Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.99999999999984 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM168201)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:38912764A>GN/A show variant in all transcripts   IGV
HGNC symbol RASGRP4
Ensembl transcript ID ENST00000454404
Genbank transcript ID NM_001146205
UniProt peptide Q8TDF6
alteration type single base exchange
alteration region CDS
DNA changes c.53T>C
cDNA.267T>C
g.4182T>C
AA changes I18T Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 18
frameshift no
known variant Reference ID: rs892055
databasehomozygous (G/G)heterozygousallele carriers
1000G77811401918
ExAC11652946321115

known disease mutation at this position, please check HGMD for details (HGMD ID CM168201)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.0590.082
1.3170.074
(flanking)-0.6760.001
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 increased4174wt: 0.8981 / mu: 0.9511 (marginal change - not scored)wt: TGCACCGGAAAAATA
mu: TGCACCGGAAAAACA		 CACC|ggaa
Donor marginally increased4179wt: 0.4304 / mu: 0.4620 (marginal change - not scored)wt: CGGAAAAATAGGAGG
mu: CGGAAAAACAGGAGG		 GAAA|aata
Donor marginally increased4175wt: 0.9679 / mu: 0.9794 (marginal change - not scored)wt: GCACCGGAAAAATAG
mu: GCACCGGAAAAACAG		 ACCG|gaaa
Donor increased4183wt: 0.69 / mu: 0.88wt: AAAATAGGAGGGCGA
mu: AAAACAGGAGGGCGA		 AATA|ggag
Donor marginally increased4187wt: 0.9139 / mu: 0.9205 (marginal change - not scored)wt: TAGGAGGGCGAGGCC
mu: CAGGAGGGCGAGGCC		 GGAG|ggcg
Donor increased4181wt: 0.83 / mu: 0.96wt: GAAAAATAGGAGGGC
mu: GAAAAACAGGAGGGC		 AAAA|tagg
distance from splice site 30
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      18KRKSHQECTGKIGGRGRPRQVRRH
mutated  not conserved    18KRKSHQECTGKTGGRGRPRQVRR
Ptroglodytes  not conserved  ENSPTRG00000010930  18KRKSHQECTGKTGGRGRPRQVRR
Mmulatta  not conserved  ENSMMUG00000020469  18KRKSHQECTGKTGGRGRPRQTRR
Fcatus  not conserved  ENSFCAG00000000827  10KSHQECPAKTGGRGRPRQARR
Mmusculus  not conserved  ENSMUSG00000030589  18KRKSHQECSGKAGGRGRSRQARR
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000061796  23KSSRKSRQE-----GGIKSRRPVQR
Dmelanogaster  no homologue    
Celegans  no alignment  F25B3.3  n/a
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
2727CONFLICTV -> A (in Ref. 1; AAK85703).might get lost (downstream of altered splice site)
49175DOMAINN-terminal Ras-GEF.might get lost (downstream of altered splice site)
7373CONFLICTG -> D (in Ref. 1; AAK85703).might get lost (downstream of altered splice site)
201432DOMAINRas-GEF.might get lost (downstream of altered splice site)
466501DOMAINEF-hand.might get lost (downstream of altered splice site)
