Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.996326700833806 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:48151822C>GN/A show variant in all transcripts   IGV
HGNC symbol RAPGEF3
Ensembl transcript ID ENST00000395358
Genbank transcript ID N/A
UniProt peptide O95398
alteration type single base exchange
alteration region CDS
DNA changes c.46G>C
cDNA.135G>C
g.13002G>C
AA changes A16P Score: 27 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 16
frameshift no
known variant Reference ID: rs11168230
databasehomozygous (G/G)heterozygousallele carriers
1000G24210031245
ExAC24141097613390
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)1.0280.758
0.4620.676
(flanking)-0.3350.603
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased13004wt: 0.9799 / mu: 0.9902 (marginal change - not scored)wt: CTGGCTGTGGAGGAT
mu: CTGCCTGTGGAGGAT		 GGCT|gtgg
distance from splice site 40
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      16WPGESCWQVGLAVEDSPALGAPRV
mutated  not conserved    16WPGESCWQVGLPVEDSPALGAPR
Ptroglodytes  all identical  ENSPTRG00000004866  16WPGESCWQVGLAVEDSPALGAPR
Mmulatta  no alignment  ENSMMUG00000000477  n/a
Fcatus  all identical  ENSFCAG00000013996  16WPGESRWQVGLAVEDSPALGASQ
Mmusculus  all identical  ENSMUSG00000022469  16WPGENHWQVGPAVVESPAVGAPQ
Ggallus  no homologue    
Trubripes  no alignment  ENSTRUG00000014445  n/a
Drerio  no alignment  ENSDARG00000079291  n/a
Dmelanogaster  no alignment  FBgn0085421  n/a
Celegans  no alignment  T20G5.5  n/a
Xtropicalis  no homologue    
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1797 / 1797
position (AA) of stopcodon in wt / mu AA sequence 599 / 599
position of stopcodon in wt / mu cDNA 1886 / 1886
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 90 / 90
chromosome 12
strand -1
last intron/exon boundary 1646
theoretical NMD boundary in CDS 1506
length of CDS 1797
coding sequence (CDS) position 46
cDNA position
(for ins/del: last normal base / first normal base)		 135
gDNA position
(for ins/del: last normal base / first normal base)		 13002
chromosomal position
(for ins/del: last normal base / first normal base)		 48151822
original gDNA sequence snippet GCTGCTGGCAGGTGGGCCTGGCTGTGGAGGATAGCCCAGCT
altered gDNA sequence snippet GCTGCTGGCAGGTGGGCCTGCCTGTGGAGGATAGCCCAGCT
original cDNA sequence snippet GCTGCTGGCAGGTGGGCCTGGCTGTGGAGGATAGCCCAGCT
altered cDNA sequence snippet GCTGCTGGCAGGTGGGCCTGCCTGTGGAGGATAGCCCAGCT
wildtype AA sequence MKVGWPGESC WQVGLAVEDS PALGAPRVGA LPDVVPEGTL LNMVLRRMHR PRSCSYQLLL
EHQRPSCIQG LRWTPLTNSE ESLDFSESLE QASTERVLRA GRQLHRHLLA TCPNLIRDRK
YHLRLYRQCC SGRELVDGIL ALGLGVHSRS QVVGICQVLL DEGALCHVKH DWAFQDRDAQ
FYRFPGPEPE PVRTHEMEEE LAEAVALLSQ RGPDALLTVA LRKPPGQRTD EELDLIFEEL
LHIKAVAHLS NSVKRELAAV LLFEPHSKAG TVLFSQGDKG TSWYIIWKGS VNVVTHGKGL
VTTLHEGDDF GQLALVNDAP RAATIILRED NCHFLRVDKQ DFNRIIKDVE AKTMRLEEHG
KVVLVLERAS QGAGPSRPPT PGRNRYTVMS GTPEKILELL LEAMGPDSSA HDPTETFLSD
FLLTHRVFMP SAQLCAALLH HFHVEPAGGS EQERSTYVCN KRQQILRLVS QWVALYGSML
HTDPVATSFL QKLSDLVGRD TRLSNLLREQ WPERRRCHRL ENGCGNASPQ MKVSAWPQFL
SSAPPGLQAP PSPPDPEGLC GRGKLSSHRH TLGSLIGVHG ALAACGALGQ AVPGGAEA*
mutated AA sequence MKVGWPGESC WQVGLPVEDS PALGAPRVGA LPDVVPEGTL LNMVLRRMHR PRSCSYQLLL
EHQRPSCIQG LRWTPLTNSE ESLDFSESLE QASTERVLRA GRQLHRHLLA TCPNLIRDRK
YHLRLYRQCC SGRELVDGIL ALGLGVHSRS QVVGICQVLL DEGALCHVKH DWAFQDRDAQ
FYRFPGPEPE PVRTHEMEEE LAEAVALLSQ RGPDALLTVA LRKPPGQRTD EELDLIFEEL
LHIKAVAHLS NSVKRELAAV LLFEPHSKAG TVLFSQGDKG TSWYIIWKGS VNVVTHGKGL
VTTLHEGDDF GQLALVNDAP RAATIILRED NCHFLRVDKQ DFNRIIKDVE AKTMRLEEHG
KVVLVLERAS QGAGPSRPPT PGRNRYTVMS GTPEKILELL LEAMGPDSSA HDPTETFLSD
FLLTHRVFMP SAQLCAALLH HFHVEPAGGS EQERSTYVCN KRQQILRLVS QWVALYGSML
HTDPVATSFL QKLSDLVGRD TRLSNLLREQ WPERRRCHRL ENGCGNASPQ MKVSAWPQFL
SSAPPGLQAP PSPPDPEGLC GRGKLSSHRH TLGSLIGVHG ALAACGALGQ AVPGGAEA*
speed 1.25 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