Very few risk factors for choanal atresia have been identified. While causes are unknown, both genetic and environmental triggers are suspected. One study suggests that chemicals that act as endocrine disrupters may put an unborn infant at risk. A 2012 epidemiological study looked at atrazine, a commonly used herbicide in the U.S., and found that women who lived in counties in Texas with the highest levels of this chemical being used to treat agricultural crops were 80 times more likely to give birth to infants with choanal atresia or stenosis compared to women who lived in the counties with the lowest levels. Another epidemiological report in 2010 found even higher associations between increased incidents of choanal atresia and exposure to second-hand-smoke, coffee consumption, high maternal zinc and B-12 intake and exposure to anti-infective urinary tract medications.

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

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.

Ectrodactyly can be caused by various changes to 7q. When 7q is altered by a deletion or a translocation ectrodactyly can sometimes be associated with hearing loss. Ectrodactyly, or Split hand/split foot malformation (SHFM) type 1 is the only form of split hand/ malformation associated with sensorineural hearing loss.

A large number of human gene defects can cause ectrodactyly. The most common mode of inheritance is autosomal dominant with reduced penetrance, while autosomal recessive and X-linked forms occur more rarely. Ectrodactyly can also be caused by a duplication on 10q24. Detailed studies of a number of mouse models for ectrodactyly have also revealed that a failure to maintain median apical ectodermal ridge (AER) signalling can be the main pathogenic mechanism in triggering this abnormality.

A number of factors make the identification of the genetic defects underlying human ectrodactyly a complicated process: the limited number of families linked to each split hand/foot malformation (SHFM) locus, the large number of morphogens involved in limb development, the complex interactions between these morphogens, the involvement of modifier genes, and the presumed involvement of multiple gene or long-range regulatory elements in some cases of ectrodactyly. In the clinical setting these genetic characteristics can become problematic and making predictions of carrier status and severity of the disease impossible to predict.

In 2011, a novel mutation in DLX5 was found to be involved in SHFM.

Ectrodactyly is frequently seen with other congenital anomalies. Syndromes in which ectrodactyly is associated with other abnormalities can occur when two or more genes are affected by a chromosomal rearrangement. Disorders associated with ectrodactyly include Ectrodactyly-Ectodermal Dysplasia-Clefting (EEC) syndrome, which is closely correlated to the ADULT syndrome and Limb-mammary (LMS) syndrome, Ectrodactyly-Cleft Palate (ECP) syndrome, Ectrodactyly-Ectodermal Dysplasia-Macular Dystrophy syndrome, Ectrodactyly-Fibular Aplasia/Hypoplasia (EFA) syndrome, and Ectrodactyly-Polydactyly. More than 50 syndromes and associations involving ectrodactyly are distinguished in the London Dysmorphology Database.

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).

According to the National Human Genome Research Institute, Poland syndrome affects males three times as often as females and affects the right side of the body twice as often as the left. The incidence is estimated to range from one in 7,000 to one in 100,000 live births.

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.

"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.

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.

The cause of Poland syndrome is unknown. However, an interruption of the embryonic blood supply to the arteries that lie under the collarbone (subclavian arteries) at about the 46th day of embryonic development is the prevailing theory.

The subclavian arteries normally supply blood to embryonic tissues that give rise to the chest wall and hand. Variations in the site and extent of the disruption may explain the range of signs and symptoms that occur in Poland syndrome. Abnormality of an embryonic structure called the apical ectodermal ridge, which helps direct early limb development, may also be involved in this disorder.

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

Occurring at a rate between 1 in 10,000 to 1 in 50,000 with a male-to-female ratio of 2.3-6:1, bladder exstrophy is relatively rare. For those individuals with bladder exstrophy who maintain their ability to reproduce, the risk of bladder exstrophy in their children is approximately 500-fold greater than the general population.

The histological and ultrastructural features of Ledderhose and Dupuytren's disease are the same, which supports the hypothesis that they have a common cause and pathogenesis. As with Dupuytren's disease, the root cause(s) of Ledderhose's disease are not yet understood. It has been noted that it is an inherited disease and of variable occurrence within families, i.e. the genes necessary for it may remain dormant for a generation or more and then surface in an individual, or be present in multiple individuals in the same generation with varying degree.

There are certain identified risk factors. The disease is more commonly associated with -

- A family history of the disease

- Higher incidence in males

- Palmar fibromatosis 10-65% of the time.

- Peyronie's disease

- Epilepsy patients

- Patients of diabetes mellitus

There is also a suspected, although unproven, link between incidence and alcoholism, smoking, liver diseases, thyroid problems, and stressful work involving the feet.

Supernumerary body parts are most commonly a congenital disorder involving the growth of an additional part of the body and a deviation from the body plan. Body parts may be easily visible or hidden away, such as internal organs.

Many additional body parts form by the same process as conjoined twins: the zygote begins to split but fails to completely separate. This condition may also be a symptom of repeated occurrences of continuous inbreeding in a genetic line.

Oligodactyly (from the Ancient Greek "oligos" meaning "few" and δάκτυλος "daktylos" meaning "finger") is the presence of fewer than five fingers or toes on a hand or foot.

It is quite often incorrectly called "hypodactyly", but the Greek prefixes and are used for scales (e.g. in hypoglycaemia and hypercholesterolemia). This as opposed to or scales, where and should be used (e.g. in oligarchy and polygamy). Oligodactyly is therefore the opposite of polydactyly. Very rare, this medical condition usually has a genetic or familial cause.

Oligodactyly is sometimes a sign or symptom of several syndromes including Poland syndrome and Weyer Ulnar Ray Syndrome. It is a type of Dysmelia.

