Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.998607451574599 (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) chr12:89917518A>GN/A show variant in all transcripts   IGV
HGNC symbol GALNT4
Ensembl transcript ID ENST00000529983
Genbank transcript ID NM_003774
UniProt peptide Q8N4A0
alteration type single base exchange
alteration region CDS
DNA changes c.809T>C
cDNA.1066T>C
g.1066T>C
AA changes I270T Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 270
frameshift no
known variant Reference ID: rs2230281
databasehomozygous (G/G)heterozygousallele carriers
1000G13579602317
ExAC28473-241794294
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-3.6970.002
2.370.955
(flanking)1.0960.972
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased1058wt: 0.40 / mu: 0.52wt: TGGAATACTTTTGAATTCTATATGCAGATAGGGGAGCCCAT
mu: TGGAATACTTTTGAATTCTATATGCAGACAGGGGAGCCCAT		 ctat|ATGC
Acc marginally increased1060wt: 0.9299 / mu: 0.9522 (marginal change - not scored)wt: GAATACTTTTGAATTCTATATGCAGATAGGGGAGCCCATGA
mu: GAATACTTTTGAATTCTATATGCAGACAGGGGAGCCCATGA		 atat|GCAG
Donor marginally increased1063wt: 0.9385 / mu: 0.9562 (marginal change - not scored)wt: TATGCAGATAGGGGA
mu: TATGCAGACAGGGGA		 TGCA|gata
Donor marginally increased1067wt: 0.9777 / mu: 0.9957 (marginal change - not scored)wt: CAGATAGGGGAGCCC
mu: CAGACAGGGGAGCCC		 GATA|gggg
distance from splice site 1066
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      270IDWNTFEFYMQIGEPMIGGFDWRL
mutated  not conserved    270IDWNTFEFYMQTGEPMIGGFDWR
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000090035  270IDWNTFEFYMQTGEPMIGGFDWR
Ggallus  no alignment  ENSGALG00000011215  n/a
Trubripes  not conserved  ENSTRUG00000011585  276IDWNTFEFYMQTEEPMIGGFDWR
Drerio  not conserved  ENSDARG00000012745  275IDWNTFEFYMQTEEPMVGGFDWR
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
36578TOPO_DOMLumenal (Potential).lost
303365REGIONCatalytic subdomain B.might get lost (downstream of altered splice site)
444577DOMAINRicin B-type lectin.might get lost (downstream of altered splice site)
457457DISULFIDBy similarity.might get lost (downstream of altered splice site)
459459MUTAGEND->H: Affects the glycopeptide specificity and abolishes ability to glycosylate Muc1, Muc2 and Muc5AC.might get lost (downstream of altered splice site)
471471CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
477477DISULFIDBy similarity.might get lost (downstream of altered splice site)
503503DISULFIDBy similarity.might get lost (downstream of altered splice site)
518518DISULFIDBy similarity.might get lost (downstream of altered splice site)
547547DISULFIDBy similarity.might get lost (downstream of altered splice site)
565565DISULFIDBy similarity.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1737 / 1737
position (AA) of stopcodon in wt / mu AA sequence 579 / 579
position of stopcodon in wt / mu cDNA 1994 / 1994
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 258 / 258
chromosome 12
strand -1
last intron/exon boundary 1
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 1737
coding sequence (CDS) position 809
cDNA position
(for ins/del: last normal base / first normal base)		 1066
gDNA position
(for ins/del: last normal base / first normal base)		 1066
chromosomal position
(for ins/del: last normal base / first normal base)		 89917518
original gDNA sequence snippet TTTTGAATTCTATATGCAGATAGGGGAGCCCATGATTGGTG
altered gDNA sequence snippet TTTTGAATTCTATATGCAGACAGGGGAGCCCATGATTGGTG
original cDNA sequence snippet TTTTGAATTCTATATGCAGATAGGGGAGCCCATGATTGGTG
altered cDNA sequence snippet TTTTGAATTCTATATGCAGACAGGGGAGCCCATGATTGGTG
wildtype AA sequence MAVRWTWAGK SCLLLAFLTV AYIFVELLVS TFHASAGAGR ARELGSRRLS DLQKNTEDLS
RPLYKKPPAD SRALGEWGKA SKLQLNEDEL KQQEELIERY AINIYLSDRI SLHRHIEDKR
MYECKSQKFN YRTLPTTSVI IAFYNEAWST LLRTIHSVLE TSPAVLLKEI ILVDDLSDRV
YLKTQLETYI SNLDRVRLIR TNKREGLVRA RLIGATFATG DVLTFLDCHC ECNSGWLEPL
LERIGRDETA VVCPVIDTID WNTFEFYMQI GEPMIGGFDW RLTFQWHSVP KQERDRRISR
IDPIRSPTMA GGLFAVSKKY FQYLGTYDTG MEVWGGENLE LSFRVWQCGG KLEIHPCSHV
GHVFPKRAPY ARPNFLQNTA RAAEVWMDEY KEHFYNRNPP ARKEAYGDIS ERKLLRERLR
CKSFDWYLKN VFPNLHVPED RPGWHGAIRS RGISSECLDY NSPDNNPTGA NLSLFGCHGQ
GGNQFFEYTS NKEIRFNSVT ELCAEVPEQK NYVGMQNCPK DGFPVPANII WHFKEDGTIF
HPHSGLCLSA YRTPEGRPDV QMRTCDALDK NQIWSFEK*
mutated AA sequence MAVRWTWAGK SCLLLAFLTV AYIFVELLVS TFHASAGAGR ARELGSRRLS DLQKNTEDLS
RPLYKKPPAD SRALGEWGKA SKLQLNEDEL KQQEELIERY AINIYLSDRI SLHRHIEDKR
MYECKSQKFN YRTLPTTSVI IAFYNEAWST LLRTIHSVLE TSPAVLLKEI ILVDDLSDRV
YLKTQLETYI SNLDRVRLIR TNKREGLVRA RLIGATFATG DVLTFLDCHC ECNSGWLEPL
LERIGRDETA VVCPVIDTID WNTFEFYMQT GEPMIGGFDW RLTFQWHSVP KQERDRRISR
IDPIRSPTMA GGLFAVSKKY FQYLGTYDTG MEVWGGENLE LSFRVWQCGG KLEIHPCSHV
GHVFPKRAPY ARPNFLQNTA RAAEVWMDEY KEHFYNRNPP ARKEAYGDIS ERKLLRERLR
CKSFDWYLKN VFPNLHVPED RPGWHGAIRS RGISSECLDY NSPDNNPTGA NLSLFGCHGQ
GGNQFFEYTS NKEIRFNSVT ELCAEVPEQK NYVGMQNCPK DGFPVPANII WHFKEDGTIF
HPHSGLCLSA YRTPEGRPDV QMRTCDALDK NQIWSFEK*
speed 1.08 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