Prolidase deficiency generally becomes evident during infancy, but initial symptoms can first manifest anytime from birth to young adulthood. The condition results in a very diverse set symptoms, the severity of which can vary significantly between patients, depending on the degree to which prolidase activity is hampered by the individual underlying mutation(s) in each case. It is even possible, though rare, for affected individuals to be asymptomatic, in which case the disorder can only be identified through laboratory screening of the prospective patient and/or their extended family.

One of the signature features of PD is the elimination of high quantities of peptides through urine.

In addition, most of those affected exhibit persistent skin lesions (starting from a mild rash) or ulcers, primarily on the legs and feet, the formation of which normally begins during childhood. Clinically, these, among other dermatological issues, represent the most distinguishing and most frequent symptoms. These may never recede, potentially leading to severe infections that can, in the worst case, necessitate amputation.

PD patients exhibit a weak immune system and markedly elevated vulnerability to infections in general, and particularly those of the respiratory system, leading some who suffer from PD to acquire recurrent lung disease. They may also have an enlarged spleen (splenomegaly), and on some occasions the spleen and liver may both be enlarged (hepatosplenomegaly). Photosensitivity and hyperkeratosis have been associated with PD. Abnormal facial characteristics, consisting of pronounced eyes which are spaced far apart (hypertelorism), a high forehead, a compressed bridge of the nose or saddle nose, and a small lower jaw and chin (micrognathia), are also observed in the majority of cases.

Those affected by PD can also suffer intellectual disabilities (approx. 75% of recorded cases do) ranging from mild to severe – mental development during childhood may therefore progress more slowly.

The specific problems produced differ according to the particular abnormal synthesis involved. Common manifestations include ataxia; seizures; retinopathy; liver fibrosis; coagulopathies; failure to thrive; dysmorphic features ("e.g.," inverted nipples and subcutaneous fat pads; and strabismus. If an MRI is obtained, cerebellar atrophy and hypoplasia is a common finding.

Ocular abnormalities of CDG-Ia include: myopia, infantile esotropia, delayed visual maturation, low vision, optic disc pallor, and reduced rod function on electroretinography.

Three subtypes of CDG I (a,b,d) can cause congenital hyperinsulinism with hyperinsulinemic hypoglycemia in infancy.

Mutations in several genes have been associated with the traditional clinical syndromes, termed muscular dystrophy-dystroglycanopathies (MDDG). A new nomenclature based on clinical severity and genetic cause was recently proposed by OMIM. The severity classifications are A (severe), B (intermediate), and C (mild). The subtypes are numbered one to six according to the genetic cause, in the following order: (1) POMT1, (2) POMT2, (3) POMGNT1, (4) FKTN, (5) FKRP, and (6) LARGE.

Most common severe types include:

Prolidase deficiency (PD) is an extremely uncommon autosomal recessive disorder associated with collagen metabolism that affects connective tissues and thus a diverse array of organ systems more broadly, though it is extremely inconsistent in its expression.

Collagen is a structural protein found i.a. in bone, skin and connective tissues that is broken down into iminodipeptides at the end of its lifecycle. Of these dipeptides, those containing C-terminal proline or hydroxyproline would normally be broken down further by the enzyme Prolidase, recovering and thus recycling the constituent amino acids.

Due to a genetic defect, prolidase activity in individuals with PD is either knocked out or severely reduced. Those affected therefore eliminate excessive amounts of iminodipeptides in their urine, wasting this precious resource, with debilitating effects.

Signs of familial dysbetaproteinemia include xanthoma striatum palmare (orange or yellow discoloration of the palms) and tuberoeruptive xanthomas over the elbows and knees. The disease leads to premature atherosclerosis and therefore a possible early onset of coronary artery disease and peripheral vascular disease leading to a heart attack, i.e. myocardial infarction, chest pain on exercise, i.e. angina pectoris or stroke in young adults or middle aged patients.

Familial dysbetalipoproteinemia or type III hyperlipoproteinemia (also known as remnant hyperlipidemia, "remnant hyperlipoproteinaemia", "broad beta disease" and "remnant removal disease") is a condition characterized by increased total cholesterol and triglyceride levels, and decreased HDL levels.

Congenital disorder of glycosylation type IIc or Leukocyte adhesion deficiency-2 (LAD2) is a type of leukocyte adhesion deficiency attributable to the absence of neutrophil sialyl-LewisX, a ligand of P- and E-selectin on vascular endothelium. It is associated with "SLC35C1".

