Table 2 NOTCH1 variants identified in the 11 families studied.

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.