540590ZN_FINGPhorbol-ester/DAG-type.might get lost (downstream of altered splice site)
548548MUTAGENF->S: Loss of cell membrane targeting.might get lost (downstream of altered splice site)
554554CONFLICTC -> R (in Ref. 1; AAK85703).might get lost (downstream of altered splice site)
671671CONFLICTL -> P (in Ref. 1; AAK85701/AAK85703).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1920 / 1920
position (AA) of stopcodon in wt / mu AA sequence 640 / 640
position of stopcodon in wt / mu cDNA 2134 / 2134
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 215 / 215
chromosome 19
strand -1
last intron/exon boundary 2078
theoretical NMD boundary in CDS 1813
length of CDS 1920
coding sequence (CDS) position 53
cDNA position
(for ins/del: last normal base / first normal base)		 267
gDNA position
(for ins/del: last normal base / first normal base)		 4182
chromosomal position
(for ins/del: last normal base / first normal base)		 38912764
original gDNA sequence snippet CCAGGAATGCACCGGAAAAATAGGAGGGCGAGGCCGGCCCC
altered gDNA sequence snippet CCAGGAATGCACCGGAAAAACAGGAGGGCGAGGCCGGCCCC
original cDNA sequence snippet CCAGGAATGCACCGGAAAAATAGGAGGGCGAGGCCGGCCCC
altered cDNA sequence snippet CCAGGAATGCACCGGAAAAACAGGAGGGCGAGGCCGGCCCC
wildtype AA sequence MNRKDSKRKS HQECTGKIGG RGRPRQVRRH KTCPSPREIS KVMASMNLGL LSEGGCSEDE
LLEKCIQSFD SAGSLCHEDH MLNMVLAMHS WVLPSADLAA RLLTSYQKAT GDTQELRRLQ
ICHLVRYWLM RHPEVMHQDP QLEEVIGRFW ATVAREGNSA QRRLGDSSDL LSPGGPGPPL
PMSSPGLGKK RKVSLLFDHL ETGELAQHLT YLEFRSFQAI TVMVLSRPGP LQRAQVLDKF
IHVAQRLHQL QNFNTLMAVT GGLCHSAISR LKDSHAHLSP DSTKALLELT ELLASHNNYA
RYRRTWAGCA GFRLPVLGVH LKDLVSLHEA QPDRLPDGRL HLPKLNNLYL RLQELVALQG
QHPPCSANED LLHLLTLSLD LFYTEDEIYE LSYAREPRCP KSLPPSPFNA PLVVEWAPGV
TPKPDRVTLG RHVEQLVESV FKNYDPEGRG TISQEDFERL SGNFPFACHG LHPPPRQGRG
SFSREELTGY LLRASAICSK LGLAFLHTFH EVTFRKPTFC DSCSGFLWGV TKQGYRCREC
GLCCHKHCRD QVKVECKKRP GAKGDAGPPG APVPSTPAPH ASCGSEENHS YTLSLEPETG
CQLRHAWTQT ESPHPSWETD TVPCPVMDPP STASSKLDS*
mutated AA sequence MNRKDSKRKS HQECTGKTGG RGRPRQVRRH KTCPSPREIS KVMASMNLGL LSEGGCSEDE
LLEKCIQSFD SAGSLCHEDH MLNMVLAMHS WVLPSADLAA RLLTSYQKAT GDTQELRRLQ
ICHLVRYWLM RHPEVMHQDP QLEEVIGRFW ATVAREGNSA QRRLGDSSDL LSPGGPGPPL
PMSSPGLGKK RKVSLLFDHL ETGELAQHLT YLEFRSFQAI TVMVLSRPGP LQRAQVLDKF
IHVAQRLHQL QNFNTLMAVT GGLCHSAISR LKDSHAHLSP DSTKALLELT ELLASHNNYA
RYRRTWAGCA GFRLPVLGVH LKDLVSLHEA QPDRLPDGRL HLPKLNNLYL RLQELVALQG
QHPPCSANED LLHLLTLSLD LFYTEDEIYE LSYAREPRCP KSLPPSPFNA PLVVEWAPGV
TPKPDRVTLG RHVEQLVESV FKNYDPEGRG TISQEDFERL SGNFPFACHG LHPPPRQGRG
SFSREELTGY LLRASAICSK LGLAFLHTFH EVTFRKPTFC DSCSGFLWGV TKQGYRCREC
GLCCHKHCRD QVKVECKKRP GAKGDAGPPG APVPSTPAPH ASCGSEENHS YTLSLEPETG
CQLRHAWTQT ESPHPSWETD TVPCPVMDPP STASSKLDS*
speed 1.01 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