Alpha-1 Antitrypsin Deficiency

Demonstration of Low Serum Concentration of the Protein Alpha-1 Antitrypsin (AAT)

A variety of techniques have been used to measure serum AAT concentration; currently the most commonly used technique is nephelometry.

• Normal serum levels are 20-53 µmol/L or approximately 100-220 mg/dL by nephelometry.
• Serum levels observed in AATD with lung disease are usually <57 mg/dL.

Identification of Biallelic Pathogenic Variants in SERPINA1

Molecular genetic testing approaches can include a combination of gene-targeted testing (single-gene testing, multigene panel) and comprehensive genomic testing (exome sequencing, exome array, genome sequencing) depending on the phenotype.

Gene-targeted testing requires that the clinician determine which gene(s) are likely involved, whereas genomic testing does not. Because the phenotype of AATD is broad, individuals with the distinctive findings described in Suggestive Findings are likely to be diagnosed using gene-targeted testing (see Option 1), whereas those in whom the diagnosis of AATD has not been considered are more likely to be diagnosed using genomic testing (see Option 2).

Option 1. When the phenotypic and laboratory findings suggest the diagnosis of AATD molecular genetic testing approaches can include single-gene testing or use of a multigene panel:

• Single-gene testing. Targeted analysis for the common PI*Z, PI*S, PI*I, and PI*F alleles (see Molecular Genetics for standard nomenclature) may be performed first.
  Sequence analysis of SERPINA1 detects other pathogenic variants such as small intragenic deletions/insertions and missense, nonsense, and splice site variants.
  Note: Depending on the sequencing method used, single-exon, multiexon, or whole-gene deletions/duplications may not be detected. If only one or no variant is detected by the sequencing method used, the next step is to perform gene-targeted deletion/duplication analysis to detect exon and whole-gene deletions or duplications.
• A multigene panel that includes SERPINA1 and other genes of interest (see Differential Diagnosis) is most likely to identify the genetic cause of the condition at the most reasonable cost while limiting identification of variants of uncertain significance and pathogenic variants in genes that do not explain the underlying phenotype. Note: (1) The genes included in the panel and the diagnostic sensitivity of the testing used for each gene vary by laboratory and are likely to change over time. (2) Some multigene panels may include genes not associated with the condition discussed in this GeneReview. (3) In some laboratories, panel options may include a custom laboratory-designed panel and/or custom phenotype-focused exome analysis that includes genes specified by the clinician. (4) Methods used in a panel may include sequence analysis, deletion/duplication analysis, and/or other non-sequencing-based tests. For this disorder a multigene panel that also includes deletion/duplication analysis is recommended (see Table 1).
  For an introduction to multigene panels click here. More detailed information for clinicians ordering genetic tests can be found here.

Option 2. When the diagnosis of AATD is not considered because an individual has atypical phenotypic features, comprehensive genomic testing (which does not require the clinician to determine which gene[s] are likely involved) is the best option. Exome sequencing is the most commonly used genomic testing method; genome sequencing is also possible.

If exome sequencing is not diagnostic, exome array (when clinically available) may be considered to detect (multi)exon deletions or duplications that cannot be detected by sequence analysis.

For an introduction to comprehensive genomic testing click here. More detailed information for clinicians ordering genomic testing can be found here.

Note: The nomenclature of SERPINA1 alleles is unconventional because it is based on electrophoretic protein variants that were identified long before the gene (SERPINA1) was identified [Cox et al 1980]. Because this older nomenclature is well established in the literature, it is used in this GeneReview.

SERPINA1 alleles encoding the variant AAT proteins were named with the prefix PI* (protease inhibitor*) serving as an alias for SERPINA1 (which had yet to be identified). The six SERPINA1 alleles discussed here are the following. (See Molecular Genetics for more details and information on other alleles.)

