Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999992851348 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM087940)
  • known disease mutation: rs2129 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:183963079C>TN/A show variant in all transcripts   IGV
HGNC symbol ALG3
Ensembl transcript ID ENST00000445626
Genbank transcript ID NM_001006941
UniProt peptide Q92685
alteration type single base exchange
alteration region CDS
DNA changes c.368G>A
cDNA.639G>A
g.4258G>A
AA changes R123Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 123
frameshift no
known variant Reference ID: rs119103236
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC055

known disease mutation: rs2129 (pathogenic for ALG3-CDG) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM087940)

known disease mutation at this position, please check HGMD for details (HGMD ID CM087940)
known disease mutation at this position, please check HGMD for details (HGMD ID CM087940)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0920.981
5.6851
(flanking)3.0161
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased4259wt: 0.5690 / mu: 0.5755 (marginal change - not scored)wt: CACTCCATCTTTGTGCTGCGGCTCTTCAATGACCCAGTGGC
mu: CACTCCATCTTTGTGCTGCAGCTCTTCAATGACCCAGTGGC		 gcgg|CTCT
Acc marginally increased4248wt: 0.8825 / mu: 0.8905 (marginal change - not scored)wt: CTTACCGTGTCCACTCCATCTTTGTGCTGCGGCTCTTCAAT
mu: CTTACCGTGTCCACTCCATCTTTGTGCTGCAGCTCTTCAAT		 atct|TTGT
distance from splice site 68
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      123ASYRVHSIFVLRLFNDPVAMVLLF
mutated  all conserved    123VLQLFNDPVAMVLL
Ptroglodytes  no homologue    
Mmulatta  no alignment  ENSMMUG00000018951  n/a
Fcatus  all identical  ENSFCAG00000016274  171ASYRVHSIFVLRLFNDPVAMALL
Mmusculus  all identical  ENSMUSG00000033809  171ASYRVHSIFVLRLFNDPVAMALL
Ggallus  all identical  ENSGALG00000008503  109ASYRIHSIFVLRLFNDPVAMAIL
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000053155  165ASYRIHSIFILRLFNDPVAMMLC
Dmelanogaster  all identical  FBgn0011297  174TSYRIHSIYVLRLFNDPVAVLLL
Celegans  all identical  K09E4.2  150TGYRIHSIFVLRLFNDPLAMMLF
Xtropicalis  all identical  ENSXETG00000017280  173ASYRVHSIFLLRLFNDPVAMVIL
protein features
start (aa)end (aa)featuredetails 
123143TRANSMEMHelical; (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1173 / 1173
position (AA) of stopcodon in wt / mu AA sequence 391 / 391
position of stopcodon in wt / mu cDNA 1444 / 1444
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 272 / 272
chromosome 3
strand -1
last intron/exon boundary 1282
theoretical NMD boundary in CDS 960
length of CDS 1173
coding sequence (CDS) position 368
cDNA position
(for ins/del: last normal base / first normal base)		 639
gDNA position
(for ins/del: last normal base / first normal base)		 4258
chromosomal position
(for ins/del: last normal base / first normal base)		 183963079
original gDNA sequence snippet CCACTCCATCTTTGTGCTGCGGCTCTTCAATGACCCAGTGG
altered gDNA sequence snippet CCACTCCATCTTTGTGCTGCAGCTCTTCAATGACCCAGTGG
original cDNA sequence snippet CCACTCCATCTTTGTGCTGCGGCTCTTCAATGACCCAGTGG
altered cDNA sequence snippet CCACTCCATCTTTGTGCTGCAGCTCTTCAATGACCCAGTGG
wildtype AA sequence MFPAQAKENA GFSGCGGDTE IDWKAYMAEV EGVINGTYDY TQLQGDTGPL VYPAGFVYIF
MGLYYATSRG TDIRMAQNIF AVLYLATLLL VFLIYHQTCK VPPFVFFFMC CASYRVHSIF
VLRLFNDPVA MVLLFLSINL LLAQRWGWGC CFFSLAVSVK MNVLLFAPGL LFLLLTQFGF
RGALPKLGIC AGLQVVLGLP FLLENPSGYL SRSFDLGRQF LFHWTVNWRF LPEALFLHRA
FHLALLTAHL TLLLLFALCR WHRTGESILS LLRDPSKRKV PPQPLTPNQI VSTLFTSNFI
GICFSRSLHY QFYVWYFHTL PYLLWAMPAR WLTHLLRLLV LGLIELSWNT YPSTSCSSAA
LHICHAVILL QLWLGPQPFP KSTQHSKKAH *
mutated AA sequence MFPAQAKENA GFSGCGGDTE IDWKAYMAEV EGVINGTYDY TQLQGDTGPL VYPAGFVYIF
MGLYYATSRG TDIRMAQNIF AVLYLATLLL VFLIYHQTCK VPPFVFFFMC CASYRVHSIF
VLQLFNDPVA MVLLFLSINL LLAQRWGWGC CFFSLAVSVK MNVLLFAPGL LFLLLTQFGF
RGALPKLGIC AGLQVVLGLP FLLENPSGYL SRSFDLGRQF LFHWTVNWRF LPEALFLHRA
FHLALLTAHL TLLLLFALCR WHRTGESILS LLRDPSKRKV PPQPLTPNQI VSTLFTSNFI
GICFSRSLHY QFYVWYFHTL PYLLWAMPAR WLTHLLRLLV LGLIELSWNT YPSTSCSSAA
LHICHAVILL QLWLGPQPFP KSTQHSKKAH *
speed 1.00 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