Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.511287622253053 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM066224)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:31347320G>AN/A show variant in all transcripts   IGV
HGNC symbol SDC3
Ensembl transcript ID ENST00000336798
Genbank transcript ID N/A
UniProt peptide O75056
alteration type single base exchange
alteration region CDS
DNA changes c.812C>T
cDNA.2305C>T
g.34289C>T
AA changes T271I Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 271
frameshift no
known variant Reference ID: rs2282440
databasehomozygous (A/A)heterozygousallele carriers
1000G159489648
ExAC175669048660

known disease mutation at this position, please check HGMD for details (HGMD ID CM066224)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.4590.971
2.2740.993
(flanking)0.4340.992
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased34294wt: 0.8540 / mu: 0.8953 (marginal change - not scored)wt: CAGCCAATGAGGTGG
mu: TAGCCAATGAGGTGG		 GCCA|atga
Donor gained342850.35mu: AACCAGACATAGCCA CCAG|acat
distance from splice site 116
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      271ELPEEETTQPDTANEVVAVGGAAA
mutated  not conserved    271ELPEEETTQPDIANEVVAVGGAA
Ptroglodytes  all identical  ENSPTRG00000000451  283PDTANEVVAVGGAA
Mmulatta  all identical  ENSMMUG00000013519  320PDTANEVVAVGGAA
Fcatus  all identical  ENSFCAG00000010378  282PDTANEVVAVGGAA
Mmusculus  all identical  ENSMUSG00000025743  329TTQPDTANEVVAVEGAA
Ggallus  not conserved  ENSGALG00000000569  298EEETTRPELGNEVVAV----
Trubripes  not conserved  ENSTRUG00000013115  139EIRDDRRND--------------
Drerio  not conserved  ENSDARG00000088962  309EIRENEVRQNNDLGRGRAVPGE-
Dmelanogaster  not conserved  FBgn0010415  345DGPRIGGNDGDITERGPGAGGSN
Celegans  all identical  F57C7.3  174NIHNDEDFFTTTTTTTYRPIVV----
Xtropicalis  not conserved  ENSXETG00000007104  274QEEDVVPQTEPPTLPDLGNEVL------
protein features
start (aa)end (aa)featuredetails 
1387TOPO_DOMExtracellular (Potential).lost
115302COMPBIASSer/Thr-rich (mucin-like).lost
314314CARBOHYDO-linked (Xyl...) (glycosaminoglycan) (Potential).might get lost (downstream of altered splice site)
367367CARBOHYDO-linked (Xyl...) (glycosaminoglycan) (Potential).might get lost (downstream of altered splice site)
383384SITECleavage of ectodomain (Potential).might get lost (downstream of altered splice site)
388408TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
409442TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
441441MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1155 / 1155
position (AA) of stopcodon in wt / mu AA sequence 385 / 385
position of stopcodon in wt / mu cDNA 2648 / 2648
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 1494 / 1494
chromosome 1
strand -1
last intron/exon boundary 2482
theoretical NMD boundary in CDS 938
length of CDS 1155
coding sequence (CDS) position 812
cDNA position
(for ins/del: last normal base / first normal base)		 2305
gDNA position
(for ins/del: last normal base / first normal base)		 34289
chromosomal position
(for ins/del: last normal base / first normal base)		 31347320
original gDNA sequence snippet AGAGACCACACAACCAGACACAGCCAATGAGGTGGTAGCTG
altered gDNA sequence snippet AGAGACCACACAACCAGACATAGCCAATGAGGTGGTAGCTG
original cDNA sequence snippet AGAGACCACACAACCAGACACAGCCAATGAGGTGGTAGCTG
altered cDNA sequence snippet AGAGACCACACAACCAGACATAGCCAATGAGGTGGTAGCTG
wildtype AA sequence MAIAYLGSSC PSQPPSSLAL SLSPTPSDFE QESGIETAMR FSPDVALAVS TTPAVLPTTN
IQPVGTPFEE LPSERPTLEP ATSPLVVTEV PEEPSQRATT VSTTMATTAA TSTGDPTVAT
VPATVATATP STPAAPPFTA TTAVIRTTGV RRLLPLPLTT VATARATTPE APSPPTTAAV
LDTEAPTPRL VSTATSRPRA LPRPATTQEP DIPERSTLPL GTTAPGPTEV AQTPTPETFL
TTIRDEPEVP VSGGPSGDFE LPEEETTQPD TANEVVAVGG AAAKASSPPG TLPKGARPGP
GLLDNAIDSG SSAAQLPQKS ILERKEVLVA VIVGGVVGAL FAAFLVTLLI YRMKKKDEGS
YTLEEPKQAS VTYQKPDKQE EFYA*
mutated AA sequence MAIAYLGSSC PSQPPSSLAL SLSPTPSDFE QESGIETAMR FSPDVALAVS TTPAVLPTTN
IQPVGTPFEE LPSERPTLEP ATSPLVVTEV PEEPSQRATT VSTTMATTAA TSTGDPTVAT
VPATVATATP STPAAPPFTA TTAVIRTTGV RRLLPLPLTT VATARATTPE APSPPTTAAV
LDTEAPTPRL VSTATSRPRA LPRPATTQEP DIPERSTLPL GTTAPGPTEV AQTPTPETFL
TTIRDEPEVP VSGGPSGDFE LPEEETTQPD IANEVVAVGG AAAKASSPPG TLPKGARPGP
GLLDNAIDSG SSAAQLPQKS ILERKEVLVA VIVGGVVGAL FAAFLVTLLI YRMKKKDEGS
YTLEEPKQAS VTYQKPDKQE EFYA*
speed 0.55 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