Café au lait spots can arise from diverse and unrelated causes:

- Having six or more café au lait spots greater than 5 mm in diameter before puberty, or greater than 15 mm in diameter after puberty, is a diagnostic feature of neurofibromatosis type I, but other features are required to diagnose NF-1.

- Familial multiple café au lait spots have been observed without NF-1 diagnosis.

- They can be caused by vitiligo in the rare McCune–Albright syndrome.

- Legius syndrome

- Tuberous sclerosis

- Fanconi anemia

- Idiopathic

- Ataxia-telangiectasia

- Basal cell nevus syndrome

- Benign congenital skin lesion

- Bloom syndrome

- Chédiak–Higashi syndrome

- Congenital naevus

- Gaucher disease

- Hunter syndrome

- Jaffe–Campanacci syndrome

- Maffucci syndrome

- Multiple mucosal neuroma syndrome

- Noonan syndrome

- Pulmonary Stenosis

- Silver–Russell syndrome

- Watson syndrome

- Wiskott–Aldrich syndrome

It is likely that this syndrome is inherited in an autosomal dominant fashion, however there may be a recessive form with hypotonia and developmental delay.

Café au lait spots are usually present at birth, permanent, and may grow in size or increase in number over time.

Cafe au lait spots are themselves benign and do not cause any illness or problems. However, they may be associated with syndromes such as Neurofibromatosis Type 1 and McCune-Albright syndrome.

The size and shape of the spots do not have any meaning or implications with regards to diagnosis of associated syndromes.

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.

The original report was of a family in Cardiff, United Kingdom. There are subsequent reports of patients from the USA, France, Australia, UAE, India and from Cuba.

Schimmelpenning syndrome appears to be sporadic rather than inherited, in almost all cases. It is thought to result from genetic mosaicism, possibly an autosomal dominant mutation arising after conception and present only in a subpopulation of cells. The earlier in embryological development such a mutation occurs, the more extensive the nevi are likely to be and the greater the likelihood of other organ system involvement.

Incontinentia pigmenti (IP) is a rare genetic disorder that affects the skin, hair, teeth, nails, and central nervous system. It is named from its appearance under a microscope. It is also known as Bloch–Siemens syndrome, Bloch–Sulzberger disease, Bloch–Sulzberger syndrome, melanoblastosis cutis, and nevus pigmentosus systematicus.

It is characterized by skin abnormalities that begin in childhood, usually a blistering rash which heals, followed by the development of harder skin growths. The skin may develop grey or brown patches which fade with time. Other symptoms can include hair loss, dental abnormalities, eye abnormalities that can lead to vision loss, and lined or pitted fingernails and toenails. Associated problems can include delayed development, intellectual disability, seizures, and other neurological problems. There is no specific treatment, individual conditions must be managed by specialists.

IP is inherited in an X-linked dominant manner. IP is lethal in most, but not all, males. A female with IP may have inherited the IKBKG mutation from either parent or have a new gene mutation. Parents may either be clinically affected or have germline mosaicism. Affected women have a 50% risk of transmitting the mutant IKBKG allele at conception; however, most affected male conceptuses miscarry. Thus, the effective ratio for liveborn children from a mother carrying the mutation is 33% unaffected females, 33% affected females, and 33% unaffected males. Genetic counseling, prenatal testing, and preimplantation genetic diagnosis is available.

In females, the cells expressing the mutated IKBKG gene due to lyonization selectively die around the time of birth so the X-inactivation is extremely skewed.

IP is caused by mutations in a gene called NEMO (NF-κB essential modulator).

If the Hirschsprung's disease is treated in time, ABCD sufferers live otherwise healthy lives. If it is not found soon enough, death often occurs in infancy. For those suffering hearing loss, it is generally regressive and the damage to hearing increases over time. Digestive problems from the colostomy and reattachment may exist, but most cases can be treated with laxatives. The only other debilitating symptom is hearing loss, which is usually degenerative and can only be treated with surgery or hearing aids.

Males are twice as likely as females to have this characteristic, and it tends to run in families. In its non-symptomatic form, it is more common among Asians and Native Americans than among other populations, and in some families there is a tendency to inherit the condition unilaterally, that is, on one hand only.

