Familial Hemophagocytic Lymphohistiocytosis-Type 3 (FHL3) via the UNC13D Gene

Hemophagocytic lymphohistiocytosis (HLH) is a rapidly progressing, hyperinflammatory condition in which activated T cells and macrophages infiltrate numerous organs. Clinical manifestations include fever, hepatosplenomegaly, pancytopenia, hemophagocytosis, severely attenuated or absent NK cell function, elevated iron levels, and elevated soluble CD25 (Henter et al. 2007. PubMed ID: 16937360). Familial (primary) HLH (FHL) and sporadic (secondary) HLH are clinically similar, and both types may be triggered by viral infections (Epstein-Barr virus, EBV), rheumatic disorders, and malignancies. The incidence of FHL is approximately 1 in 50,000 live births with 70-80% of patients showing clinical symptoms during infancy (Aricò et al. 1996. PubMed ID: 8637226; Janka. 1983. PubMed ID: 6354720). Though rare, cases of late-onset, adult FHL have been reported in patients ranging in age from their twenties to sixties (Allen et al. 2001. PubMed ID: 11410413; Clementi et al. 2002. PubMed ID: 12229880; Nagafuji et al. 2007. PubMed ID: 17606450). Males with HLH may have X-linked lymphoproliferative disorder (XLP) that may include gammaglobulinemia and lymphoma (Coffey et al. 1998. PubMed ID: 9771704; Arico et al. 2001. PubMed ID: 11159547; Rigaud et al. 2006. PubMed ID: 17080092; Booth et al. 2011. PubMed ID: 20926771).

FHL is primarily an autosomal recessive or X-linked disorder, though a few autosomal dominant conditions are associated with FHL. Over 75% of FHL cases can be attributed to pathogenic variants in one of six genes: PRF1 (FHL type 2), UNC13D (FHL type 3), STX11 (FHL type 4), STXBP2 (FHL type 5), and the XIAP and SH2D1A genes (both are associated with X-linked FHL). Pathogenic variants in PRF1 account for 20-40% of all FHL cases and pathogenic variants in UNC13D, STX11, and STXBP2 account for approximately 20-25%, 14%, and 10% of FHL cases, respectively (Gholam et al. 2011. PubMed ID: 21303357). Around 60% of X-linked FHL is caused by pathogenic variants in the SH2D1A gene (Coffey et al. 1998. PubMed ID: 9771704; Gilmour et al. 2000. PubMed ID: 10898506; Yin et al. 1999. PubMed ID: 10598819; Nichols et al. 1998. PubMed ID: 9811875). Most of the FHL genes encode proteins that help regulate lytic granule targeting, docking, and membrane fusion during CTL and NK cell degranulation; PRF1 encodes a primary component of lytic granule cargo involved directly in membrane disruption of target cells at the immunological synapse (Gholam et al. 2011. PubMed ID: 21303357).  

Pathogenic variants are located throughout the UNC13D gene and comprise primarily missense or nonsense variants, splice-site variants, and small insertions and deletions. Most variants are inherited from parental carriers; de novo variants are rare. Large copy number variants are rare, with only one large duplication having been reported to date (Feldmann et al. 2003. PubMed ID: 14622600; Yamamoto et al. 2004. PubMed ID: 15466010; Zur Stadt et al. 2006. PubMed ID: 16278825; Hiejima et al. 2018. PubMed ID: 29596912).

UNC13D encodes the Munc13-4 protein which regulates SNARE-mediated lytic granule exocytosis in CTLs and NK cells (Feldmann et al. 2003. PubMed ID: 14622600). UNC13D has been cited as a nonessential gene for growth of human tissue culture cells (Online Gene Essentiality, ogee.medgenius.info).

Mouse models in which Unc13d is absent have shown a complete loss of platelet dense granule secretion and attenuated platelet aggregation.  Mice lacking Unc13d also had prolonged bleeding times, which is consistent with the Unc13d gene product serving a critical role during proper platelet function (Ren et al. 2010. PubMed ID: 20435885).

This test does include analysis of a known pathogenic inversion involving the UNC13D gene that was observed in 7% of FHL patients in one report (Meeths et al. 2011. PubMed ID: 21931115; Qian et al. 2014. PubMed ID: 24470399). This test also includes coverage of an intronic variant associated with FHL defined as c.118-308C>T (Meeths et al. 2011. PubMed ID: 21931115).

Over 75% of familial hemophagocytic lymphohistiocytosis (FHL) cases can be attributed to pathogenic variants in one of six genes: PRF1 (FHL type 2), UNC13D (FHL type 3), STX11 (FHL type 4), STXBP2 (FHL type 5), XIAP, and SH2D1A. Pathogenic variants in UNC13D account for 20-25% of cases (Gholam et al. 2011. PubMed ID: 21303357).

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

This test provides 100% coverage of all coding exons of the UNC13D 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 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).

This test also includes analysis of a known pathogenic inversion involving the UNC13D gene and an intronic variant defined as c.118-308C>T (Qian et al. 2014. PubMed ID: 24470399; Meeths et al. 2011. PubMed ID: 21931115).

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).