PolyPhenDbColumns: PolyPhenDb Columns

In Bioconductor/VariantAnnotation: Annotation of Genetic Variants

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

Bioconductor/VariantAnnotation documentation built on March 28, 2024, 10 a.m.