Malformations of the upper extremities can occur In the third to seventh embryonic week. In some cases the TPT is hereditary. In these cases, there is a mutation on chromosome 7q36. If the TPT is hereditary, it is mostly inherited as an autosomal dominant trait, non-opposable and bilateral. The sporadic cases are mostly opposable and unilateral.

Triphalangeal thumb can occur in syndromes but it can also be isolated. The triphalangeal thumb can appear in combination with other malformations or syndromes.

Syndromes include:

- Holt-Oram syndrome

- Aase syndrome

- Blackfan-Diamond syndrome

- Townes-Brocks syndrome

Malformations include:

- Radial polydactyly

- Syndactyly

- Claw-like hand or foot

Not much research has been done on the epidemiology of congenital trigger thumbs. There are a few reports on the incidence in their respective studies. The most recent data comes from a Japanese study by Kukichi and Ogino where they found an incidence 3.3 trigger thumbs per 1,000 live births in 1 year old children.

It is unclear whether the cause of the trigger thumb is congenital or acquired. The occurrence of bilateral incidence and trigger thumbs in both children of twins are an indication for a congenital cause. Trigger thumb in children is also associated with trisomy of chromosome 13. For these reasons it was assumed that trigger thumbs in children are to be of congenital cause. However, more and more evidence which point towards an acquired cause have been found in recent studies. Therefore the name pediatric trigger thumb is also widely used (and currently preferred by some) for the same disorder.

"Infant’s persistent thumb-clutched hand, flexion-adduction deformity of the thumb, pollex varus, thumb in the hand deformity."

Congenital clasped thumb describes an anomaly which is characterized by a fixed thumb into the palm at the metacarpophalangeal joint in one or both hands.

The incidence and genetic background are unknown. A study of Weckesser et al. showed that boys are twice as often affected with congenital clasped thumb compared to girls. The anomaly is in most cases bilateral (present in both hands).

A congenital clasped thumb can be an isolated anomaly, but can also be attributed to several syndromes.

Diagnosing the congenital clasped thumb is difficult in the first three to four months of life, as it is normal when the thumb is clutched into the palm in these first months.

Diagnoses that cause the same flexion or adduction abnormalities of the thumb are:

- Congenital clasped thumb

- Congenital Trigger thumb (flexion of the interphalangeal joint) - Trigger finger

- Spasticity: overstimulation of muscles

Syndrome associated flexion-adduction of the thumb:

- Freeman-Sheldon syndrome (a congenital, heritable affection of the face, the hands, the feet and some joints)

- Distal arthrogryposis

- MASA syndrome

- X-linked hydrocephalus

- Adducted thumb syndrome

- Waardenburg syndrome

- Whistling face syndrome (Freeman-Sheldon syndrome)

- Digitotalar dysmorphism

- Multiple pterygium syndrome

Hand-foot-genital syndrome is inherited in an autosomal dominant manner. The proportion of cases caused by de novo mutations is unknown because of the small number of individuals described. If a parent of the proband is affected, the risk to the siblings is 50%. When the parents are clinically unaffected, the risk to the sibs of a proband appears to be low. Each child of an individual with HFGS has a 50% chance of inheriting the mutation. Prenatal testing may be available through laboratories offering custom prenatal testing for families in which the disease-causing mutation has been identified in an affected family member.

Thumb hypoplasia is a spectrum of congenital abnormalities of the thumb varying from small defects to absolute retardation of the thumb. It can be isolated, when only the thumb is affected, and in 60% of the cases it is associated with radial dysplasia (or radial club, radius dysplasia, longitudinal radial deficiency). Radial dysplasia is the condition in which the forearm bone and the soft tissues on the thumb side are underdeveloped or absent.

In an embryo the upper extremities develop from week four of the gestation. During the fifth to eighth week the thumb will further develop. In this period something goes wrong with the growth of the thumb but the exact cause of thumb hypoplasia is unknown.

One out of every 100,000 live births shows thumb hypoplasia. In more than 50% of the cases both hands are affected, otherwise mainly the right hand is affected.

About 86% of the children with hypoplastic thumb have associated abnormalities. Embryological hand development occurs simultaneously with growth and development of the cardiovascular, neurologic and hematopoietic systems. Thumb hypoplasia has been described in 30 syndromes wherein those abnormalities have been seen. A syndrome is a combination of three or more abnormalities. Examples of syndromes with an hypoplastic thumb are Holt-Oram syndrome, VACTERL association and thrombocytopenia absent radius (TAR syndrome).

When it comes to treatment it is important to differentiate a thumb that needs stability, more web width and function, or a thumb that needs to be replaced by the index finger. Severe thumb hypoplasia is best treated by pollicization of the index finger. Less severe thumb hypoplasia can be reconstructed by first web space release, ligament reconstruction and muscle or tendon transfer.

It has been recommended that pollicization is performed before 12 months, but a long-term study of pollicizations performed between the age of 9 months and 16 years showed no differences in function related to age at operation.

