Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999998800698 (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 CM100499)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:57870155A>CN/A show variant in all transcripts   IGV
HGNC symbol ARHGAP9
Ensembl transcript ID ENST00000430041
Genbank transcript ID NM_001080156
UniProt peptide Q9BRR9
alteration type single base exchange
alteration region CDS
DNA changes c.556T>G
cDNA.988T>G
g.12443T>G
AA changes S186A Score: 99 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 186
frameshift no
known variant Reference ID: rs11544238
databasehomozygous (C/C)heterozygousallele carriers
1000G4349861420
ExAC16976-118515791

known disease mutation at this position, please check HGMD for details (HGMD ID CM100499)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
CTCF, Transcription Factor, CCCTC-binding factor (1)
DNase1, Open Chromatin, DNase1 Hypersensitive Site
EBF, Transcription Factor, EBF Transcription Factor Binding
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
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
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)3.2140.118
-0.3810.001
(flanking)-0.2840
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc lost124510.20wt: ACAGCGCCCTCCTCAGGCTGGGTGAGTGTGAGCGAGAGGCG ctgg|GTGA
Donor increased12445wt: 0.53 / mu: 0.60wt: TCCTCAGGCTGGGTG
mu: TCCGCAGGCTGGGTG		 CTCA|ggct
distance from splice site 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      186FYREPPPTAPSSGWGPAGSRPESS
mutated  all conserved    186PTAPSAGWGPAGSRPES
Ptroglodytes  all identical  ENSPTRG00000005134  370PTAPSSGWGPAGSRPES
Mmulatta  all identical  ENSMMUG00000022060  449PTAPSSGWGPAGSRPES
Fcatus  no alignment  ENSFCAG00000002082  n/a
Mmusculus  not conserved  ENSMUSG00000040345  107FYRERPPQSASLQG
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000013390  147FFKDPKSQNPES-WKPGNSRPES
Dmelanogaster  no homologue    
Celegans  not conserved  C38D4.5  438LYKDQKSAEKH---GKHYDAPQG
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
213247DOMAINWW.might get lost (downstream of altered splice site)
322336STRANDmight get lost (downstream of altered splice site)
322435DOMAINPH.might get lost (downstream of altered splice site)
346361STRANDmight get lost (downstream of altered splice site)
368370HELIXmight get lost (downstream of altered splice site)
380384STRANDmight get lost (downstream of altered splice site)
389392STRANDmight get lost (downstream of altered splice site)
394396TURNmight get lost (downstream of altered splice site)
398406STRANDmight get lost (downstream of altered splice site)
412416STRANDmight get lost (downstream of altered splice site)
420439HELIXmight get lost (downstream of altered splice site)
475475MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
542749DOMAINRho-GAP.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1644 / 1644
position (AA) of stopcodon in wt / mu AA sequence 548 / 548
position of stopcodon in wt / mu cDNA 2076 / 2076
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 433 / 433
chromosome 12
strand -1
last intron/exon boundary 1905
theoretical NMD boundary in CDS 1422
length of CDS 1644
coding sequence (CDS) position 556
cDNA position
(for ins/del: last normal base / first normal base)		 988
gDNA position
(for ins/del: last normal base / first normal base)		 12443
chromosomal position
(for ins/del: last normal base / first normal base)		 57870155
original gDNA sequence snippet CACCGCCGACAGCGCCCTCCTCAGGCTGGGTGAGTGTGAGC
altered gDNA sequence snippet CACCGCCGACAGCGCCCTCCGCAGGCTGGGTGAGTGTGAGC
original cDNA sequence snippet CACCGCCGACAGCGCCCTCCTCAGGCTGGGGACCAGCGGGT
altered cDNA sequence snippet CACCGCCGACAGCGCCCTCCGCAGGCTGGGGACCAGCGGGT
wildtype AA sequence MSEPPVYCNL VDLRRCPRSP PPGPACPLLQ RLDAWEQHLD PNSGRCFYIN SLTGCKSWKP
PRRSRSETNP GSMEGTQTLK RNNDVLQPQA KGFRSDTGTP EPLDPQGSLS LSQRTSQLDP
PALQAPRPLP QLLDDPHEVE KSGLLNMTKI AQGGRKLRKN WGPSWVVLTG NSLVFYREPP
PTAPSSGWGP AGSRPESSVD LRGAALAHGR HLSSRRNVLH IRTIPGHEFL LQSDHETELR
AWHRALRTVI ERLDRENPLE LRLSGSGPAE LSAGEDEEEE SELVSKPLLR LSSRRSSIRG
PEGTEQNRVR NKLKRLIAKR PPLQSLQERG LLRDQVFGCQ LESLCQREGD TVPSFLRLCI
AAVDKRGLDV DGIYRVSGNL AVVQKLRFLV DRERAVTSDG RYVFPEQPGQ EGRLDLDSTE
WDDIHVVTGA LKLFLRELPQ PLVPPLLLPH FRAALALSES EQCLSQIQEL IGSMPKPNHD
TLRYLLEHLC RVIAHSDKNR MTPHNLGIVF GPTLFRPEQE TSDPAAHALY PGQLVQLMLT
NFTSLFP*
mutated AA sequence MSEPPVYCNL VDLRRCPRSP PPGPACPLLQ RLDAWEQHLD PNSGRCFYIN SLTGCKSWKP
PRRSRSETNP GSMEGTQTLK RNNDVLQPQA KGFRSDTGTP EPLDPQGSLS LSQRTSQLDP
PALQAPRPLP QLLDDPHEVE KSGLLNMTKI AQGGRKLRKN WGPSWVVLTG NSLVFYREPP
PTAPSAGWGP AGSRPESSVD LRGAALAHGR HLSSRRNVLH IRTIPGHEFL LQSDHETELR
AWHRALRTVI ERLDRENPLE LRLSGSGPAE LSAGEDEEEE SELVSKPLLR LSSRRSSIRG
PEGTEQNRVR NKLKRLIAKR PPLQSLQERG LLRDQVFGCQ LESLCQREGD TVPSFLRLCI
AAVDKRGLDV DGIYRVSGNL AVVQKLRFLV DRERAVTSDG RYVFPEQPGQ EGRLDLDSTE
WDDIHVVTGA LKLFLRELPQ PLVPPLLLPH FRAALALSES EQCLSQIQEL IGSMPKPNHD
TLRYLLEHLC RVIAHSDKNR MTPHNLGIVF GPTLFRPEQE TSDPAAHALY PGQLVQLMLT
NFTSLFP*
speed 1.51 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