Variant Effect Scores and Experimental Data: parameters and notes¶

See the tutorial for usage and examples.

Each function includes its purpose, API, inputs, outputs, example code and result description. Prepare any required credentials, local files and optional dependencies; remote results vary with database releases and query time.

Retrieve AlphaMissense classifications across a protein¶

dnakit.databases.alpha_missense_get_protein_scores(*, uniprot_id, max_residues=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`uniprot_id`	string	Required	UniProt accession ID (e.g., 'P00533' for EGFR, 'P01116' for KRAS, 'P04637' for TP53).
`max_residues`	integer \| null	None	Optional cap on the number of residues fetched. 0 / null / omitted = no cap (fetch every residue of the protein, recommended for whole-protein analysis). Positive integer = fetch only the first N residues (useful for fast diagnostic calls on very long proteins).
`verbose`	bool	True	Progress flag.

Retrieve substitution classes and mean scores at a residue¶

dnakit.databases.alpha_missense_get_residue_scores(*, uniprot_id, position, verbose=True)

Parameter	Type	Required / default	Description and constraints
`uniprot_id`	string	Required	UniProt accession ID (e.g., 'P00533' for EGFR)
`position`	integer	Required	Amino acid position in the protein (1-indexed)
`verbose`	bool	True	Progress flag.

Classify a missense variant with AlphaMissense¶

dnakit.databases.alpha_missense_get_variant_score(*, uniprot_id, variant, verbose=True)

Parameter	Type	Required / default	Description and constraints
`uniprot_id`	string	Required	UniProt accession ID (e.g., 'P00533' for EGFR)
`variant`	string	Required	Variant in protein notation: p.X123Y or X123Y where X is reference amino acid, 123 is position, Y is variant (e.g., 'p.R123H', 'V600E')
`verbose`	bool	True	Progress flag.

Retrieve CADD scores for substitutions at a position¶

dnakit.databases.cadd_get_position_scores(*, chrom, pos, version=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`chrom`	string	Required	Chromosome (1-22, X, Y, MT)
`pos`	integer	Required	Genomic position (1-based)
`version`	string	None	CADD version and genome build
`verbose`	bool	True	Progress flag.

Retrieve CADD scores across a genomic interval¶

dnakit.databases.cadd_get_range_scores(*, chrom, start, end, version=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`chrom`	string	Required	Chromosome (1-22, X, Y, MT)
`start`	integer	Required	Start position (1-based, inclusive)
`end`	integer	Required	End position (1-based, inclusive). Max range: 100bp.
`version`	string	None	CADD version and genome build
`verbose`	bool	True	Progress flag.

Retrieve indexed CADD annotations through MyVariant¶

dnakit.databases.cadd_get_scores(*, variant, assembly='hg38', verbose=True)

Parameter	Type	Required / default	Description and constraints
`variant`	string	Required	Variant query used to retrieve indexed CADD annotations through MyVariant.
`assembly`	string	'hg38'	Reference genome assembly, for example hg38.
`verbose`	bool	True	Progress flag.

Retrieve a variant's CADD deleteriousness score¶

dnakit.databases.cadd_get_variant_score(*, chrom, pos, ref, alt, version=None, include_annotations=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`chrom`	string	Required	Chromosome (1-22, X, Y, MT). Can include 'chr' prefix.
`pos`	integer	Required	Genomic position (1-based)
`ref`	string	Required	Reference allele (e.g., 'A', 'G')
`alt`	string	Required	Alternate allele (e.g., 'T', 'C')
`version`	string	None	CADD version and genome build
`include_annotations`	boolean	None	Include full annotation details in response
`verbose`	bool	True	Progress flag.

Check EVE score availability for a gene¶

dnakit.databases.eve_get_gene_info(*, gene_symbol, verbose=True)

Parameter	Type	Required / default	Description and constraints
`gene_symbol`	string	Required	Gene symbol (e.g., 'TP53', 'BRCA1', 'EGFR')
`verbose`	bool	True	Progress flag.

Retrieve an EVE variant pathogenicity score¶

dnakit.databases.eve_get_variant_score(*, variant=None, chrom=None, pos=None, ref=None, alt=None, species=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`variant`	string	None	Variant in HGVS format (e.g., 'ENST00000269305.4:c.100G>A', 'NM_000546.5:c.215C>G')
`chrom`	string	None	Chromosome (1-22, X, Y). Use with pos, ref, alt instead of variant.
`pos`	integer	None	Genomic position (GRCh38)
`ref`	string	None	Reference allele
`alt`	string	None	Alternate allele
`species`	string	None	Species (default: human)
`verbose`	bool	True	Progress flag.

Build an amino acid effect matrix from MaveDB scores¶

dnakit.databases.mave_db_get_effect_matrix(*, urn, uniprot_id=None, score_field=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`urn`	string	Required	MaveDB score set URN (e.g., 'urn:mavedb:00000115-a-7'). Obtain from MaveDB_search_score_sets.
`uniprot_id`	string \| null	None	Optional UniProt accession (e.g., 'P01116' for KRAS). If supplied, the tool fetches the canonical sequence and verifies the MaveDB position numbering against it via a landmark check; sets numbering_offset and surfaces a warning in numbering_check if the positions don't match (silent off-by-N is the #1 silent bug in DMS analysis).
`score_field`	string \| null	None	Optional explicit column name to use as the variant score (e.g., 'score', 'ddG', 'fitness'). If omitted, tries 'score' → 'ddG' → 'fitness' → first numeric non-HGVS field in that order. The actual field used is reported in data.score_field_used.
`verbose`	bool	True	Progress flag.

Retrieve multiple variant pathogenicity prediction scores¶

dnakit.databases.my_variant_get_pathogenicity_scores(*, variant_id, fields=None, assembly=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`variant_id`	string	Required	Variant ID: rsID (e.g., rs45478192) or HGVS genomic (e.g., chr16:g.23635348A>C). Both formats work; an HGVS id must be expressed in the assembly given by the 'assembly' parameter.
`fields`	string	None	Fields to return (pre-configured for pathogenicity scores)
`assembly`	string	None	Reference genome assembly for both the HGVS variant_id and the returned coordinates: 'hg19' (GRCh37, the default) or 'hg38' (GRCh38).
`verbose`	bool	True	Progress flag.