This disorder was discovered in two unrelated Israeli boys 3 and 5 years of age, each the offspring of consanguineous parents. Both had severe mental retardation, short stature, a distinctive facial appearance, and the Bombay (hh) blood phenotype, and both were secretor- and Lewis-negative. They both had had recurrent severe bacterial infections similar to those seen in patients with LAD1, including pneumonia, peridontitis, otitis media, and localized cellulitis. Similar to that in patients with LAD1, their infections were accompanied by pronounced leukocytosis (30,000 to 150,000/mm) but an absence of pus formation at sites of recurrent cellulitis. In vitro studies revealed a pronounced defect in neutrophil motility. Because the genes for the red blood cell H antigen and for the secretor status encode for distinct α1,2-fucosyltransferases and the synthesis of Sialyl-LewisX requires an α1,3-fucosyltransferase, it was postulated that a general defect in fucose metabolism is the basis for this disorder. It was subsequently found that GDP-L-fucose transport into Golgi vesicles was specifically impaired, and then missense mutations in the GDP-fucose transporter cDNA of three patients with LAD2 were discovered. Thus, GDP-fucose transporter deficiency is a cause of LAD2.

Glycerol Kinase Deficiency causes the condition known as hyperglycerolemia, an accumulation of glycerol in the blood and urine. This excess of glycerol in bodily fluids can lead to many more potentially dangerous symptoms. Common symptoms include vomiting and lethargy. These tend to be the only symptoms, if any, present in adult GKD which has been found to present with fewer symptoms than infant or juvenile GKD. When GKD is accompanied by Duchenne Muscular Dystrophy and Adrenal Hypoplasia Congenita, also caused by mutations on the Xp21 chromosome, the symptoms can become much more severe. Symptoms visible at or shortly after birth include:

- cryptorchidism

- strabismus

- seizures

Some other symptoms that become more noticeable with time would be:

- metabolic acidosis

- hypoglycemia

- adrenal cortex insufficiency

- learning disabilities

- osteoporosis

- myopathy

Many of the physically visible symptoms, such as cryptorchidism, strabismus, learning disabilities, and myopathy, tend to have an added psychological effect on the subject due to the fact that they can set him or her apart from those without GKD. Cryptorchidism, the failure of one or both of the testes to descend to the scrotum, has been known to lead to sexual identity confusion amongst young boys because it is such a major physiological anomaly. Strabismus is the misalignment of one’s eyes. Typically, one is focused but the other is “lazy” and is directed inward or out ward (up and down is less common but does occur).

High cholesterol levels normally do not cause any symptoms. Yellow deposits of cholesterol-rich fat may be seen in various places on the body such as around the eyelids (known as xanthelasma palpebrarum), the outer margin of the iris (known as arcus senilis corneae), and in the tendons of the hands, elbows, knees and feet, particularly the Achilles tendon (known as a tendon xanthoma).

Accelerated deposition of cholesterol in the walls of arteries leads to atherosclerosis, the underlying cause of cardiovascular disease. The most common problem in FH is the development of coronary artery disease (atherosclerosis of the coronary arteries that supply the heart) at a much younger age than would be expected in the general population. This may lead to angina pectoris (chest pain or tightness on exertion) or heart attacks. Less commonly, arteries of the brain are affected; this may lead to transient ischemic attacks (brief episodes of weakness on one side of the body or inability to talk) or occasionally stroke. Peripheral artery occlusive disease (obstruction of the arteries of the legs) occurs mainly in people with FH who smoke; this can cause pain in the calf muscles during walking that resolves with rest (intermittent claudication) and problems due to a decreased blood supply to the feet (such as gangrene).

Atherosclerosis risk is increased further with age and in those who smoke, have diabetes, high blood pressure and a family history of cardiovascular disease.

Glycerol Kinase Deficiency (GKD) is an X-linked recessive enzyme defect that is heterozygous in nature. Three clinically distinct forms of this deficiency have been proposed, namely infantile, juvenile, and adult. National Institutes of Health and its Office of Rare Diseases Research (ORDR) branch classifies GKD as a rare disease, known to affect fewer than 200,000 individuals in the United States. The responsible gene lies in a region containing genes in which deletions can cause Duchenne muscular dystrophy and adrenal hypoplasia congenita. Combinations of these three genetic defects including GKD are addressed medically as Complex GKD.

Remarks:

- Some GSDs have different forms, e.g. infantile, juvenile, adult (late-onset).

