diff --git a/src/ontology/reports/mondo_base_current_release-report.tsv b/src/ontology/reports/mondo_base_current_release-report.tsv index a2dba8bd6a..92d5da7045 100644 --- a/src/ontology/reports/mondo_base_current_release-report.tsv +++ b/src/ontology/reports/mondo_base_current_release-report.tsv @@ -10322,6 +10322,7 @@ "achondrogenesis type IA" "Achondrogenesis type 1A (ACG1A), a form of achondrogenesis, is a very rare, lethal skeletal dysplasia characterized by dwarfism with extremely short limbs, narrow chest, short ribs that are easily fractured, soft skull bones and distinctive histological features of the cartilage." "" "achondrogenesis" "Achondrogenesis describes a rare group of lethal skeletal dysplasias characterized by an endochondral ossification deficiency that leads to dwarfism with extreme micromelia, a small thorax, a prominent abdomen, anasarca and polyhydramnios. There are three types of achondrogenesis that exist and that differ clinically, radiologically, histologically and genetically: achondrogensis type 1a, type 1b and type 2." "" "severe spondylodysplastic dysplasia" "An instance of spondylodysplastic dysplasia that has a high degree of severity." "" + "TRIP11-related skeletal dysplasia" "Any skeletal dysplasia in which the cause of the disease is a variation in the TRIP11 gene. Reduced protein function in TRIP11 causes a spectrum of skeletal symptoms from a more mild phenotype, called ondontochondrodysplasia, with features including short stature and joint laxity to a more severe phenotype, called achondrogenesis type 1A, which presents as a lethal prenatal or neonatal skeletal dysplasia. The clinical severity of achondrogenesis compared to ondontochondrodysplasia is related to the residual function of the gene which is not currently possible to anticipate based on genotype alone. The phenotype cannot fully be predicted by genotype alone, evidenced by variants being reported with both phenotypes." "" "achondrogenesis type II" "Achondrogenesis type 2 (ACG2), a form of achondrogenesis, is a very rare and lethal skeletal dysplasia and part of the spectrum of type 2 collagen-related bone disorders, characterizedby severe micromelia, short neck with large head, small thorax, protuberant abdomen, underdeveloped lungs, distinctive facial features such as a prominent forehead, a small chin, a cleft palate (in some) and distinctive histological features of the cartilage." "" "acromesomelic dysplasia 2A" "An autosomal recessively inherited form of acromesomelic dysplasia characterized by severe dwarfism at birth, abnormalities confined to limbs, severe shortening and deformity of long bones, fusion or absence of carpal and tarsal bones, ball shaped fingers and, occasionally, polydactyly and absent joints. As seen in acromesomelic dysplasia, Hunter-Thomson type and acromesomelic dysplasia, Maroteaux Type, facial features and intelligence are normal." "" "short-limb skeletal dysplasia with severe combined immunodeficiency" "Short-limb skeletal dysplasia with severe combined immunodeficiency is an extremely rare type of SCID characterized by the classical signs of T-B- SCID (severe and recurrent infections, diarrhea, failure to thrive, absence of T and B lymphocytes), associated with skeletal anomalies like short stature, bowing of the long bones and metaphyseal abnormalities of variable degree of severity." "" @@ -13390,6 +13391,7 @@ "colobomatous macrophthalmia-microcornea syndrome" "" "megalencephaly-capillary malformation-polymicrogyria syndrome" "A polymalfomative syndrome characterized by cutaneous capillary malformations, megalencephaly, cortical brain malformations (most distinctively polymicrogyria), abnormalities of somatic growth with body and brain asymmetry, developmental delay, and characteristic facial dysmorphism." "" "overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes" "A disease caused by mosaic gain-of-function (GoF) of several genes in the MTOR pathway (MTOR, PIK3CA, PIK3R2 and AKT3) are functionally the same despite significant phenotypic variability. These GoF variants result in overgrowth due to an over-activation of key genes in this