PolyPhen-2 annotation summary report explained

Following is a description of PolyPhen-2 annotation summary report. Reports in this format are produced by both PolyPhen-2 Batch query web service, as well as by standalone PolyPhen-2 software. It is a plain text tab-separated file with each line annotating single protein variant (amino acid residue substitution).

Fourteen columns highlighted below (1-2, 6-11, 41, 45-48, 91) are the ones included in the Short version of the report available via Batch query web page. These are sufficient if you are interested in PolyPhen-2 prediction outcome and prediction confidence scores. The rest of the columns in Full report version are mostly useful only if you want to investigate all features supporting the prediction in detail.

Column No.	Column Name	Description
Original query (as copied from user input):
1	query_no	input query ordinal
2	o_acc	original protein identifier
3	o_pos	original substitution position in the protein sequence
4	o_aa1	original wild type (reference) amino acid residue
5	o_aa2	original mutant (substitution) amino acid residue
Annotated query:
6	rsid	dbSNP reference SNP identifier (rsID) if available
7	acc	UniProtKB accession if known protein, otherwise same as o_acc
8	length	Length of the protein sequence
9	pos	substitution position in UniProtKB protein sequence, otherwise same as o_pos
10	aa1	wild type amino acid residue in relation to UniProtKB sequence
11	aa2	mutant amino acid residue in relation to UniProtKB sequence
Nucleotide sequence context annotations:
12	chr_pos	SNP chromosome:position (chromosome coordinates are 1-based)
13	str	transcript strand (“+” or “-”)
14	gene	gene symbol
15	transcript	UCSC transcript name (unique identifier)
16	canon	UCSC knowCanonical representative transcript flag: 1 - canonical, 0 - alternative
17	cid	UCSC knownCanonical cluster identifier (number)
18	txcov	transcript coverage, the number of transcipts in UCSC cluster overlapping the mutation position / total number of transcripts in the cluster
19	ntlen	full transcript length (number of nucleotides)
20	ntpos	mutation position in the full transcript nucleotide sequence (in the direction of transcription)
21	nt1	reference nucleotide (transcript strand)
22	nt2	variant nucleotide (transcript strand)
23	PtGgPaNl	orthologous alleles in chimp (Pt), gorilla (Gg), Orangutan (Pa) and gibbon (Nl) if different from human reference allele, ? - otherwise; . - data not available
24	dref	putative derived allele found in human reference, score: 0 - no evidence, 1 - variant allele matches orthologous ancestral allele, 2 - dbSNP minor allele matches reference allele, 3 - both dbSNP and orthologous evidence present, ? - not enough evidence to score
25	gerprs	Genomic Evolutionary Rate Profiling (GERP++) position-specific conservation score, RS; 0 - when alignment coverage is insufficient
26	phylop	conservation scoring by phyloP (phylogenetic p-values) from the PHAST package for multiple alignments of 99 vertebrate genomes to the human genome
27	trv	transversion mutation flag: 0 - transition, 1 - transversion
28	CpG	CpG context: 0 - non-CpG context retained, 1 - mutation removes CpG site, 2 - mutation creates new CpG site, 3 - CpG context retained: C(C/G)G substitution
29	JXmin	distance from mutation position to the nearest exon / intron junction (“-” for upstream, “+” for downstream)
30	JXc	mutation in a codon that is split across two exons: ? - no, 1 - yes
31	exon	mutation in exon # / of total exons (exons are enumerated in the direction of transcription)
32	cexon	same as above but only coding (CDS) exons are being enumerated
33	cdnpos	number of the mutated codon within transcript's CDS (1-base)
34	frame	mutation position offset within the codon (0..2)
35	dgn	degeneracy index for mutated codon position, by Nei & Kumar (2000) “Molecular Evolution and Phylogenetics”, page 64: 0 - non-degenerate, 2 - simple 2-fold degenerate, 3 - complex 2-fold degenerate, 4 - 4-fold degenerate
36	cdn1	reference codon
37	cdn2	mutated codon
dbNSP annotations:
38	dbrsid	dbSNP SNP rsID
39	dbminor	dbSNP minor allele nucleotide (transcript strand)
40	dbmaf	dbSNP minor allele frequency
PolyPhen-2 prediction outcome:
41	prediction	qualitative ternary classification appraised at 5%/10% (HumDiv) or 10%/15% (HumVar) False Discovery Rate (FDR) thresholds: “benign”, “possibly damaging”, “probably damaging”
PolyPhen-1 prediction description (obsolete, please ignore):
42	based_on	prediction basis
