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 ENST00000393469
Genbank transcript ID NM_001195483
UniProt peptide A0AV02
alteration type single base exchange
alteration region CDS
DNA changes c.1991G>A
cDNA.2041G>A
g.195134G>A
AA changes R664Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 664
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      664RSLLLPSCRSLRSPQEQIILAPSL
mutated  all conserved    664RSLQSPQEQIILAPS
Ptroglodytes  all identical  ENSPTRG00000015317  664RSLRSPQEQIILAPS
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000035506  655KSFLVPSCRSLRSAQ
Ggallus  not conserved  ENSGALG00000012045  680RRPSPKEQIVVTPA
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000074384  655NLGRQNGALQDQIVVTPS
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 2145 / 2145
position (AA) of stopcodon in wt / mu AA sequence 715 / 715
position of stopcodon in wt / mu cDNA 2195 / 2195
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 51 / 51
chromosome 3
strand -1
last intron/exon boundary 2033
theoretical NMD boundary in CDS 1932
length of CDS 2145
coding sequence (CDS) position 1991
cDNA position
(for ins/del: last normal base / first normal base)		 2041
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 MTQMSQVQEL FHEAAQQDAL AQPQPWWKTQ LFMWEPVLFG TWDGVFTSCM INIFGVVLFL
RTGWLVGNTG VLLGMFLVSF VILVALVTVL SGIGVGERSS IGSGGVYSMI SSVLGGQTGG
TIGLLYVFGQ CVAGAMYITG FAESISDLLG LGNIWAVRGI SVAVLLALLG INLAGVKWII
RLQLLLLFLL AVSTLDFVVG SFTHLDPEHG FIGYSPELLQ NNTLPDYSPG ESFFTVFGVF
FPAATGVMAG FNMGGDLREP AASIPPGSLA AVGISWFLYI IFVFLLGAIC TREALRYDFL
IAEKVSLMGF LFLLGLYISS LASCMGGLYG APRILQCIAQ EKVIPALACL GQGKGPNKTP
VAAICLTSLV TMAFVFVGQV NVLAPIVTIN FMLTYVAVDY SYFSLSMCSC SLTPVPEPVL
REGAEGLHCS EHLLLEKAPS YGSEGPAQRV LEGTLLEFTK DMDQLLQLTR KLESSQPRQG
EGNRTPESQK RKSKKATKQT LQDSFLLDLK SPPSFPVEIS DRLPAASWEG QESCWNKQTS
KSEGTQPEGT YGEQLVPELC NQSESSGEDF FLKSRLQEQD VWRRSTSFYT HMCNPWVSLL
GAVGSLLIMF VIQWVYTLVN MGVAAIVYFY IGRASPGLHL GSASNFSFFR WMRSLLLPSC
RSLRSPQEQI ILAPSLAKVD MEMTQLTQEN ADFATRDRYH HSSLVNREQL MPHY*
mutated AA sequence MTQMSQVQEL FHEAAQQDAL AQPQPWWKTQ LFMWEPVLFG TWDGVFTSCM INIFGVVLFL
RTGWLVGNTG VLLGMFLVSF VILVALVTVL SGIGVGERSS IGSGGVYSMI SSVLGGQTGG
TIGLLYVFGQ CVAGAMYITG FAESISDLLG LGNIWAVRGI SVAVLLALLG INLAGVKWII
RLQLLLLFLL AVSTLDFVVG SFTHLDPEHG FIGYSPELLQ NNTLPDYSPG ESFFTVFGVF
FPAATGVMAG FNMGGDLREP AASIPPGSLA AVGISWFLYI IFVFLLGAIC TREALRYDFL
IAEKVSLMGF LFLLGLYISS LASCMGGLYG APRILQCIAQ EKVIPALACL GQGKGPNKTP
VAAICLTSLV TMAFVFVGQV NVLAPIVTIN FMLTYVAVDY SYFSLSMCSC SLTPVPEPVL
REGAEGLHCS EHLLLEKAPS YGSEGPAQRV LEGTLLEFTK DMDQLLQLTR KLESSQPRQG
EGNRTPESQK RKSKKATKQT LQDSFLLDLK SPPSFPVEIS DRLPAASWEG QESCWNKQTS
KSEGTQPEGT YGEQLVPELC NQSESSGEDF FLKSRLQEQD VWRRSTSFYT HMCNPWVSLL
GAVGSLLIMF VIQWVYTLVN MGVAAIVYFY IGRASPGLHL GSASNFSFFR WMRSLLLPSC
RSLQSPQEQI ILAPSLAKVD MEMTQLTQEN ADFATRDRYH HSSLVNREQL MPHY*
speed 0.66 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