pathway. The phenotypic variability is generally attributed to the mosaic fraction and affected tissue types. For example, macrocephaly is noted if the variant is identified in the brain, but non symmetric overgrowth of that limb is noted when the variant is only present in the affected limb. The pathologies of the affected tissue often reveal similar characteristics such as cellular overgrowth. However, this is not always the case especially with focal cortical dysplasia. At times the characteristics pathologies are not present in the tissue but sampling biases are an issue. FCD resections often involve a very small area and so a very small amount of tissue is available for pathology and it is not guaranteed that lesional tissue is sent. Therefore, having a single disease term which can encompass the phenotypic variability yet provide a unifying molecular diagnosis name makes sense given the common functional mechanism." "" + "PIK3CA-related overgrowth spectrum" "Any overgrowth syndrome resulting from pathogenic gain-of-function variants in the PIK3CA gene. The variants can be germline or somatic" "" "pseudoacromegaly with severe insulin resistance" "" "Bartter disease type 4A" "Any Bartter syndrome in which the cause of the disease is a mutation in the BSND gene." "" "grange syndrome" "Grange syndrome is characterized by stenosis or occlusion of multiple arteries (including the renal, cerebral and abdominal vessels), hypertension, brachysyndactyly, syndactyly, increased bone fragility, and learning difficulties or borderline intellectual deficit. Congenital heart defects were also reported in some cases." "" @@ -13468,6 +13470,7 @@ "thyroid carcinoma, nonmedullary, with or without cell oxyphilia" "" "megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 1" "Any megalencephaly-polymicrogyria-postaxial polydactyly-hydrocephalus syndrome in which the cause of the disease is a mutation in the PIK3R2 gene." "" "megalencephaly-polymicrogyria-postaxial polydactyly-hydrocephalus syndrome" "Megalencephaly-polymicrogyria-postaxial polydactyly-hydrocephalus syndrome is characterized by megalencephaly, polymicrogyria, and hydrocephalus with variable polydactyly. It has been described in six unrelated patients. Intellectual deficit or slow development is also present. The mode of inheritance of this syndrome is unknown since all cases were sporadic." "" + "PIK3R2-related overgrowth spectrum" "Any overgrowth syndrome resulting from pathogenic gain-of-function variants in the PIK3R2 gene. The variants can be germline or somatic" "" "Graves disease, susceptibility to, 2" "" "Osebold skeletal dysplasia/osteolysis syndrome" "" "osteosclerotic chondrodysplasia, lethal, with intracellular inclusions" "" @@ -15990,6 +15993,7 @@ "holoprosencephaly 11" "Any holoprosencephaly in which the cause of the disease is a mutation in the CDON gene." "" "hyperuricemic nephropathy, familial juvenile type 3" "" "Charcot-Marie-Tooth disease axonal type 2O" "Any Charcot-Marie-Tooth disease in which the cause of the disease is a mutation in the DYNC1H1 gene." "" + "dyneinopathy" "A spectrum of diseases related to monoallelic variants in DYNC1H1 and characterized by variable neuromuscular and/or neurodevelopmental presentations. While not absolute, there appear to be genotype-phenotype correlations based on the location of the variant. Patients with variants in the stem domain of DYNC1H1 have been reported with a predominantly neuromuscular presentation, including congenital myopathy, spinal muscular atrophy, Charcot-Marie-Tooth (CMT), and less frequently, intellectual disability and autism. Patients with variants in the motor domain predominantly present with neurodevelopmental presentations including intellectual disability, seizures, malformations of cortical development (abnormal brain MRI findings such as pachygyria, heterotopias, enlarged ventricles, hypoplasia of CC, brain stem, cerebellum), autism, and less frequently, neuromuscular phenotypes." "" "autosomal recessive spinocerebellar ataxia 11" "Any autosomal recessive syndromic cerebellar ataxia in which the cause of the disease is a mutation in