Table 2.
NOTCH1 variants identified in the 11 families studied.
| Family | Ethnicity | Testing method for proband | NOTCH1 variant | Interpretation | Rationale documenting clinical relevance using ACMG criteria |
|---|---|---|---|---|---|
| A | Native Canadian | Research GS: proband + affected sibling. | 127 kbp deletion 9q34.3-9q34.3 (encompassing entire NOTCH1 gene and no other OMIM morbid map genes) | Pathogenic |
Variant previously reported: Similar deletion reported in Kerstjens-Frederikse et al. [13]. ACMG criteria (copy number LOSS): 2A - Complete overlap of haploinsufficient gene NOTCH1 (+1.00). |
| B | European | Research GS: trio |
c.13_14dupCT p.Ala6Trpfs*28 |
Likely pathogenic |
Variant previously reported: No ACMG criteria PVS1 – Frameshift, where LOF is a known mechanism of disease. PM2 – Absent from gnomAD. |
| C | European | Clinical NOTCH1 sequencing: singleton + research GS: quad (in parallel) |
c.2995G>A p.Val999Met |
VUS |
Variant previously reported: ClinVar ID: 1036675. Family previously reported in Gordon et al. [31]. ACMG criteria: PM2 – Present at low frequency in controls (total AF = 0.00001474; maximal AF = 0.00008253 in South Asian subpopulation). PP1 – Segregates with CHD in 3 family members. PP2 – NOTCH1 is intolerant to missense variation. |
| D | African/European | Research GS: proband + affected sibling. |
c.141-1G>C p.? |
Likely pathogenic |
Variant previously reported: No ACMG criteria: PVS1 – Variant is in the canonical splice site, where LOF is a known mechanism of disease. PM2 – Absent from gnomAD |
| E | European/Native Canadian | Research GS: proband + 3 affected relatives |
c.568C>T p.Arg190Cys |
VUS |
Variant previously reported: No ACMG criteria: PM2 – Present at low frequency in controls (total AF = 0.000001429; maximal AF = 0.000001852 in Non-Finnish European subpopulation) PP1 – Segregates with CHD in 4 family members. PP2 – NOTCH1 is intolerant to missense variation. |
| F | European | Clinical NOTCH1 sequencing: singleton + research GS: trio (in parallel) |
c.5814C>G p.Tyr1938* |
Likely pathogenic |
Variant previously reported: No ACMG criteria: PVS1 – Nonsense variant, where LOF is a known mechanism of disease. PM2 – Absent from gnomAD. |
| G | African/European/Middle Eastern | Clinical ES: trio |
c.3654T>A p.Cys1218* |
Pathogenic |
Variant previously reported: No ACMG criteria: PVS1 – Nonsense variant, where LOF is a known mechanism of disease. PS2 – De novo variant where parentage is confirmed. PM2 – Absent from gnomAD. |
| H | Eastern European/Ashkenazi Jewish | Clinical AOS gene panel: singleton |
c.4415G>A p.Cys1472Tyr |
Likely pathogenic |
Variant previously reported: No. ACMG criteria: PM2 – Absent from gnomAD. PM5 – Another variant at the same amino acid (p.Cys1472Trp) is reported as likely pathogenic in Alankarage et al. [32]. PP1 (Moderate) – Segregates with CHD/cutis aplasia in 4 family members. PP2 – NOTCH1 is intolerant to missense variation. PP3 – Variant is predicted damaging by all in silico tools (CADD = 26.7; REVEL = 0.836) |
| I | European | Clinical AOS gene panel: singleton |
c.4579C>T p.Gln1527* |
Pathogenic |
Variant previously reported: No ACMG criteria: PVS1 – Nonsense variant, where LOF is a known mechanism of disease. PM2 – Absent from gnomAD. PP1_Strong: Previously reported to segregate with disease. |
| J | European | Research GS: trio |
c.866-2A>G p.? |
Likely pathogenic |
Variant previously reported: No ACMG criteria: PVS1 – Variant is in the canonical splice site, where LOF is a known mechanism of disease. PM2 – Absent from gnomAD |
| K | European | Research GS: trio |
c.5349del p.Arg1784Glyfs*14 |
Likely pathogenic |
Variant previously reported: No ACMG criteria: PVS1 – Nonsense variant, where LOF is a known mechanism of disease. PM2 – Absent from gnomAD. |
Transcript referenced is NM_017617. Variants were interpreted using guidelines outlined by the American College of Medical Genetics (ACMG) [29, 30]. Allele frequencies referenced are from gnomAD v4.1.0. The level of evidence supporting segregation data (PP1) was adjusted based on guidelines from Jarvik and Browning (2016) [43].
AF allele frequency, AOS Adams–Oliver syndrome, CHD congenital heart disease, ES exome sequencing, gnomAD genome aggregation database, GS genome sequencing, LOF loss of function, VUS variant of uncertain significance.