Table 2 Potentially causative variants identified by exome sequencing.

From: TBK1 and TNFRSF13B mutations and an autoinflammatory disease in a child with lethal COVID-19

Gene transcript

HGVS rs-ID

Zyg.

Associated disease (Inheritance)

gnomAD allele count

gnomAD constraint metrics

TBK1

NM_013254.4

c.1760 + 4_1760 + 7del; p.?

rs753802322

hom

Severe COVID-19 (AD); Susceptibility to acute infection-induced encephalopathy 8 (AD); Frontotemporal dementia and/or amyotrophic lateral sclerosis 4 (AD)

1 (het) / 0 (hom)

pLI: 0.08

Missense-Z: 1.9

o/e (LoF): 0.25 (0.16-0.42)

o/e (Missense): 0.72 (0.65-0.79)

TNFRSF13B

NM_012452.2

c.310 T > C; p.(Cys104Arg)

rs34557412

hom

Common variable immune deficiency 2 (AD / AR); Immunoglobulin A deficiency 2 (?)

983 (het) / 4 (hom)

pLI: 0

Missense-Z: −1.2

o/e (LoF): 1.73 (1.14-1.96)

o/e (Missense): 1.26 (1.13-1.41)

  1. Note that gene symbols are italicized.
  2. HGVS sequence variant description in accordance with the recommendations of the human genome variation society, rs-ID dbSNP reference single-nucleotide polymorphism number, Zyg Zygosity, hom homozygous, het heterozygous, AD autosomal-dominant, AR autosomal-recessive, pLI probability of loss of function intolerance, Missense-Z Z-score indicating the depletion of missense variants from a gene, o/e observed/expected metric with its 90% confidence interval shown in brackets for loss-of-function (LoF) or missense variants.
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