Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999987150053 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM065199)
  • known disease mutation: rs7796 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:166615372G>TN/A show variant in all transcripts   IGV
HGNC symbol GALNT3
Ensembl transcript ID ENST00000409882
Genbank transcript ID N/A
UniProt peptide Q14435
alteration type single base exchange
alteration region CDS
DNA changes c.290C>A
cDNA.303C>A
g.35821C>A
AA changes T97K Score: 78 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 97
frameshift no
known variant Reference ID: rs137853091
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs7796 (pathogenic for Hyperphosphatemic familial tumoral calcinosis 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM065199)

known disease mutation at this position, please check HGMD for details (HGMD ID CM065199)
known disease mutation at this position, please check HGMD for details (HGMD ID CM065199)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3030.999
5.6511
(flanking)4.6791
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Acceptor lost35818.5sequence motif lost- wt: ttca|GAAC
 mu: ttca.GAAA
Donor gained358170.99mu: TTTTCAGAAAACCCA TTCA|gaaa
distance from splice site 3
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      97QRRKDETYPIKTPTFAGGLFSISK
mutated  not conserved    97QRRKDETYPIKKPTFAGGLFSIS
Ptroglodytes  all identical  ENSPTRG00000012593  359QRRKDETYPIKTPTFAGGLFSIS
Mmulatta  all identical  ENSMMUG00000019177  359QRRKDETYPIKTPTFAGGLFSIS
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000026994  359QRRKDETYPIKTPTFAGGLFSIS
Ggallus  all identical  ENSGALG00000010960  358KRRKDETYPIRTPTFAGGLFSIS
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000063724  43RRRKDETYPIKTPTFAGGLFSIS
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000020839  351TRRKDETYPIKTPTFAGGLFSIS
protein features
start (aa)end (aa)featuredetails 
38633TOPO_DOMLumenal (Potential).lost
132132CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
184293REGIONCatalytic subdomain A.might get lost (downstream of altered splice site)
297297CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
356418REGIONCatalytic subdomain B.might get lost (downstream of altered splice site)
481481CONFLICTQ -> R (in Ref. 1; CAA63371).might get lost (downstream of altered splice site)
484484CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
504630DOMAINRicin B-type lectin.might get lost (downstream of altered splice site)
517517DISULFIDBy similarity.might get lost (downstream of altered splice site)
535535DISULFIDBy similarity.might get lost (downstream of altered splice site)
561561DISULFIDBy similarity.might get lost (downstream of altered splice site)
574574DISULFIDBy similarity.might get lost (downstream of altered splice site)
605605DISULFIDBy similarity.might get lost (downstream of altered splice site)
618618DISULFIDBy similarity.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1116 / 1116
position (AA) of stopcodon in wt / mu AA sequence 372 / 372
position of stopcodon in wt / mu cDNA 1129 / 1129
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 14 / 14
chromosome 2
strand -1
last intron/exon boundary 1007
theoretical NMD boundary in CDS 943
length of CDS 1116
coding sequence (CDS) position 290
cDNA position
(for ins/del: last normal base / first normal base)		 303
gDNA position
(for ins/del: last normal base / first normal base)		 35821
chromosomal position
(for ins/del: last normal base / first normal base)		 166615372
original gDNA sequence snippet CAATGGATTATTTTTCAGAACACCCACTTTTGCAGGAGGAC
altered gDNA sequence snippet CAATGGATTATTTTTCAGAAAACCCACTTTTGCAGGAGGAC
original cDNA sequence snippet TGAAACCTACCCAATTAAAACACCCACTTTTGCAGGAGGAC
altered cDNA sequence snippet TGAAACCTACCCAATTAAAAAACCCACTTTTGCAGGAGGAC
wildtype AA sequence MYGYGCNIFP PSPSNLKGEC FYGWLEPLLA RIAENYTAVV SPDIASIDLN TFEFNKPSPY
GSNHNRGNFD WSLSFGWESL PDHEKQRRKD ETYPIKTPTF AGGLFSISKE YFEYIGSYDE
EMEIWGGENI EMSFRVWQCG GQLEIMPCSV VGHVFRSKSP HSFPKGTQVI ARNQVRLAEV
WMDEYKEIFY RRNTDAAKIV KQKAFGDLSK RFEIKHRLQC KNFTWYLNNI YPEVYVPDLN
PVISGYIKSV GQPLCLDVGE NNQGGKPLIM YTCHGLGGNQ YFEYSAQHEI RHNIQKELCL
HAAQGLVQLK ACTYKGHKTV VTGEQIWEIQ KDQLLYNPFL KMCLSANGEH PSLVSCNPSD
PLQKWILSQN D*
mutated AA sequence MYGYGCNIFP PSPSNLKGEC FYGWLEPLLA RIAENYTAVV SPDIASIDLN TFEFNKPSPY
GSNHNRGNFD WSLSFGWESL PDHEKQRRKD ETYPIKKPTF AGGLFSISKE YFEYIGSYDE
EMEIWGGENI EMSFRVWQCG GQLEIMPCSV VGHVFRSKSP HSFPKGTQVI ARNQVRLAEV
WMDEYKEIFY RRNTDAAKIV KQKAFGDLSK RFEIKHRLQC KNFTWYLNNI YPEVYVPDLN
PVISGYIKSV GQPLCLDVGE NNQGGKPLIM YTCHGLGGNQ YFEYSAQHEI RHNIQKELCL
HAAQGLVQLK ACTYKGHKTV VTGEQIWEIQ KDQLLYNPFL KMCLSANGEH PSLVSCNPSD
PLQKWILSQN D*
speed 0.82 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