Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999865 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:65150485C>TN/A show variant in all transcripts   IGV
HGNC symbol GNS
Ensembl transcript ID ENST00000543646
Genbank transcript ID N/A
UniProt peptide P15586
alteration type single base exchange
alteration region CDS
DNA changes c.250G>A
cDNA.380G>A
g.2743G>A
AA changes G84R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 84
frameshift no
known variant Reference ID: rs2620733
databasehomozygous (T/T)heterozygousallele carriers
1000G15267932319
ExAC226723544621
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.0660.103
-0.0670.013
(flanking)0.1330.005
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 increased2743wt: 0.9982 / mu: 0.9992 (marginal change - not scored)wt: AGCTAGGACAAGAGC
mu: AGCTAAGACAAGAGC		 CTAG|gaca
Donor increased2738wt: 0.91 / mu: 1.00wt: GGAAGAGCTAGGACA
mu: GGAAGAGCTAAGACA		 AAGA|gcta
Donor marginally increased2745wt: 0.8438 / mu: 0.9211 (marginal change - not scored)wt: CTAGGACAAGAGCAT
mu: CTAAGACAAGAGCAT		 AGGA|caag
distance from splice site 39
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      84NCQTGLQGEELGQEHLRTYLEPSR
mutated  not conserved    84NCQTGLQGEELRQEHLRTYLEPS
Ptroglodytes  not conserved  ENSPTRG00000005176  84-----------------------
Mmulatta  not conserved  ENSMMUG00000006481  84-----------------------
Fcatus  not conserved  ENSFCAG00000000437  85-----------------------
Mmusculus  not conserved  ENSMUSG00000034707  76-----------------------
Ggallus  not conserved  ENSGALG00000009856  76----------------
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000023766  70-----------------------
Dmelanogaster  not conserved  FBgn0033836  65-----------------------
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000007318  90-----------------------
protein features
start (aa)end (aa)featuredetails 
9191MOD_RES3-oxoalanine (Cys) (By similarity).might get lost (downstream of altered splice site)
9191METALCalcium; via 3-oxoalanine (By similarity).might get lost (downstream of altered splice site)
111111CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
117117CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
183183CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
198198CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
210210CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
252252CONFLICTF -> C (in Ref. 2; BAD97204).might get lost (downstream of altered splice site)
279279CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
317317CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
326326METALCalcium (By similarity).might get lost (downstream of altered splice site)
327327METALCalcium (By similarity).might get lost (downstream of altered splice site)
362362CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
387387CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
405405CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
422422CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
449449CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
480480CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1755 / 1755
position (AA) of stopcodon in wt / mu AA sequence 585 / 585
position of stopcodon in wt / mu cDNA 1885 / 1885
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 131 / 131
chromosome 12
strand -1
last intron/exon boundary 1807
theoretical NMD boundary in CDS 1626
length of CDS 1755
coding sequence (CDS) position 250
cDNA position
(for ins/del: last normal base / first normal base)		 380
gDNA position
(for ins/del: last normal base / first normal base)		 2743
chromosomal position
(for ins/del: last normal base / first normal base)		 65150485
original gDNA sequence snippet GACTCCAAGGGGAAGAGCTAGGACAAGAGCATTTGAGAACT
altered gDNA sequence snippet GACTCCAAGGGGAAGAGCTAAGACAAGAGCATTTGAGAACT
original cDNA sequence snippet GACTCCAAGGGGAAGAGCTAGGACAAGAGCATTTGAGAACT
altered cDNA sequence snippet GACTCCAAGGGGAAGAGCTAAGACAAGAGCATTTGAGAACT
wildtype AA sequence MRLLPLAPGR LRRGSPRHLP SCSPALLLLV LGGCLGVFGV AAGTRRPNVV LLLTDDQDEV
LGGMAFSEYS TTNCQTGLQG EELGQEHLRT YLEPSRTPLK KTKALIGEMG MTFSSAYVPS
ALCCPSRASI LTGKYPHNHH VVNNTLEGNC SSKSWQKIQE PNTFPAILRS MCGYQTFFAG
KYLNEYGAPD AGGLEHVPLG WSYWYALEKN SKYYNYTLSI NGKARKHGEN YSVDYLTDVL
ANVSLDFLDY KSNFEPFFMM IATPAPHSPW TAAPQYQKAF QNVFAPRNKN FNIHGTNKHW
LIRQAKTPMT NSSIQFLDNA FRKRWQTLLS VDDLVEKLVK RLEFTGELNN TYIFYTSDNG
YHTGQFSLPI DKRQLYEFDI KVPLLVRGPG IKPNQTSKML VANIDLGPTI LDIAGYDLNK
TQMDGMSLLP ILRGASNLTW RSDVLVEYQG EGRNVTDPTC PSLSPGVSQC FPDCVCEDAY
NNTYACVRTM SALWNLQYCE FDDQEVFVEV YNLTADPDQI TNIAKTIDPE LLGKMNYRLM
MLQSCSGPTC RTPGVFDPGY RFDPRLMFSN RGSVRTRRFS KHLL*
mutated AA sequence MRLLPLAPGR LRRGSPRHLP SCSPALLLLV LGGCLGVFGV AAGTRRPNVV LLLTDDQDEV
LGGMAFSEYS TTNCQTGLQG EELRQEHLRT YLEPSRTPLK KTKALIGEMG MTFSSAYVPS
ALCCPSRASI LTGKYPHNHH VVNNTLEGNC SSKSWQKIQE PNTFPAILRS MCGYQTFFAG
KYLNEYGAPD AGGLEHVPLG WSYWYALEKN SKYYNYTLSI NGKARKHGEN YSVDYLTDVL
ANVSLDFLDY KSNFEPFFMM IATPAPHSPW TAAPQYQKAF QNVFAPRNKN FNIHGTNKHW
LIRQAKTPMT NSSIQFLDNA FRKRWQTLLS VDDLVEKLVK RLEFTGELNN TYIFYTSDNG
YHTGQFSLPI DKRQLYEFDI KVPLLVRGPG IKPNQTSKML VANIDLGPTI LDIAGYDLNK
TQMDGMSLLP ILRGASNLTW RSDVLVEYQG EGRNVTDPTC PSLSPGVSQC FPDCVCEDAY
NNTYACVRTM SALWNLQYCE FDDQEVFVEV YNLTADPDQI TNIAKTIDPE LLGKMNYRLM
MLQSCSGPTC RTPGVFDPGY RFDPRLMFSN RGSVRTRRFS KHLL*
speed 0.64 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