Table 1

Anonymised phenotypic and research molecular diagnosis data for the probands in the congenital malformations caused by ciliopathies cohort

Research number	Recruitment category	Most likely clinical diagnosis based on HPO terms	Does recruitment category match most likely clinical diagnosis?	GEL GMC exit report	Research molecular diagnosis	Gene	Is identified diagnosis a ciliopathy?	Diagnostic confidence
1	JBTS	JBTS	Yes	Sol	CHARGE Syn	CHD7	No	Conf
2	BBS	Non-cil MS cond	No	Sol	Alström Syn	ALMS1	Yes	Conf
3	BBS	BBS	Yes	Sol	BBS +RP	ARL6 +IMPG2	Yes	Conf
4	BBS	BBS	Yes	Sol	RP	RPGR	Yes	Conf
5	BBS	Non-cil MS cond	No	Sol	Retinal cil, possibly syndromic	CEP290	Yes	Conf
6	JBTS	JBTS	Yes	Sol	JBTS	KIAA0586	Yes	Conf
7	RMCD	OFD-like cil	Yes	Sol	OFD1, PKD +inherited cataract	OFD1, PKD1, CRYBB1	Yes (OFD1)	OFD1 Conf, PKD1 +CRYYB1 Poss
8	BBS	Isol RD	No	Sol	RP	PRPF8	No	Conf
9	RMCD	JBTS-like MS cil	Yes	Uns	Seckel Syn	CEP152	No	Poss
10	JBTS	JBTS	Yes	Sol	JBTS	CEP290	Yes	Conf
11	RMCD	Jeune-like cil	Yes	Unr	Feingold Syn	MYCN	No	Conf
12	JBTS	JBTS	Yes	Unr	JBTS	ARMC9	Yes	Conf
13	BBS	BBS	Yes	Unr	Tubulinopathy	TUBA1A	No	Poss
14	RMCD	Jeune-like cil	Yes	Unr	Jeune Syn	WDR19	Yes	Conf
15	BBS	Isol RD	No	Unr	RP	RHO	No	Conf
16	RMCD	Non-cil MS cond	No	VUS	STAG1 syndromic ID syn	STAG1	No	Prob
17	BBS	BBS	Yes	Sol	BBS	BBS1	Yes	Conf
18	BBS	BBS	Yes	Sol	Neurodevelopmental disorder	RERE	No	Conf
19	BBS	BBS	Yes	Sol	Alström Syn	ALMS1	Yes	Conf
20	BBS	Isol eye cond (not RD)	No	Sol	BBS	BBS2	Yes	Conf
21	JBTS	JBTS	Yes	Unr	Poretti-Boltshauser Syn+Arboleda Tham Syn	LAMA1, KAT6A	No	LAMA1 Prob, KAT6A Poss
22	BBS	BBS	Yes	Sol	BBS	MKKS	Yes	Conf
23	JBTS	JBTS	Yes	Sol	JBTS	CEP290	Yes	Prob
24	BBS	Non-cil MS cond	No	Uns				Uns
25	BBS	BBS	Yes	Sol	Smith Magenis Syn	RAI1	No	Conf
26	BBS	BBS	Yes	Sol	Cone-rod dystrophy	PROM1	No	Conf
27	JBTS	Non-cil MS cond	No	Unr	Luscan-Lumish Syn	SETD2	No	Conf
28	BBS	Non-cil MS cond	No	Sol	Optic Atrophy	OPA1	No	Conf
29	BBS	Non-cil MS cond	No	Sol	Alström Syn	ALMS1	Yes	Conf
30	BBS	BBS	Yes	Sol	Chung-Jansen Syn	PHIP	No	Conf
31	BBS	Isol RD	No	Sol	Cone-rod dystrophy	RAB28	Yes	Conf
32	BBS	BBS	Yes	Sol	None: Unsolved	ALMS1	N/a	False+ve
33	RMCD	Non-cil MS cond	No	Uns				Uns
34	RMCD	Non-cil MS cond	No	Uns	Van Esch-O'Driscoll Syn	POLA1	No	Poss
35	JBTS	JBTS	Yes	Uns				Uns
36	JBTS	JBTS	Yes	Uns				Uns
37	RMCD	Non-cil MS cond	No	Uns				Uns
