monarch-initiative/mondo: v2025-10-07

<details> <summary>New terms: 27</summary>

| Term | ----| | DNAJC21-related Shwachman Diamond syndrome (MONDO:0700311) | | systemic lupus erythematosus related to C1S (MONDO:1060176) | | combined immunodeficiency syndrome (MONDO:0700289) | | diffuse midline glioma, H3 K27-altered (MONDO:1060171) | | CHD7-related CHARGE syndrome (MONDO:1010178) | | IRF4-related combined immunodeficiency (MONDO:1010173) | | POLD3-related combined immunodeficiency (MONDO:1010176) | | PTEN harmartoma tumor syndrome with immune disorder (MONDO:0700330) | | NFATC1-related combined immunodeficiency (MONDO:1010174) | | FASLG-related immunodeficiency (MONDO:0700306) | | systemic lupus erythematosus related to C1QA (MONDO:1060174) | | idiopathic pulmonary fibrosis (MONDO:0800504) | | TREX1-related autosomal dominant Aicardi-Goutieres syndrome (MONDO:0700333) | | HAVCR2-related cancer predisposition (MONDO:1060169) | | IKZF2-related combined immunodeficiency (MONDO:1010177) | | interstitial lung disease 2 (MONDO:0800497) | | giant cell hepatitis with autoimmune hemolytic anemia (MONDO:1060166) | | argyrophilic grain disease (MONDO:0700351) | | POLD2-related combined immunodeficiency (MONDO:1010175) | | ELANE-related neutropenia (MONDO:1060165) | | IRF4-related immune disorder (MONDO:0700327) | | complex movement disorder with or without neurodevelopmental features (MONDO:1060159) | | FLNB-associated autosomal dominant filamin related bone disorder (MONDO:1060173) | | TNFRSF9-related immunodeficiency (MONDO:0700308) | | inherited distal renal tubular acidosis (MONDO:1060161) | | acquired distal renal tubular acidosis (MONDO:1060162) | | ACO2-related optic atrophy with or without extraocular features (MONDO:1060120) |

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<details> <summary>Terms renamed: 14</summary>

| ID | Old Label | New Label | ----|----|----| | MONDO:0970950 | Rothmund-Thomson syndrome, type 4 | Rothmund-Thomson syndrome type 4 | | MONDO:0014347 | Rothmund-Thomson syndrome, type 3 | Rothmund-Thomson syndrome type 3 | | MONDO:0004742 | primary cerebellar degeneration | obsolete primary cerebellar degeneration | | MONDO:0025303 | anaplasmosis | obsolete anaplasmosis | | MONDO:0003723 | blunt duct adenosis of breast | obsolete blunt duct adenosis of breast | | MONDO:0800460 | ASAH1-related disorders | obsolete ASAH1-related disorders | | MONDO:0006518 | sporadic Creutzfeld Jacob disease | obsolete sporadic Creutzfeld Jacob disease | | MONDO:0005118 | human granulocytic ehrlichiosis | human granulocytic anaplasmosis | | MONDO:0020474 | cheirospondyloenchondromatosis | obsolete cheirospondyloenchondromatosis | | MONDO:0800029 | interstitial lung disease 2 | obsolete interstitial lung disease 2 | | MONDO:0018603 | SFTPC- related interstitial lung disease | SFTPC-related interstitial lung disease | | MONDO:0000638 | benign glioma | obsolete benign glioma | | MONDO:0017770 | Robinow-like syndrome | obsolete Robinow-like syndrome | | MONDO:0002492 | acute kidney failure | acute kidney injury |

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<details> <summary>Text definitions added: 35</summary>

