Table 4. Identification of 13 heterozygous, rare and non-synonymous candidate de novo variants.
The 124 non-synonymous candidate de novo variants were systematically evaluated based on the potential to be damaging to gene and protein function and the possible involvement in the patient’s immunological phenotype.
| Patient nr. | Sex | Age range at sampling | Phenotype (IUIS classification) | De novo variant | GnomAD AF in % | in-house AF in % | PhyloP | CADD | VarMap | MetaDome | Coding DNV in denovo-db (protein effect) | LOEUF | Function | Literature | Comments |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Missense SNVs | |||||||||||||||
| 1 | M | 11–15 | SCID | PSMB10 Chr16(GRCh37): g.67968809C>T NM_002801.3: c.601G>A p.(Gly201Arg) |
0 | 0 | 5 | 32 | Likely deleterious | Neutral | - | 1.37 | Immuno- and thymoproteasome subunit | Homozygous Psmb10 variant in mice causes SCID and systemic autoinflammation (Treise et al., 2018). Homozygous PSMB10 variant in humans cause PRAAS, no immunodeficiency (Sarrabay et al., 2020). | Revertant somatic mosaicism (VAF: 39.7%). Additional inherited SNV and partial somatic UPD16 (Table 1—source data 1). |
| 9 | M | 6–10 | Predominantly antibody deficiency, hypogamma-globulinemia | RPL27A Chr11(GRCh37): g.8707228T>C NM_000990.4: c.322T>C p.(Tyr108His) |
0.0032 | 0.0041 | 7.4 | 27.4 | Likely deleterious | Intolerant | - | 0.39 | Ribosomal subunit | Ribosomopathies may include immunological defects (Khan et al., 2011). | |
| 27 | M | 11–15 | Autoinflammatory disorder | TAOK2 Chr16(GRCh37): g.29997683C>T NM_016151.3: c.2090C>T p.(Ala697Val) |
0 | 0 | 4.8 | 22.5 | Possibly deleterious | Slightly intolerant | 6 (4 mis) | 0.24 | Serine/threonine-protein kinase (p38 MAPK pathway) | Homozygous TAOK2 variant causes abnormal T cell activation in two patients with inflammatory bowel disease (Molho-Pessach et al., 2017). | |
| 28 | F | 16–20 | Predominantly antibody deficiency, hypogamma-globulinemia | KCTD9 Chr8(GRCh37): g.25292997C>T NM_017634.3: c.695G>A p.(Arg232His) |
0 | 0.0082 | 5.8 | 32 | Likely deleterious | Intolerant | - | 0.52 | Substrate-specific adapter | Involved in NK cell activation (Chen et al., 2013). | |
| 52 | M | 11–15 | Predominantly antibody deficiency, hypogamma-globulinemia | SCRIB Chr8(GRCh37): g.144874432C>T NM_182706.4: c.4472G>A p.(Arg1491Gln) |
0.0032 | 0 | 4.2 | 29.9 | Possibly deleterious | Intolerant | 5 (4 mis) | 0.31 | Scaffold protein | Involved in uropod and immunological synapse formation, and ROS production by antigen-presenting cells (Barreda et al., 2020). | |
| 58 | F | 21–25 | Unclassified | CTCF Chr16(GRCh37): g.67645905G>T NM_006565.4: c.833G>T p.(Arg278Leu) |
0 | 0 | 9.7 | 24.7 | Possibly deleterious | Highly intolerant | 12 (11 mis) | 0.15 | Transcriptional insulator | CTCF variants cause neurodevelopmental disorders, sometimes associated with recurrent infections and minor facial dysmorphisms (Konrad et al., 2019). | Published (Konrad et al., 2019). |
| 75 | F | 6–10 | Bone marrow failure | FUBP1 Chr1(GRCh37): g.78435621A>C NM_001303433.1: c.199T>G p.(Leu67Val) |
0 | 0 | 2.6 | 24.8 | Possibly deleterious | Intolerant | 1 (0 mis) | 0.12 | Transcriptional regulator that binds FUSE upstream of the c-myc promoter | Essential for long-term repopulating hematopoietic stem cell renewal (Rabenhorst et al., 2015). Fubp1 KO mice show cerebral hyperplasia, pulmonary hypoplasia, pale livers, hypoplastic spleen, thymus, and bone marrow, cardiac hypertrophy, placental distress, and small size (Zhou et al., 2016). | |
