PolyPhenDbColumns {VariantAnnotation} | R Documentation

## 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.

- rsid : rsid

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

### Author(s)

Valerie Obenchain

### See Also

`?PolyPhenDb`

[Package VariantAnnotation version 1.36.0 Index]