PolyPhenDbColumns: PolyPhenDb Columns
Description
Description of the PolyPhen Sqlite Database Columns
Column descriptions
These column names are displayed when columns is called on a
PolyPhenDb object. Original query :
- OSNPID : original SNP identifier from user input
- OSNPACC : original protein identifier from user input
- OPOS : original substitution position in the protein sequence
from user input
- OAA1 : original wild type (reference) aa residue from user input
- OAA2 : original mutant (reference) aa residue from user input
Mapped query :
- SNPID : SNP identifier mapped to dbSNP rsID if available,
otherwise same as o_snp_id. This value was used as the
rsid column
- ACC : protein UniProtKB accession if known protein, otherwise
same as o_acc
- POS : substitution position mapped to UniProtKB protein sequence
if known, otherwise same as o_pos
- AA1 : wild type aa residue
- AA2 : mutant aa residue
- NT1 : wild type allele nucleotide
- NT2 : mutant allele nucleotide
PolyPhen-2 prediction :
- PREDICTION : qualitative ternary classification FPR thresholds
PolyPhen-1 prediction :
- BASEDON : prediction basis
- EFFECT : predicted substitution effect on the protein structure or
function
PolyPhen-2 classifiers :
- PPH2CLASS : binary classifier outcome ("damaging" or "neutral")
- PPH2PROB : probability of the variation being dammaging
- PPH2FPR : false positive rate at the pph2_prob level
- PPH2TPR : true positive rate at the pph2_prob level
- PPH2FDR : false discovery rate at the pph2_prob level
UniProtKB-SwissProt derived protein sequence annotations :
- SITE : substitution SITE annotation
- REGION : substitution REGION annotation
- PHAT : PHAT matrix element for substitution in the
TRANSMEM region
Multiple sequence alignment scores :
- DSCORE : difference of PSIC scores for two aa variants
(Score1 - Score2)
- SCORE1 : PSIC score for wild type aa residue (aa1)
- SCORE2 : PSIC score for mutant aa residue (aa2)
- NOBS : number of residues observed at the substitution position
in the multiple alignment (sans gaps)
Protein 3D structure features :
- NSTRUCT : initial number of BLAST hits to similar proteins with
3D structures in PDB
- NFILT : number of 3D BLAST hits after identity threshold filtering
- PDBID : protein structure identifier from PDB
- PDBPOS : position of substitution in PDB protein sequence
- PDBCH : PDB polypeptide chain identifier
- IDENT : sequence identity between query and aligned PDB sequences
- LENGTH : PDB sequence alignment length
- NORMACC : normalized accessible surface
- SECSTR : DSSP secondary structure assignment
- MAPREG : region of the phi-psi (Ramachandran) map derived from the
residue dihedral angles
- DVOL : change in residue side chain volume
- DPROP : change in solvent accessible surface propensity resulting
from the substitution
- BFACT : normalized B-factor (temperature factor) for the residue
- HBONDS : number of hydrogen sidechain-sidechain and
sidechain-mainchain bonds formed by the residue
- AVENHET : average number of contacts with heteroatoms per residue
- MINDHET : closest contact with heteroatom
- AVENINT : average number of contacts with other chains per residue
- MINDINT : closest contact with other chain
- AVENSIT : average number of contacts with critical sites per
residue
- MINDSIT : closest contact with a critical site
Nucleotide sequence features (CpG/codon/exon junction) :
- TRANSV : whether substitution is a transversion
- CODPOS : position of the substitution within the codon
- CPG : whether or not the substitution changes CpG context
- MINDJNC : substitution distance from exon/intron junction
Pfam protein family :
- PFAMHIT : Pfam identifier of the query protein
Substitution scores :
- IDPMAX : maximum congruency of the mutant aa residue to all
sequences in multiple alignment
- IDPSNP : maximum congruency of the mutant aa residue to the
sequence in alignment with the mutant residue
- IDQMIN : query sequence identity with the closest homologue
deviating from the wild type aa residue
Comments :
- COMMENTS : Optional user comments