Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999926684 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM014567)
  • known disease mutation: rs4367 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:55318045T>GN/A show variant in all transcripts   IGV
HGNC symbol DHCR24
Ensembl transcript ID ENST00000535035
Genbank transcript ID N/A
UniProt peptide Q15392
alteration type single base exchange
alteration region CDS
DNA changes c.1289A>C
cDNA.1372A>C
g.34847A>C
AA changes Y430S Score: 144 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 430
frameshift no
known variant Reference ID: rs28939092
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs4367 (pathogenic for Desmosterolosis) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM014567)

known disease mutation at this position, please check HGMD for details (HGMD ID CM014567)
known disease mutation at this position, please check HGMD for details (HGMD ID CM014567)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.4220.923
5.0071
(flanking)5.0071
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased34839wt: 0.70 / mu: 0.77wt: CTCTGCCTCTGCAGCTTCCAGATGCTGTATGCCGACTGCTA
mu: CTCTGCCTCTGCAGCTTCCAGATGCTGTCTGCCGACTGCTA		 ccag|ATGC
Acc increased34838wt: 0.71 / mu: 0.82wt: TCTCTGCCTCTGCAGCTTCCAGATGCTGTATGCCGACTGCT
mu: TCTCTGCCTCTGCAGCTTCCAGATGCTGTCTGCCGACTGCT		 tcca|GATG
Acc marginally increased34848wt: 0.6335 / mu: 0.6721 (marginal change - not scored)wt: TGCAGCTTCCAGATGCTGTATGCCGACTGCTACATGAACCG
mu: TGCAGCTTCCAGATGCTGTCTGCCGACTGCTACATGAACCG		 gtat|GCCG
Acc gained348520.43mu: GCTTCCAGATGCTGTCTGCCGACTGCTACATGAACCGGGAG gccg|ACTG
distance from splice site 15
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      430FVRSVHGFQMLYADCYMNREEFWE
mutated  not conserved    430RSVHGFQMLSADCYMNREEFW
Ptroglodytes  all identical  ENSPTRG00000000779  471FVRSVHGFQMLYADCYMNREEFW
Mmulatta  all identical  ENSMMUG00000021577  471FVRSVHGFQMLYADCYMNREEFW
Fcatus  all identical  ENSFCAG00000003989  394FVRSVHGFQMLYADCYMSREEFW
Mmusculus  all identical  ENSMUSG00000034926  471FVRSVHGFQMLYADCYMNREEFW
Ggallus  all identical  ENSGALG00000010798  471FVRSVHGFQMLYADCYMTREEFW
Trubripes  all identical  ENSTRUG00000016297  474FVRDVHGFQMLYADVYMNREEFW
Drerio  all identical  ENSDARG00000013236  471FVRDVHGFQMLYADVYMERKEFW
Dmelanogaster  no homologue    
Celegans  all identical  F52H2.6  480FVRSVNGFQMTYADIYMTRAEYA
Xtropicalis  all identical  ENSXETG00000020010  471FVRDVHGFQMLYADCYMSREEFW
protein features
start (aa)end (aa)featuredetails 
53516TOPO_DOMCytoplasmic (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1428 / 1428
position (AA) of stopcodon in wt / mu AA sequence 476 / 476
position of stopcodon in wt / mu cDNA 1511 / 1511
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 84 / 84
chromosome 1
strand -1
last intron/exon boundary 1358
theoretical NMD boundary in CDS 1224
length of CDS 1428
coding sequence (CDS) position 1289
cDNA position
(for ins/del: last normal base / first normal base)		 1372
gDNA position
(for ins/del: last normal base / first normal base)		 34847
chromosomal position
(for ins/del: last normal base / first normal base)		 55318045
original gDNA sequence snippet CTGCAGCTTCCAGATGCTGTATGCCGACTGCTACATGAACC
altered gDNA sequence snippet CTGCAGCTTCCAGATGCTGTCTGCCGACTGCTACATGAACC
original cDNA sequence snippet GCATGGCTTCCAGATGCTGTATGCCGACTGCTACATGAACC
altered cDNA sequence snippet GCATGGCTTCCAGATGCTGTCTGCCGACTGCTACATGAACC
wildtype AA sequence MGAGEQNRQS AHCVQGICGY LEGDEEGEEG EVRSTQVREW KEQGSKTFMC TGRPGWLTVS
LRVGKYKKTH KNIMINLMDI LEVDTKKQIV RVEPLVTMGQ VTALLTSIGW TLPVLPELDD
LTVGGLIMGT GIESSSHKYG LFQHICTAYE LVLADGSFVR CTPSENSDLF YAVPWSCGTL
GFLVAAEIRI IPAKKYVKLR FEPVRGLEAI CAKFTHESQR QENHFVEGLL YSLDEAVIMT
GVMTDEAEPS KLNSIGNYYK PWFFKHVENY LKTNREGLEY IPLRHYYHRH TRSIFWELQD
IIPFGNNPIF RYLFGWMVPP KISLLKLTQG ETLRKLYEQH HVVQDMLVPM KCLQQALHTF
QNDIHVYPIW LCPFILPSQP GLVHPKGNEA ELYIDIGAYG EPRVKHFEAR SCMRQLEKFV
RSVHGFQMLY ADCYMNREEF WEMFDGSLYH KLREKLGCQD AFPEVYDKIC KAARH*
mutated AA sequence MGAGEQNRQS AHCVQGICGY LEGDEEGEEG EVRSTQVREW KEQGSKTFMC TGRPGWLTVS
LRVGKYKKTH KNIMINLMDI LEVDTKKQIV RVEPLVTMGQ VTALLTSIGW TLPVLPELDD
LTVGGLIMGT GIESSSHKYG LFQHICTAYE LVLADGSFVR CTPSENSDLF YAVPWSCGTL
GFLVAAEIRI IPAKKYVKLR FEPVRGLEAI CAKFTHESQR QENHFVEGLL YSLDEAVIMT
GVMTDEAEPS KLNSIGNYYK PWFFKHVENY LKTNREGLEY IPLRHYYHRH TRSIFWELQD
IIPFGNNPIF RYLFGWMVPP KISLLKLTQG ETLRKLYEQH HVVQDMLVPM KCLQQALHTF
QNDIHVYPIW LCPFILPSQP GLVHPKGNEA ELYIDIGAYG EPRVKHFEAR SCMRQLEKFV
RSVHGFQMLS ADCYMNREEF WEMFDGSLYH KLREKLGCQD AFPEVYDKIC KAARH*
speed 1.23 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