While there is no cure for BGS, symptoms can be treated as they arise. Surgery shortly after birth can repair craniosynostosis, as well as defects in the hand to create a functional grasp. There are risks associated with untreated craniosynostosis, therefore surgery is often needed to separate and reshape the bones. Since patients with a RECQL4 mutation may be at an increased risk of developing cancer, surveillance is recommended.

A 2007 study followed 112 individuals for a mean of 12 years (mean age 25.3, range 12–71). No patient died during follow-up, but several required medical interventions. The mean final heights were 167 and 153 cm for men and women, respectively, which is approximately 2 standard deviations below normal.

Rothmund–Thomson syndrome (RTS), also known as poikiloderma atrophicans with cataract or poikiloderma congenitale, is a rare autosomal recessive skin condition originally described by August von Rothmund (1830–1906) in 1868. Matthew Sydney Thomson (1894–1969) published further descriptions in 1936.

There have been several reported cases associated with osteosarcoma. A hereditary genetic basis, mutations in the DNA Helicase "RECQL4" gene, causing problems during initiation of DNA replication has been implicated in the syndrome

Kindler syndrome is an autosomal recessive genodermatosis. The KIND1 gene mutated in Kindler syndrome codes for the protein kindlin-1, which is thought to be active in the interactions between actin and the extracellular matrix (focal adhesion plaques). Kindler syndrome was first described in 1954 by Theresa Kindler.

Kindler syndrome (also known as "bullous acrokeratotic poikiloderma of kindler and weary", is a rare congenital disease of the skin caused by a mutation in the KIND1 gene.

Smith Martin Dodd syndrome is a very rare genetic disorder first described by Smith et al. in 1994. It is characterized by small eyes, a diaphragmatic hernia, and Tetralogy of Fallot, a congenital heart defect. The only known case is of a 9-year-old boy with several congenital anomalies including a diaphragmatic hernia, microphthalmia, and Tetralogy of Fallot. It was found that the boy had a reciprocal translocation t(1;15)(q41;q21.2). A congenital diaphragmatic hernia is consistent with chromosome 1q41-q42 deletion syndrome, and the report by Smith et al. suggested that genes involved in the translocation may be important for the development of morphological characteristics, especially those of the eye or heart.

Noonan syndrome (NS) is a relatively common autosomal dominant congenital disorder and is named after Jacqueline Noonan, a pediatric cardiologist. It is referred to as the male version of Turner's syndrome; however, the genetic causes of Noonan syndrome and Turner syndrome are distinct and both males and females are affected. The principal features include congenital heart defect (typicall pulmonary valve stenosis with dysplastic pulmonary valve also atrial septal defect and hypertrophic cardiomyopathy), short stature, learning problems, pectus excavatum, impaired blood clotting, and a characteristic configuration of facial features including a webbed neck and a flat nose bridge. NS is a RASopathy, and is one of several disorders that are caused by a disruption of RAS-MAPK signaling pathway.

It is believed that between approximately 1 in 1,000 and 1 in 2,500 children worldwide are born with NS. It is one of the most common genetic syndromes associated with congenital heart disease, similar in frequency to Down syndrome. However, the range and severity of features can vary greatly in patients with NS. Therefore, the syndrome is not always identified at an early age.

Baller–Gerold syndrome (BGS) is a rare genetic syndrome that involves premature fusion of the skull bones and malformations of facial, forearm and hand bones. The symptoms of Baller–Gerold syndrome overlap with features of a few other genetics disorders: Rothmund-Thomson syndrome and RAPADILINO syndrome. The prevalence of BGS is unknown, as there have only been a few reported cases, but it is estimated to be less than 1 in a million. The name Baller-Gerold comes from the researchers Baller and Gerold who discovered the first three cases.

Available treatments address the symptoms of CCD, not the underlying defect. Early diagnosis and aggressive salt replacement therapy result in normal growth and development, and generally good outcomes. Replacement of NaCl and KCl has been shown to be effective in children.

A potential treatment is butyrate.

Observations leading to the characterization of the SLC26 family were based on research on rare human diseases. Three rare recessive diseases in humans have been shown to be caused by genes of this family. Diastrophic dysplasia, congenital chloride diarrhea, and Pendred syndrome are caused by the highly related genes SLC26A2 (first called DTDST), SLC26A3 (first called CLD or DRA), and SLC26A4 (first called PDS), respectively. Two of these diseases, diastrophic dysplasia and congenital chloride diarrhea, are Finnish heritage diseases.

