Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.000109120079758181 (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 CM167853)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:56771251A>CN/A show variant in all transcripts   IGV
HGNC symbol ARHGEF3
Ensembl transcript ID ENST00000495373
Genbank transcript ID N/A
UniProt peptide Q9NR81
alteration type single base exchange
alteration region CDS
DNA changes c.1003T>G
cDNA.1154T>G
g.342107T>G
AA changes L335V Score: 32 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 335
frameshift no
known variant Reference ID: rs3772219
databasehomozygous (C/C)heterozygousallele carriers
1000G48511071592
ExAC77401728725027

known disease mutation at this position, please check HGMD for details (HGMD ID CM167853)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.2061
0.6290.994
(flanking)0.9160.991
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased342103wt: 0.5047 / mu: 0.5337 (marginal change - not scored)wt: TCCCTGATCGACAGCTCTCGAGTCTTGTGTTGTCATGGTGA
mu: TCCCTGATCGACAGCTCTCGAGTCGTGTGTTGTCATGGTGA		 tcga|GTCT
Donor marginally increased342108wt: 0.2383 / mu: 0.2609 (marginal change - not scored)wt: AGTCTTGTGTTGTCA
mu: AGTCGTGTGTTGTCA		 TCTT|gtgt
Donor marginally increased342103wt: 0.9494 / mu: 0.9913 (marginal change - not scored)wt: TCTCGAGTCTTGTGT
mu: TCTCGAGTCGTGTGT		 TCGA|gtct
Donor gained3421010.46mu: GCTCTCGAGTCGTGT TCTC|gagt
distance from splice site 39
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      335QKDSLIDSSRVLCCHGELKNNRGV
mutated  all conserved    335QKDSLIDSSRVVCCHGELKNNRG
Ptroglodytes  all identical  ENSPTRG00000015041  367DSSRVLCCHGELKNNRG
Mmulatta  all identical  ENSMMUG00000010163  367DSSRVLCCHGELKNNRG
Fcatus  all identical  ENSFCAG00000003569  367DSSRVLCCHGELKNNRG
Mmusculus  all identical  ENSMUSG00000021895  341QKDSLIDSSRVLCCHGELKNNRG
Ggallus  all identical  ENSGALG00000005481  335QRDSLIDNSRVLCCHGELKNNRG
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000013834  368ESSRILICHGELKNNRG
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000000921  303RVLLCVQKDLINSRS
protein features
start (aa)end (aa)featuredetails 
291449DOMAINPH.lost
410410CONFLICTI -> T (in Ref. 3; AAP97313).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1251 / 1251
position (AA) of stopcodon in wt / mu AA sequence 417 / 417
position of stopcodon in wt / mu cDNA 1402 / 1402
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 152 / 152
chromosome 3
strand -1
last intron/exon boundary 1193
theoretical NMD boundary in CDS 991
length of CDS 1251
coding sequence (CDS) position 1003
cDNA position
(for ins/del: last normal base / first normal base)		 1154
gDNA position
(for ins/del: last normal base / first normal base)		 342107
chromosomal position
(for ins/del: last normal base / first normal base)		 56771251
original gDNA sequence snippet TGATCGACAGCTCTCGAGTCTTGTGTTGTCATGGTGAACTG
altered gDNA sequence snippet TGATCGACAGCTCTCGAGTCGTGTGTTGTCATGGTGAACTG
original cDNA sequence snippet TGATCGACAGCTCTCGAGTCTTGTGTTGTCATGGTGAACTG
altered cDNA sequence snippet TGATCGACAGCTCTCGAGTCGTGTGTTGTCATGGTGAACTG
wildtype AA sequence MVAKDYPFYL TVKRANCSLE LPPASGPAKD AEEPSNKRVK PLSRVTSLAN LIPPVKATPL
KRFSQTLQRS ISFRSESRPD ILAPRPWSRN AAPSSTKRRD SKLWSETFDV CVNQMLTSKE
IKRQEAIFEL SQGEEDLIED LKLAKKAYHD PMLKLSIMTE QELNQIFGTL DSLIPLHEEL
LSQLRDVRKP DGSTEHVGPI LVGWLPCLSS YDSYCSNQVA AKALLDHKKQ DHRVQDFLQR
CLESPFSRKL DLWNFLDIPR SRLVKYPLLL REILRHTPND NPDQQHLEEA INIIQGIVAE
INTKTGESEC RYYKERLLYL EEGQKDSLID SSRVLCCHGE LKNNRGVKLH VFLFQEVLVI
TRAVTHNEQL CYQLYRQPIP VKDLLLEDLQ DGEVRLGGSL RGAFSNNERS MDSSRG*
mutated AA sequence MVAKDYPFYL TVKRANCSLE LPPASGPAKD AEEPSNKRVK PLSRVTSLAN LIPPVKATPL
KRFSQTLQRS ISFRSESRPD ILAPRPWSRN AAPSSTKRRD SKLWSETFDV CVNQMLTSKE
IKRQEAIFEL SQGEEDLIED LKLAKKAYHD PMLKLSIMTE QELNQIFGTL DSLIPLHEEL
LSQLRDVRKP DGSTEHVGPI LVGWLPCLSS YDSYCSNQVA AKALLDHKKQ DHRVQDFLQR
CLESPFSRKL DLWNFLDIPR SRLVKYPLLL REILRHTPND NPDQQHLEEA INIIQGIVAE
INTKTGESEC RYYKERLLYL EEGQKDSLID SSRVVCCHGE LKNNRGVKLH VFLFQEVLVI
TRAVTHNEQL CYQLYRQPIP VKDLLLEDLQ DGEVRLGGSL RGAFSNNERS MDSSRG*
speed 1.24 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