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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