Disorders of Copper Metabolism Panel

Copper is an essential trace element for normal human metabolism (Kardos et al. 2018. PubMed ID: 30348177). Copper facilitates electron transfer reactions and is incorporated into many enzymes and transcription factors involved in cellular integrity, energy production, signaling, proliferation, oxidation and radiation defense (Kardos et al. 2018. PubMed ID: 30348177). Several disorders are associated with abnormal copper metabolism, these include Menkes disease, occipital horn syndrome (OHS), Wilson disease, aceruloplasminemia, Huppke-Brendel syndrome (HBS), MEDNIK syndrome, and MEDNIK-like syndrome. Genetic testing may aide in establishing a differential diagnosis, predicting the course of disease, and may assist reproductive planning.

Menkes disease is a severe X-linked disorder of generalized copper deficiency, while OHS is an X-linked connective tissue disorder. Both disorders are caused by pathogenic variants in the ATP7A gene are associated with low serum copper and ceruloplasmin concentration (Kaler. 2016. PubMed ID: 20301586). Classic Menkes disease may characterized by failure to thrive, developmental delay, hypotonia, and seizures. Affected individuals may also develop hair anomalies, distinctive facies, skin laxity, as well as umbilical or inguinal hernias. Female ATP7A carriers are typically asymptomatic (likely due to favorable X-inactivation), however 50% of carriers may have pili torti (Kaler. 2016. PubMed ID: 20301586). Onset typically occurs between 3 to 6 months. In some cases (but not all), early treatment with copper replacement therapy may improve developmental and neurologic outcomes (Kaler. 2016. PubMed ID: 20301586). The prevalence of Menkes disease is approximately 1 case per 100,000 births (Kaler. 2016. PubMed ID: 20301586). Comparably, OHS is characterized by wedge-shaped calcifications at the sites of certain muscle attachments to the occipital bone (occipital horns), joint laxity, skin laxity, bladder diverticula, nguinal hernias, vascular tortuosity, chronic diarrhea, orthostatic hypotension, and mild cognitive deficits (Kaler. 2016. PubMed ID: 20301586). Onset typically occurs in early to late childhood. The exact prevalence of OHS is presently unknown, but is considered rare.

Wilson disease is caused by pathogenic variants in the ATP7B gene. This autosomal recessive disorder is associated with low serum ceruloplasmin concentration, abnormal serum copper and non-ceruloplasmin-bound copper concentrations, high urinary copper and increased hepatic copper concentration (Weiss et al. 2016. PubMed ID: 20301685). Serum ceruloplasmin concentration may be normal in some affected individuals. Wilson disease typically presents with variable hepatic, neurologic and/or psychiatric disturbances, as well as Kayser-Fleischer rings. Onset may occur between the ages of 3 to 50 years. Administration of chelating agents or zinc can prevent symptoms in asymptomatic individuals (Weiss et al. 2016. PubMed ID: 20301685). The prevalence of Wilson disease is estimated at approximately 1 in 30,000 individuals, however prevalence varies significantly by geographic location (Weiss. 2016. PubMed ID: 20301685; Chang and Hahn. 2017. PubMed ID: 28433102).

Aceruloplasminemia is caused by pathogenic variants in the CP gene. This autosomal recessive disorder is associated with very low or absent serum ceruloplasmin concertation, low serum copper and iron concentrations, and elevated serum ferritin and hepatic iron concentration. It is characterized by iron accumulation in the brain and viscera, retinal degeneration, diabetes mellitus, anemia, and neurologic disease (Miyajima and Hosoi. 2018. PubMed ID: 20301666). Onset typically occurs between 30 to 70 years of age. Administration of iron chelating agents and fresh frozen human plasma may aide to decrease iron accumulation in the liver (Miyajima and Hosoi. 2018. PubMed ID: 20301666). The exact prevalence of aceruloplasminemia is presently unknown, but is estimated to be approximately 1 case per 2 million individuals in Japan (Miyajima et al. 1999. PubMed ID: 10449129).

HBS is caused by pathogenic variants in the SLC33A1 gene. This autosomal recessive disorder is associated with very low or absent serum copper and ceruloplasmin concentration. It is characterized by bilateral congenital cataracts, sensorineural hearing loss, axial hypotonia, severe developmental delay, structural brain changes, and progressive neurologic disease (Bindu et al. 2019. PubMed ID: 31194315). Onset occurs in infancy with death in childhood. Medical management may include surveillance, cataract removal, and feeding and developmental support (Bindu et al. 2019. PubMed ID: 31194315). The exact prevalence of HBS is presently unknown, but is considered rare.

Autosomal recessive MEDNIK and MEDNIK-like syndrome are associated with a limited number of pathogenic variants in the AP1S1 and AP1B1 genes, respectively (Montpetit et al. 2008. PubMed ID: 19057675; Martinelli et al. 2013. PubMed ID: 23423674; Asaif et al. 2019. PubMed ID: 31630791). MEDNIK is an acronym for mental retardation, enteropathy, deafness, neuropathy, ichthyosis, and keratodermia. This disorder displays overlapping features with both Menkes and Wilson disease. This disorder is associated with low serum copper and ceruloplasmin concentration (Martinelli et al. 2013. PubMed ID: 23423674; Asaif et al. 2019. PubMed ID: 3163079). MEDNIK-like syndrome is also referred to as keratitis-ichthyosis-deafness syndrome. The exact prevalence of MEDNIK and MEDNIK-like syndrome are presently unknown, but are considered rare.

