Missense mutations associated with variable onset of FHL or found to be nonpathogenic
| Patient . | Age, y . | Gene . | Allele 1 . | Allele 2 . | Experimental outcome (% of WT activity) . | Allele Frequency (gnomAD36) . |
|---|---|---|---|---|---|---|
| Category I: mutations associated with an early (patients aged <5 years) onset of FHL | ||||||
| P137 | 0.167 | UNC13D | c.1208T>C p.L403P | c.1208T>C p.L403P | Null (supplemental Figure 8) | - |
| P238 | 0.167, 4, 5 | STX11 | c.173T>C p.L58P | c.173T>C p.L58P | Null (Figure 4B) | <0.1% |
| P339 | 0.167 | PRF1 | c.666C>A p.H222Q | c.666C>A p.H222Q | Null (Figure 4A; supplemental Figure 9) | <0.1% |
| P440 | 0.583 | STXBP2 | c.1621G>A p.G541S | c.1621G>A p.G541S | Null (supplemental Figure 8) | <0.1% |
| P541 | 2 | STXBP2 | c.728T>G p.L243R | c.1247-1G>C p.V417LfsX126∗ | Null / Null (Figure 4C) | - / <0.1% |
| P6 (case #1)26 | 0.08 | UNC13D | c.1232G>A p.R411Q | c.2588G>A p.G863D | Normal / 22% (Figure 3A; supplemental Figure 8) | 0.8% / 0.37% East Asian |
| Category II: mutations associated with a late (patients aged >5 years) onset of FHL | ||||||
| P742 | 8 | PRF1 | c.577T>C p.F193L | c. 1229G>C p.R410P18 | 21% / TS18 (supplemental Figure 8) | - / <0.1% |
| P837 | 10 | PRF1 | c.601C>A p.P201T | c.853_855del p.K285del43 | 17% / Null (Figure 4A; supplemental Figure 9) | - / <0.1% |
| P944 | 18 | PRF1 | c.1066C>T p.R356W | c.1349C>T p.T450M18 | 13%/TS18 (supplemental Figure 8) | <0.1% / <0.1% |
| P1015 | 9, 13 | UNC13D | c.1240C>T p.R414C | c.2753C>A p.A918D | 20%/17% (Figure 4D) | <0.1% / - |
| P11 (case #2) | 44 | UNC13D | c.1135G>A p.E379K | c.1135G>A p.E379K | 15% (Figure 3D) | - |
| P1245 | 45 | STXBP2 | c.1001C>T p.P334L | c.474_483del_insGA p.C158Wfs∗78∗ | 67%†/null (Figure 4C) | 0.1% / 0.1% Ashkenazi Jewish |
| P1346 | 14, 14, 15, 36, 42, 56 | STX11 | c.146G>A p.R49Q | - | Normal (supplemental Figure 8) | 6.5% East Asian, 1.7% African American |
| Category III: carriers of digenic mutations47 | ||||||
| P14 | 0.92 | PRF1 | c.992C>T p.S331L | - | 17% (supplemental Figure 8) | <0.1% |
| UNC13D | c.1232G>A p.R411Q | - | Normal (supplemental Figure 8) | 0.8% East Asian | ||
| P15 | 2.25 | PRF1 | c.272C>T p.A91V | - | Normal (supplemental Figure 10) | 4.3% European |
| UNC13D | c.227C>T p.T76M | - | 22% (supplemental Figure 8) | 0.5% African American | ||
| P16 | 3 | PRF1 | c.272C>T p.A91V | - | Normal (supplemental Figure 10) | 4.3% European |
| UNC13D | c.2243C>T p.A748V | - | Normal (supplemental Figure 8) | <0.1% | ||
| P17 | 9, 13 | PRF1 | c.272C>T p.A91V | - | Normal (supplemental Figure 10) | 4.3% European |
| UNC13D | c.2896C>T p.R966W | - | Normal (supplemental Figure 8) | 0.7% European | ||
| P18 | 28 | PRF1 | c.272C>T p.A91V | - | Normal (supplemental Figure 10) | 4.3% European |
| UNC13D | c.182A>G p.Y61C | - | Normal (supplemental Figure 8) | - | ||
| P19 | 0.167 | UNC13D | c.2030T>C p.I677T∗ | - | Not tested | - |
| STX11 | c.221C>T p.T74M | - | Normal (Figure 4B) | 0.7% South Asian | ||
| P20 | 5, 10 | PRF1 | c.272C>T p.A91V | - | Normal (supplemental Figure 10) | 4.3% European |
| STXBP2 | c.1034C>T p.T345M | - | Normal (supplemental Figure 8) | 1.6% European | ||
| P21 | 21 | PRF1 | c.272C>T p.A91V | - | Normal (supplemental Figure 10) | 4.3% European |
| STXBP2 | c.1586G>C p.R529P | - | Normal (supplemental Figure 8) | 0.24% European | ||
| P22 | 24 | PRF1 | c.50 delT p.L17Rfs∗29∗ | - | Null | 0.3% African American |
| STXBP2 | c.1459G>A p.V487M | - | Null (supplemental Figure 8) | 0.57% African American | ||
| Patient . | Age, y . | Gene . | Allele 1 . | Allele 2 . | Experimental outcome (% of WT activity) . | Allele Frequency (gnomAD36) . |
|---|---|---|---|---|---|---|
| Category I: mutations associated with an early (patients aged <5 years) onset of FHL | ||||||