the SYT14 gene." "" "chromosome 8q21.11 deletion syndrome" "Heterozygous overlapping microdeletions on chromosome 8q21.11 resulting in intellectual disability, facial dysmorphism comprising a round face, ptosis, short philtrum, Cupid's bow and prominent low-set ears, nasal speech and mild finger and toe anomalies." "" "obsolete primary microcephaly-epilepsy-permanent neonatal diabetes syndrome" "" "true" @@ -17016,7 +17020,7 @@ "developmental and epileptic encephalopathy, 30" "Any early infantile epileptic encephalopathy in which the cause of the disease is a mutation in the SIK1 gene." "" "lissencephaly 7 with cerebellar hypoplasia" "" "immunodeficiency 39" "Any primary immunodeficiency disease in which the cause of the disease is a mutation in the IRF7 gene." "" - "developmental and epileptic encephalopathy, 31" "Any early infantile epileptic encephalopathy in which the cause of the disease is a mutation in the DNM1 gene." "" + "developmental and epileptic encephalopathy, 31A" "Any developmental and epileptic encephalopathy in which the cause of the disease is a heterozygous mutation in the DNM1 gene." "" "intellectual disability, autosomal dominant 34" "Any autosomal dominant non-syndromic intellectual disability in which the cause of the disease is a mutation in the COL4A3BP gene." "" "dyskeratosis congenita, autosomal recessive 6" "Any dyskeratosis congenita in which the cause of the disease is a mutation in the PARN gene." "" "autosomal recessive spinocerebellar ataxia 20" "Any autosomal recessive cerebellar ataxia in which the cause of the disease is a mutation in the SNX14 gene." "" @@ -17101,6 +17105,7 @@ "ATF6-related retinopathy" "A retinopathy caused by biallelic variants in the AFT6 gene." "" "intellectual disability, autosomal dominant 39" "Any autosomal dominant non-syndromic intellectual disability in which the cause of the disease is a mutation in the MYT1L gene." "" "polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis" "" + "PI4KA-related disorder" "Any human disease in which the cause of the disease is a variation in the PI4KA gene. This disease is characterized primarily by neurologic dysfunction (limb spasticity, developmental delay, intellectual disability, seizures, ataxia, nystagmus), gastrointestinal manifestations (multiple intestinal atresia, inflammatory bowel disease), and combined immunodeficiency (leukopenia, variable immunoglobulin defects). Age of onset is typically antenatal or in early childhood; individuals can present with any combination of these features. Rare individuals present with later-onset hereditary spastic paraplegia. Brain MRI findings can include hypomyelinating leukodystrophy, cerebellar hypoplasia/atrophy, thin or dysplastic corpus callosum, and/or perisylvian polymicrogyria." "" "herpes simplex encephalitis, susceptibility to, 7" "A Mendelian susceptibility or predisposition to herpes simplex infection induced encephalitis in which the cause of the diseas is a mutation in the IRF3 gene." "" "thyroid cancer, nonmedullary, 4" "Any thyroid cancer, nonmedullary in which the cause of the disease is a mutation in the FOXE1 gene." "" "thyroid cancer, nonmedullary, 5" "Any thyroid cancer, nonmedullary in which the cause of the disease is a mutation in the HABP2 gene." "" @@ -17798,7 +17803,7 @@ "lethal recessive chondrodysplasia" "Lethal recessive chondrodysplasia is an extremely rare lethal form of chondrodysplasia characterized by severe micromelic dwarfism, short and incurved limbs with normal hands and feet, facial dysmorphism (disproportionately large skull, frontal prominence, slightly flattened nasal bridge and short neck), muscular hypotonia, hyperlaxity of the extremities, and a narrow thorax. Most patients die of respiratory distress during the first hours or weeks of life. There have been no further descriptions in the literature since 1988." "" "chondrodysplasia" "" "choroidal atrophy-alopecia syndrome" "Choroidal atrophy - alopecia is a very rare ectodermal dysplasia syndrome, characterized by the association of choroidal atrophy (sometimes regional), together with other ectodermal dysplasia features including fine