Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999995172904117 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM950090)
  • known disease mutation: rs2393 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:131894454T>CN/A show variant in all transcripts   IGV
HGNC symbol ARG1
Ensembl transcript ID ENST00000368087
Genbank transcript ID NM_000045
UniProt peptide P05089
alteration type single base exchange
alteration region CDS
DNA changes c.32T>C
cDNA.171T>C
g.171T>C
AA changes I11T Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 11
frameshift no
known variant Reference ID: rs28941474
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs2393 (pathogenic for Arginase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950090)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950090)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950090)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.5970.864
3.970.887
(flanking)-0.6340.745
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased170wt: 0.20 / mu: 0.61wt: GGATTATTGGAGCTC
mu: GGATTACTGGAGCTC		 ATTA|ttgg
Donor marginally increased163wt: 0.6439 / mu: 0.7063 (marginal change - not scored)wt: ACCATAGGGATTATT
mu: ACCATAGGGATTACT		 CATA|ggga
distance from splice site 26
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      11 MSAKSRTIGIIGAPFSKGQPRGG
mutated  not conserved    11MSAKSRTIGITGAPFSKGQPRG
Ptroglodytes  all identical  ENSPTRG00000018600  11MSAKSRTIGIIGAPFSKGQPRG
Mmulatta  all identical  ENSMMUG00000017540  11MSAKSRTIGIIGAPFSKGQPRG
Fcatus  all identical  ENSFCAG00000002068  11MSSKSKSIGIIGVPFSKGQLK-
Mmusculus  all identical  ENSMUSG00000019987  11MSSKPKSLEIIGAPFSKGQPRG
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000002189  33VGLIGAPFAKGQPRP
Drerio  all identical  ENSDARG00000071703  31SVGIIGAPFSKGQQKD
Dmelanogaster  all identical  FBgn0023535  35QSLGIIGVPFAKGQAKQ
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
713STRANDlost
2226HELIXmight get lost (downstream of altered splice site)
2733HELIXmight get lost (downstream of altered splice site)
3642HELIXmight get lost (downstream of altered splice site)
4652STRANDmight get lost (downstream of altered splice site)
4848CONFLICTK -> E (in Ref. 3; AAL71547).might get lost (downstream of altered splice site)
6769STRANDmight get lost (downstream of altered splice site)
7089HELIXmight get lost (downstream of altered splice site)
8686CONFLICTE -> Q (in Ref. 1; AAA51776).might get lost (downstream of altered splice site)
9399STRANDmight get lost (downstream of altered splice site)
101101METALManganese 1.might get lost (downstream of altered splice site)
101103HELIXmight get lost (downstream of altered splice site)
104114HELIXmight get lost (downstream of altered splice site)
119126STRANDmight get lost (downstream of altered splice site)
124124METALManganese 2.might get lost (downstream of altered splice site)
124124METALManganese 1.might get lost (downstream of altered splice site)
126126METALManganese 2.might get lost (downstream of altered splice site)
126130REGIONSubstrate binding.might get lost (downstream of altered splice site)
128128METALManganese 1.might get lost (downstream of altered splice site)
132134TURNmight get lost (downstream of altered splice site)
137139REGIONSubstrate binding.might get lost (downstream of altered splice site)
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 2.might get lost (downstream of altered splice site)
232232METALManganese 1.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 969 / 969
position (AA) of stopcodon in wt / mu AA sequence 323 / 323
position of stopcodon in wt / mu cDNA 1108 / 1108
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 140 / 140
chromosome 6
strand 1
last intron/exon boundary 942
theoretical NMD boundary in CDS 752
length of CDS 969
coding sequence (CDS) position 32
cDNA position
(for ins/del: last normal base / first normal base)		 171
gDNA position
(for ins/del: last normal base / first normal base)		 171
chromosomal position
(for ins/del: last normal base / first normal base)		 131894454
original gDNA sequence snippet GTCCAGAACCATAGGGATTATTGGAGCTCCTTTCTCAAAGG
altered gDNA sequence snippet GTCCAGAACCATAGGGATTACTGGAGCTCCTTTCTCAAAGG
original cDNA sequence snippet GTCCAGAACCATAGGGATTATTGGAGCTCCTTTCTCAAAGG
altered cDNA sequence snippet GTCCAGAACCATAGGGATTACTGGAGCTCCTTTCTCAAAGG
wildtype AA sequence MSAKSRTIGI IGAPFSKGQP RGGVEEGPTV LRKAGLLEKL KEQECDVKDY GDLPFADIPN
DSPFQIVKNP RSVGKASEQL AGKVAEVKKN GRISLVLGGD HSLAIGSISG HARVHPDLGV
IWVDAHTDIN TPLTTTSGNL HGQPVSFLLK ELKGKIPDVP GFSWVTPCIS AKDIVYIGLR
DVDPGEHYIL KTLGIKYFSM TEVDRLGIGK VMEETLSYLL GRKKRPIHLS FDVDGLDPSF
TPATGTPVVG GLTYREGLYI TEEIYKTGLL SGLDIMEVNP SLGKTPEEVT RTVNTAVAIT
LACFGLAREG NHKPIDYLNP PK*
mutated AA sequence MSAKSRTIGI TGAPFSKGQP RGGVEEGPTV LRKAGLLEKL KEQECDVKDY GDLPFADIPN
DSPFQIVKNP RSVGKASEQL AGKVAEVKKN GRISLVLGGD HSLAIGSISG HARVHPDLGV
IWVDAHTDIN TPLTTTSGNL HGQPVSFLLK ELKGKIPDVP GFSWVTPCIS AKDIVYIGLR
DVDPGEHYIL KTLGIKYFSM TEVDRLGIGK VMEETLSYLL GRKKRPIHLS FDVDGLDPSF
TPATGTPVVG GLTYREGLYI TEEIYKTGLL SGLDIMEVNP SLGKTPEEVT RTVNTAVAIT
LACFGLAREG NHKPIDYLNP PK*
speed 1.32 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