| P137 | 0.167 | UNC13D | c.1208T>C p.L403P | c.1208T>C p.L403P | Null (supplemental Figure 8) | - |
| P238 | 0.167, 4, 5 | STX11 | c.173T>C p.L58P | c.173T>C p.L58P | Null (Figure 4B) | <0.1% |
| P339 | 0.167 | PRF1 | c.666C>A p.H222Q | c.666C>A p.H222Q | Null (Figure 4A; supplemental Figure 9) | <0.1% |
| P440 | 0.583 | STXBP2 | c.1621G>A p.G541S | c.1621G>A p.G541S | Null (supplemental Figure 8) | <0.1% |
| P541 | 2 | STXBP2 | c.728T>G p.L243R | c.1247-1G>C p.V417LfsX126∗ | Null / Null (Figure 4C) | - / <0.1% |
| P6 (case #1)26 | 0.08 | UNC13D | c.1232G>A p.R411Q | c.2588G>A p.G863D | Normal / 22% (Figure 3A; supplemental Figure 8) | 0.8% / 0.37% East Asian |
| Category II: mutations associated with a late (patients aged >5 years) onset of FHL | ||||||
| P742 | 8 | PRF1 | c.577T>C p.F193L | c. 1229G>C p.R410P18 | 21% / TS18 (supplemental Figure 8) | - / <0.1% |
| P837 | 10 | PRF1 | c.601C>A p.P201T | c.853_855del p.K285del43 | 17% / Null (Figure 4A; supplemental Figure 9) | - / <0.1% |
| P944 | 18 | PRF1 | c.1066C>T p.R356W | c.1349C>T p.T450M18 | 13%/TS18 (supplemental Figure 8) | <0.1% / <0.1% |
| P1015 | 9, 13 | UNC13D | c.1240C>T p.R414C | c.2753C>A p.A918D | 20%/17% (Figure 4D) | <0.1% / - |
| P11 (case #2) | 44 | UNC13D | c.1135G>A p.E379K | c.1135G>A p.E379K | 15% (Figure 3D) | - |
| P1245 | 45 | STXBP2 | c.1001C>T p.P334L | c.474_483del_insGA p.C158Wfs∗78∗ | 67%†/null (Figure 4C) | 0.1% / 0.1% Ashkenazi Jewish |
| P1346 | 14, 14, 15, 36, 42, 56 | STX11 | c.146G>A p.R49Q | - | Normal (supplemental Figure 8) | 6.5% East Asian, 1.7% African American |
| Category III: carriers of digenic mutations47 | ||||||
| P14 | 0.92 | PRF1 | c.992C>T p.S331L | - | 17% (supplemental Figure 8) | <0.1% |
| UNC13D | c.1232G>A p.R411Q | - | Normal (supplemental Figure 8) | 0.8% East Asian | ||
| P15 | 2.25 | PRF1 | c.272C>T p.A91V | - | Normal (supplemental Figure 10) | 4.3% European |
| UNC13D | c.227C>T p.T76M | - | 22% (supplemental Figure 8) | 0.5% African American | ||
| P16 | 3 | PRF1 | c.272C>T p.A91V | - | Normal (supplemental Figure 10) | 4.3% European |
| UNC13D | c.2243C>T p.A748V | - | Normal (supplemental Figure 8) | <0.1% | ||
| P17 | 9, 13 | PRF1 | c.272C>T p.A91V | - | Normal (supplemental Figure 10) | 4.3% European |
| UNC13D | c.2896C>T p.R966W | - | Normal (supplemental Figure 8) | 0.7% European | ||
| P18 | 28 | PRF1 | c.272C>T p.A91V | - | Normal (supplemental Figure 10) | 4.3% European |
| UNC13D | c.182A>G p.Y61C | - | Normal (supplemental Figure 8) | - | ||
| P19 | 0.167 | UNC13D | c.2030T>C p.I677T∗ | - | Not tested | - |
| STX11 | c.221C>T p.T74M | - | Normal (Figure 4B) | 0.7% South Asian | ||
| P20 | 5, 10 | PRF1 | c.272C>T p.A91V | - | Normal (supplemental Figure 10) | 4.3% European |
| STXBP2 | c.1034C>T p.T345M | - | Normal (supplemental Figure 8) | 1.6% European | ||
| P21 | 21 | PRF1 | c.272C>T p.A91V | - | Normal (supplemental Figure 10) | 4.3% European |
| STXBP2 | c.1586G>C p.R529P | - | Normal (supplemental Figure 8) | 0.24% European | ||
| P22 | 24 | PRF1 | c.50 delT p.L17Rfs∗29∗ | - | Null | 0.3% African American |
| STXBP2 | c.1459G>A p.V487M | - | Null (supplemental Figure 8) | 0.57% African American | ||
% of killing is based on day 7 data for all mutants.
Mutations in italic were previously tested by us using Prf1−/− CTLs18 or PRF1-KO human NK-cell line KHYG1.43
P10 represents 2 siblings with same compound heterozygote UNC13D mutations.15
TS, temperature sensitive. These 2 PRF1 mutants have been previously extensively tested in our laboratory and found to be misfolded and temperature sensitive.18
Mutations not tested in our system (most due to frameshift/deletion).
This mutant showed 30% cytotoxicity on day 4; despite a significant recovery of function, the degranulation remained severely reduced on day 7 (Figure 4C).