Ectrodactyly is an extreme instance of oligodactyly, involving the absence of one or more central digits of the hand or foot and is also known as split hand/split foot malformation (SHFM). The hands and feet of people with ectrodactyly are often described as "claw-like" and may include only the thumb and one finger (usually either the little finger, ring finger, or a syndactyly of the two) with similar abnormalities of the feet.

People with oligodactyly often have full use of the remaining digits and adapt well to their condition. They are not greatly hindered in their daily activities, if at all. Even those with the most extreme forms are known to engage in tasks that require fine control, such as writing and bootmaking as well as working as a cab driver.

Vadoma people of Zimbabwe have a high frequency of oligodactyly.

It can be unilateral or bilateral.

- Sometimes, a unilateral choanal atresia is not detected until much later in life because the baby manages to get along with only one nostril available for breathing.

- Bilateral choanal atresia is a very serious life-threatening condition because the baby will then be unable to breathe directly after birth as babies are obligate nasal breathers (they mainly use their noses to breathe). In some cases, this may present as cyanosis while the baby is feeding, because the oral air passages are blocked by the tongue, further restricting the airway. The cyanosis may improve when the baby cries, as the oral airway is used at this time. These babies may require airway resuscitation soon after birth.

Specific types of additional body parts include:

- Accessory breast – one or more additional breasts

- Accessory spleen – one or more additional spleens

- Cervical rib – an additional rib

- Diphallia - Having two penes/penises.

- Hermaphroditism – having both sexes' sex organs

- Hyperdontia – additional teeth

- Pelvic digit – a bony growth in the soft tissue of the pelvic region

- Polycephaly – an extra head

- Polydactyly – additional fingers or toes

- Polymelia — an extra arm or leg.

- Polyorchidism – having three or more testicles

- Supernumerary bones – these additional bones are fairly common, particularly in the feet, and are frequently mistaken for fractures on x-rays.

- Supernumerary kidney – a third kidney

- Supernumerary nipples – an additional nipple

- Supernumerary phantom limbs – where the brain acts as though a limb were there, but it is not.

- Syndactyly – webbing between the fingers or toes

- Uterus didelphys – two vaginal canals and/or uteri

Cranioschisis (Greek: "κρανιον - kranion" "skull", and "schisis - σχίσις" - "split") is a developmental birth defect involving the skull. In this disease, the cranium fails to close completely (especially at the occipital region). Thus, the brain is exposed to the amnios, and eventually degenerates, causing anencephaly.

Leri-Weill dyschondrosteosis is a pseudoautosomal dominant disorder which occurs more frequently in females and is due to a mutation, deletion or duplication of the SHOX gene. The SHOX gene plays a particularly important role in the growth and maturation of bones in the arms and legs. The SHOX gene is located within band Xp22.3 of the pseudoautosomal region of the X chromosome, which escapes X-inactivation. Homozygous SHOX gene mutations result in Langer mesomelic dysplasia.

Radial dysplasia, also known as radial club hand or radial longitudinal deficiency, is a congenital difference occurring in a longitudinal direction resulting in radial deviation of the wrist and shortening of the forearm. It can occur in different ways, from a minor anomaly to complete absence of the radius, radial side of the carpal bones and thumb. Hypoplasia of the distal humerus may be present as well and can lead to stiffnes of the elbow. Radial deviation of the wrist is caused by lack of support to the carpus, radial deviation may be reinforced if forearm muscles are functioning poorly or have abnormal insertions. Although radial longitudinal deficiency is often bilateral, the extent of involvement is most often asymmetric.

The incidence is between 1:30,000 and 1:100,000 and it is more often a sporadic mutation rather than an inherited condition. In case of an inherited condition, several syndromes are known for an association with radial dysplasia, such as the cardiovascular Holt-Oram syndrome, the gastrointestinal VATER syndrome and the hematologic Fanconi anemia and TAR syndrome. Other possible causes are an injury to the apical ectodermal ridge during upper limb development, intrauterine compression, or maternal drug use (thalidomide).

Ectrodactyly–ectodermal dysplasia–cleft syndrome, or EEC, and also referred to as EEC syndrome (also known as "Split hand–split foot–ectodermal dysplasia–cleft syndrome") is a rare form of ectodermal dysplasia, an autosomal dominant disorder inherited as an genetic trait. EEC is characterized by the triad of ectrodactyly, ectodermal dysplasia, and facial clefts. Other features noted in association with EEC include vesicoureteral reflux, recurrent urinary tract infections, obstruction of the nasolacrimal duct, decreased pigmentation of the hair and skin, missing or abnormal teeth, enamel hypoplasia, absent punctae in the lower eyelids, photophobia, occasional cognitive impairment and kidney anomalies, and conductive hearing loss.

Roberts syndrome is an extremely rare condition that only affects about 150 reported individuals. Although there have been only about 150 reported cases, the affected group is quite diverse and spread worldwide. Parental consanguinity (parents are closely related) is common with this genetic disorder. The frequency of Roberts syndrome carriers is unknown.

Rachischisis (Greek: "rhachis - ῥάχις" - spine, and "schisis - σχίσις" - split) is a developmental birth defect involving the neural tube. This anomaly occurs in utero, when the posterior neuropore of the neural tube fails to close by the 27th intrauterine day. As a consequence the vertebrae overlying the open portion of the spinal cord do not fully form and remain unfused and open, leaving the spinal cord exposed. Patients with rachischisis have motor and sensory deficits, chronic infections, and disturbances in bladder function. This defect often occurs with anencephaly.

Craniorachischisis is a variant of rachischisis that occurs when the entire spinal cord and brain are exposed - simultaneous complete rachischisis and anencephaly. It is incompatible with life; affected pregnancies often end in miscarriage or stillbirth. Infants born alive with craniorachischisis die soon after birth.