It is important to know that every reconstruction of the thumb never gives a normal thumb, because there is always a decline of function. When a child has a good index finger, wrist and fore-arm the maximum strength of the thumb will be 50% after surgery in comparison with a normal thumb. The less developed the index finger, wrist and fore-arm is, the less strength the reconstructed thumb will have after surgery.

Type VII of radial polydactyly is associated with several syndromes:

Holt–Oram syndrome, Fanconi anemia (aplastic anemia by the age of 6), Townes–Brocks syndrome, and Greig cephalopolysyndactyly (also known to occur with ulnar polydactyly).

The syndromes associated with central polydactyly are:

Bardet–Biedl syndrome,

Meckel syndrome,

Pallister–Hall syndrome,

Legius syndrome,

Holt–Oram syndrome,

Also, central polydactyly can be associated with syndactyly and cleft hand.

Other syndromes including polydactyly include acrocallosal syndrome, basal cell nevus syndrome, Biemond syndrome, ectrodactyly-ectodermal dysplasias-cleft lip/palate syndrome, mirror hand deformity, Mohr syndrome, oral-facial-digital syndrome, Rubinstein-Taybi syndrome, short rib polydactyly, and VATER association.

It can also occur with a triphalangeal thumb.

It remains unconfirmed whether composer Sergei Rachmaninoff's abnormally large reach on a piano was a result of arachnodactyly due to Marfan syndrome, as the pianist exhibited no other signs of the disease.

Diagnosis is based on physical examination including radiographs of the hands and feet and imaging studies of the kidneys, bladder, and female reproductive tract. HOXA13 is the only gene known to be associated with HFGS. Approximately 60% of mutations are polyalanine expansions. Molecular genetic testing is clinically available.

This feature can occur on its own, with no underlying health problems. However, it can also be associated with certain medical conditions. Examples include Marfan syndrome, Ehlers-Danlos syndrome, Loeys–Dietz syndrome, congenital contractural arachnodactyly, and homocystinuria.

Arachnodactyly has been linked to mutations in both fibrillin-1 and fibrillin-2 genes.

Ape hand deformity, also known as simian hand, is a deformity in humans who cannot move the thumb away from the rest of the hand. It is an inability to abduct the thumb. Abduction of the thumb refers to the specific capacity to orient the thumb perpendicularly to the ventral (palmar) surface of the hand. Opposition refers specifically the ability to "swing" the first metacarpal such that the tip of the thumb may touch the distal end of the 5th phalanx and if we put the hand on the table as the palm upward the thumb can not point to the sky. The Ape Hand Deformity is caused by damage to the distal median nerve (also called a Median Claw lesion), and subsequent loss of opponens pollicis muscle function. The name "ape hand deformity" is misleading, as apes have opposable thumbs.

It can occur with an injury of the median nerve either at the elbow or the wrist, impairing the thenar muscles and opponens pollicis muscle.

Ape hand deformity is one aspect of median nerve palsy, which is usually caused by deep injuries to the arm, forearm and wrist area.

Ape hand caused by median and ulnar nerve lesions

There are few good estimates of prevalence for pes cavus in the general community. While pes cavus has been reported in between 2 and 29% of the adult population, there are several limitations of the prevalence data reported in these studies. Population-based studies suggest the prevalence of the cavus foot is approximately 10%.

Arthrogryposis is a rare condition. Some authors say the overall prevalence is one in 3000 and others say it is one in 11000-12000 among European live births. Congenital clubfoot is the most common single contracture and its prevalence is one in 500 live births.

YVS has been described relatively recently in the 1980s and since then less than 15 cases have been reported around the world. Many of the infants did not survive beyond one year of age.

When an individual is born with phocomelia due to drugs or pharmaceuticals, it is known as thalidomide syndrome. The symptoms of thalidomide syndrome are defined by absent or shortened limbs; causing flipper hands and feet. According to Anthony J Perri III, and Sylvia Hsu they can additionally receive:

- Palsy disorder of the face

- Ear and eye abnormalities; resulting in limited/complete loss of hearing or sight

- Gastrointestinal and genitourinary tract disorders

- Ingrown genitalia

- Undeveloped/missing lungs

- Distorted digestive tract, heart, kidney

- disorders to the limbs

The infants that were exposed to thalidomide during development phases had a 40% chance of survival. The McMredie-McBride hypothesis explains that the limbs of the infants become malformed as a result of the thalidomide harming the neural tissue—simply because the neural tissue has such a large impact on formation and development of the limbs.

Phocomelia is a condition that involves malformations of the arms and legs. Although many factors can cause phocomelia, the prominent roots come from the use of the drug thalidomide and from genetic inheritance. Occurrence in an individual results in various abnormalities to the face, limbs, ears, nose, vessels and many other underdevelopments. Although operations may improve some abnormalities, many are not surgically treatable due to the lack of nerves and other related structures.

