Table 1 InpherNet supports each prediction with referenced observations.
From: InpherNet accelerates monogenic disease diagnosis using patients’ candidate genes’ neighbors
Patient ID | Patient phenotypes | Number of candidate genes | Causative gene & disease diagnosis | Relevant causative gene phenotypes from our HPO-A | Other tools rank: Phranken_HPOA/Phrank_HPOA/PhenIX/Phevor_HPOA/ Phevor_All/Phive/hiPhive | InpherNet rank | Strongest explanatory neighbor | Neighbor gene | Select neighbor gene phenotypes | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
96 | Hair, frontal upsweep (HP:0002236) Childhood-onset truncal obesity (HP:0008915) Gynecomastia (HP:0000771) Brachydactyly (HP:0001156) Generalized hypopigmentation (HP:0007513) Achilles tendon contracture (HP:0001771) | 364 | CTNNB1 Neurodevelopmental disorder with spastic diplegia and visual defects (MIM 615075) | Abnormality of the hair (HP:0001595) Abnormality of skin pigmentation (HP:0001000) Obesity (HP:0001513) | 8 | 22 | 34 | 45 | 30 | 29 | 5 | 1 | Mouse Ortholog | Ctnnb1 | Abnormal forelimb morphology (MP:0000550) Abnormal hindlimb morphology (MP:0000556) Abnormal melanogenesis (MP:0005077) Abnormality of hair growth (HP:0040170) |
128 | Motor delay (HP:0001270) Delayed speech and language development (HP:0000750) Developmental regression (HP:0002376) Intellectual disability (HP:0001249) Hypotonia (HP:0001252) Seizures (HP:0001250) Renal Fanconi syndrome (HP:0001994) Decreased circulating phosphate level (HP:0002148), Sensorineural hearing impairment (HP:0000407) | 389 | KCNA2 Developmental and epileptic encephalopathy 32 (MIM 616366) | Intellectual disability (HP:0001249) Seizures (HP:0001250) | 20 | 53 | 121 | 244 | 143 | 146 | 31 | 1 | Paralog | KCNA1 | Abnormality of movement (HP:0100022), Global developmental delay (HP:0001263) Hearing impairment (HP:0000365) Hypotonia (HP:0001252) Intellectual disability (HP:0001249) Intellectual disability, progressive (HP:0006887) Seizures (HP:0001250) |
123 | Motor delay (HP:0001270) Developmental regression (HP:0002376) Progressive language deterioration (HP:0007064) Autism (HP:0000717) Intellectual disability (HP:0001249) Tonic–clonic seizures (HP:0002069) Macrocephaly (HP:0000256) | 312 | GNB1 Mental retardation, autosomal dominant 42 (MIM 616973) | Abnormality of the head (HP:0000234) EEG abnormality (HP:0002353) Global developmental delay (HP:0001263) Intellectual disability (HP:0001249) Neurodevelopmental abnormality (HP:0012759) Seizure (HP:0001250) | 5 | 26 | 164 | 173 | 42 | 245 | 25 | 1 | Pathway | ITPR1 | Global developmental delay (HP:0001263) Intellectual disability (HP:0001249) Involuntary movements (HP:0004305) Motor delay (HP:0001270) Neurodevelopmental abnormality (HP:0012759) Neurodevelopmental delay (HP:0012758) |
73 | Microcephaly (HP:0000252) Attention deficit hyperactivity disorder (ADHD; HP:0007018) Delayed speech and language developmental (HP:0000750) Repetitive compulsive behavior (HP:0008762) Global developmental delay (HP:0001263) Hypermetropia (HP:0000540) | 321 | PHF8 Mental retardation syndrome, X-linked, Siderius type (MIM 300263) | Abnormality of higher mental function (HP:0011446) Delayed speech and language developmental (HP:0000750) Intellectual disability (HP:0001249) Neurodevelopmental delay (HP:0012758) | 28 | 29 | 27 | 160 | 160 | 63 | 11 | 1 | Interaction Partner | TAF1 | Behavioral abnormality (HP:0000708) Delayed gross motor developmental (HP:0002194) Delayed speech and language developmental (HP:0000750) Microcephaly (HP:0000252) Neurodevelopmental delay (HP:0012758) |
