Background
Methods
Patients
Genetic analysis
Cytokine determination
Degranulation assays with flow cytometry
Clinical data
Statistical analysis
Results
Genetic results
Case | Gender | Age | Candidate gene | Exon/intron | Nucleotide change | Amino acid change | Genotype |
---|---|---|---|---|---|---|---|
P2 | F | 6Y3M |
PRF1
| Exon3 | c.757G>A c.1061A>T | p.Glu253Lys p.Asp354Val | heterozygous heterozygous |
P16 | M | 3Y3M |
SH2D1A
| Exon2 | c.191G>A | p.Trp64Ter | hemizygous |
P17 | M | 11M24D |
SH2D1A
| Exon2 | c.162C>G | p.Tyr54Ter | hemizygous |
P26 | M | 11M17D |
SH2D1A
| Exon2 | c.163C>T | p.Arg55 Ter | hemizygous |
P1 | M | 1Y5M |
PRF1
| Exon2 | c.385T>A | p.Trp129Arg | heterozygous |
P3 | M | 4Y5M |
UNC13D
| Exon6 | c.478G>A | p.Val160 Met | heterozygous |
P4 | M | 2Y8M |
UNC13D
| Exon6 | c.518C>T | p.Thr173Met | heterozygous |
P5 | F | 1Y7M |
UNC13D
| Exon10 | c.760C>T | p.Arg254Cys | heterozygous |
P6 | M | 8D |
UNC13D
| Exon23 | c.2296C>T | p.Glu766Ter | heterozygous |
P7 | M | 25D |
UNC13D
| Exon32 | c.3259C>T | p.Arg1087Trp | heterozygous |
XIAP
| Exon5 | c.1268A>C | p.Gln423Proa
| hemizygous | |||
P8 | M | 7Y9M |
STXBP2
| Exon7 | c.497C>T | p.Thr166Meta
| heterozygous |
P9 | M | 11Y11M |
STXBP2
| Exon7 | c.497C>T | p.Thr166 Meta
| heterozygous |
P10 | F | 5Y8M |
STXBP2
| Exon7 | c.575G>A | p.Arg192His | heterozygous |
P11 | M | 1Y1M |
STXBP2
| Exon9 | c.767T>C | p.Leu256Pro | heterozygous |
P38 | M | 1Y1M |
XIAP
| Exon5 | c.1268A>C | p.Gln423Proa
| hemizygous |
P45 | M | 4Y |
UNC13D
| Intron1 | c.118-307G>A | Unknown | heterozygous |
Case | Candidate gene | Nucleotide change | Amino acid change | ExAC allele frequency | HGMD/GS references | Polyphen-2 | SIFT | CD107a |
---|---|---|---|---|---|---|---|---|
P2 |
PRF1
| c.757G>A c.1061A>T | p.Glu253Lys p.Asp354Val | 0.00003296 Not reported | [33] No reference | PROBABLY DAMAGING with a score of 0.962 POSSIBLY DAMAGING with a score of 0.952 | AFFECT PROTEIN FUNCTION with a score of 0.01 AFFECT PROTEIN FUNCTION with a score of 0.02 | 32.28 |
P16 |
SH2D1A
| c.191G>A | p.Trp64Ter | Not reported | Not Available | Not Available | 33.83 | |
P17 |
SH2D1A
| c.162C>G | p.Tyr54 Ter | Not reported | [36] | Not Available | Not Available | 0.72 |
P26 |
SH2D1A
| c.163C>T | p.Arg55 Ter | Not reported | Not Available | Not Available | No done | |
P1 |
PRF1
| c.385T>A | p.Trp129Arg | Not reported | No reference | PROBABLY DAMAGING with a score of 1.000 | AFFECT PROTEIN FUNCTION with a score of 0.00 | 3.24 |
P3 |
UNC13D
| c.478G>A | p.Val160 Met | Not reported | No reference | PROBABLY DAMAGING with a score of 0.999 | AFFECT PROTEIN FUNCTION with a score of 0.05 | 35.14 |
P4 |
UNC13D
| c.518C>T | p.Thr173Met | 0.00001670 | No reference | PROBABLY DAMAGING with a score of 1.000 | AFFECT PROTEIN FUNCTION with a score of 0.01 | 0.43 |
P5 |
UNC13D
| c.760C>T | p.Arg254Cys | 0.0003450 | No reference | PROBABLY DAMAGING with a score of 0.987 | AFFECT PROTEIN FUNCTION with a score of 0.02 | 5.69 |
P6 |
UNC13D
| c.2296C>T | p.Glu766 Ter | Not reported | Not Available | Not Available | 0.51 | |
P7 |
UNC13D
| c.3259C>T | p.Arg1087Trp | 0.0001438 | No reference | BENIGN with a score of 0.002 | AFFECT PROTEIN FUNCTION with a score of 0.00 | 2.64 |
XIAP
