LLGMFLVSFV ILVALVTVLS
GIGVGERSSI GSGGVYSMIS SVLGGQTGGT IGLLYVFGQC VAGAMYITGF AESISDLLGL
GNIWAVRGIS VAVLLALLGI NLAGVKWIIR LQLLLLFLLA VSTLDFVVGS FTHLDPEHGF
IGYSPELLQN NTLPDYSPGE SFFTVFGVFF PAATGVMAGF NMGGDLREPA ASIPPGSLAA
VGISWFLYII FVFLLGAICT REALRYDFLI AEKVSLMGFL FLLGLYISSL ASCMGGLYGA
PRILQCIAQE KVIPALACLG QGKGPNKTPV AAICLTSLVT MAFVFVGQVN VLAPIVTINF
MLTYVAVDYS YFSLSMCSCS LTPVPEPVLR EGAEGLHCSE HLLLEKAPSY GSEGPAQRVL
EGTLLEFTKD MDQLLQLTRK LESSQPRQGE GNRTPESQKR KSKKATKQTL QDSFLLDLKS
PPSFPVEISD RLPAASWEGQ ESCWNKQTSK SEGTQPEGTY GEQLVPELCN QSESSGEDFF
LKSRLQEQDV WRRSTSFYTH MCNPWVSLLG AVGSLLIMFV IQWVYTLVNM GVAAIVYFYI
GRASPGLHLG SASNFSFFRW MRSLLLPSCR SLQSPQEQII LAPSLAKVDM EMTQLTQENA
DFATRDRYHH SSLVNREQLM PHY*
speed 1.36 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