Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999993112 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM093085)
  • known disease mutation: rs3193 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr18:46645236A>GN/A show variant in all transcripts   IGV
HGNC symbol DYM
Ensembl transcript ID ENST00000442713
Genbank transcript ID N/A
UniProt peptide Q7RTS9
alteration type single base exchange
alteration region CDS
DNA changes c.1054T>C
cDNA.1375T>C
g.342482T>C
AA changes C352R Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 352
frameshift no
known variant Reference ID: rs120074165
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs3193 (pathogenic for Smith-McCort dysplasia 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM093085)

known disease mutation at this position, please check HGMD for details (HGMD ID CM093085)
known disease mutation at this position, please check HGMD for details (HGMD ID CM093085)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.9221
4.8961
(flanking)1.3211
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased342487wt: 0.66 / mu: 0.82wt: TGCCTGACAAATTCC
mu: CGCCTGACAAATTCC		 CCTG|acaa
distance from splice site 61
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      352VIRMMLEIINSCLTNSLHHNPNLV
mutated  not conserved    352VIRMMLEIINSRLTNSLHHN
Ptroglodytes  all identical  ENSPTRG00000010011  542VIRMMLEIINSCLTNSLHHNPNL
Mmulatta  no homologue    
Fcatus  not conserved  ENSFCAG00000012954  542XXXXXXXXXXXXXXXXXXXXXXX
Mmusculus  all identical  ENSMUSG00000035765  542VIRMMLEIINSCLTNSLHHNPNL
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000009986  543VIRMMLEIINSCLCNSLHHNPNL
Drerio  no homologue    
Dmelanogaster  all identical  FBgn0027607  568VLRMVLEILNSCLTNQLVYCPNL
Celegans  not conserved  C47D12.2  565GIRTLLEIINSALCGGLRHNS
Xtropicalis  all identical  ENSXETG00000020310  543VIRMMLEIINSCLTNSLHHNPNM
protein features
start (aa)end (aa)featuredetails 
381381CONFLICTE -> G (in Ref. 3; BAF83992).might get lost (downstream of altered splice site)
408408CONFLICTD -> Y (in Ref. 4; AAH64394).might get lost (downstream of altered splice site)
453453CONFLICTR -> K (in Ref. 3; BAF83992).might get lost (downstream of altered splice site)
458458MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
537537CONFLICTE -> G (in Ref. 3; BAF83992).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1440 / 1440
position (AA) of stopcodon in wt / mu AA sequence 480 / 480
position of stopcodon in wt / mu cDNA 1761 / 1761
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 322 / 322
chromosome 18
strand -1
last intron/exon boundary 1612
theoretical NMD boundary in CDS 1240
length of CDS 1440
coding sequence (CDS) position 1054
cDNA position
(for ins/del: last normal base / first normal base)		 1375
gDNA position
(for ins/del: last normal base / first normal base)		 342482
chromosomal position
(for ins/del: last normal base / first normal base)		 46645236
original gDNA sequence snippet TGTTAGAGATCATCAACTCCTGCCTGACAAATTCCCTTCAC
altered gDNA sequence snippet TGTTAGAGATCATCAACTCCCGCCTGACAAATTCCCTTCAC
original cDNA sequence snippet TGTTAGAGATCATCAACTCCTGCCTGACAAATTCCCTTCAC
altered cDNA sequence snippet TGTTAGAGATCATCAACTCCCGCCTGACAAATTCCCTTCAC
wildtype AA sequence MGSNSSRIGD LPKNEYLKKL SGTESISEND PFWNQLLSFS FPAPTSSSEL KLLEEATISV
CRSLAGLWTV FTLGGVGSKA AASPELSSPL ANQSLLLLLV LANLTDASDA PNPYRQAIMS
FKNTQDSSPF PSSIPHAFQI NFNSLYTALC EQQTSDQATL LLYTLLHQNS NIRTYMLART
DMENLVLPIL EILYHVEERN SHHVYMALII LLILTEDDGF NRSIHEVILK NITWYSERVL
TEISLGSLLI LVVIRTIQYN MTRTRDKYLH TNCLAALANM SAQFRSLHQY AAQRIISLFS
LLSKKHNKVL EQATQSLRGS LSSNDVPLPD YAQDLNVIEE VIRMMLEIIN SCLTNSLHHN
PNLVYALLYK RDLFEQFRTH PSFQDIMQNI DLVISFFSSR LLQAGAELSV ERVLEIIKQG
VVALPKDRLK KFPELKFKYV EEEQPEEFFI PYVWSLVYNS AVGLYWNPQD IQLFTMDSD*
mutated AA sequence MGSNSSRIGD LPKNEYLKKL SGTESISEND PFWNQLLSFS FPAPTSSSEL KLLEEATISV
CRSLAGLWTV FTLGGVGSKA AASPELSSPL ANQSLLLLLV LANLTDASDA PNPYRQAIMS
FKNTQDSSPF PSSIPHAFQI NFNSLYTALC EQQTSDQATL LLYTLLHQNS NIRTYMLART
DMENLVLPIL EILYHVEERN SHHVYMALII LLILTEDDGF NRSIHEVILK NITWYSERVL
TEISLGSLLI LVVIRTIQYN MTRTRDKYLH TNCLAALANM SAQFRSLHQY AAQRIISLFS
LLSKKHNKVL EQATQSLRGS LSSNDVPLPD YAQDLNVIEE VIRMMLEIIN SRLTNSLHHN
PNLVYALLYK RDLFEQFRTH PSFQDIMQNI DLVISFFSSR LLQAGAELSV ERVLEIIKQG
VVALPKDRLK KFPELKFKYV EEEQPEEFFI PYVWSLVYNS AVGLYWNPQD IQLFTMDSD*
speed 0.71 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