. 2020 May 4;267(9):2533–2545. doi: 10.1007/s00415-020-09865-6

Table 3.

Top ranked putative pathogenic variants shared by three affected siblings

Gene gnomAD constraint metrics	Transcript ID	c. notation p. notation	Classification^a	Phenotype; MIM number; inheritance	Pathogenicity predictions^b		Subjects: clinical findings
Gene gnomAD constraint metrics	Transcript ID	c. notation p. notation	Classification^a	Phenotype; MIM number; inheritance	CADD/REVEL/M-CAP/ClinPred	Impact on splicing	Subjects: clinical findings
NEK4 misZ = 0.88 pLI = 0.0	NM_003157	c.190A>T p.Asn64Tyr	VUS_PM1+PM2+PP3	n.r	23.7/0.452/0.113/0.984	n.d	IA7: 2 IA IA8: 1 IA + 1 aSAH IA15: 6 IA
EDIL3 misZ = 1.16 pLI = 0.0	NM_005711	c.383G>A p.Cys128Tyr	VUS_PM1+PM2+PP3	n.r	29.1/0.946/0.523/0.998	n.d
EDNRB misZ = 1.18 pLI = 0.01	NM_001201397	c.891T>G p.Ser297Arg	VUS_PM2	Waardenburg syndrome, type 4A; 277580; AD, AR; ABCD syndrome, 600501, AR; Hirschsprung disease, susceptibility to, 2, 600155, AD	23.7/0.303/0.020/0.972	Gain of ESS site (HSF); no impact (NG2, MES)
DNAH9 misZ = − 0.04 pLI = 0.0	NM_001372	c.13304T>C p.Ile4435Thr	VUS_PM2	Ciliary dyskinesia, primary, 40; 618300; AR	24.5/0.203/0.010/0.983	n.d
GGA3 misZ = − 0.01 pLI = 0.0	NM_138619	c.16G>A p.Gly6Arg	VUS_PM2+PP3	n.r	33.0/0.299/0.049/0.988	n.d

Sequence alterations were identified by filtering the exome sequencing data as described in the text. gnomAD constraint metrics (v2.1.1) including missense Z score (misZ; intolerance to variation) and pLI score (probability of loss-of-function intolerance) are given. Transcript IDs correspond to the NCBI Reference Sequence (RefSeq) project. Nucleotide and amino acid changes are given according to the indicated transcript ID. Nucleotide numbering uses + 1 as the A of the ATG translation initiation codon in the reference sequence, with the initiation codon as codon 1

AD autosomal dominant, AR autosomal recessive, ESS Exonic Splicing Silencer, aSAH aneurysmal subarachnoid hemorrhage, IA intracranial aneurysm (including unruptured and ruptured IA), MIM Mendelian inheritance in man, n.d. not determined, n.r. none reported

^aVariant classification: VUS, variant of uncertain significance; classification criteria PM1, PM2, PP3 and BP4 are explained in the Supplementary Methods. PM1 was assigned to the NEK4 p.Asn64Tyr variant, because of the critical position in the so-called tyrosine-down motif (references see Supplementary Information). PM1 was assigned to the EDIL3 p.Cys128Tyr variant, because of its critical position in an EGF-like domain (see “Discussion”)

^bDetails on pathogenicity predictors and respective thresholds [CADD (≥ 20), REVEL (≥ 0.5), M-CAP (≥ 0.025), ClinPred (≥ 0.5)] as well as on splice site predictions with HSF, NetGene2 (NG2), MaxEntScan (MES) and BDGP are given in the Supplementary Methods. Scores ≥ thresholds are shown in bold numbers