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)
  • 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 ENST00000269445
Genbank transcript ID NM_017653
UniProt peptide Q7RTS9
alteration type single base exchange
alteration region CDS
DNA changes c.1624T>C
cDNA.2082T>C
g.342482T>C
AA changes C542R Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 542
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      542VIRMMLEIINSCLTNSLHHNPNLV
mutated  not conserved    542SRLTNSLHHNPNL
Ptroglodytes  all identical  ENSPTRG00000010011  542SCLTNSLHHNPNL
Mmulatta  no homologue    
Fcatus  not conserved  ENSFCAG00000012954  542XXXXXXXXXXXXX
Mmusculus  all identical  ENSMUSG00000035765  542SCLTNSLHHNPNL
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000009986  542INSCLCNSLHHNPNL
Drerio  no homologue    
Dmelanogaster  all identical  FBgn0027607  568VLRMVLEILNSCLTNQLVYCPNL
Celegans  not conserved  C47D12.2  565GIRTLLEIINSALCGGLRHNSHL
Xtropicalis  all identical  ENSXETG00000020310  543INSCLTNSLHHNPNM
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2010 / 2010
position (AA) of stopcodon in wt / mu AA sequence 670 / 670
position of stopcodon in wt / mu cDNA 2468 / 2468
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 459 / 459
chromosome 18
strand -1
last intron/exon boundary 2319
theoretical NMD boundary in CDS 1810
length of CDS 2010
coding sequence (CDS) position 1624
cDNA position
(for ins/del: last normal base / first normal base)		 2082
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
CRSLVENNPR TGNLGALIKV FLSRTKELKL SAECQNHIFI WQTHNALFII CCLLKVFICQ
MSEEELQLHF TYEEKSPGNY SSDSEDLLEE LLCCLMQLIT DIPLLDITYE ISVEAISTMV
VFLSCQLFHK EVLRQSISHK YLMRGPCLPY TSKLVKTLLY NFIRQEKPPP PGAHVFPQQS
DGGGLLYGLA SGVATGLWTV 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
CRSLVENNPR TGNLGALIKV FLSRTKELKL SAECQNHIFI WQTHNALFII CCLLKVFICQ
MSEEELQLHF TYEEKSPGNY SSDSEDLLEE LLCCLMQLIT DIPLLDITYE ISVEAISTMV
VFLSCQLFHK EVLRQSISHK YLMRGPCLPY TSKLVKTLLY NFIRQEKPPP PGAHVFPQQS
DGGGLLYGLA SGVATGLWTV 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 1.34 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