| Term | New Text Definition | ----|----| | POLD3-related combined immunodeficiency (MONDO:1010176) | A combined immunodeficiency in which the cause of the disease is a variation in the POLD3 gene. | | idiopathic pulmonary fibrosis (MONDO:0800504) | An interstitial lung disease with a poor prognosis, that is characterized by the progressive formation of scar tissue within the lungs in the absence of any known cause. | | FLNB-associated autosomal dominant filamin related bone disorder (MONDO:1060173) | Any autosomal dominant filamin related bone disorder in which the cause of the disease is a variation in FLNB gene. | | argyrophilic grain disease (MONDO:0700351) | A tauopathy characterized pathologically by the presence of silver stain positive lesions called argyrophilic grains, oligodendrocytic coiled bodies, and neuronal tau-positive pretangles. | | IKZF2-related combined immunodeficiency (MONDO:1010177) | A combined immunodeficiency syndrome in which the cause of the disease is a variation in the IKZF2 gene. | | developmental delay with variable intellectual impairment and behavioral abnormalities (MONDO:0032745) | A neurodevelopmental disorder caused by a mutation in TCF gene, characterized by impaired intellectual development with speech difficulties and behavioral abnormalities, most commonly autism spectrum disorder (ASD), defects in attention, and/or hyperactivity. | | neurodevelopmental disorder with hypotonia, brain anomalies, distinctive facies, and absent language (MONDO:0971172) | A syndromic neurodevelopmental disorder in which the cause of the disease is a variation in RNU4-2 gene and is inherited in an autosomal dominant pattern. It is characterized by moderate to severe global developmental delay/intellectual disability, speech anomalies (mostly non-verbal), hypotonia, abnormal brain MRI (reduced white matter volume, hypoplasia of the corpus callosum, ventriculomegaly, and delayed myelination), dysmorphic facial features, short stature, microcephaly, behavioral issues, seizures and feeding difficulties, as well as variable vision, gastrointestinal, endocrine, skeletal, genitourinary, cardiac, and cutaneous anomalies. It has autosomal dominant inheritance. | | TREX1-related autosomal dominant Aicardi-Goutieres syndrome (MONDO:0700333) | Autosomal dominant form of Aicardi-Goutieres syndrome 1. | | ACCES syndrome (MONDO:0859262) | A rare congenital disease caused by a mutation in the UBA2 gene, charcterized by scalp defects, digital and skeletal anomalies, early growth deficiency, and neurodevelopmental delay. Ectrodactyly presents in some cases. | | giant cell hepatitis with autoimmune hemolytic anemia (MONDO:1060166) | A rare autoimmune disease of early childhood, marked by the simultaneous or sequential immune attack on red blood cells and liver cells. | | tumor predisposition syndrome 3 (MONDO:0014368) | Any hereditary cancer predisposition due to variation(s) in the POT1 gene, which confers a predisposition to development of various types of benign and malignant neoplasms. | | complex movement disorder with or without neurodevelopmental features (MONDO:1060159) | A movement disorder characterized by having one or more different types of movement disorders, such as abnormal muscle tone, abnormal degree of movement, dystonia or torsion, which may occur with or without neurodevelopmental features, such as developmental delay or intellectual disability. | | serpinopathy (MONDO:0027749) | Hereditary disease by a qualitative or quantitative deficiencies or overexpression and/or abnormal accumulation of SERPIN; SERPINs are members of the serpin (serine proteinase inhibitors) superfamily which includes proteins with serine protease inhibitor activity and some that do not exhibit this inhibitory activity against serine proteases. | | POLD2-related combined immunodeficiency (MONDO:1010175) | A non-severe combined immunodeficiency due to polymerase delta deficiency in which the cause of the disease is a variation in the POLD2 gene. | | FASLG-related immunodeficiency (MONDO:0700306) | An immunodeficiency disease in which the cause of the disease is a variation in the FASLG gene. | | systemic lupus erythematosus related to C1S (MONDO:1060176) | Any systemic lupus erythematosus in which the cause of the disease is a variation in the C1S gene. | | DNAJC21-related Shwachman Diamond syndrome (MONDO:0700311) | A Shwachman Diamond syndrome in which the cause of the disease is a variation in the DNAJC21 gene. | | interstitial lung disease 2 (MONDO:0800497) | An interstitial lung disease in which the cause of the disease is a variation in the SFTPA2 gene. | | ACO2-related optic atrophy with or without extraocular features (MONDO:1060120) | An optic atrophy in which the cause of the disease is monoallelic or biallelic variants in the ACO2 gene. ACO2 is a mitochondrial protein and thus, in addition to the optic atrophy features, features of this disease include abnormal mitochondrial morphology and can affect other organ systems. Extraocular features can include ataxia, spastic paraplegia, CNS abnormalities, neurodevelopmental phenotypes, and retinal degeneration. | | ELANE-related neutropenia (MONDO:1060165) | Any neutropenia in which the cause of the disease is a mutation in the ELANE gene. | | IRF4-related immune disorder (MONDO:0700327) | An immune disorder in which the cause of the disease is a variation in the interferon activation domain of the IRF4 gene. | | TNFRSF9-related immunodeficiency (MONDO:0700308) | An immunodeficiency disease in which the cause of the disease is a variation in the TNFRSF9 gene. | | Shwachman-Diamond syndrome 1 (MONDO:0044204) | A Shwachman Diamond syndrome in which the cause of the disease is a variation in the SBDS gene. | | CHD7-related CHARGE syndrome (MONDO:1010178) | A CHARGE syndrome in which the cause of the disease is a variation in the CHD7 gene. | | interstitial lung disease 1 (MONDO:0030608) | An interstitial lung disease in which the cause of the disease is a variation in the SFTPA1 gene. | | systemic lupus erythematosus related to C1QA (MONDO:1060174) | Any systemic lupus erythematosus in which the cause of the disease is a variation in the C1QA gene. | | inherited distal renal tubular acidosis (MONDO:1060161) | A form of distal renal tubular acidosis that is inherited. | | IRF4-related combined immunodeficiency (MONDO:1010173) | A combined immunodeficiency in which the cause of the disease is a variation in the IRF4 gene. | | acquired distal renal tubular acidosis (MONDO:1060162) | A form of distal renal tular acidosis that develops secondary to another condition, usually disease or drug. | | combined immunodeficiency syndrome (MONDO:0700289) | A combined immunodeficiency in which other clinical features are present in other organ systems in addition to immunodeficiency. | | HAVCR2-related cancer predisposition (MONDO:1060169) | Hereditary cancer predisposition due to variation(s) in the HAVCR2 gene, which confers the predisposition to susceptibility to subcutaneous panniculitis-like T-cell lymphoma (SPTCL) and hemophagocytic lymphohistiocytosis (HLH). Affected individuals typically present with multiple subcutaneous nodules and systemic B symptoms. | | cardiac anomalies - developmental delay - facial dysmorphism syndrome (MONDO:0014773) | A rare, genetic syndromic intellectual disability characterized by developmental delay, mild to severe intellectual disability, facial features (bulbous nasal tip, and macroglossia, macrostomia, or open mouth appearance) and a wide spectrum of other nonspecific variable clinical features, such as cardiac defects. | | NFATC1-related combined immunodeficiency (MONDO:1010174) | A combined immunodeficiency in which the cause of the disease is a variation in the NFATC1 gene. | | inherited interstitial lung disease (MONDO:0031199) | An instance of interstitial lung disease that is caused by an inherited modification of the individual's genome. | | diffuse midline glioma, H3 K27-altered (MONDO:1060171) | A diffuse midline glioma characterized by H3 K27 alteration and usually either a histone H3 K27M mutation, an EGFR mutation, or aberrant overexpression of EZHIP. The prognosis is poor. |

