Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.99938097846693 (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) chr9:35662251T>CN/A show variant in all transcripts   IGV
HGNC symbol ARHGEF39
Ensembl transcript ID ENST00000378387
Genbank transcript ID NM_032818
UniProt peptide Q8N4T4
alteration type single base exchange
alteration region CDS
DNA changes c.917A>G
cDNA.1035A>G
g.13613A>G
AA changes H306R Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 306
frameshift no
known variant Reference ID: rs2297879
databasehomozygous (C/C)heterozygousallele carriers
1000G3019291230
ExAC67631924126004
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
H2BK20ac, Histone, Histone 2B Lysine 20 Acetylation
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K36ac, Histone, Histone 3 Lysine 36 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)-2.3930.036
0.6690.408
(flanking)0.5410.64
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased13618wt: 0.21 / mu: 0.26wt: AGCTGTCCTTCCCTCATGAGAAGCTACTGCTTATGTCCACA
mu: AGCTGTCCTTCCCTCGTGAGAAGCTACTGCTTATGTCCACA		 gaga|AGCT
Acc marginally increased13614wt: 0.9612 / mu: 0.9644 (marginal change - not scored)wt: CTCTAGCTGTCCTTCCCTCATGAGAAGCTACTGCTTATGTC
mu: CTCTAGCTGTCCTTCCCTCGTGAGAAGCTACTGCTTATGTC		 tcat|GAGA
Acc increased13612wt: 0.78 / mu: 0.93wt: CTCTCTAGCTGTCCTTCCCTCATGAGAAGCTACTGCTTATG
mu: CTCTCTAGCTGTCCTTCCCTCGTGAGAAGCTACTGCTTATG		 cctc|ATGA
Acc increased13605wt: 0.60 / mu: 0.76wt: GTGGTCTCTCTCTAGCTGTCCTTCCCTCATGAGAAGCTACT
mu: GTGGTCTCTCTCTAGCTGTCCTTCCCTCGTGAGAAGCTACT		 gtcc|TTCC
Acc increased13607wt: 0.43 / mu: 0.52wt: GGTCTCTCTCTAGCTGTCCTTCCCTCATGAGAAGCTACTGC
mu: GGTCTCTCTCTAGCTGTCCTTCCCTCGTGAGAAGCTACTGC		 cctt|CCCT
Acc marginally increased13609wt: 0.8486 / mu: 0.9262 (marginal change - not scored)wt: TCTCTCTCTAGCTGTCCTTCCCTCATGAGAAGCTACTGCTT
mu: TCTCTCTCTAGCTGTCCTTCCCTCGTGAGAAGCTACTGCTT		 ttcc|CTCA
distance from splice site 14
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      306PCGGLLSLSFPHEKLLLMSTDQEE
mutated  not conserved    306SLSFPREKLLLMSTDQE
Ptroglodytes  all identical  ENSPTRG00000020915  306SLSFPHEKLLLMSTDQE
Mmulatta  all identical  ENSMMUG00000016323  306SLSFPHEKLLLMSTDQE
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000051517  306SLSFPHEKLLLMSTDQE
Ggallus  all identical  ENSGALG00000002599  314E-GGLLSLSFPHKT
Trubripes  not conserved  ENSTRUG00000012270  312NFPKAKLLLMSSSQE
Drerio  not conserved  ENSDARG00000013476  310ARAKLLLMSDDQV
Dmelanogaster  no alignment  FBgn0035761  n/a
Celegans  no alignment  C02F12.4  n/a
Xtropicalis  not conserved  ENSXETG00000020139  319R-GGLISLTFAKEKLLLMSTDQK
protein features
start (aa)end (aa)featuredetails 
227331DOMAINPH.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1008 / 1008
position (AA) of stopcodon in wt / mu AA sequence 336 / 336
position of stopcodon in wt / mu cDNA 1126 / 1126
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 119 / 119
chromosome 9
strand -1
last intron/exon boundary 1111
theoretical NMD boundary in CDS 942
length of CDS 1008
coding sequence (CDS) position 917
cDNA position
(for ins/del: last normal base / first normal base)		 1035
gDNA position
(for ins/del: last normal base / first normal base)		 13613
chromosomal position
(for ins/del: last normal base / first normal base)		 35662251
original gDNA sequence snippet TCTCTAGCTGTCCTTCCCTCATGAGAAGCTACTGCTTATGT
altered gDNA sequence snippet TCTCTAGCTGTCCTTCCCTCGTGAGAAGCTACTGCTTATGT
original cDNA sequence snippet GCTCAGTCTGTCCTTCCCTCATGAGAAGCTACTGCTTATGT
altered cDNA sequence snippet GCTCAGTCTGTCCTTCCCTCGTGAGAAGCTACTGCTTATGT
wildtype AA sequence MELSCPGSRC PVQEQRARWE RKRACTAREL LETERRYQEQ LGLVATYFLG ILKAKGTLRP
PERQALFGSW ELIYGASQEL LPYLEGGCWG QGLEGFCRHL ELYNQFAANS ERSQTTLQEQ
LKKNKGFRRF VRLQEGRPEF GGLQLQDLLP LPLQRLQQYE NLVVALAENT GPNSPDHQQL
TRAARLISET AQRVHTIGQK QKNDQHLRRV QALLSGRQAK GLTSGRWFLR QGWLLVVPPH
GEPRPRMFFL FTDVLLMAKP RPPLHLLRSG TFACKALYPM AQCHLSRVFG HSGGPCGGLL
SLSFPHEKLL LMSTDQEELS RWYHSLTWAI SSQKN*
mutated AA sequence MELSCPGSRC PVQEQRARWE RKRACTAREL LETERRYQEQ LGLVATYFLG ILKAKGTLRP
PERQALFGSW ELIYGASQEL LPYLEGGCWG QGLEGFCRHL ELYNQFAANS ERSQTTLQEQ
LKKNKGFRRF VRLQEGRPEF GGLQLQDLLP LPLQRLQQYE NLVVALAENT GPNSPDHQQL
TRAARLISET AQRVHTIGQK QKNDQHLRRV QALLSGRQAK GLTSGRWFLR QGWLLVVPPH
GEPRPRMFFL FTDVLLMAKP RPPLHLLRSG TFACKALYPM AQCHLSRVFG HSGGPCGGLL
SLSFPREKLL LMSTDQEELS RWYHSLTWAI SSQKN*
speed 0.10 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