Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 5.90950428153431e-12 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM910048)
  • known disease mutation: rs2389 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:131904948C>GN/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.611C>G
cDNA.668C>G
g.10665C>G
AA changes T204S Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 204
frameshift no
known variant Reference ID: rs104893942
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs2389 (pathogenic for Arginase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM910048)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910048)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910048)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.2590.095
1.0510.1
(flanking)0.1870.093
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 increased10657wt: 0.2407 / mu: 0.2524 (marginal change - not scored)wt: CCAGAAGAAGTAACT
mu: CCAGAAGAAGTAAGT		 AGAA|gaag
Donor decreased10660wt: 0.90 / mu: 0.77wt: GAAGAAGTAACTCGA
mu: GAAGAAGTAAGTCGA		 AGAA|gtaa
Donor increased10659wt: 0.72 / mu: 1.00wt: AGAAGAAGTAACTCG
mu: AGAAGAAGTAAGTCG		 AAGA|agta
Donor increased10664wt: 0.25 / mu: 0.97wt: AAGTAACTCGAACAG
mu: AAGTAAGTCGAACAG		 GTAA|ctcg
distance from splice site 5
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      204LGIKYFSMTEVTRTVNTAVAITLA
mutated  all conserved    204LGIKYFSMTEVSRTVNTAVAITL
Ptroglodytes  not conserved  ENSPTRG00000018600  204LGIKYFSMTEVDR
Mmulatta  not conserved  ENSMMUG00000017540  211LGIKYFSMTEVDR
Fcatus  all identical  ENSFCAG00000002068  276EVTRTVNTAVTVTL
Mmusculus  not conserved  ENSMUSG00000019987  204LGIKYFSMTEVDK
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000002189  226LGAKVFSMTEVDR
Drerio  not conserved  ENSDARG00000071703  224LGIKTFSMTEVDR
Dmelanogaster  not conserved  FBgn0023535  235VGIRYYAMDTIDR
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
200206HELIXlost
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 611
cDNA position
(for ins/del: last normal base / first normal base)		 668
gDNA position
(for ins/del: last normal base / first normal base)		 10665
chromosomal position
(for ins/del: last normal base / first normal base)		 131904948
original gDNA sequence snippet GAAGACACCAGAAGAAGTAACTCGAACAGTGAACACAGCAG
altered gDNA sequence snippet GAAGACACCAGAAGAAGTAAGTCGAACAGTGAACACAGCAG
original cDNA sequence snippet CTTTTCAATGACTGAAGTAACTCGAACAGTGAACACAGCAG
altered cDNA sequence snippet CTTTTCAATGACTGAAGTAAGTCGAACAGTGAACACAGCAG
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 TPLTTTSGNL HGQPVSFLLK ELKGKIPDVP GFSWVTPCIS AKDIVYIGLR
DVDPGEHYIL KTLGIKYFSM TEVSRTVNTA VAITLACFGL AREGNHKPID YLNPPK*
speed 1.27 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