Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999984857781 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM022481)
  • known disease mutation: rs2130 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:183963586A>GN/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.67T>C
cDNA.338T>C
g.3751T>C
AA changes W23R Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 23
frameshift no
known variant Reference ID: rs119103237
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs2130 (pathogenic for ALG3-CDG) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM022481)

known disease mutation at this position, please check HGMD for details (HGMD ID CM022481)
known disease mutation at this position, please check HGMD for details (HGMD ID CM022481)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.0951
4.2221
(flanking)3.3711
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 increased3742wt: 0.3767 / mu: 0.4272 (marginal change - not scored)wt: CTTGTCTTCTTCCAGACACAGAGATTGACTGGAAGGCCTAC
mu: CTTGTCTTCTTCCAGACACAGAGATTGACCGGAAGGCCTAC		 acag|AGAT
Donor marginally increased3751wt: 0.9050 / mu: 0.9580 (marginal change - not scored)wt: TTGACTGGAAGGCCT
mu: TTGACCGGAAGGCCT		 GACT|ggaa
Donor increased3750wt: 0.81 / mu: 0.97wt: ATTGACTGGAAGGCC
mu: ATTGACCGGAAGGCC		 TGAC|tgga
distance from splice site 15
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      23FSGCGGDTEIDWKAYMAEVEGVIN
mutated  not conserved    23FSGCGGDTEIDRKAYMAEVEGVI
Ptroglodytes  no homologue    
Mmulatta  no alignment  ENSMMUG00000018951  n/a
Fcatus  all identical  ENSFCAG00000016274  71TEIDWKAYMAQVEGVI
Mmusculus  all identical  ENSMUSG00000033809  71TEIDWKAYMAQVEGFI
Ggallus  all identical  ENSGALG00000008503  9DTEIDWQAYMQEVEGFA
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000053155  65TEIDWKAYMDEVEGVI
Dmelanogaster  all identical  FBgn0011297  74TEIDWVAYMQECEGFL
Celegans  all identical  K09E4.2  49TEIDWSTYMQQVECYV
Xtropicalis  all identical  ENSXETG00000017280  73TEIDWKAYMDEVEGVL
protein features
start (aa)end (aa)featuredetails 
4161TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
95115TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
123143TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
149169TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
172192TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
203223TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
231251TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
289309TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
332352TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
356376TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
407427TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
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 67
cDNA position
(for ins/del: last normal base / first normal base)		 338
gDNA position
(for ins/del: last normal base / first normal base)		 3751
chromosomal position
(for ins/del: last normal base / first normal base)		 183963586
original gDNA sequence snippet TTCCAGACACAGAGATTGACTGGAAGGCCTACATGGCCGAG
altered gDNA sequence snippet TTCCAGACACAGAGATTGACCGGAAGGCCTACATGGCCGAG
original cDNA sequence snippet GGGGAGACACAGAGATTGACTGGAAGGCCTACATGGCCGAG
altered cDNA sequence snippet GGGGAGACACAGAGATTGACCGGAAGGCCTACATGGCCGAG
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 IDRKAYMAEV 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 *
speed 1.39 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