Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 1.47720585950402e-09 (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 ENST00000356962
Genbank transcript ID NM_001244438
UniProt peptide P05089
alteration type single base exchange
alteration region CDS
DNA changes c.893C>G
cDNA.951C>G
g.10665C>G
AA changes T298S Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 298
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 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 67
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      298NPSLGKTPEEVTRTVNTAVAITLA
mutated  all conserved    298NPSLGKTPEEVSRT
Ptroglodytes  all identical  ENSPTRG00000018600  290NPSLGKTPEEVTRT
Mmulatta  all identical  ENSMMUG00000017540  297NPSLGKTPEEVTRT
Fcatus  all identical  ENSFCAG00000002068  276NPSLGKTPEEVTRT
Mmusculus  not conserved  ENSMUSG00000019987  290NPTLGKTAEEVKST
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000002189  312NPLRGPTEHAIQSTVNTAVDL
Drerio  not conserved  ENSDARG00000071703  310NPKLGRTADEIKSTVNAAVD
Dmelanogaster  not conserved  FBgn0023535  318VRTTVESGLEILK
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
286303HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 993 / 993
position (AA) of stopcodon in wt / mu AA sequence 331 / 331
position of stopcodon in wt / mu cDNA 1051 / 1051
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 59 / 59
chromosome 6
strand 1
last intron/exon boundary 885
theoretical NMD boundary in CDS 776
length of CDS 993
coding sequence (CDS) position 893
cDNA position
(for ins/del: last normal base / first normal base)		 951
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 GAAGACACCAGAAGAAGTAACTCGAACAGTGAACACAGCAG
altered cDNA sequence snippet GAAGACACCAGAAGAAGTAAGTCGAACAGTGAACACAGCAG
wildtype AA sequence MSAKSRTIGI IGAPFSKGQP RGGVEEGPTV LRKAGLLEKL KEQVTQNFLI LECDVKDYGD
LPFADIPNDS PFQIVKNPRS VGKASEQLAG KVAEVKKNGR ISLVLGGDHS LAIGSISGHA
RVHPDLGVIW VDAHTDINTP LTTTSGNLHG QPVSFLLKEL KGKIPDVPGF SWVTPCISAK
DIVYIGLRDV DPGEHYILKT LGIKYFSMTE VDRLGIGKVM EETLSYLLGR KKRPIHLSFD
VDGLDPSFTP ATGTPVVGGL TYREGLYITE EIYKTGLLSG LDIMEVNPSL GKTPEEVTRT
VNTAVAITLA CFGLAREGNH KPIDYLNPPK *
mutated AA sequence MSAKSRTIGI IGAPFSKGQP RGGVEEGPTV LRKAGLLEKL KEQVTQNFLI LECDVKDYGD
LPFADIPNDS PFQIVKNPRS VGKASEQLAG KVAEVKKNGR ISLVLGGDHS LAIGSISGHA
RVHPDLGVIW VDAHTDINTP LTTTSGNLHG QPVSFLLKEL KGKIPDVPGF SWVTPCISAK
DIVYIGLRDV DPGEHYILKT LGIKYFSMTE VDRLGIGKVM EETLSYLLGR KKRPIHLSFD
VDGLDPSFTP ATGTPVVGGL TYREGLYITE EIYKTGLLSG LDIMEVNPSL GKTPEEVSRT
VNTAVAITLA CFGLAREGNH KPIDYLNPPK *
speed 1.30 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