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 ENST00000397089
Genbank transcript ID N/A
UniProt peptide O95398
alteration type single base exchange
alteration region CDS
DNA changes c.82G>C
cDNA.224G>C
g.13002G>C
AA changes A28P Score: 27 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 28
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      28WPGESCWQVGLAVEDSPALGAPRV
mutated  not conserved    28WPGESCWQVGLPVEDSPALGAPR
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 2607 / 2607
position (AA) of stopcodon in wt / mu AA sequence 869 / 869
position of stopcodon in wt / mu cDNA 2749 / 2749
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 143 / 143
chromosome 12
strand -1
last intron/exon boundary 2631
theoretical NMD boundary in CDS 2438
length of CDS 2607
coding sequence (CDS) position 82
cDNA position
(for ins/del: last normal base / first normal base)		 224
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 MAQREEIKRP LWETVGWPGE SCWQVGLAVE DSPALGAPRV GALPDVVPEG TLLNMVLRRM
HRPRSCSYQL LLEHQRPSCI QGLRWTPLTN SEESLDFSES LEQASTERVL RAGRQLHRHL
LATCPNLIRD RKYHLRLYRQ CCSGRELVDG ILALGLGVHS RSQVVGICQV LLDEGALCHV
KHDWAFQDRD AQFYRFPGPE PEPVRTHEME EELAEAVALL SQRGPDALLT VALRKPPGQR
TDEELDLIFE ELLHIKAVAH LSNSVKRELA AVLLFEPHSK AGTVLFSQGD KGTSWYIIWK
GSVNVVTHGK GLVTTLHEGD DFGQLALVND APRAATIILR EDNCHFLRVD KQDFNRIIKD
VEAKTMRLEE HGKVVLVLER ASQGAGPSRP PTPGRNRYTV MSGTPEKILE LLLEAMGPDS
SAHDPTETFL SDFLLTHRVF MPSAQLCAAL LHHFHVEPAG GSEQERSTYV CNKRQQILRL
VSQWVALYGS MLHTDPVATS FLQKLSDLVG RDTRLSNLLR EQWPERRRCH RLENGCGNAS
PQMKARNLPV WLPNQDEPLP GSSCAIQVGD KDAIGLQPDA RGVATSLGLN ERLFVVNPQE
VHELIPHPDQ LGPTVGSAEG LDLVSAKDLA GQLTDHDWSL FNSIHQVELI HYVLGPQHLR
DVTTANLERF MRRFNELQYW VATELCLCPV PGPRAQLLRK FIKLAAHNSA ISRLAHTWER
LPHKVRKLYS ALERLLDPSW NHRVYRLALA KLSPPVIPFM PLLLKDMTFI HEGNHTLVEN
LINFEKMRMM ARAARMLHHC RSHNPVPLSP LRSRVSHLHE DSQVARISTC SEQSLSTRSP
ASTWAYVQQL KVIDNQRELS RLSRELEP*
mutated AA sequence MAQREEIKRP LWETVGWPGE SCWQVGLPVE DSPALGAPRV GALPDVVPEG TLLNMVLRRM
HRPRSCSYQL LLEHQRPSCI QGLRWTPLTN SEESLDFSES LEQASTERVL RAGRQLHRHL
LATCPNLIRD RKYHLRLYRQ CCSGRELVDG ILALGLGVHS RSQVVGICQV LLDEGALCHV
KHDWAFQDRD AQFYRFPGPE PEPVRTHEME EELAEAVALL SQRGPDALLT VALRKPPGQR
TDEELDLIFE ELLHIKAVAH LSNSVKRELA AVLLFEPHSK AGTVLFSQGD KGTSWYIIWK
GSVNVVTHGK GLVTTLHEGD DFGQLALVND APRAATIILR EDNCHFLRVD KQDFNRIIKD
VEAKTMRLEE HGKVVLVLER ASQGAGPSRP PTPGRNRYTV MSGTPEKILE LLLEAMGPDS
SAHDPTETFL SDFLLTHRVF MPSAQLCAAL LHHFHVEPAG GSEQERSTYV CNKRQQILRL
VSQWVALYGS MLHTDPVATS FLQKLSDLVG RDTRLSNLLR EQWPERRRCH RLENGCGNAS
PQMKARNLPV WLPNQDEPLP GSSCAIQVGD KDAIGLQPDA RGVATSLGLN ERLFVVNPQE
VHELIPHPDQ LGPTVGSAEG LDLVSAKDLA GQLTDHDWSL FNSIHQVELI HYVLGPQHLR
DVTTANLERF MRRFNELQYW VATELCLCPV PGPRAQLLRK FIKLAAHNSA ISRLAHTWER
LPHKVRKLYS ALERLLDPSW NHRVYRLALA KLSPPVIPFM PLLLKDMTFI HEGNHTLVEN
LINFEKMRMM ARAARMLHHC RSHNPVPLSP LRSRVSHLHE DSQVARISTC SEQSLSTRSP
ASTWAYVQQL KVIDNQRELS RLSRELEP*
speed 1.08 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