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<details> <summary>Text definitions changed: 19</summary>

| Term | Old Text Definition | New Text Definition | ----|----|----| | distal renal tubular acidosis (MONDO:0015827) | Distal renal tubular acidosis (dRTA) is a disorder of impaired net acid secretion by the distal tubule characterized by hyperchloremic metabolic acidosis. The classic form is often associated with hypokalemia whereas other forms of acquired dRTA may be associated with hypokalemia, hyperkalemia or normokalemia. | A kidney disorder of impaired net acid secretion by the distal tubule characterized by hyperchloremic metabolic acidosis. Primary distal renal tubular acidosis is often associated with hypokalemia whereas acquired form may be associated with hypokalemia, hyperkalemia or normokalemia. | | obsolete blunt duct adenosis of breast (MONDO:0003723) | Breast adenosis characterized by the presence of ducts with distended lumen and columnar cell metaplasia. | OBSOLETE. Breast adenosis characterized by the presence of ducts with distended lumen and columnar cell metaplasia. | | Boomerang dysplasia (MONDO:0007208) | Boomerang dysplasia (BD) is a rare lethal skeletal dysplasia characterized by severe short-limbed dwarfism, dislocated joints, club feet, distinctive facies and diagnostic x-ray findings of underossified and dysplastic long tubular bones, with a boomerang-like bowing. | A rare lethal skeletal dysplasia characterized by severe short-limbed dwarfism, dislocated joints, club feet, distinctive facies and diagnostic x-ray findings of underossified and dysplastic long tubular bones, with a boomerang-like bowing. | | obsolete primary cerebellar degeneration (MONDO:0004742) | A heterogenous group of degenerative syndromes marked by progressive cerebellar dysfunction either in isolation or combined with other neurologic manifestations. Sporadic and inherited subtypes occur. Inheritance patterns include autosomal dominant, autosomal recessive, and X-linked. | OBSOLETE. A heterogenous group of degenerative syndromes marked by progressive cerebellar dysfunction either in isolation or combined with other neurologic manifestations. Sporadic and inherited subtypes occur. Inheritance patterns include autosomal dominant, autosomal recessive, and X-linked. | | autosomal dominant distal renal tubular acidosis (MONDO:0008368) | Autosomal dominant distal renal tubular acidosis (AD dRTA) is an inherited form of distal renal tubular acidosis (dRTA) characterized by hyperchloremic metabolic acidosis often but not always associated with hypokalemia. | A distal renal tubular acidosis that is caused by the mutation in SLC4A1 gene and follows the autosomal dominant inheritance. It is characterized by reduced ability to acidify urine, variable hyperchloremic hypokalemic metabolic acidosis, nephrocalcinosis, nephrolithiasis, and metabolic bone disease. | | torsion dystonia 2 (MONDO:0009141) | Primary dystonia DYT2 type is characterized by segmental dystonia that manifests with involuntary posturing affecting predominantly the feet. | A dystonia characterized by segmental dystonia that predominantly affects the distal limbs and leads to abnormal posture. This disease has a progressive clinical course and may develop into generalized dystonia but remains mild overall. | | Sandhoff disease (MONDO:0010006) | Sandhoff disease is a lysosomal storage disorder from the GM2 gangliosidosis family and is characterized by central nervous system degeneration. | A lysosomal disorder from the GM2 gangliosidosis family, caused by biallelic pathogenic variants in the HEXB gene, characterized by GM2 ganglioside accumulation in the nervous system and progressive central nervous system degeneration. | | atelosteogenesis type I (MONDO:0007167) | Atelosteogenesis I is a perinatally lethal skeletal dysplasia characterized by severe short-limbed dwarfism, joint dislocations, club feet along with distinctive facies and radiographic findings. | A perinatally lethal skeletal dysplasia characterized by severe short-limbed dwarfism, joint dislocations, club feet along with distinctive facies and radiographic findings. | | mucopolysaccharidosis type 3 (MONDO:0018937) | Mucopolysaccharidosis type III (MPS III) is a lysosomal storage disease belonging to the group of mucopolysaccharidoses and characterized by severe and rapid intellectual deterioration. | A lysosomal disease characterized by progressive neurocognitive decline, severe intellectual deterioration, loss of functional abilities, and premature death. | | obsolete cheirospondyloenchondromatosis (MONDO:0020474) | Cheirospondyloenchondromatosis is an extremely rare type of enchondromatosis of very early onset (from neonatal period to infancy) characterized by symmetrical multiple enchondromas with metacarpal and phalangeal involvement resulting in short hands and feet, platyspondyly, mild to moderate short stature and intellectual disability. | OBSOLETE. Cheirospondyloenchondromatosis is an extremely rare type of enchondromatosis of very early onset (from neonatal period to infancy) characterized by symmetrical multiple enchondromas with metacarpal and phalangeal involvement resulting in short hands and feet, platyspondyly, mild to moderate short stature and intellectual disability. | | autosomal recessive distal renal tubular acidosis (MONDO:0018440) | Autosomal recessive distal renal tubular