- Some GSDs have different subtypes, e.g. GSD1a / GSD1b, GSD9A1 / GSD9A2 / GSD9B / GSD9C / GSD9D.

- GSD type 0: Although glycogen synthase deficiency does not result in storage of extra glycogen in the liver, it is often classified with the GSDs as type 0 because it is another defect of glycogen storage and can cause similar problems.

- GSD type VIII (GSD 8): In the past it was considered a distinct condition, however it is now classified with GSD type VI or GSD IXa1; it has been described as X-linked recessive inherited.

- GSD type XI (GSD 11): Fanconi-Bickel syndrome, hepatorenal glycogenosis with renal Fanconi syndrome, no longer considered a glycogen storage disease.

- GSD type XIV (GSD 14): Now classed as Congenital disorder of glycosylation type 1 (CDG1T), affects the phosphoglucomutase enzyme (gene PGM1).

- Lafora disease is considered a complex neurodegenerative disease and also a glycogen metabolism disorder.

Hypertryptophanemia, also called familial hypertryptophanemia, is a rare autosomal recessive metabolic disorder that results in a massive buildup of the amino acid tryptophan in the blood, with associated symptoms and tryptophanuria ("-uria" denotes "in the urine").

Elevated levels of tryptophan are also seen in Hartnup disease, a disorder of amino acid transport. However, the increase of tryptophan in that disorder is negligible when compared to that of hypertryptophanemia.

Mauriac syndrome is a rare complication of diabetes mellitus type 1 characterized by extreme hepatomegaly due to glycogen deposition, along with growth failure and delayed puberty. It occurs in children and adolescents with type 1 diabetes as a result of abnormally high blood sugar levels and the symptoms tend to rectify with attainment of normal blood sugar levels. Abnormally high blood sugar levels are relatively common among patients with type I diabetes, but Mauriac syndrome is rare suggesting that a factor affecting glycogen metabolism in addition to the high level of blood sugar is necessary to cause the syndrome. A study of an adolescent boy with severe Mauriac syndrome found a mutation in PHKG2 which is the catalytic subunit of glycogen phosphorylase kinase (PhK). PhK is a large enzyme complex responsible for the activation of glycogen phosphorylase, the first enzyme in the pathway of glycogen metabolism. Expression of the mutant PHKG2 in a human liver cell line inhibited the enzyme activity of the PhK complex and increased glycogen levels. The mother of the boy with Mauriac syndrome possessed the mutant PHKG2, but did not have diabetes or a clinically detectable enlarged liver. The father of the boy had type 1 diabetes with abnormally high blood sugar levels and the size of his liver and his growth were normal. The study suggests that a mutant enzyme of glycogen metabolism in addition to an abnormally high blood glucose level is necessary to cause Mauriac syndrome.

Quite often, the presenting symptom of ornithine aminotransferase (OAT) deficiency is myopia which progresses to night blindness. The onset of myopia is often in early childhood. Ophthalmological findings in affected individuals include constricted visual fields, posterior subcapsular cataracts (can begin in late teens), elevated dark adaptation thresholds and decreased or absent electroretinographic responses. Symptoms of OAT deficiency are progressive, and between the ages of 45 and 65, most affected individuals are almost completely blind.

In some cases, affected individuals will present in the neonatal period with disease that closely mimics a classic urea cycle defect, such as ornithine transcarbamylase deficiency, as the block in ornithine metabolism leads to secondary dysfunction of the urea cycle. These individuals present with hyperammonemia, poor feeding, failure to thrive and increased excretion of orotic acid.

Lenz–Majewski syndrome is a skin condition characterized by hyperostosis, craniodiaphyseal dysplasia, dwarfism, cutis laxa, proximal symphalangism, syndactyly, brachydactyly, mental retardation, enamel hypoplasia, and hypertelorism.

In 2013, whole-exome sequencing showed that a missense mutation resulting in overactive phosphatidylserine synthase 1 was the cause of LMS, making it the first known human disease to be caused by disrupted phosphatidylserine metabolism. The researchers suggested a link between the condition and bone metabolism.

Glycogen storage disease type IV, also known as Anderson’s Disease, is a form of glycogen storage disease, which is caused by an inborn error of metabolism. It is the result of a mutation in the GBE1 gene, which causes a defect in the glycogen branching enzyme. Therefore, glycogen is not made properly and abnormal glycogen molecules accumulate in cells; most severely in cardiac and muscle cells. The severity of this disease varies on the amount of enzyme produced. Glycogen Storage Disease Type IV is autosomal recessive, which means each parent has a mutant copy of the gene but show no symptoms of the disease. It affects 1 in 800,000 individuals worldwide, with 3% of all Glycogen Storage Diseases being type IV.