The presence of a single transverse palmar crease can be, but is not always, a symptom associated with abnormal medical conditions, such as fetal alcohol syndrome, or with genetic chromosomal abnormalities, including Down Syndrome (chromosome 21), cri du chat syndrome (chromosome 5), Klinefelter syndrome, Wolf-Hirschhorn Syndrome, Noonan syndrome (chromosome 12), Patau syndrome (chromosome 13), IDIC 15/Dup15q (chromosome 15), Edward's syndrome (chromosome 18), and Aarskog-Scott syndrome (X-linked recessive), or autosomal recessive disorder, such as Leaukocyte adhesion deficiency-2 (LAD2). A unilateral single palmar crease was also reported in a case of chromosome 9 mutation causing Nevoid basal cell carcinoma syndrome and Robinow syndrome. It is also sometimes found on the hand of the affected side of patients with Poland Syndrome, and craniosynostosis.

At this time, there are no other phenotypes (observable expressions of a gene) that have been discovered for mutations in the ESCO2 gene.

Respiratory complications are often cause of death in early infancy.

Hay–Wells syndrome is also known as AEC syndrome; this is short for "ankyloblepharon–ectodermal dysplasia–clefting syndrome", "ankyloblepharon filiforme adnatum–ectodermal dysplasia–cleft palate syndrome", "ankyloblepharon–ectodermal defects–cleft lip/palate (AEC) syndrome", "ankyloblepharon–ectodermal defect–cleft lip and/or palate syndrome", or "ankyloblepharon ectodermal dysplasia and clefting". Hay–Wells syndrome, or Ankyloblepharon-Ectodermal Dysplasia-Clefting (AEC) syndrome, is one of over one-hundred forms of ectodermal dysplasia; a collection of inherited diseases that cause atypical development of nails, glands, teeth, and hair. Males and females are equally affected by Hay–Wells syndrome. No demographic has been shown to be especially susceptible to the syndrome. In the United States, Hay-Wells like syndromes occur in only one in 100,000 births. Symptoms are apparent at birth, or become apparent when atypical development of teeth occurs. Major symptoms of Hay–Wells syndrome include: sparse hair and eyelashes, missing teeth, cleft palate, cleft lip with fusing of the upper and lower eyelids, and deformed nails. Therefore, a diagnosis of Hay–Wells syndrome is largely based upon the physical clinical presentation of the patient.

While not always pathological, it can present as a birth defect in multiple syndromes including:

- Catel–Manzke syndrome

- Bloom syndrome

- Coffin–Lowry syndrome

- congenital rubella

- Cri du chat syndrome

- DiGeorge's syndrome

- Ehlers-Danlos syndrome

- fetal alcohol syndrome

- Hallermann-Streiff syndrome

- Hemifacial microsomia (as part of Goldenhar syndrome)

- Juvenile idiopathic arthritis

- Marfan syndrome

- Noonan syndrome

- Pierre Robin syndrome

- Prader–Willi syndrome

- Progeria

- Russell-Silver syndrome

- Seckel syndrome

- Smith-Lemli-Opitz syndrome

- Treacher Collins syndrome

- Trisomy 13 (Patau syndrome)

- Trisomy 18 (Edwards syndrome)

- Wolf–Hirschhorn syndrome

- X0 syndrome (Turner syndrome)

The RASopathies are developmental syndromes caused by germline mutations (or in rare cases by somatic mosaicism) in genes that alter the Ras subfamily and mitogen-activated protein kinases that control signal transduction, including:

- Capillary malformation-AV malformation syndrome

- Autoimmune lymphoproliferative syndrome

- Cardiofaciocutaneous syndrome

- Hereditary gingival fibromatosis type 1

- Neurofibromatosis type 1

- Noonan syndrome

- Costello syndrome, Noonan-like

- Legius syndrome, Noonan-like

- Noonan syndrome with multiple lentigines, formerly called LEOPARD syndrome, Noonan-like

Some people may have some mental slowness, but children with this condition often have good social skills. Some males may have problems with fertility.

Schimmelpenning syndrome is a neurocutaneous condition characterized by one or more sebaceous nevi, usually appearing on the face or scalp, associated with anomalies of the central nervous system, ocular system, skeletal system, cardiovascular system, and genitourinary system.