and sparse hair, absent or decreased lashes and eyebrows, and possibly mild visual loss and dysplastic/thick/grooved nails." "" - "choroideremia-hypopituitarism syndrome" "True" + "obsolete choroideremia-hypopituitarism syndrome" "" "true" "ring chromosome 1" "Ring chromosome 1 syndrome is an autosomal anomaly characterized by variable clinical features, most commonly including significant intrauterine and postnatal growth failure, developmental delay, intellectual disability, microcephaly, and dysmorphic facial features. Some less frequent clinical features are dysgenesis of corpus callosum, atrial septal defect, rocker bottom feet and clinodactyly." "" "chromosome 1 disorder" "Chromosomal disorder in which chromosome 1 is affected." "" "ring chromosome 10" "Ring chromosome 10 syndrome is characterized by intellectual deficit, growth retardation, and various dysmorphic features. Less than 20 cases have been described. The main features are low birth weight, microcephaly, stubby nose with a prominent nasal bridge, hypertelorism, strabismus, wide-set nipples, single transverse palmar creases, and clinodactyly. Boys have undescended testes and hypoplastic scrotum. Congenital heart disease, hydronephrosis or renal hypoplasia was present in some of the cases." "" @@ -19384,6 +19389,7 @@ "obsolete syndrome with limb reduction defects" "" "true" "obsolete dysostosis with combined reduction defects of upper and lower limbs" "" "true" "obsolete syndrome with limb duplication, polydactyly, syndactyly, and/or hyperphalangy" "" "true" + "IRF6-related condition" "Van der Woude syndrome, popliteal pterygium syndrome, cleft lip with or without palate, or a spectrum of one or two of those conditions in which the cause of the disease is a mutation in the IRF6 gene." "" "amelia of upper limb" "A non-syndromic amelia that involves the forelimb." "" "amelia of lower limb" "A non-syndromic amelia that involves the hindlimb." "" "tetra-amelia" "" @@ -23517,7 +23523,6 @@ "leukoencephalopathy, hereditary diffuse, with spheroids" "" "Teebi hypertelorism syndrome" "" "gastrointestinal defects and immunodeficiency syndrome 2" "A severe autosomal recessive developmental disorder characterized by multiple intestinal atresia apparent soon after birth. Affected infants have a distended abdomen and do not pass meconium. There is some evidence of inflammatory bowel disease. Death occurs in the first weeks of life. Some patients may also have immunodeficiency." "" - "gastrointestinal defect and immunodeficiency syndrome" "" "spastic paraplegia 86, autosomal recessive" "" "Teebi hypertelorism syndrome 2" "" "parkinsonism-dystonia 3, childhood-onset" "" @@ -23589,6 +23594,7 @@ "renal hypodysplasia/aplasia 4" "" "macrothrombocytopenia, isolated, 2, autosomal dominant" "" "macrothrombocytopenia, isolated" "" + "gastrointestinal defect and immunodeficiency syndrome" "" "developmental delay, impaired growth, dysmorphic facies, and axonal neuropathy" "" "neurodevelopmental disorder with microcephaly, impaired language, epilepsy, and gait abnormalities" "An autosomal dominant neurodevelopmental disorder characterized by global developmental delay apparent in infancy. Affected individuals have delayed walking with variable gait abnormalities, including ataxia and spasticity, impaired intellectual development with poor or absent speech and language, and progressive microcephaly. Dysmorphic facial features may also be observed. Most patients have early-onset seizures; some may develop a demyelinating peripheral neuropathy. The clinical features suggest involvement of both the central and peripheral nervous systems." "" "thyroid hormone metabolism, abnormal, 2" "" @@ -25735,6 +25741,7 @@ "obsolete Mycobacterium tuberculosis, protection against" "" "true" "ACD-related telomere biology disorder" "A complex set of inherited conditions caused by a pathogenic variant(s) in the ACD gene that results in aberrant telomere biology." "" "ACD-related long telomere syndrome" "A telomere biology disorder typically characterized by increased telomere length due to a pathogenic variant in the ACD gene that may cause familial