acidosis (AR dRTA) is an inherited form of distal renal tubular acidosis (dRTA) characterized by hypokalemic hyperchloremic metabolic acidosis. Deafness often occurs either early or later on in life but may be absent or never be diagnosed. | The autosomal recessive form of distal renal tubular acidosis (dRTA) characterized by hypokalemic hyperchloremic metabolic acidosis. Deafness often occurs either early or later on in life but may be absent or never be diagnosed. | | renal tubular acidosis, distal, 4, with hemolytic anemia (MONDO:0012700) | Distal renal tubular acidosis (dRTA) with anemia is a very rare form of distal renal tubular acidosis (dRTA) characterized by a defect in renal acidification and hereditary hemolytic anemia. | A very rare form of distal renal tubular acidosis (dRTA) characterized by a defect in renal acidification and hereditary hemolytic anemia. | | ASAH1-related sphingolipidosis (MONDO:0100524) | A spectrum of disorders that includes Farber disease and spinal muscular atrophy with progressive myoclonic epilepsy. Both disorders are caused by mutations in the ASAH1 gene that encodes the lysosomal hydrolase that breaks down the bioactive lipid, ceramide. | A spectrum of disorders caused by variation(s) in the ASAH1 genel this spectrum includes Farber disease and spinal muscular atrophy with progressive myoclonic epilepsy. The ASAH1 gene encodes the lysosomal hydrolase that breaks down the bioactive lipid, ceramide. | | MYH7-related skeletal myopathy (MONDO:0008050) | Laing distal myopathy, also called myopathy distal, type 1 (MPD1), is characterized by early-onset selective weakness of the great toe and ankle dorsiflexors, and a very slowly progressive course. | A rare autosomal dominant distal myopathy characterized by preferential weakness of the great toe, ankle dorsiflexor, finger extensor and neck flexor. Progression is slow with variations in age of onset, severity, weakness, cardiac, and respiratory involvement. | | microcephaly with or without chorioretinopathy, lymphedema, or intellectual disability (MONDO:0007918) | Microcephaly with or without chorioretinopathy, lymphedema or intellectual disability (MCLID) is a rare autosomal dominant condition characterized by variable expression of microcephaly, ocular disorders including chorioretinopathy, congenital lymphedema of the lower limbs, and mild to moderate intellectual disability. | A microcephaly caused by a mutation in KIF11 gene and follows autosomal dominant inheritance. It is characterized by variable expression of microcephaly, ocular disorders including chorioretinopathy, congenital lymphedema of the lower limbs, and mild to moderate intellectual disability. | | obsolete Robinow-like syndrome (MONDO:0017770) | Robinow-like syndrome is characterized by the association of the clinical features present in Robinow syndrome (short stature, mesomelic brachymelia, macrocephaly, and hypoplastic genitalia), with anterior chamber cleavage anomalies. It has been described in two sisters and is transmitted as an autosomal recessive trait. | OBSOLETE. Robinow-like syndrome is characterized by the association of the clinical features present in Robinow syndrome (short stature, mesomelic brachymelia, macrocephaly, and hypoplastic genitalia), with anterior chamber cleavage anomalies. It has been described in two sisters and is transmitted as an autosomal recessive trait. | | facioscapulohumeral muscular dystrophy 1 (MONDO:0008030) | Any facioscapulohumeral muscular dystrophy in which the cause of the disease is a mutation in the FRG1 gene. | Any facioscapulohumeral muscular dystrophy associated with contraction of the D4Z4 macrosatellite repeat in the subtelomeric region of chromosome 4q35. | | Larsen syndrome (MONDO:0007875) | Larsen syndrome (LS) is a rare skeletal dysplasia characterized by congenital dislocation of large joints, foot deformities, cervical spine dysplasia, scoliosis, spatula-shaped distal phalanges and distinctive craniofacial abnormalities, including cleft palate. | A rare skeletal dysplasia characterized by congenital dislocation of large joints, foot deformities, cervical spine dysplasia, scoliosis, spatula-shaped distal phalanges and distinctive craniofacial abnormalities, including cleft palate. | | sporadic Creutzfeldt-Jakob disease (MONDO:0016079) | Sporadic Creutzfeldt-Jakob disease (sCJD) is a subacute fatal neurodegenerative disease belonging to the group of prion diseases, characterized by a clinical triad of dementia, myoclonus, and EEG anomalies, along with neuropathological evidence of neuronal loss, spongiform changes, and astrocytosis. There are three types of CJD: sporadicCJD (sCJD), inherited CJD, and iatrogenic and variant CJD (vCJD). | A rare sporadic human prion disease characterized by rapidly progressive cognitive impairment in combination with variable neurologic signs and symptoms including myoclonus, visual or cerebellar problems, pyramidal or extrapyramidal features, or akinetic mutism. Brain imaging may show high signal intensity in caudate, putamen, and/or cortical regions, and a typical EEG pattern consisting of generalized periodic sharp wave complexes is observed in many cases. The disease is invariably fatal within less than two years. Neuropathologic examination reveals deposition of abnormal prion protein in brain tissue, as well as spongiform change and massive neuronal loss and gliosis. |

