Hereditary Hemochromatosis via the SLC40A1 Gene

Hereditary hemochromatosis (HH) is a disorder characterized by excess iron overload. In type 4 HH, iron overload is due to alterations in ferroportin, the iron transporting protein found on macrophages and on the basolateral surface of enterocytes. There are two different forms of type 4 HH: classical (45% cases) and non-classical (30%). In 25% of cases, distinguishing type 4 classical or non-classical forms is unclear (Mayr et al. 2010). In patients with classical type 4 HH, iron accumulation occurs in macrophages, mainly Kupffer cells in the liver whereas non-classical type 4 HH patients show hepatocyte iron deposition similar to patients with type 1 HH. Symptom onset is primarily after the third decade of life with patients initially presenting with fatigue and arthritis (typically in metacarpophalangeal joints). Chronic iron deposition can result in advanced fibrotic liver disease, cirrhosis, hepatocellular carcinoma, atherosclerosis, arthritis, fatigue, diabetes, hypogonadism, cardiomyopathy, and diffuse skin pigmentation (Mayr et al. 2010).

There are six types of hemochromatosis each due to a different genetic cause: type 1- HFE, type 2- HAMP or HFE2/HJV, type 3- TFR2, type 4- SLC40A1, type 5- FTH1, and type 6- FTL. Type 1 hemochromatosis is the most prevalent form of the disease and represents >90% of cases (Vujic 2014). Genetic testing can be helpful in differential diagnosis of HH from other liver function disorders and for determining the underlying cause of hemochromatosis (Zarrilli et al. 2013). Phlebotomy is standard treatment to reduce serum iron levels and prevent progressive liver damage.

Hemochromatosis is inherited in an autosomal recessive mode through pathogenic variants in the HFE, HAMP, HFE2/HJV, or TRF2 genes or an autosomal dominant pattern through pathogenic variants in the SLC40A1, FTH1, or FTL genes (Santos et al. 2012; Njajou et al. 2001). The SLC40A1 gene encodes ferroportin, an iron transporting protein that is negatively regulated by hepcidin. To date, missense variants account for >90% of the causative variants and nonsense, gross deletions and frameshift variants have not been reported in the SLC40A1 gene (Détivaud et al. 2013; Callebaut et al. 2014). An in-frame deletion and splice site alteration have been reported in two individuals (Wallace et al. 2002; Lee et al. 2007). In classical type 4 HH patients, loss of function variants lead to loss of ferroportin expression and intracellular retention of iron within cells, primarily macrophages. Non-classic type 4 HH patients have gain of function variants disrupting interactions with the negative regulator hepcidin. Penetrance for type 4 HH is variable and influenced by both environmental factors and HFE pathogenic variants (Le Lan et al. 2011).

Analytical sensitivity for detection of variants in the SLC40A1 gene is > 99%. In hyperferritinemia patients where types 1-3 and 6 HH were ruled out, pathogenic variants in the SLC40A1 gene were found in all 44 patients (Callebaut et al 2014).

This test provides full coverage of all coding exons of the SLC40A1 gene 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 full 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).