| 118 | F | 0–5 | Immune dysregulation, autoimmunity and others | RUNX3 Chr1(GRCh37): g.25256227C>T NM_004350.2: c.133G>A p.(Gly45Arg) |
0 | 0 | 2.4 | 18 | Possibly deleterious | Slightly tolerant | 1 (1 mis) | 0.42 | Transcriptional regulator | RUNX3 regulates CD8+T cell thymocyte development, maturation of cytotoxic CD8+T cells and the function of innate lymphoid cells 3 via stimulation of RORγt (Ebihara et al., 2015). Runx3 KO mice spontaneously develop inflammatory bowel disease and gastric lesions (Brenner et al., 2004). | |
| Frameshift SNVs | |||||||||||||||
| 49 | M | 26–30 | Predominantly antibody deficiency, hypogamma-globulinemia | DDX1 Chr2(GRCh37): g.15769802dup NM_004939.2: c.1952dup p.(Trp652fs) |
0 | 0 | - | - | - | - | 4 (0 fs) | 0.28 | RNA helicase | Part of a dsRNA sensor that activates the NF-κB pathway and type I interferon responses (Zhang et al., 2011). | |
| 78 | F | 6–10 | CID, syndromal | KMT2C Chr7(GRCh37): g.151860074del NM_170606.2: c.10588del p.(Ser3530Leufs*3) |
0 | 0 | - | - | - | - | 19 (4 fs) | 0.12 | Histone methyltransferase | KMT2C de novo variant causes Kleefstra syndrome 2, sometimes associated with recurrent respiratory infections (Koemans et al., 2017). | |
| Small in-frame indel | |||||||||||||||
| 108 | M | 21–25 | Bone marrow failure | NSD2 Chr4(GRCh37): g.1959681_1959687delins TTTTTCT NM_133330.2: c.2903_2909delins TTTTTCT p. (Arg968_Arg970delinsLeuPheLeu) |
- | - | - | - | - | - | 0.12 | Histone methyltransferase | NSD2 de novo LoF variant causes mild Wolf-Hirschhorn syndrome (Barrie et al., 2019). Unclear role in immunity. | Postzygotic mosaicism (VAF 29%). | |
| Patient nr. | Sex | Age range at sampling | Phenotype (IUIS classification) | De novo variant | GnomAD AF in % | in-house AF in % | PhyloP | CADD | SpliceAI Acceptor Gain | SpliceAI Acceptor Loss | Coding DNV in denovo-db (protein effect) | LOEUF | Function | Literature | Comments |
| Splice site SNVs | |||||||||||||||
| 53 | F | 11–15 | Autoinflammatory disorder | FBXW11 Chr5(GRCh37): g.171295802T>C NM_012300.2: c.1468–2A>G p.? |
0 | 0 | 7.9 | 34 | 0.0134 | 0.9862 | 2 (0 ss) | 0.31 | Component of SCF (SKP1-CUL1-F-box) E3 ubiquitin ligase complex | Involved in the regulation of NF-κB signalling (Wang et al., 2018). | |
| 119 | F | 11–15 | Autoinflammatory disorder | RELA Chr11(GRCh37): g.65423234C>T NM_021975.3: c.959–1G>A p.? |
0 | 0 | 3.5 | 34 | 0.7968 | 0.9991 | - | 0.18 | Transcription factor p65 (NF-κB subunit) | Heterozygous RELA variant causes chronic mucocutaneous ulceration (Badran et al., 2017). | |
Abbreviations: IUIS = International Union of Immunological Societies; GnomAD = Genome Aggregation Database; AF = allele frequency; CADD = Combined Annotation Dependent Depletion; DNV = de novo variant; LOEUF = loss-of-function observed/expected upper bound fraction; SNV = single nucleotide variant; indel = insertion-deletion; (S)CID = severe combined immunodeficiency; NA = not applicable; mis = missense; fs = frameshift; ss = splice site; MAPK = mitogen-activated protein kinase; FUSE = far upstream element; PRAAS = proteasome-associated autoinflammatory syndrome; NK = natural killer; ROS = reactive oxygen species; KO = knockout; dsRNA = double-stranded RNA; NF-κB = nuclear factor kappa-light-chain-enhancer of activated B cells; LoF = loss-of-function; VAF = variant allele fraction; UPD16 = uniparental disomy of chromosome 16.