melanoma." "" + "MTOR-related overgrowth spectrum" "Any overgrowth syndrome in which the cause of the disease is a pathogenic gain-of-function variants in the MTOR gene. The variants can be germline or somatic." "" "uterine ligament adenosarcoma" "An extremely rare adenosarcoma that arises from the uterine ligament." "" "obsolete chromate resistance" "" "true" "SSR3-CDG" "A congenital disorder of glycosylation with a SSR3 deficiency that affects the brain, lungs and gastrointestinal system, and presents with clinical phenotypes such as seizures, intellectual disability, developmental delay, microcephaly and abnormal brain structure." "" @@ -26721,7 +26728,7 @@ "oocyte/zygote/embryo maturation arrest 19" "" "cone-rod dystrophy 24" "" "congenital myopathy 22A, classic" "" - "developmental and epileptic encephalopathy 31B" "" + "developmental and epileptic encephalopathy, 31B" "Any developmental and epileptic encephalopathy in which the cause of the disease is a homozygous mutation in the DNM1 gene." "" "spermatogenic failure 82" "" "spermatogenic failure 83" "" "ciliary dyskinesia, primary, 50" "" @@ -27110,6 +27117,8 @@ "MHC class II deficiency 3" "" "MHC class II deficiency 4" "" "MHC class II deficiency 5" "" + "neurodevelopmental disorder with hypotonia, feeding difficulties, facial dysmorphism, and brain abnormalities" "" + "Ehlers-Danlos syndrome, classic-like, 3" "" "pythiosis" "A granulomatous disease caused by the aquatic organism pythium insidiosum occurring rarely in humans. It is classified into three forms: ocular, cutaneous, and arterial." "" "epilepsy, non-human animal" "Epilepsy that occurs in non-human animals." "" "myoclonus, non-human animal" "Myoclonus that occurs in non-human animals." "" @@ -28720,6 +28729,7 @@ "corneal sequestra, non-human animal" "" "osseous choristoma of the ciliary body, non-human animal" "" "hyperinsulinemic hypoglycemia with polycystic kidney disease" "Any hyperinsulinemic hypoglycemia which is accompanied by cystic structures in the kidneys, and in which the cause of the disease is a variation in the PMM2 promoter." "" + "GBA1-related Parkinson disease, susceptibility" "A susceptibility or predisposition to Parkinsons disease in which the cause of the disease is the presence of a monoallelic pathogenic variant or risk allele in the GBA1 gene." "" "infectious discitis" "An infection of the intervertebral disk space." "" "staphylococcus discitis" "Discitis caused by infection with Staphylococcus." "" "escherichia coli discitis" "Discitis caused by infection with Escherichia coli." "" diff --git a/src/ontology/reports/mondo_obsoletioncandidates.tsv b/src/ontology/reports/mondo_obsoletioncandidates.tsv index f63c72d441..394259c994 100644 --- a/src/ontology/reports/mondo_obsoletioncandidates.tsv +++ b/src/ontology/reports/mondo_obsoletioncandidates.tsv @@ -1,7 +1,7 @@ mondo_id label comment issue obsoletion_date MONDO:0000014 colorblindness, partial Reason of obsoletion: out of scope - MONDO:excludeHistoricalDisease. Term to consider: - https://github.com/monarch-initiative/mondo/issues/7700 2024-09-01 MONDO:0000114 cerebelloparenchymal disorder Reason of obsoletion: out of scope - MONDO:excludeHistoricalDisease. Term to consider: - https://github.com/monarch-initiative/mondo/issues/7700 2024-09-01 -MONDO:0000169 microphthalmia, isolated, with cataract Reason of obsoletion: out of scope - MONDO:excludeHistoricalDisease. Term to consider: microphthalmia, isolated, with cataract 1-MONDO:0007995 https://github.com/monarch-initiative/mondo/issues/7554 2024-07-01 +MONDO:0000169 microphthalmia, isolated, with cataract Reason of obsoletion: out of scope - MONDO:excludeHistoricalDisease. Term to consider: microphthalmia, isolated, with cataract 1-MONDO:0007995 https://github.com/monarch-initiative/mondo/issues/7554|https://github.com/monarch-initiative/mondo/issues/7766 2024-07-01 MONDO:0000224 acquired carbohydrate metabolism disease Reason of obsoletion: out of scope - MONDO:excludeHistoricalDisease. Term to consider: - https://github.com/monarch-initiative/mondo/issues/7700 2024-09-01 MONDO:0000251 diarrheal disease secondary to altered bowel motility