Table 3.

Gene-based tests (MAF < 0.1%) separately by variant category.

Gene	p value	q value	Test	Variant category	EDS gene
COL2A1	2.00E−04	0.0318	kbac	Intronic variants	Non-EDS gene
TNXB	3.00E−04	0.0318	CMC	Nonsynonymous variants and in-frame indels	EDS gene
TNXB	4.00E−04	0.0318	kbac	Nonsynonymous variants and in-frame indels	EDS gene
ZNF469	4.00E−04	0.0318	kbac	Nonsynonymous variants and in-frame indels	EDS gene
TNXB	5.00E−04	0.0318	skat	Nonsynonymous variants and in-frame indels	EDS gene
ZNF469	6.00E−04	0.0318	kbac	Synonymous variants	EDS gene
TNXB	6.00E−04	0.0318	vt	Nonsynonymous variants and in-frame indels	EDS gene
ZNF469	6.00E−04	0.0318	vt	Nonsynonymous variants and in-frame indels	EDS gene
COL5A1	6.00E−04	0.0318	skat	Synonymous variants	EDS gene
COL2A1	0.001	0.0446	vt	Intronic variants	Non-EDS gene
COL2A1	0.0013	0.0516	CMC	Intronic variants	Non-EDS gene
ZNF469	0.0019	0.0714	CMC	Nonsynonymous variants and in-frame indels	EDS gene
ZNF469	0.003	0.1004	vt	Synonymous variants	EDS gene
ZNF469	0.0032	0.1004	CMC	Synonymous variants	EDS gene
PARP2	0.0043	0.1268	skat	Nonsynonymous variants and in-frame indels	Non-EDS gene
MMP9	0.0046	0.1282	kbac	Intronic variants	Non-EDS gene
TF	0.0056	0.1365	kbac	Synonymous variants	Non-EDS gene
TF	0.0058	0.1365	vt	Synonymous variants	Non-EDS gene
COL5A1	0.0058	0.1365	skat	Intronic variants	EDS gene
COL12A1	0.0062	0.1382	vt	Intronic variants	EDS gene
COL12A1	0.0067	0.1396	skat	Synonymous variants	EDS gene
PARP2	0.0072	0.1396	kbac	Nonsynonymous variants and in-frame indels	Non-EDS gene
COL5A1	0.0072	0.1396	kbac	Synonymous variants	EDS gene
COL5A1	0.0078	0.1449	kbac	Intronic variants	EDS gene
MMP9	0.0082	0.1462	calpha	Intronic variants	Non-EDS gene

Full results are shown in Supplementary Table S4ter.

Vt Variable Thresholds methods, kbac kernel-based adaptive cluster, CMC Combined and Multivariate collapsing, skat SNP-set (Sequence) Kernel Association Method, EDS Ehlers–Danlos Syndrome.