Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.000250721754984067 (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) chr12:89916811C>TN/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.1516G>A
cDNA.1773G>A
g.1773G>A
AA changes V506I Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 506
frameshift no
known variant Reference ID: rs2230283
databasehomozygous (T/T)heterozygousallele carriers
1000G138752890
ExAC49282291127839
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.2450.992
5.6530.996
(flanking)0.2190.536
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 increased1764wt: 0.2734 / mu: 0.2799 (marginal change - not scored)wt: AGTTATGTGCAGAGG
mu: AGTTATGTGCAGAGA		 TTAT|gtgc
Donor increased1775wt: 0.27 / mu: 0.66wt: GAGGTACCTGAGCAA
mu: GAGATACCTGAGCAA		 GGTA|cctg
Donor marginally increased1771wt: 0.9004 / mu: 0.9102 (marginal change - not scored)wt: TGCAGAGGTACCTGA
mu: TGCAGAGATACCTGA		 CAGA|ggta
Donor marginally increased1766wt: 0.9712 / mu: 0.9751 (marginal change - not scored)wt: TTATGTGCAGAGGTA
mu: TTATGTGCAGAGATA		 ATGT|gcag
Donor gained17690.74mu: TGTGCAGAGATACCT TGCA|gaga
distance from splice site 1773
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      506RFNSVTELCAEVPEQKNYVGMQNC
mutated  all conserved    506RFNSVTELCAEIPEQKNYVGMQN
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000090035  506RFNSVTELCAEVPQQKDYVGMQN
Ggallus  no alignment  ENSGALG00000011215  n/a
Trubripes  all identical  ENSTRUG00000011585  512RFNTVTELCAEVVEGRASIGMKH
Drerio  all identical  ENSDARG00000012745  511RFNSVTELCAEVQDGMTHIGMKH
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
36578TOPO_DOMLumenal (Potential).lost
444577DOMAINRicin B-type lectin.lost
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 1516
cDNA position
(for ins/del: last normal base / first normal base)		 1773
gDNA position
(for ins/del: last normal base / first normal base)		 1773
chromosomal position
(for ins/del: last normal base / first normal base)		 89916811
original gDNA sequence snippet TGACAGAGTTATGTGCAGAGGTACCTGAGCAAAAAAATTAT
altered gDNA sequence snippet TGACAGAGTTATGTGCAGAGATACCTGAGCAAAAAAATTAT
original cDNA sequence snippet TGACAGAGTTATGTGCAGAGGTACCTGAGCAAAAAAATTAT
altered cDNA sequence snippet TGACAGAGTTATGTGCAGAGATACCTGAGCAAAAAAATTAT
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 WNTFEFYMQI GEPMIGGFDW RLTFQWHSVP KQERDRRISR
IDPIRSPTMA GGLFAVSKKY FQYLGTYDTG MEVWGGENLE LSFRVWQCGG KLEIHPCSHV
GHVFPKRAPY ARPNFLQNTA RAAEVWMDEY KEHFYNRNPP ARKEAYGDIS ERKLLRERLR
CKSFDWYLKN VFPNLHVPED RPGWHGAIRS RGISSECLDY NSPDNNPTGA NLSLFGCHGQ
GGNQFFEYTS NKEIRFNSVT ELCAEIPEQK NYVGMQNCPK DGFPVPANII WHFKEDGTIF
HPHSGLCLSA YRTPEGRPDV QMRTCDALDK NQIWSFEK*
speed 1.05 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