Reason of obsoletion: out of scope - MONDO:excludeHistoricalDisease. Term to consider: - https://github.com/monarch-initiative/mondo/issues/7700 2024-09-01 MONDO:0000379 malignant Sertoli-Leydig cell tumor Reason of obsoletion: out of scope - MONDO:excludeHistoricalDisease. Term to consider: - https://github.com/monarch-initiative/mondo/issues/7700 2024-09-01 @@ -49,7 +49,6 @@ MONDO:0015174 autoimmune enteropathy type 3 Reason of obsoletion: out of scope - MONDO:0015256 blepharoptosis-cleft palate-ectrodactyly-dental anomalies syndrome Reason of obsoletion: out of scope - MONDO:excludeHistoricalDisease. Term to consider: - https://github.com/monarch-initiative/mondo/issues/7700 2024-09-01 MONDO:0015257 sino-auricular heart block Reason of obsoletion: out of scope - MONDO:excludeHistoricalDisease. Term to consider: - https://github.com/monarch-initiative/mondo/issues/7700 2024-09-01 MONDO:0015424 lethal chondrodysplasia, Moerman type Reason of obsoletion: out of scope - MONDO:excludeHistoricalDisease. Term to consider: - https://github.com/monarch-initiative/mondo/issues/7700|https://github.com/monarch-initiative/mondo/issues/6751 2024-09-01 -MONDO:0015429 choroideremia-hypopituitarism syndrome Reason of obsoletion: duplicate. This will be merged with MONDO:0022737 choroideremia hypopituitarism https://github.com/monarch-initiative/mondo/issues/7553 2024-07-01 MONDO:0015468 craniosynostosis-cataract syndrome Reason of obsoletion: out of scope - MONDO:excludeHistoricalDisease. Term to consider: - https://github.com/monarch-initiative/mondo/issues/6751|https://github.com/monarch-initiative/mondo/issues/7700 2024-09-01 MONDO:0015559 lymphoadenopathic mastocytosis with eosinophilia Reason of obsoletion: out of scope - MONDO:excludeHistoricalDisease. Term to consider: - https://github.com/monarch-initiative/mondo/issues/7700 2024-09-01 MONDO:0015907 epimetaphyseal skeletal dysplasia Reason of obsoletion: out of scope - MONDO:excludeHistoricalDisease. Term to consider: - https://github.com/monarch-initiative/mondo/issues/6751|https://github.com/monarch-initiative/mondo/issues/7700 2024-09-01 @@ -392,4 +391,4 @@ MONDO:0100112 acyl-CoA binding domain containing protein 5 deficiency Reason of MONDO:0100113 hearing loss with skin disease Reason of obsoletion: out of scope - MONDO:excludeHistoricalDisease. Term to consider: - https://github.com/monarch-initiative/mondo/issues/7700 2024-09-01 MONDO:0800112 non-atopic asthma Reason of obsoletion: duplicate. This will be merged with MONDO:0004765 intrinsic asthma https://github.com/monarch-initiative/mondo/issues/5261|https://github.com/monarch-initiative/mondo/issues/7691 2024-08-01 MONDO:0859345 branchial arch abnormalities, choanal atresia, athelia, hearing loss, and hypothyroidism syndrome Reason of obsoletion: duplicate. This will be merged with MONDO:0859345 branchial arch abnormalities, choanal atresia, athelia, hearing loss, and hypothyroidism syndrome https://github.com/monarch-initiative/mondo/issues/7560 2024-07-01 -MONDO:0957319 pseudohypoaldosteronism, type I Reason: duplicate. This will be merged with MONDO:0019161 pseudohypoaldosteronism type 1 https://github.com/monarch-initiative/mondo/issues/7273 2024-05-01 +MONDO:0957319 pseudohypoaldosteronism, type I Reason: duplicate. This will be merged with MONDO:0019161 pseudohypoaldosteronism type 1 https://github.com/monarch-initiative/mondo/issues/7766|https://github.com/monarch-initiative/mondo/issues/7273 2024-05-01 diff --git a/src/ontology/reports/mondo_release_diff_changed_terms.tsv b/src/ontology/reports/mondo_release_diff_changed_terms.tsv index fc74fa24ef..279b2231d3 100644 --- a/src/ontology/reports/mondo_release_diff_changed_terms.tsv +++ b/src/ontology/reports/mondo_release_diff_changed_terms.tsv @@ -5,13 +5,18 @@ MONDO:0006788 label hydrophthalmos obsolete hydrophthalmos MONDO:0009586 label mesangial sclerosis, diffuse renal, with ocular abnormalities obsolete mesangial sclerosis, diffuse renal, with ocular abnormalities MONDO:0013881 label pidermolysis bullosa, junctional 7, with interstitial lung disease and nephrotic syndrome epidermolysis bullosa, junctional 7, with