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<details> <summary>Terms obsoleted with replacement: 4</summary>

| Term | Replacement | ----|----| | obsolete ASAH1-related disorders (MONDO:0800460) | ASAH1-related sphingolipidosis (MONDO:0100524) | | obsolete sporadic Creutzfeld Jacob disease (MONDO:0006518) | sporadic Creutzfeldt-Jakob disease (MONDO:0016079) | | obsolete anaplasmosis (MONDO:0025303) | human granulocytic anaplasmosis (MONDO:0005118) | | obsolete benign glioma (MONDO:0000638) | low grade glioma (MONDO:0021637) |

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<details> <summary>Terms obsoleted without replacement: 5</summary>

| Term | ----| | obsolete primary cerebellar degeneration (MONDO:0004742) | | obsolete cheirospondyloenchondromatosis (MONDO:0020474) | | obsolete Robinow-like syndrome (MONDO:0017770) | | obsolete blunt duct adenosis of breast (MONDO:0003723) | | obsolete interstitial lung disease 2 (MONDO:0800029) |

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<details> <summary>New obsoletion candidates: 4</summary>

| Mondo ID | Label | |:---|:---| | MONDO:0005731 | dipetalonemiasis | | MONDO:0100317 | deficiency of adenosine deaminase 2 | | MONDO:0800197 | achromatopsia 6 | | MONDO:0800369 | Parkinson disease 19B, early-onset |

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<details> <summary>Terms that were previously candidates for obsoletion and are now not anymore: 0</summary>

No changes.

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