43	effect	predicted substitution effect on the protein structure or function
PolyPhen-2 classifier outcome and scores:
44	pph2_class	probabilistic binary classifier outcome: “damaging” or “neutral”
45	pph2_prob	classifier probability of the variation being damaging
46	pph2_FPR	classifier model False Positive Rate (1 - specificity) at the above probability
47	pph2_TPR	classifier model True Positive Rate (sensitivity) at the above probability
48	pph2_FDR	classifier model False Discovery Rate at the above probability
UniProtKB/Swiss-Prot/Pfam protein annotations:
49	PfamHit	Pfam identifier of the protein family or domain to which substitution maps
50	site	substitution SITE annotation
51	region	substitution REGION annotation
52	PHAT	PHAT matrix element for substitutions in the TRANSMEM region
Multiple sequence alignment scores:
53	dScore	difference of PSIC scores for two amino acid residue variants (Score1-Score2)
54	Score1	PSIC score for wild type amino acid residue (aa1)
55	Score2	PSIC score for mutant amino acid residue (aa2)
56	MSAv	version of the multiple sequence alignment used in conservation scores calculations: 1 - pairwise BLAST HSP (obsolete), 2 - MAFFT-Leon-Cluspack (default), 3 - MultiZ CDS
57	Nobs	number of residues observed at the substitution position in multiple alignment (without gaps)
58	Nseqs	number of sequences observed at the substitution position in multiple alignment (including gaps)
59	Nsubs	number of residues different from reference residue (aa1) observed at the substitution position in multiple alignment
60	Nvars	number of residues same as substitution residue (aa2) observed at the substitution position in multiple alignment (without gaps)
61	Nres	number of unique residues observed at the substitution position in multiple alignment (without gaps)
Substitution scores:
62	IdPmax	maximum congruency of the substitution amino acid residue across all sequences with a substitution at the substitution position in multiple alignment
63	IdPSNP	maximum congruency of the substitution amino acid residue to the sequences in multiple alignment with the substitution residue at the substitution position in multiple alignment
64	IdQmax	query sequence identity with the closest homologue deviating from the wild type amino acid residue (aa1)
Phylogenetic tree based scores:
65	DistPmin	minimum normalized distance along the phylogenetic tree across all substitution types encountered at the substitution position
66	DistPSNP	minimum normalized distance along the phylogenetic tree for substitution residues (aa2) encountered at the substitution position
67	DistQmin	minimum distance (sum of branch lengths) along the phylogenetic tree across all substitution types encountered at the substitution position
68	BaRE	Bayesian Rate Estimator for scoring evolutionary conservation, D.M. Jordan (2015)
Gene-based scores:
69	RVISraw	Residual Variation Intolerance Score (raw), Petrovski et al. (2013)
70	RVISranked	Residual Variation Intolerance Score (normalized by rank), Petrovski et al. (2013)
RCSB PDB annotations:
71	Nstruct	initial number of BLAST hits to similar proteins with 3D structures in PDB
72	Nfilt	number of 3D BLAST hits after identity threshold filtering
73	PDB_id	PDB protein structure identifier
74	PDB_ch	PDB polypeptide chain identifier
75	PDB_len	PDB sequence alignment length
76	PDB_pos	position of substitution in the PDB protein sequence
77	PDB_idn	sequence identity between query sequence and the aligned PDB sequence
Amino acid residues structural features:
78	dVol	change in residue side chain volume
79	dProp	change in solvent accessible surface propensity resulting from the substitution
Protein 3D structure features:
80	SecStr	DSSP secondary structure assignment
81	MapReg	region of the phi-psi map (Ramachandran map) derived from the residue dihedral angles
82	NormASA	normalized accessible surface
83	B-fact	normalized B-factor (temperature factor) for the residue
84	H-bonds	number of hydrogen sidechain-sidechain and sidechain-mainchain bonds formed by the residue
85	AveNHet	number of residue contacts with heteroatoms, average per homologous PDB chain
86	MinDHet	closest residue contact with a heteroatom, Å
87	AveNInt	number of residue contacts with other chains, average per homologous PDB chain
88	MinDInt	closest residue contact with other chain, Å
89	AveNSit	number of residue contacts with critical sites, average per homologous PDB chain
90	MinDSit	closest residue contact with a critical site, Å
Comments:
91	Comments	optional user comments, copied from input