Synonyms include: "Linear nevus sebaceous syndrome (LNSS)", "Schimmelpenning-Feuerstein-Mims syndrome", "Feuerstein-Mims syndrome", "sebaceous nevus syndrome", "Solomon syndrome", and "Jadassohn's nevus phakomatosis". "Nevus" is sometimes spelled "naevus" and "sebaceous" may also be spelled "sebaceus". "Epidermal nevus syndrome" is sometimes used as a synonym, but more often as a broader term referring to Schimmelpenning syndrome in addition to nevus comedonicus syndrome, CHILD syndrome, Becker's nevus syndrome, and phakomatosis pigmentokeratotica.

The classic Schimmelpenning syndrome diagnosis comprises a triad of sebaceous nevi, seizures, and mental retardation. The condition was first reported by Gustav Schimmelpenning in 1957 and independently reported by Feuerstein and Mims in 1962.

The first gene that could cause the syndrome is described recently and is called NF1X (chromosome 19: 19p13.1).

Overall, the estimated prevalence of Stickler syndrome is about 1 in 10,000 people. Stickler syndrome affects 1 in 7,500 to 9,000 newborns.

It can be detected by the naked eye as well as dental or skull X-Ray testing.

Many professionals that are likely to be involved in the treatment of those with Stickler's syndrome, include anesthesiologists, oral and maxillofacial surgeons; craniofacial surgeons; ear, nose, and throat specialists, ophthalmologists, optometrists, audiologists, speech pathologists, physical therapists and rheumatologists.

Hay–Wells syndrome (also known as AEC syndrome; see "Naming") is one of at least 150 known types of ectodermal dysplasia.These disorders affect tissues that arise from the ectodermal germ layer, such as skin, hair, and nails.

Researchers in the past 20 years have determined that a gene mutation, specifically a homozygous mutation in the EDNRB gene, is the cause of ABCD syndrome. The advancement of technology led to new DNA material testing methods and this discovery changed the view of ABCD syndrome completely. A homozygous mutation means that there was an identical mutation on both the maternal and paternal genes. The identifying clinical report stated the test was done by scanning the Kurdish family for mutations in the EDNRB gene and the EDN3 gene by using a test called denaturing gradient gel electrophoresis. The electrophoresis test takes advantage of electrical currents and differences in melting points of fragments of DNA or RNA to move them based on their molecular weight; the differences in mobility of the fragments then can be analyzed to determine different sequences and to detect individual alleles. Different nucleotides in DNA are codes for certain proteins, which are formed by different patterns of the base pairs adenine, thymine, guanine, and cytosine. The combination of adenine and thymine and guanine and cytosine align on the double strands of DNA. The test results found "an aberrant DGGE pattern of exon 3 of the EDNRB gene. The mutation was determined to be a homozygous C to T base pair transition at the amino acid level, causing a premature stop in gene translation." This specialized testing enables geneticists to recognize the gene mutation that is the cause of ABCD syndrome.

New findings introduced an important break in the beliefs about ABCD syndrome because the endothelin B gene is a gene involved in Shah-Waardenburg syndrome. The endothelin receptor B produces Waardenburg syndrome type IV. Researchers began discussing the possibility that ABCD syndrome was in fact not a syndrome; rather it was a type of another syndrome known as Waardenburg. Discovering that the same gene is involved in ABCD and Waardenburg syndrome is important because researchers can now look further into ways to fix this crucial gene.

Recent findings in genetic research have suggested that a large number of genetic disorders, both genetic syndromes and genetic diseases, that were not previously identified in the medical literature as related, may be, in fact, highly related in the genotypical root cause of these widely varying, phenotypically-observed disorders. Orofaciodigital syndrome has been found to be a ciliopathy. Other known ciliopathies include primary ciliary dyskinesia, Bardet-Biedl syndrome, polycystic kidney disease and polycystic liver disease, nephronophthisis, Alstrom syndrome, Meckel-Gruber syndrome and some forms of retinal degeneration.

Low-set ears are ears with depressed positioning of the pinna two or more standard deviations below the population average.

It can be associated with conditions such as:

- Down's syndrome

- Turner Syndrome

- Noonan syndrome

- Patau syndrome

- DiGeorge syndrome

- Cri du chat syndrome

- Edwards syndrome

- Fragile X syndrome

It is usually bilateral, but can be unilateral in Goldenhar syndrome.