Pathogenic variants in one or more of the genes included as part of this panel are reported to be associated with additional phenotypes including (but not limited to) spinal muscular atrophy, cerebellar ataxia, and spastic paraplegia.

Disorders of copper metabolism are inherited in an autosomal recessive (AP1B1, AP1S1, ATP7B, CP, SLC33A1) or X-linked (ATP7A) manner. Pathogenic variants are typically inherited from a carrier parent. However, approximately a third of pathogenic variants in the ATP7A gene are reported to arise de novo (Moizard et al. 2011. PubMed ID: 21208200; Prasad et al. 2011. PubMed ID: 21924848). To date, there are no reports of individuals with aceruloplasminemia, MEDNIK syndrome, MEDNIK-like syndrome, Menkes disease or HBS having affected offspring (Kaler. 2016. PubMed ID: 20301586; Miyajima and Hosoi. 2018. PubMed ID: 20301666; Bindu et al. 2019. PubMed ID: 31194315). The risk of an individual with Wilson disease having an affected offspring is low, with the exception of consanguinity or populations with a high incidence of disease (Weiss. 2016. PubMed ID: 20301685). Small deletions, nonsense, splice site, frameshift, missense, and regulatory pathogenic variants are reported for the ATP7A, ATP7B and CP genes. A limited number of pathogenic missense, nonsense, splicing and frameshift variants are reported for the SLC33A1 gene (Bindu et al. 2019. PubMed ID: 31194315). A pathogenic splicing variant and gross deletion are reported for the AP1B1 gene (Asaif et al. 2019. PubMed ID: 31630791). A pathogenic splicing and frameshift variant are reported for the AP1S1 gene (Montpetit et al. 2008. PubMed ID: 19057675; Martinelli et al. 2013. PubMed ID: 23423674). Pathogenic structural variants, predominantly in the form of gross deletions, are reported for the ATP7A, ATP7B and CP genes (Kaler. 2016. PubMed ID: 20301586; Weiss. 2016. PubMed ID: 20301685; Miyajima and Hosoi. 2018. PubMed ID: 20301666).

Pathogenic allele enrichment in specific populations is reported for several of these genes. In the ATP7B gene p.His1069Gln accounts for approximately 30% to 70% of pathogenic alleles in European populations; p.Arg778Leu accounts for approximately 57% of pathogenic alleles in individuals of Asian ancestry and who are aged <18 years; and the promoter deletion c.-441_-427del15 is highly enriched in Sardinia (Weiss. 2016. PubMed ID: 20301685; Chang and Hahn. 2019. PubMed ID: 28433102). In the AP1S1 gene, a splice variant c.183-2A>G (also known as IVS2.2A>G) is prevalent in the Kamouraska region of the province of Quebec (Montpetit et al. 2008. PubMed ID: 19057675). Targeted variant testing may be considered in individuals from these specific populations.

The AP1B1, AP1S1, ATP7A, ATP7B, CP, and SLC33A1 genes encode proteins that are either directly or indirectly related to copper metabolism and homeostasis. AP1B1 encodes the large beta subunit of the adaptor protein 1 (AP-1) complex, while AP1S1 encodes the small subunit of the AP-1 complex (Montpetit et al. 2008. PubMed ID: 19057675; Asaif et al. 2019. PubMed ID: 3163079). The AP-1 complex directs clathrin coat assembly, mediates trafficking between the transGolgi network, endosomes, and the plasma, and also directs the trafficking of copper ATPases (Montpetit et al. 2008. PubMed ID: 19057675; Marinelli and Dionisi-Vicki. 2014. PubMed ID: 24754424). The ATP7A and ATP7B genes each encode a transmembrane copper-transporting P-type ATPase (Vulpe et al. 1993. PubMed ID: 8490659; Lim et al. 2006. PubMed ID: 16554302). CP encodes a plasma metalloprotein that binds plasma copper and also maintains iron homeostasis (Vassiliev et al. 2005. PubMed ID: 16269323). SLC33A1 encodes an acetyl CoA transporter that is required for acetylation of gangliosides and glycoproteins, and possibly the copper ATPases (Huppke et al. 2012. PubMed ID: 22243965).

See individual gene summaries for more information about the molecular biology of gene products and spectra of pathogenic variants.

Due to the genetic heterogeneity of the disorders tested in this panel, the clinical sensitivity of this specific grouping of genes is difficult to estimate. The clinical sensitivity for ATP7A-Related Copper Transport Disorders should be close to 100% with concurrent sequencing and structural variant analysis (Kaler. 2016. PubMed ID: 20301586). Approximately 80% of individuals with suspected Wilson disease based on biochemical and clinical testing harbor pathogenic ATP7B variants (Chang and Hahn. 2017. PubMed ID: 28433102). Clinical sensitivity for the CP gene is difficult to estimate as the differential diagnosis is broad and includes disorders of copper and iron metabolism, as well as various neurodegenerative disorders (Miyajima and Hosoi. 2018. PubMed ID: 20301666). Estimates of clinical sensitive are limited for the AP1B1, AP1S1 and SLC33A1 genes, as to date only isolated cases have been reported (Montpetit et al. 2008. PubMed ID: 19057675; Martinelli et al. 2013. PubMed ID: 23423674; Asaif et al. 2019. PubMed ID: 31630791; Bindu et al. 2019. PubMed ID: 31194315).

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This panel typically provides 98.7% coverage of all coding exons of the genes plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define coverage as ≥20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).