Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999843083692 (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) chr20:62038277T>GN/A show variant in all transcripts   IGV
HGNC symbol KCNQ2
Ensembl transcript ID ENST00000359125
Genbank transcript ID NM_172107
UniProt peptide O43526
alteration type single base exchange
alteration region CDS
DNA changes c.2339A>C
cDNA.2514A>C
g.65717A>C
AA changes N780T Score: 65 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 780
frameshift no
known variant Reference ID: rs1801475
databasehomozygous (G/G)heterozygousallele carriers
1000G91111352046
ExAC19837-690712930
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.5840.891
0.7740.871
(flanking)1.4460.695
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased65711wt: 0.23 / mu: 0.32wt: CCCGGGCTGCAGGCCCCCCGAGGGGAACCTGCGGGACAGCG
mu: CCCGGGCTGCAGGCCCCCCGAGGGGACCCTGCGGGACAGCG		 ccga|GGGG
distance from splice site 452
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      780EDTPGCRPPEGNLRDSDTSISIPS
mutated  not conserved    780EDTPGCRPPEGTLRDSDTSISIP
Ptroglodytes  not conserved  ENSPTRG00000013736  713EDTPGCRPPEGTLRDSDTSISIP
Mmulatta  not conserved  ENSMMUG00000015918  767EDAPGCRPPEGTLRDSDTSISIP
Fcatus  not conserved  ENSFCAG00000008923  684----LRDSDTSISIP
Mmusculus  not conserved  ENSMUSG00000016346  778ALRDSDTSISIP
Ggallus  not conserved  ENSGALG00000005822  761ALRDSDTSISIP
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no alignment  FBgn0033494  n/a
Celegans  no alignment  C25B8.1  n/a
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
313872TOPO_DOMCytoplasmic (Potential).lost
854854CONFLICTR -> C (in Ref. 4; AAD16988).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2619 / 2619
position (AA) of stopcodon in wt / mu AA sequence 873 / 873
position of stopcodon in wt / mu cDNA 2794 / 2794
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 176 / 176
chromosome 20
strand -1
last intron/exon boundary 2063
theoretical NMD boundary in CDS 1837
length of CDS 2619
coding sequence (CDS) position 2339
cDNA position
(for ins/del: last normal base / first normal base)		 2514
gDNA position
(for ins/del: last normal base / first normal base)		 65717
chromosomal position
(for ins/del: last normal base / first normal base)		 62038277
original gDNA sequence snippet CTGCAGGCCCCCCGAGGGGAACCTGCGGGACAGCGACACGT
altered gDNA sequence snippet CTGCAGGCCCCCCGAGGGGACCCTGCGGGACAGCGACACGT
original cDNA sequence snippet CTGCAGGCCCCCCGAGGGGAACCTGCGGGACAGCGACACGT
altered cDNA sequence snippet CTGCAGGCCCCCCGAGGGGACCCTGCGGGACAGCGACACGT
wildtype AA sequence MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG
GAGAGKPPKR NAFYRKLQNF LYNVLERPRG WAFIYHAYVF LLVFSCLVLS VFSTIKEYEK
SSEGALYILE IVTIVVFGVE YFVRIWAAGC CCRYRGWRGR LKFARKPFCV IDIMVLIASI
AVLAAGSQGN VFATSALRSL RFLQILRMIR MDRRGGTWKL LGSVVYAHSK ELVTAWYIGF
LCLILASFLV YLAEKGENDH FDTYADALWW GLITLTTIGY GDKYPQTWNG RLLAATFTLI
GVSFFALPAG ILGSGFALKV QEQHRQKHFE KRRNPAAGLI QSAWRFYATN LSRTDLHSTW
QYYERTVTVP MYSSQTQTYG ASRLIPPLNQ LELLRNLKSK SGLAFRKDPP PEPSPSKGSP
CRGPLCGCCP GRSSQKVSLK DRVFSSPRGV AAKGKGSPQA QTVRRSPSAD QSLEDSPSKV
PKSWSFGDRS RARQAFRIKG AASRQNSEEA SLPGEDIVDD KSCPCEFVTE DLTPGLKVSI
RAVCVMRFLV SKRKFKESLR PYDVMDVIEQ YSAGHLDMLS RIKSLQSRVD QIVGRGPAIT
DKDRTKGPAE AELPEDPSMM GRLGKVEKQV LSMEKKLDFL VNIYMQRMGI PPTETEAYFG
AKEPEPAPPY HSPEDSREHV DRHGCIVKIV RSSSSTGQKN FSAPPAAPPV QCPPSTSWQP
QSHPRQGHGT SPVGDHGSLV RIPPPPAHER SLSAYGGGNR ASMEFLRQED TPGCRPPEGN
LRDSDTSISI PSVDHEELER SFSGFSISQS KENLDALNSC YAAVAPCAKV RPYIAEGESD
TDSDLCTPCG PPPRSATGEG PFGDVGWAGP RK*
mutated AA sequence MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG
GAGAGKPPKR NAFYRKLQNF LYNVLERPRG WAFIYHAYVF LLVFSCLVLS VFSTIKEYEK
SSEGALYILE IVTIVVFGVE YFVRIWAAGC CCRYRGWRGR LKFARKPFCV IDIMVLIASI
AVLAAGSQGN VFATSALRSL RFLQILRMIR MDRRGGTWKL LGSVVYAHSK ELVTAWYIGF
LCLILASFLV YLAEKGENDH FDTYADALWW GLITLTTIGY GDKYPQTWNG RLLAATFTLI
GVSFFALPAG ILGSGFALKV QEQHRQKHFE KRRNPAAGLI QSAWRFYATN LSRTDLHSTW
QYYERTVTVP MYSSQTQTYG ASRLIPPLNQ LELLRNLKSK SGLAFRKDPP PEPSPSKGSP
CRGPLCGCCP GRSSQKVSLK DRVFSSPRGV AAKGKGSPQA QTVRRSPSAD QSLEDSPSKV
PKSWSFGDRS RARQAFRIKG AASRQNSEEA SLPGEDIVDD KSCPCEFVTE DLTPGLKVSI
RAVCVMRFLV SKRKFKESLR PYDVMDVIEQ YSAGHLDMLS RIKSLQSRVD QIVGRGPAIT
DKDRTKGPAE AELPEDPSMM GRLGKVEKQV LSMEKKLDFL VNIYMQRMGI PPTETEAYFG
AKEPEPAPPY HSPEDSREHV DRHGCIVKIV RSSSSTGQKN FSAPPAAPPV QCPPSTSWQP
QSHPRQGHGT SPVGDHGSLV RIPPPPAHER SLSAYGGGNR ASMEFLRQED TPGCRPPEGT
LRDSDTSISI PSVDHEELER SFSGFSISQS KENLDALNSC YAAVAPCAKV RPYIAEGESD
TDSDLCTPCG PPPRSATGEG PFGDVGWAGP RK*
speed 0.73 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