The common cause is congenital, but it can also be caused by maternal steroids passed on through breast milk to the newborn. It is different from breast feeding-associated jaundice (breast-fed infants have higher bilirubin levels than formula-fed ones).

A defect in the UGT1A1-gene, also linked to Crigler–Najjar syndrome and Gilbert's syndrome, is responsible for the congenital form of Lucey–Driscoll syndrome.

Pentosuria is a condition where the sugar xylitol, a pentose, presents in the urine in unusually high concentrations. It was characterized as an inborn error of carbohydrate metabolism in 1908. It is associated with a deficiency of L-xylulose reductase, necessary for xylitol metabolism. L-Xylulose is a reducing sugar, so it may give false diagnosis of diabetes, as it is found in high concentrations in urine. However glucose metabolism is normal in people with pentosuria, and they are not diabetic. Patients of pentosuria have a low concentration of the sugar d-xyloketose. Using, Phenyl pentosazone crystals, phloroglucin reaction, and absorption spectrum, pentose can be traced back as the reducing substance in urine, with those that have pentosuria.

Research has shown that pentosuria appears in 3 forms. The most widely studied is essential pentosuria, where a couple of grams of L-xylusol are released into a person’s system daily. L-xylulose reductase, contained in red blood cells, is composed of both a major and minor isozyme. For those diagnosed with essential pentosuria, the major isozyme appears to be the same as the minor one. Alimentary pentosuria can be acquired through fruits high in pentose. Finally, drug-induced pentosuria can be developed by those exposed to morphine, fevers, allergies, and some hormones.

Those diagnosed with Pentosuria are predominantly of Jewish root. However, it is a harmless defect, and no cure is needed.

It is also known as:

- Glycogenosis type IV

- Glycogen branching enzyme deficiency

- Polyglucosan body disease

- Amylopectinosis

The eponym "Andersen's disease" is sometimes used, for Dorothy Hansine Andersen.

Mutations in GBE1 can also cause a milder disease in adults called adult polyglucosan body disease.

Generally, the majority of individuals with creatine transporter defect express the following symptoms with varying levels of severity: developmental delay and regression, mental retardation, and abnormalities in expressive and cognitive speech. However, several studies have shown a wider variety of symptoms including, but not limited to attention deficit and hyperactivity with impulsivity, myopathy, hypotonia, semantic-pragmatic language disorder, oral dyspraxia, extrapyramidal movement disorder, constipation, absent speech development, seizures, and epilepsy. Furthermore, symptoms can significantly vary between hemizygous males and heterozygous females, although, symptoms are generally more severe in hemizygous males. Hemizygous males more commonly express seizures, growth deficiency, severe mental retardation, and severe expressive language impairment. Heterozygous females more commonly express mild retardation, impairments to confrontational naming and verbal memory, and learning and behavior problems.

Histidinemia, also referred to as histidinuria, is a rare autosomal recessive metabolic disorder caused by a deficiency of the enzyme histidase. Histidase is needed for the metabolism of the amino acid histidine. Although originally thought to be linked to multiple developmental disorders histidinemia is now accepted as a relatively benign disorder, leading to a reduction in the prevalence of neonatal screening procedures.

Galactosemia (British galactosaemia) is a rare genetic metabolic disorder that affects an individual's ability to metabolize the sugar galactose properly. Galactosemia follows an autosomal recessive mode of inheritance that confers a deficiency in an enzyme responsible for adequate galactose degradation.

Friedrich Goppert (1870–1927), a German physician, first described the disease in 1917, with its cause as a defect in galactose metabolism being identified by a group led by Herman Kalckar in 1956.

Its incidence is about 1 per 60,000 births for people of European ancestry. In other populations the incidence rate differs. Galactosaemia is about one hundred times more common (1:480 births) within the Irish Traveller population.

The low incidence of this syndrome is often related to aldolase A's essential glycolytic role along with its exclusive expression in blood and skeletal muscle. Early developmental reliance and constitutive function prevents severe mutation in successful embryos. Infrequent documentation thus prevents clear generalisation of symptoms and causes. However five cases have been well described. ALDOA deficiency is diagnosed through reduced aldoA enzymatic activity, however, both physiological response and fundamental causes vary.