The term is from Ancient Greek φώκη "phōkē", "seal (animal)" + "-o-" interfix + μέλος "melos", "limb" + English suffix "-ia") is an extremely rare congenital disorder involving malformation of the limbs (dysmelia). Étienne Geoffroy Saint-Hilaire coined the term in 1836.

Pes cavus may be hereditary or acquired, and the underlying cause may be neurological, orthopedic, or neuromuscular. Pes cavus is sometimes—but not always—connected through Hereditary Motor and Sensory Neuropathy Type 1 (Charcot-Marie-Tooth disease) and Friedreich's Ataxia; many other cases of pes cavus are natural.

The cause and deforming mechanism underlying pes cavus is complex and not well understood. Factors considered influential in the development of pes cavus include muscle weakness and imbalance in neuromuscular disease, residual effects of congenital clubfoot, post-traumatic bone malformation, contracture of the plantar fascia, and shortening of the Achilles tendon.

Among the cases of neuromuscular pes cavus, 50% have been attributed to Charcot-Marie-Tooth disease, which is the most common type of inherited neuropathy with an incidence of 1 per 2,500 persons affected. Also known as Hereditary Motor and Sensory Neuropathy (HMSN), it is genetically heterogeneous and usually presents in the first decade of life with delayed motor milestones, distal muscle weakness, clumsiness, and frequent falls. By adulthood, Charcot-Marie-Tooth disease can cause painful foot deformities such as pes cavus. Although it is a relatively common disorder affecting the foot and ankle, little is known about the distribution of muscle weakness, severity of orthopaedic deformities, or types of foot pain experienced. There are no cures or effective courses of treatment to halt the progression of any form of Charcot-Marie-Tooth disease.

The development of the cavus foot structure seen in Charcot-Marie-Tooth disease has been previously linked to an imbalance of muscle strength around the foot and ankle. A hypothetical model proposed by various authors describes a relationship whereby weak evertor muscles are overpowered by stronger invertor muscles, causing an adducted forefoot and inverted rearfoot. Similarly, weak dorsiflexors are overpowered by stronger plantarflexors, causing a plantarflexed first metatarsal and anterior pes cavus.

Pes cavus is also evident in people without neuropathy or other neurological deficit. In the absence of neurological, congenital, or traumatic causes of pes cavus, the remaining cases are classified as being ‘idiopathic’ because their aetiology is unknown.

Some studies suggest a hormonal link. Specifically, the hormone relaxin has been indicated.

A genetic factor is indicated since the trait runs in families and there is an increased occurrence in some ethnic populations (e.g., Native Americans, Lapps / Sami people). A locus has been described on chromosome 13. Beukes familial dysplasia, on the other hand, was found to map to an 11-cM region on chromosome 4q35, with nonpenetrant carriers not affected.

The diagnosis of PPS has been made in several ethnic groups, including Caucasian, Japanese, and sub-Saharan African. Males and females are equally likely to suffer from the syndrome. Since the disorder is very rare, its incidence rate is difficult to estimate, but is less than 1 in 10,000.

Some of the different types of AMC include:

- Arthrogryposis multiplex due to muscular dystrophy.

- Arthrogryposis ectodermal dysplasia other anomalies, also known as Cote Adamopoulos Pantelakis syndrome, Trichooculodermovertebral syndrome, syndrome and Alves syndrome.

- Arthrogryposis epileptic seizures migrational brain disorder.

- Arthrogryposis thoracic dystrophy, also known as Van Bervliet syndrome.

- Arthrogryposis like disorder, also known as Kuskokwim disease.

- Arthrogryposis-like hand anomaly and sensorineural deafness.

- Arthrogryposis multiplex congenita calcification.

- Arthrogryposis multiplex congenita distal (), also known as X-linked spinal muscular atrophy type 2

- Gordon Syndrome, also known as Distal Arthrogryposis, Type 2A.

- Arthrogryposis multiplex congenita, distal type 2B, also known as Freeman-Sheldon syndrome variant.

- Arthrogryposis multiplex congenita neurogenic type (). This particular type of AMC has been linked to the gene on locus 5q35. Arthrogryposis multiplex congenita pulmonary hypoplasia, also with a large number of synonyms.

- Arthrogryposis multiplex congenita whistling face, also known as Illum syndrome.

- Arthrogryposis multiplex congenita, distal type 1 ().

- Arthrogryposis ophthalmoplegia retinopathy, also known as Oculomelic amyoplasia.

- Arthrogryposis renal dysfunction cholestasis syndrome, also known as Syndrome.

Hip dysplasia is considered to be a multifactorial condition. That means that several factors are involved in causing the condition to manifest.

The cause of this condition is unknown; however, some factors of congenital hip dislocation are through heredity and racial background. It is also thought that the higher rates in some ethnic groups (such as some Native American groups) is due to the practice swaddling of infants, which is known to be a potential risk factor for developing dysplasia. It also has a low risk in African Americans and southern Chinese.