In humans, individuals with RTS, and carrying the "RECQL4" germline mutation, can have several clinical features of accelerated aging. These features include atrophic skin and pigment changes, alopecia, osteopenia, cataracts and an increased incidence of cancer. Also in mice, "RECQL4" mutants show features of accelerated aging.

Aplasia cutis congenita (ACC) is a rare disorder characterized by congenital absence of skin. Frieden classified ACC in 1986 into 9 groups on the basis of location of the lesions and associated congenital anomalies. The scalp is the most commonly involved area with lesser involvement of trunk and extremities. Frieden classified ACC with fetus papyraceus as type 5. This type presents as truncal ACC with symmetrical absence of skin in stellate or butterfly pattern with or without involvement of proximal limbs.]It is the most common congenital cicatricial alopecia, and is a congenital focal absence of epidermis with or without evidence of other layers of the skin.

The exact etiology of ACC is still unclear but intrauterine infection by varicella or herpes virus, drugs such as methimazole, misoprostol, valproate, cocaine, marijuana etc., fetus papyraceus, feto-fetal transfusion, vascular coagulation defects, amniotic membrane adherence, abnormal elastic fiber biomechanical forces and trauma are implicated. It can be associated with Johanson-Blizzard syndrome, Adams-Oliver syndrome, trisomy 13, and Wolf-Hirschhorn syndrome.

It can also seen with exposure to methimazole and carbimazole in utero. This dermatological manifestation has been linked to Peptidase D haploinsufficiency and a deletion in Chromosome 19.

This condition has been linked to mutations in the ribosomal GTPase BMS1 gene.

Hereditary sclerosing poikiloderma is an autosomal dominant conditions with skin changes consisting of generalized poikiloderma appearing in childhood.

Neurocristopathy is a diverse class of pathologies that may arise from defects in the development of tissues containing cells commonly derived from the embryonic neural crest cell lineage. The term was coined by Robert P. Bolande in 1974.

Accepted examples are piebaldism, Waardenburg syndrome, Hirschsprung disease, Ondine's curse (congenital central hypoventilation syndrome), pheochromocytoma, paraganglioma, Merkel cell carcinoma, multiple endocrine neoplasia, neurofibromatosis type I, CHARGE syndrome, familial dysautonomia, DiGeorge syndrome, Axenfeld-Rieger syndrome, Goldenhar syndrome (a.k.a. hemifacial microsomia), craniofrontonasal syndrome, congenital melanocytic nevus, melanoma, and certain congenital heart defects of the outflow tract, in particular.

Multiple sclerosis has also been suggested as being neurocristopathic in origin.

The usefulness of the definition resides in its ability to refer to a potentially common etiological factor for certain neoplasms and/or congenital malformation associations that are otherwise difficult to group with other means of nosology.

Hemimelia comprises

- Fibular hemimelia, Congenital longitudinal deficiency of the fibula or Fibular longitudinal meromelia

- Tibial hemimelia, Congenital longitudenal deficiency of the tibia, Congenital aplasia and dysplasia of the tibia with intact fibula, Congenital longitudinal deficiency of the tibia or Tibial longitudinal meromelia

- Radial Hemimelia, Congenital longitudinal deficiency of the radius, Radial clubhand, Radial longitudinal meromelia or Radial ray agenesis

- Ulnar hemimelia, Congenital longitudinal deficiency of the ulna, Ulnar clubhand or Ulnar longitudinal meromelia

Regular administration of exogenous granulocyte colony-stimulating factor (filgrastim) clinically improves neutrophil counts and immune function and is the mainstay of therapy, although this may increase risk for myelofibrosis and acute myeloid leukemia in the long term.

Over 90% of SCN responds to treatment with granulocyte colony-stimulating factor (filgrastim), which has significantly improved survival.

Once a patient with neurocutaneous melanosis becomes symptomatic, little can be done to improve prognosis as there is no effective treatment for the disorder. Most therapies are designed to treat the symptoms associated with the disorder, mainly those related to hydrocephalus. A ventriculoperitoneal shunt to relieve intracranial pressure is the preferred method.

Chemotherapy and radiotherapy have been shown to be ineffective in cases of neurocutaneous melanosis where malignancy is present. Additionally, due to the total infiltration of the central nervous system by these lesions, surgical resection is not a viable treatment option.

