Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.0239034344806119 (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 CM140548)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr8:97614661T>AN/A show variant in all transcripts   IGV
HGNC symbol SDC2
Ensembl transcript ID ENST00000302190
Genbank transcript ID NM_002998
UniProt peptide P34741
alteration type single base exchange
alteration region CDS
DNA changes c.211T>A
cDNA.1132T>A
g.109083T>A
AA changes S71T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 71
frameshift no
known variant Reference ID: rs1042381
databasehomozygous (A/A)heterozygousallele carriers
1000G1498821031
ExAC24361756620002

known disease mutation at this position, please check HGMD for details (HGMD ID CM140548)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0150.981
0.910.983
(flanking)3.6750.98
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased109075wt: 0.75 / mu: 0.92wt: AGAGCTGACAACATC
mu: AGAGCTGACAACAAC		 AGCT|gaca
Donor gained1090780.51mu: GCTGACAACAACTCG TGAC|aaca
distance from splice site 39
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      71DEDVESPELTTSRPLPKILLTSAA
mutated  all conserved    71EDVESPELTTTRPLPKILLTSA
Ptroglodytes  all identical  ENSPTRG00000020443  71EDVESPELTTSRPLPKIPFTSA
Mmulatta  all identical  ENSMMUG00000000963  71EDVESPELTTSRPLPKIPFTSA
Fcatus  all identical  ENSFCAG00000014598  51DEDVESPEMTTSRPLPKIGFT
Mmusculus  all identical  ENSMUSG00000022261  71EDIESPVLTTSQLIPRIPLTSA
Ggallus  all identical  ENSGALG00000015999  70STVTTTSRIVPKLPTTSD
Trubripes  all identical  ENSTRUG00000004101  68GEEVVEEAVTISTVYIK------
Drerio  not conserved  ENSDARG00000002731  72GEVIEDPVTVNTLFFVPKAEPTQD
Dmelanogaster  no alignment  FBgn0010415  n/a
Celegans  not conserved  F57C7.3  100PPSSATTKSDKVTSPSHAVVTAK
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
19144TOPO_DOMExtracellular (Potential).lost
101101CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
142143SITECleavage of ectodomain (Potential).might get lost (downstream of altered splice site)
145169TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
150150CONFLICTI -> T (in Ref. 2; BAB15150).might get lost (downstream of altered splice site)
170201TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 606 / 606
position (AA) of stopcodon in wt / mu AA sequence 202 / 202
position of stopcodon in wt / mu cDNA 1527 / 1527
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 922 / 922
chromosome 8
strand 1
last intron/exon boundary 1364
theoretical NMD boundary in CDS 392
length of CDS 606
coding sequence (CDS) position 211
cDNA position
(for ins/del: last normal base / first normal base)		 1132
gDNA position
(for ins/del: last normal base / first normal base)		 109083
chromosomal position
(for ins/del: last normal base / first normal base)		 97614661
original gDNA sequence snippet AGAGTCCAGAGCTGACAACATCTCGACCACTTCCAAAGATA
altered gDNA sequence snippet AGAGTCCAGAGCTGACAACAACTCGACCACTTCCAAAGATA
original cDNA sequence snippet AGAGTCCAGAGCTGACAACATCTCGACCACTTCCAAAGATA
altered cDNA sequence snippet AGAGTCCAGAGCTGACAACAACTCGACCACTTCCAAAGATA
wildtype AA sequence MRRAWILLTL GLVACVSAES RAELTSDKDM YLDNSSIEEA SGVYPIDDDD YASASGSGAD
EDVESPELTT SRPLPKILLT SAAPKVETTT LNIQNKIPAQ TKSPEETDKE KVHLSDSERK
MDPAEEDTNV YTEKHSDSLF KRTEVLAAVI AGGVIGFLFA IFLILLLVYR MRKKDEGSYD
LGERKPSSAA YQKAPTKEFY A*
mutated AA sequence MRRAWILLTL GLVACVSAES RAELTSDKDM YLDNSSIEEA SGVYPIDDDD YASASGSGAD
EDVESPELTT TRPLPKILLT SAAPKVETTT LNIQNKIPAQ TKSPEETDKE KVHLSDSERK
MDPAEEDTNV YTEKHSDSLF KRTEVLAAVI AGGVIGFLFA IFLILLLVYR MRKKDEGSYD
LGERKPSSAA YQKAPTKEFY A*
speed 0.28 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