| c.1268A>C | p.Gln423Pro | 0.3334 | BENIGN with a score of 0.002 | TOLERATED with a score of 0.30 | |||
P8 |
STXBP2
| c.497C>T | p.Thr166Met | 0.0002454 | No reference | BENIGN with a score of 0.022 | TOLERATED with a score of 0.10 | 3.51 |
P9 |
STXBP2
| c.497C>T | p.Thr166 Met | 0.0002454 | No reference | BENIGN with a score of 0.022 | TOLERATED with a score of 0.10 | 13.37 |
P10 |
STXBP2
| c.575G>A | p.Arg192His | Not reported | [15] | PROBABLY DAMAGING with a score of 1.000 | AFFECT PROTEIN FUNCTION with a score of 0.00 | 13.73 |
P11 |
STXBP2
| c.767T>C | p.Leu256Pro | Not reported | No reference | PROBABLY DAMAGING with a score of 1.000 | AFFECT PROTEIN FUNCTION with a score of 0.00 | 4.7 |
P38 |
XIAP
| c.1268A>C | p.Gln423Pro | 0.3334 | BENIGN with a score of 0.002 | TOLERATED with a score of 0.30 | 0.07 | |
P45 |
UNC13D
| c.118-307G>A | Unknown | Not reported | Not Available | Not Available | 3.07 |
Cytokine levels
Degranulation and clinical data
Total (n = 45) | Primary (n = 4) | Secondary (n = 41) |
P-value | |
---|---|---|---|---|
Age at diagnosis | ||||
≤12 months | 9/45 | 2/4 | 7/41 | 0.116 |
>12 months | 36/45 | 2/4 | 34/41 | |
Mean age (year, range) | 3.7 (0–12.3) | 2.9 (1.0–6.3) | 3.8 (0–12.3) | 0.646 |
Sex (M/F) | 27/18 | 3/1 | 24/17 | 0.521 |
Fever | 45/45 | 4/4 | 41/41 | |
Hemoglobin (<90 g/L) | 16/45 | 1/4 | 15/41 | 0.644 |
Mean (g/L, range) | 94.0 (46.0–135.0) | 93.8 (84.0–102.0) | 94.0 (46.0–135.0) | 0.905 |
Platelets (<100x109/L) | 30/45 | 2/4 | 28/41 | 0.459 |
Mean (100x109/L, range) | 82.5 (32.0–400.0) | 100.0 (5.0–215.0) | 80.8 (3.0–400.0) | 0.661 |
White blood cells | ||||
Mean (1x109/L, range) | 7.5 (0.3–41.3) | 6.5 (1.0–9.7) | 7.6 (0.3–41.3) | 0.842 |
Percentage of neutrophils | ||||
Mean (%, range) | 38.2 (2.0–81.5) | 12.8 (6.9–19.4) | 40.7 (2.0–81.5) | 0.012 |
Total neutrophils (<1x109/L) | 20/45 | 2/4 | 18/41 | 0.815 |
Mean (1x109/L, range) | 2.9 (0.1–22.1) | 0.9 (0.1–1.3) | 3.1 (0.1–22.1) | 0.413 |
Percentage of lymphocytes | ||||
Mean (%, range) | 50.4 (7.9–88) | 75.3 (71.8–77.7) | 48.0 (7.9–88.0) | 0.012 |
Total lymphocytes | ||||
Mean (1x109/L, range) | 3.6 (0.2–28.1) | 4.9 (0.7–7.5) | 3.4 (0.2–28.1) | 0.175 |
Triglycerides (>3.0 mmol/L) | 15/45 | 3/4 | 12/41 | 0.064 |
Mean (mmol/L, range) | 2.7 (0.8–8.9) | 3.0 (1.3–4.1) | 2.7 (0.8–8.9) | 0.425 |
Fibrinogen (<1.5 g/L) | 30/45 | 4/4 | 26/41 | 0.138 |
Mean (g/L, range) | 1.5 (0.2–4.9) | 0.9 (0.5–1.2) | 1.5 (0.2–4.9) | 0.14 |
LDH (>500 IU/L) | 32/45 | 3/4 | 29/41 | 0.857 |
Mean (IU/L, range) | 1018.0 (167.0–6565.0) | 814.0 (363.0–1644.0) | 1037.9 (167.0–6565.0) | 0.842 |
Ferritin (>500 μg/L) | 45/45 | 4/4 | 41/41 | |
Mean (μg/L, range) | 1477.7 (895.0–1500.0) | 1500.0 (1500.0–1500.0) | 1474.2 (895.0–1500.0) | 0.655 |
sIL2R (≥2400 U/ml) | 26/27 | 4/4 | 22/23 | 0.671 |
Mean (U/ml, range) | 34092.7 (155.6–85787.7) | 27198.1 (14250.9–38203.1) | 35239.6 (155.6–85787.7) | 0.922 |
sIL2R/Ferritin | ||||
Mean (U/pg, range) | 23.0 (0.1–57.2) | 18.4 (9.5–25.5) | 23.8 (0.1–57.2) | 0.811 |
Degranulation (CD107a <5 %) | 16/36 | 1/3 | 15/33 | 0.795 |
Mean (%, range) | 10.3 (0.1–35.1) | 22.3 (0.7–33.8) | 9.2 (0.1–35.1) | 0.407 |
EBV-DNA (>1000 copies) | 26/45 | 2/4 | 24/41 | 0.741 |
CMV-DNA (>1000 copies) | 1/45 | 0/4 | 1/41 | 0.752 |