genes_to_phenotype.txt

In the genes_to_phenotypes.txt file, we list for each gene the most specific HPO-classes (and not all the ancestors). The following table shows an excerpt from the file. The table provides the NCBI Gene identifier, the gene symbol, the HPO identifier and term name. If available, the frequency is shown. For instance, mutation in the AARS1 gene cause Leukoencephalopathy, hereditary diffuse, with spheroids 2. The frequency of the HPO term Sensory ataxia was annotated to be 1 in 2 because of information in Sundal C, et al., PMID:31775912 (See entry in table below). The HPO resource offers annotations made by the HPO team (using disease identifiers from OMIM) as well as annotations provided by the Orphanet team (using ORPHA disease identifiers). In this case, gene to phenotype annotations are shown separately.

File format

ncbi_gene_id	gene_symbol	hpo_id	hpo_name	frequency	disease_id
10	NAT2	HP:0000007	Autosomal recessive inheritance	-	OMIM:243400
10	NAT2	HP:0001939	Abnormality of metabolism/homeostasis	-	OMIM:243400
16	AARS1	HP:0002460	Distal muscle weakness	15/15	OMIM:613287
16	AARS1	HP:0002451	Limb dystonia	3/3	OMIM:616339
16	AARS1	HP:0010871	Sensory ataxia	1/2	OMIM:619661
16	AARS1	HP:0009886	Trichorrhexis nodosa	1/2	OMIM:619691
16	AARS1	HP:0002421	Poor head control	HP:0040283	ORPHA:442835
16	AARS1	HP:0001298	Encephalopathy	HP:0040281	ORPHA:442835
16	AARS1	HP:0001290	Generalized hypotonia	HP:0040282	ORPHA:442835
16	AARS1	HP:0001273	Abnormal corpus callosum morphology	HP:0040283	ORPHA:442835
16	AARS1	HP:0001268	Mental deterioration	HP:0040283	ORPHA:442835
16	AARS1	HP:0001268	Mental deterioration	2/2	OMIM:619661