interstitial lung disease and nephrotic syndrome MONDO:0014347 label short stature with microcephaly and distinctive facies Rothmund-Thomson syndrome, type 3 +MONDO:0014598 label developmental and epileptic encephalopathy, 31 developmental and epileptic encephalopathy, 31A +MONDO:0015429 label choroideremia-hypopituitarism syndrome obsolete choroideremia-hypopituitarism syndrome MONDO:0100032 label familial temporal lobe epilepsy syndrome obsolete familial temporal lobe epilepsy syndrome +MONDO:0957248 label developmental and epileptic encephalopathy 31B developmental and epileptic encephalopathy, 31B MONDO:0002839 definition A cancer-related condition in which the gastric wall becomes thickened and rubbery (leather-bottle stomach). It is most often associated with diffuse gastric adenocarcinomas. MONDO:0006788 definition Abnormal enlargement of the eye MONDO:0100016 definition A generalized isolated dystonia characterized by early-onset, which may be clinically indistinguishable from DYT-TOR1A and may be the most common cause of early-onset generalized dystonia, at least outside the Askenazi Jewish population. MONDO:0859050 definition An inherited predisposition to Schistosoma mansoni infection intensity and reinfection after treatment. +MONDO:0014598 definition Any early infantile epileptic encephalopathy in which the cause of the disease is a mutation in the DNM1 gene. Any developmental and epileptic encephalopathy in which the cause of the disease is a heterozygous mutation in the DNM1 gene. MONDO:0060778 definition Probably related to a recessive gene, this is Fanconi Syndrome, characterized by adult onset. A Fanconi renotubular syndrome that occurs in an adult. Adult Fanconi syndrome is typically acquired. MONDO:0100032 definition This syndrome is identified in an individual who has seizures with temporal lobe features with a family history of similar seizures. Seizures often comprise such mild symptoms that they are undiagnosed. There are no implications expected for development or learning and seizures are typically infrequent and well controlled. +MONDO:0957248 definition Any developmental and epileptic encephalopathy in which the cause of the disease is a homozygous mutation in the DNM1 gene. MONDO:0000014 obsoletion_candidate True MONDO:0000093 obsoletion_candidate True MONDO:0000114 obsoletion_candidate True @@ -70,6 +75,7 @@ MONDO:0015256 obsoletion_candidate True MONDO:0015257 obsoletion_candidate True MONDO:0024322 obsoletion_candidate True MONDO:0015424 obsoletion_candidate True +MONDO:0015429 obsoletion_candidate True MONDO:0015468 obsoletion_candidate True MONDO:0015559 obsoletion_candidate True MONDO:0015907 obsoletion_candidate True @@ -373,4 +379,5 @@ MONDO:0000093 obsolete True MONDO:0002839 obsolete True MONDO:0006788 obsolete True MONDO:0009586 obsolete True +MONDO:0015429 obsolete True MONDO:0100032 obsolete True diff --git a/src/ontology/reports/mondo_release_diff_new_terms.tsv b/src/ontology/reports/mondo_release_diff_new_terms.tsv index edee1ce085..a64d1a4d54 100644 --- a/src/ontology/reports/mondo_release_diff_new_terms.tsv +++ b/src/ontology/reports/mondo_release_diff_new_terms.tsv @@ -1,4 +1,5 @@ mondo_id label definition obsolete obsoletion_candidate +MONDO:0100572 MTOR-related overgrowth spectrum Any overgrowth syndrome in which the cause of the disease is a pathogenic gain-of-function variants in the MTOR gene. The variants can be germline or somatic. MONDO:0968990 genetic central precocious puberty in male MONDO:0968991 non-genetic central precocious puberty in male MONDO:0970943 spermatogenic failure, x-linked, 8 @@ -36,6 +37,8 @@ MONDO:0971013 MHC class II deficiency 2 MONDO:0971014 MHC class II deficiency 3 MONDO:0971015 MHC class II deficiency 4 MONDO:0971016 MHC class II deficiency 5 +MONDO:0971043 neurodevelopmental disorder with hypotonia, feeding difficulties, facial dysmorphism, and brain abnormalities +MONDO:0971044 Ehlers-Danlos syndrome, classic-like, 3 MONDO:1011400 pituitary-dependent hyperadrenocorticism, non-human animal Pituitary-dependent hyperadrenocorticism that occurs in non-human animals. MONDO:1011401 type 1 diabetes