• PI*M. The most common allele in all populations described to date. Some benign variants of the PI*M allele are designated M1, M2, M3, etc.
• PI*Z. The most common pathogenic allele, resulting in a quantitatively and functionally deficient AAT protein. Individuals homozygous for PI*Z (i.e., PI*ZZ) have severe alpha-1 antitrypsin deficiency (AATD).
• PI*S. A pathogenic allele resulting in a quantitatively and functionally deficient AAT. It is usually of clinical consequence only in the compound heterozygous state with another pathogenic allele (e.g., PI*SZ) and when the serum AAT level is <57 mg/dL.
• PI*F. A pathogenic allele that is distinctive because the resulting protein is functionally impaired in binding neutrophil elastase but quantitatively normal
• PI*I. An allele that is associated with mild quantitative deficiency
• Null alleles (sometimes designated PI*QO). Pathogenic alleles that result in either no mRNA product or no protein production

Detection of a Functionally Deficient AAT Protein Variant by Protease Inhibitor (PI) Typing

PI typing is performed by polyacrylamide gel isoelectric focusing (IEF) electrophoresis of serum in a gradient between pH 4 and 5. Note: IEF is no longer in common use in clinical practice.

• Electrophoretic AAT protein variants (isoforms) are designated by letters based on their migration pattern. For example, the normal AAT protein (designated M) migrates in the middle of the isoelectric field. The abnormal AAT deficiency protein (designated Z) migrates most slowly. Other variants have been given additional alphabetic designations; some rare variants have been named by place of origin of the proband.
• Because a range of AAT protein variants from normal to deficient can be observed in an IEF assay, a reference of 13 common and five rare AAT protein variants is used to identify the specific AAT protein [Greene et al 2013].
• The limitations of IEF include inability to interpret an atypical electrophoretic pattern resulting from rare AAT protein variants and absence of AAT protein resulting from a SERPINA1 pathogenic null allele.
• IEF, the biochemical gold standard test for establishing the diagnosis of AATD, may be less costly than molecular genetic testing.

Though the optimal algorithm for laboratory testing is not well defined and recommendations in available guidelines differ [Attaway et al 2019], the guidelines for the diagnosis and management of AATD by the American Thoracic Society / European Respiratory Society include recommended indications for genetic testing for AATD [American Thoracic Society & European Respiratory Society 2003].

Lung Disease

Adult-onset lung disease. Chronic obstructive pulmonary disease (COPD), specifically emphysema and/or chronic bronchitis, is the most common clinical manifestation of AATD. Bronchiectasis is also associated with AATD.

In adults, smoking is the major factor in accelerating the development of COPD. Although the natural history of AATD varies, depending in part on what has brought the individual to medical attention (e.g., lung symptoms, liver symptoms, asymptomatic relative of an affected individual), the onset of respiratory disease in smokers with AATD is characteristically between ages 40 and 50 years [Tanash et al 2008]. Nonsmokers may have a normal life span, but can also develop lung and/or liver disease.

Individuals with severe AATD may manifest the usual signs and symptoms of obstructive lung disease, asthma, and chronic bronchitis (e.g., dyspnea, cough, wheezing, and sputum production) [McElvaney et al 1997]. For example, in the National Heart, Lung, and Blood Institute Registry, of 1,129 participants with severe deficiency of AAT, 84% described dyspnea, 76% wheezed with an upper respiratory tract infection, and 50% reported cough and phlegm [McElvaney et al 1997, Eden et al 2003]. Of note, the prevalence of AATD in persons with asthma does not differ from that found in the general population [Wencker et al 2002, Miravitlles et al 2003].

Most individuals (~95%) with severe AATD have evidence of bronchiectasis on chest CT, with 27% demonstrating clinical symptoms of bronchiectasis [Parr et al 2007].

• Chest CT shows loss of lung parenchyma and hyperlucency. In contrast to the usual pattern observed in centriacinar emphysema (emphysematous changes more pronounced in the lung apices than bases), the pattern observed in two thirds of individuals with AATD is that of more pronounced emphysematous changes in the bases than apices [Parr et al 2004].
• Lung function tests show decreased expiratory airflow, increased lung volumes, and decreased diffusing capacity. Approximately 60% of individuals with AATD-associated emphysema demonstrate a component of reversible airflow obstruction, defined as a 200-mL and 12% increase in the post-bronchodilator FEV₁ and/or FVC.

Childhood-onset lung disease. Although reported, emphysema in children with AATD is extremely rare and may result from the coexistence of other unidentified genetic factors affecting the lung [Cox & Talamo 1979].

