Skip to main content
. 2020 Nov 5;107(5):963–976. doi: 10.1016/j.ajhg.2020.10.002

Table 1.

Summary of NCKAP1 Variants Identified in NDD-Affected Individuals

Family Index Cohort Cohort Size Methods gDNA Change (chr2, hg19) Function NT Change aa Change Inheritance gnomAD Clinical Significance
LGD Variants
1 SSC 2,508 WES g.183866861_183866862insTG frameshift c.523_524insCA p.Gly175Alafs∗14 de novo 0 P
3 GeneDx 31,111 WES g.183860531_183860532insA frameshift c.656_657insT p.Tyr220Ilefs∗9 de novo 0 P
5 Lyon 200 WES g.183859579T>A stopgain c.796A>T p.Lys266∗ de novo 0 P
6 GeneDx 31,111 WES g.183826886C>T splicing c.1899+1G>A – unknown 0 LP
7 Parkville 160 WES g.183821230G>A stopgain c.2131C>T p.Arg711∗ paternal 0 P
8 ASID 10,927 target g.183817939del frameshift c.2292del p.Ile765Leufs∗18 maternal 0 LP
9 Poitiers 224–350 WES g.183817632G>A stopgain c.2410C>T p.Arg804∗ not maternal 0 LP
10 Lausanne – WES g.183817632G>A stopgain c.2410C>T p.Arg804∗ not maternal 0 LP
12 ACGC 2,926 target g.183792844C>T splicing c.3198+1G>A – de novo 0 P
13 Lyon 200 WES g.183791591_183791592dup frameshift c.3240_3241dup p.Lys1081Ilefs∗15 de novo 0 P
14 SSC 2,508 WES g.183791570G>T stopgain c.3262G>T p.Glu1088∗ de novo 0 P
15 Riyadh 105 WES g.183790537C>A stopgain c.3298G>T p.Glu1100∗ paternal 0 P
De Novo Intronic Variants
2 SSC 2,508 WES g.183866852T>C splicing c.530+3A>G – de novo 0 P
4 Riyadh 2,219 WES g.183859618T>G splicing c.760−3A>C – de novo 0 VUS
11 GeneDx 31,111 WES g.183817233G>C splicing c.2522−3C>G – maternal 0 LP
Microdeletion
16 Odense – aCGH g.183762482-184182761del microdeletion 240 kb deletion – de novo 0 P
Chromosome Inversion
17 Colorado – MPS inv(2)(2pter®p23.1(30340928)::2q32.1(183896661)®p23.1(30340928)::2q32.1(183896662) ®2qter). inversion – – de novo – P
De Novo Missense Variants
18 GeneDx 31,111 WES g.183902823G>C missense c.5C>G p.Ser2Trp de novo 0 VUS
19 GeneDx 31,111 WES g.183832053C>T missense c.1537G>A p.Ala513Thr de novo 1 VUS
20 GeneDx 31,111 WES g.183790473G>A missense c.3362C>T p.Ala1121Val de novo 0 VUS

NCKAP1 isoform is GenBank: NM_205842.3. MPS, mate pair sequencing of inversion; P, pathogenic; LP, likely pathogenic; VUS, variants of uncertain significance.