mellitus, non-human animal Type 1 diabetes mellitus that occurs in non-human animals. MONDO:1011402 type 2 diabetes mellitus, non-human animal Type 2 diabetes mellitus that occurs in non-human animals. @@ -640,3 +643,10 @@ MONDO:1012002 vitreous degeneration, non-human animal MONDO:1012003 corneal sequestra, non-human animal MONDO:1012004 osseous choristoma of the ciliary body, non-human animal MONDO:1030002 dysplasia of the proximal femoral epiphyses A developmental disorder affecting the growth and development of the proximal end of the femur (thigh bone) near the hip joint characterized by avascular necrosis of the femoral head, cystic changes of the femoral head, and/or sclerosis of the femoral head. It is a relatively milder form of the other skeletal disorders associated with COL2A1. +MONDO:1040002 PIK3CA-related overgrowth spectrum Any overgrowth syndrome resulting from pathogenic gain-of-function variants in the PIK3CA gene. The variants can be germline or somatic +MONDO:1040004 PIK3R2-related overgrowth spectrum Any overgrowth syndrome resulting from pathogenic gain-of-function variants in the PIK3R2 gene. The variants can be germline or somatic +MONDO:1040009 TRIP11-related skeletal dysplasia Any skeletal dysplasia in which the cause of the disease is a variation in the TRIP11 gene. Reduced protein function in TRIP11 causes a spectrum of skeletal symptoms from a more mild phenotype, called ondontochondrodysplasia, with features including short stature and joint laxity to a more severe phenotype, called achondrogenesis type 1A, which presents as a lethal prenatal or neonatal skeletal dysplasia. The clinical severity of achondrogenesis compared to ondontochondrodysplasia is related to the residual function of the gene which is not currently possible to anticipate based on genotype alone. The phenotype cannot fully be predicted by genotype alone, evidenced by variants being reported with both phenotypes. +MONDO:1040010 IRF6-related condition Van der Woude syndrome, popliteal pterygium syndrome, cleft lip with or without palate, or a spectrum of one or two of those conditions in which the cause of the disease is a mutation in the IRF6 gene. +MONDO:1040012 PI4KA-related disorder Any human disease in which the cause of the disease is a variation in the PI4KA gene. This disease is characterized primarily by neurologic dysfunction (limb spasticity, developmental delay, intellectual disability, seizures, ataxia, nystagmus), gastrointestinal manifestations (multiple intestinal atresia, inflammatory bowel disease), and combined immunodeficiency (leukopenia, variable immunoglobulin defects). Age of onset is typically antenatal or in early childhood; individuals can present with any combination of these features. Rare individuals present with later-onset hereditary spastic paraplegia. Brain MRI findings can include hypomyelinating leukodystrophy, cerebellar hypoplasia/atrophy, thin or dysplastic corpus callosum, and/or perisylvian polymicrogyria. +MONDO:1040030 GBA1-related Parkinson disease, susceptibility A susceptibility or predisposition to Parkinsons disease in which the cause of the disease is the presence of a monoallelic pathogenic variant or risk allele in the GBA1 gene. +MONDO:1040031 dyneinopathy A spectrum of diseases related to monoallelic variants in DYNC1H1 and characterized by variable neuromuscular and/or neurodevelopmental presentations. While not absolute, there appear to be genotype-phenotype correlations based on the location of the variant. Patients with variants in the stem domain of DYNC1H1 have been reported with a predominantly neuromuscular presentation, including congenital myopathy, spinal muscular atrophy, Charcot-Marie-Tooth (CMT), and less frequently, intellectual disability and autism. Patients with variants in the motor domain predominantly present with neurodevelopmental presentations including intellectual disability, seizures, malformations of cortical development (abnormal brain MRI findings such as pachygyria, heterotopias, enlarged ventricles, hypoplasia of CC, brain stem, cerebellum), autism, and less frequently, neuromuscular phenotypes.