Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999999873 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM950091)
  • known disease mutation: rs2394 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:131902466G>TN/A show variant in all transcripts   IGV
HGNC symbol ARG1
Ensembl transcript ID ENST00000476845
Genbank transcript ID N/A
UniProt peptide P05089
alteration type single base exchange
alteration region CDS
DNA changes c.413G>T
cDNA.470G>T
g.8183G>T
AA changes G138V Score: 109 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 138
frameshift no
known variant Reference ID: rs104893943
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs2394 (pathogenic for Arginase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950091)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950091)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950091)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.0950.998
5.7330.999
(flanking)-0.6390.703
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 increased8174wt: 0.9674 / mu: 0.9862 (marginal change - not scored)wt: GACAACCACAAGTGG
mu: GACAACCACAAGTGT		 CAAC|caca
Donor increased8176wt: 0.54 / mu: 0.87wt: CAACCACAAGTGGAA
mu: CAACCACAAGTGTAA		 ACCA|caag
Donor increased8181wt: 0.64 / mu: 0.87wt: ACAAGTGGAAACTTG
mu: ACAAGTGTAAACTTG		 AAGT|ggaa
distance from splice site 53
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      138TDINTPLTTTSGNLHGQPVSFLLK
mutated  not conserved    138TDINTPLTTTSVNLHGQPVSFLL
Ptroglodytes  all identical  ENSPTRG00000018600  138TDINTPLTTTSGNLHGQPVSFLL
Mmulatta  all identical  ENSMMUG00000017540  145TDINTPLTTTTGNLHGQPVSFLL
Fcatus  all identical  ENSFCAG00000002068  124TDINTPLTTTSGNLHGQPVSFLL
Mmusculus  all identical  ENSMUSG00000019987  138TDINTPLTTSSGNLHGQPVSFLL
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000002189  160DVNTALTTPTGNLHGQPMSFLL
Drerio  all identical  ENSDARG00000071703  158ADINTPLTTPTGNIHGQPMSYLI
Dmelanogaster  all identical  FBgn0023535  169ADINLHSTSQSGNIHGMPVSFLL
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
137139REGIONSubstrate binding.lost
140142HELIXmight get lost (downstream of altered splice site)
144148HELIXmight get lost (downstream of altered splice site)
150152HELIXmight get lost (downstream of altered splice site)
153155TURNmight get lost (downstream of altered splice site)
171173HELIXmight get lost (downstream of altered splice site)
174179STRANDmight get lost (downstream of altered splice site)
183183BINDINGSubstrate.might get lost (downstream of altered splice site)
184193HELIXmight get lost (downstream of altered splice site)
196199STRANDmight get lost (downstream of altered splice site)
200206HELIXmight get lost (downstream of altered splice site)
202202CONFLICTE -> K (in Ref. 3; AAL71547).might get lost (downstream of altered splice site)
208220HELIXmight get lost (downstream of altered splice site)
221223STRANDmight get lost (downstream of altered splice site)
227232STRANDmight get lost (downstream of altered splice site)
230230MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
232232METALManganese 1.might get lost (downstream of altered splice site)
232232METALManganese 2.might get lost (downstream of altered splice site)
233235HELIXmight get lost (downstream of altered splice site)
234234METALManganese 2.might get lost (downstream of altered splice site)
238240TURNmight get lost (downstream of altered splice site)
243246STRANDmight get lost (downstream of altered splice site)
254267HELIXmight get lost (downstream of altered splice site)
270276STRANDmight get lost (downstream of altered splice site)
280282HELIXmight get lost (downstream of altered splice site)
286303HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 711 / 711
position (AA) of stopcodon in wt / mu AA sequence 237 / 237
position of stopcodon in wt / mu cDNA 768 / 768
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 58 / 58
chromosome 6
strand 1
last intron/exon boundary 664
theoretical NMD boundary in CDS 556
length of CDS 711
coding sequence (CDS) position 413
cDNA position
(for ins/del: last normal base / first normal base)		 470
gDNA position
(for ins/del: last normal base / first normal base)		 8183
chromosomal position
(for ins/del: last normal base / first normal base)		 131902466
original gDNA sequence snippet TCCACTGACAACCACAAGTGGAAACTTGCATGGACAACCTG
altered gDNA sequence snippet TCCACTGACAACCACAAGTGTAAACTTGCATGGACAACCTG
original cDNA sequence snippet TCCACTGACAACCACAAGTGGAAACTTGCATGGACAACCTG
altered cDNA sequence snippet TCCACTGACAACCACAAGTGTAAACTTGCATGGACAACCTG
wildtype AA sequence MSAKSRTIGI IGAPFSKGQP RGGVEEGPTV LRKAGLLEKL KEQECDVKDY GDLPFADIPN
DSPFQIVKNP RSVGKASEQL AGKVAEVKKN GRISLVLGGD HSLAIGSISG HARVHPDLGV
IWVDAHTDIN TPLTTTSGNL HGQPVSFLLK ELKGKIPDVP GFSWVTPCIS AKDIVYIGLR
DVDPGEHYIL KTLGIKYFSM TEVTRTVNTA VAITLACFGL AREGNHKPID YLNPPK*
mutated AA sequence MSAKSRTIGI IGAPFSKGQP RGGVEEGPTV LRKAGLLEKL KEQECDVKDY GDLPFADIPN
DSPFQIVKNP RSVGKASEQL AGKVAEVKKN GRISLVLGGD HSLAIGSISG HARVHPDLGV
IWVDAHTDIN TPLTTTSVNL HGQPVSFLLK ELKGKIPDVP GFSWVTPCIS AKDIVYIGLR
DVDPGEHYIL KTLGIKYFSM TEVTRTVNTA VAITLACFGL AREGNHKPID YLNPPK*
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