It has been demonstrated that early embryonic, post-zygotic somatic mutations in the NRAS gene are implicated in the pathogenesis of NCM. Recently, experimental treatment with MEK162, a MEK inhibitor, has been tried in a patient with NCM and progressive symptomatic leptomeningeal melanocytosis. Pathological studies with immunohistochemical and Western Blot analyses using Ki67 and pERK antibodies showed a potential effect of MEK inhibiting therapy. Further studies are needed to determine whether MEK inhibitors can effectively target NRAS-mutated symptomatic NCM.

Microcoria is a congenital disease in which the pupils of the subject are narrower than 2 mm in diameter. Microcoria is associated with juvenile-onset glaucoma. It is also associated with Pierson syndrome chararacterized by microcoria and congenital nephrotic syndrome. The defect is in the Laminin beta 2 gene on chromosome 3p21 which encodes a protein essential to the glomerular basement membrane.

It is also part of the known manifestations of a born infant to a mother suffering from uncontrolled hyperglycemia. Other symptoms include transposition of great vessels, respiratory distress secondary to surfactant defect, sacral agensis, jitteriness, irritability, and lethargy due to rebound fetal hypoglycemia. Congenital microcoria is an autosomal dominant trait. However, it can also occur sporadically.

Prosthetic replacement of missing teeth is possible using dental implant technology or dentures. This treatment can be successful in giving patients with anodontia a more aesthetically pleasing appearance. The use of an implant prosthesis in the lower jaw could be recommended for younger patients as it is shown to significantly improve the craniofacial growth, social development and self-image. The study associated with this evidence worked with individuals who had ectodermal dysplasia of varying age groups of up to 11, 11 to 18 and more than 18 years. It was noted that the risk of implant failure was significantly higher in patients younger than 18 years, but there is significant reason to use this methodology of treatment in those older. Overall the use of an implant-prosthesis has a considerable functional, aesthetic and psychological advantage when compared to a conventional denture, in the patients.

Studies suggest that prenatal care for mothers during their pregnancies can prevent congenital amputation. Knowing environmental and genetic risks is also important. Heavy exposure to chemicals, smoking, alcohol, poor diet, or engaging in any other teratogenic activities while pregnant can increase the risk of having a child born with a congenital amputation. Folic acid is a multivitamin that has been found to reduce birth defects.

Congenital lactic acidosis (CLA) is a rare disease caused by mutations in mitochondrial DNA (mtDNA) that affect the ability of cells to use energy and cause too much lactic acid to build up in the body, a condition called lactic acidosis.

Lip pits are harmless and do not usually require any treatment, although in some reported cases surgical excision has been used.

Kostmann disease is a form of severe congenital neutropenia (SCN), specifically type 3 (SCN3), which is a rare autosomal recessive condition in which severe chronic neutropenia is detected soon after birth. The disorder was discovered in 1956 in an extended family in northern Sweden by Rolf Kostmann, a Swedish doctor.

Severe congenital neutropenia (SCN) is used as the overarching term for all diseases that affect myelopoiesis most prominently. Kostmann syndrome can restrictively refer to Kostmann disease specifically, or can be used synonymously with SCN as an umbrella term. These syndrome subtypes are phenotypically similar despite arising from different gene abnormalities.

Although mutations of more than 15 genes cause severe congenital neutropenia (in a general sense) not all of these are usually considered as SCN. Clinical usage excludes two broad categories of congenital neutropenia. Diseases are excluded that overtly affect multiple systems rather than impacting myelopoiesis most prominently. Thus SCN excludes the severe neutropenia which can occur in congenital diseases such as Shwachman–Diamond syndrome, Barth syndrome, Chédiak–Higashi syndrome, WHIM syndrome, and glycogen storage disease type Ib. A further group of other miscellaneous inherited disorders, such as hyper IgM syndrome, Hermansky–Pudlak syndrome (HPS), Griscelli syndrome (GS), PN, P14 deficiency, Cohen syndrome, Charcot–Marie–Tooth disease (CMT) can show congenital neutropenia, but lack bone marrow findings typical of SCN.

This group of diseases may also have additional features such as partial albinism, retinopathy, or neuropathy, and are not inclined to degenerate into acute myelogenous leukemia.

There is no proven treatment for congenital lactic acidosis. Treatments that are occasionally used or that are under investigation include the ketogenic diet and dichloroacetate. Other treatments aim to relieve symptoms – for example, anticonvulsants may be used to relieve seizures.