Studies that followed newborns with severe AAT deficiency through age 32 years showed that most adults did not smoke and lacked physiologic and CT evidence of emphysema [Mostafavi et al 2018]. Longer-term follow-up studies are not currently available. In most observational studies, the mean age of individuals with lung disease is in the fifth decade [Seersholm et al 1997, Alpha-1 Antitrypsin Deficiency Registry Study Group 1998].

Risk for lung disease in PI*MZ heterozygotes. Approximately 2%-3% of North Americans are PI*MZ heterozygotes. Nonsmoking PI*MZ heterozygotes are generally not considered to be at significantly increased risk for clinical emphysema [Molloy et al 2014]. Specifically, population-based studies show no significant spirometric differences between matched PI*MZ and PI*MM cohorts [Al Ashry & Strange 2017]. However, smoking PI*MZ heterozygotes are at increased risk for COPD [Hersh et al 2004, Sørheim et al 2010, Molloy et al 2014]. Of note, slight abnormalities of lung function can be present without clinical symptoms. Alternatively, spirometry can miss at least 10% of patients with a clinical diagnosis of COPD and emphysema on CT scan [Smith et al 2014, Lutchmedial et al 2015].

Risk for lung disease in persons with the PI*SZ genotype. Individuals who smoke and have the PI*SZ genotype with serum AAT levels below the protective threshold value have a slightly increased disease risk.

Note: An attempt to correlate serum AAT levels with protein variants in children showed trends similar to those seen in adults [Donato et al 2012].

Liver Disease

Childhood-onset liver disease. The most common manifestation of AATD-associated liver disease is neonatal cholestasis: jaundice, with hyperbilirubinemia and raised serum aminotransferase levels in the early days and months of life.

Liver abnormalities develop in only a portion of children with AATD. In a study of 200,000 Swedish children who were followed up after newborn screening for AATD, 18% of those with the PI*ZZ genotype developed clinically recognized liver abnormalities and 2.4% developed liver cirrhosis with death in childhood [Sveger 1976, Sveger 1988, Strnad et al 2020]. Liver damage may progress slowly [Volpert et al 2000].

In a follow-up study of 44 children with AATD-associated liver disease initially manifesting as cirrhosis or portal hypertension, outcomes ranged from liver transplantation in two to relatively healthy lives up to 23 years after diagnosis in seven [Migliazza et al 2000].

It is not known why only a small proportion of children with early hyperbilirubinemia have continued liver destruction leading to cirrhosis. The overall risk that an individual with the PI*ZZ genotype will develop severe liver disease in childhood is generally low (~2%); the risk is higher among sibs of a child with the PI*ZZ genotype and liver disease.

• When liver abnormalities in the proband are mild and resolve, the risk of liver disease in sibs with the PI*ZZ genotype is approximately 13%.
• When liver disease in the proband is severe, the risk for severe liver disease in sibs with the PI*ZZ genotype may be approximately 40% [Cox 2004].

The PI*MZ and PI*SZ genotypes are not associated with an increased risk for childhood liver disease; however, on occasion, elevated levels of liver enzymes that resolve have been observed. In a study of 58 children with heterozygous genotypes showing signs of liver involvement during the first six months of life, almost all had normal values of liver enzymes at ages 12 months, five years, and ten years [Pittschieler 2002].

Adult-onset liver disease. Liver disease in adults (manifesting as cirrhosis and fibrosis) may occur in the absence of a history of neonatal or childhood liver disease. Liver disease is more common in men than women.

The risk for liver disease at age 20-40 years is approximately 2% and at age 41-50 years approximately 4% [Cox & Smyth 1983].

Autopsy studies suggest that the prevalence of liver disease may be as high as 40% in older individuals who have never smoked and do not have COPD [Eriksson 1987]. Liver disease was subclinical at death in some of these individuals.

Hepatocellular carcinoma (HCC). The risk for HCC among individuals with AATD and the PI*ZZ genotype is several times that typically associated with liver cirrhosis. This increased risk has been attributed to failure of apoptosis of injured cells with retained Z protein, which sends a chronic regeneration signal to hepatocytes with a lesser load of retained Z protein [Perlmutter 2006].

Liver pathology. AATD liver inclusions are visualized as bright pink globules of various sizes, using periodic acid-Schiff