Gene–Disease Evidence, Dosage and Actionability: 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 ClinGen gene dosage sensitivity curations¶

dnakit.databases.clin_gen_dosage_by_gene(*, gene=None, gene_symbol=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`gene`	string	None	Gene symbol to search for (e.g., 'BRCA1', 'MECP2', 'TP53'). Case-insensitive.
`gene_symbol`	string	None	DNAKit optional alias for gene
`verbose`	bool	True	Progress flag.

Search ClinGen dosage sensitivity by genomic interval¶

dnakit.databases.clin_gen_dosage_region_search(*, chromosome, start, end, assembly=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`chromosome`	string	Required	Chromosome (e.g., '17', 'X').
`start`	integer	Required	Start position.
`end`	integer	Required	End position.
`assembly`	string	None	Genome assembly version.
`verbose`	bool	True	Progress flag.

Retrieve adult clinical actionability curations¶

dnakit.databases.clin_gen_get_actionability_adult(*, gene=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`gene`	string	None	Optional: Filter by gene symbol
`verbose`	bool	True	Progress flag.

Retrieve pediatric clinical actionability curations¶

dnakit.databases.clin_gen_get_actionability_pediatric(*, gene=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`gene`	string	None	Optional: Filter by gene symbol
`verbose`	bool	True	Progress flag.

Retrieve ClinGen dosage sensitivity records¶

dnakit.databases.clin_gen_get_dosage_sensitivity(*, gene=None, include_regions=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`gene`	string	None	Optional: Filter by gene symbol
`include_regions`	boolean	None	Include recurrent CNV regions (default: false)
`verbose`	bool	True	Progress flag.

Retrieve ClinGen gene–disease validity curations¶

dnakit.databases.clin_gen_get_gene_validity(*, gene=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`gene`	string	None	Optional: Filter by gene symbol
`verbose`	bool	True	Progress flag.

Retrieve ClinGen variant classifications¶

dnakit.databases.clin_gen_get_variant_classifications(*, gene=None, variant=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`gene`	string	None	Optional: Filter by gene symbol
`variant`	string	None	Optional: filter to one variant. Accepts a ClinGen canonical allele ID ('CA16020993', with or without a 'CAR:' prefix), a ClinVar VariationID ('370074'), full HGVS ('NM_000277.3:c.1315+1G>T'), or a protein change ('p.Arg408Trp'). The form supplied selects the matching server-side filter. HGVS and protein-change strings match on substring, so a short fragment can return many rows -- combine with 'gene' to scope them.
`verbose`	bool	True	Progress flag.

Search gene actionability across adult and pediatric contexts¶

dnakit.databases.clin_gen_search_actionability(*, gene, verbose=True)

Parameter	Type	Required / default	Description and constraints
`gene`	string	Required	Gene symbol to search (e.g., BRCA1, MLH1, LDLR)
`verbose`	bool	True	Progress flag.

Search dosage sensitivity scores by gene symbol¶

dnakit.databases.clin_gen_search_dosage_sensitivity(*, gene, verbose=True)

Parameter	Type	Required / default	Description and constraints
`gene`	string	Required	Gene symbol to search (e.g., MECP2, PMP22, RAI1)
`verbose`	bool	True	Progress flag.

Search gene–disease validity by gene symbol¶

dnakit.databases.clin_gen_search_gene_validity(*, gene, verbose=True)

Parameter	Type	Required / default	Description and constraints
`gene`	string	Required	Gene symbol to search (e.g., BRCA1, TP53, CFTR)
`verbose`	bool	True	Progress flag.