38	BBS	BBS	Yes	Uns				Uns
39	BBS	BBS	Yes	Uns				Uns
40	BBS	BBS	Yes	Uns				Uns
41	JBTS	JBTS	Yes	Uns	JBTS	CSPP1	Yes	Prob
42	JBTS	JBTS	Yes	Unr	JBTS	PIBF1	Yes	Prob
43	BBS	BBS	Yes	Uns				Uns
44	RMCD	Non-cil MS cond	No	Uns				Uns
45	BBS	Isol polydactyly	No	Uns				Uns
46	RMCD	MKS/JBTS-like MS cil	Yes	Uns				Uns
47	BBS	Non-cil MS cond	No	Unr				Uns
48	RMCD	BBS-like MS cil	Yes	Uns	Candidate cil	LRRC45	Candidate	Poss
49	RMCD	Non-cil MS cond	No	Unr				Uns
50	BBS	BBS	Yes	Unr				Uns
51	RMCD	DM	DM	Unr				Uns
52	RMCD	JBTS-like MS cil	Yes	Unr				Uns
53	RMCD	Isol GI disorder	No	Unr				Uns
54	RMCD	Non-cil MS cond	No	Uns				Uns
55	JBTS	JBTS	Yes	Uns				Uns
56	BBS	Isol eye cond (not RD)	No	VUS	BBS	BBS9	Yes	Poss
57	JBTS	JBTS	Yes	Uns				Uns
58	RMCD	JBTS-like MS cil	Yes	Uns				Uns
59	BBS	BBS	Yes	Uns				Uns
60	BBS	BBS	Yes	Uns				Uns
61	RMCD	Non-cil MS cond	No	Unr	WT1-related disorder	WT1	No	Conf
62	RMCD	Non-cil MS cond	No	Uns				Uns
63	RMCD	Non-cil MS cond	No	Uns				Uns
64	RMCD	JBTS-like MS cil	Yes	Uns				Uns
65	BBS	BBS	Yes	Uns				Uns
66	RMCD	BBS-like MS cil	Yes	Uns				Uns
67	BBS	Non-cil MS cond	No	VUS	Alström Syn	ALMS1	Yes	Poss
68	JBTS	JBTS	Yes	Uns				Uns
69	BBS	BBS	Yes	Sol	BBS	BBS1	Yes	Conf
70	BBS	Non-cil MS cond	No	Uns				Uns
71	RMCD	Non-cil MS cond	No	Unr	Shukla-Vernon Syn	BCORL1	No	Poss
72	BBS	BBS	Yes	Unr	Sifrim-Hitz-Weiss Syn	CHD4	No	Poss
73	RMCD	Isol GI disorder	No	Uns				Uns
74	BBS	Non-cil MS cond	No	Uns				Uns
75	BBS	DM	DM	Unr	BBS	BBS4	Yes	Poss
76	BBS	BBS	Yes	VUS	BBS	BBS10	Yes	Poss
77	BBS	BBS	Yes	Uns				Uns
78	BBS	BBS	Yes	Uns				Uns
79	BBS	BBS	Yes	Uns				Uns
80	BBS	BBS	Yes	Uns				Uns
81	BBS	BBS	Yes	Uns				Uns
82	BBS	Non-cil MS cond	No	Unr	Attenuated mucopolysaccharidosis 1	IDUA	No	Prob
83	BBS	BBS	Yes	Uns				Uns

Table includes the recruitment category, designated ‘most likely’ clinical diagnosis based on entered HPO terms alone, GEL GMC exit questionnaire reporting outcome, research molecular diagnosis (determined by genotype), responsible gene, whether the identified diagnosis is a ciliopathy and diagnostic confidence. Note: individual variant information, including data taken into consideration in forming ACMG classifications, can be found in online supplemental table 4.
BBS, Bardet-Biedl syndrome; Cil, ciliopathy; Cond, condition; Conf, confident; DM, data missing; GEL, Genomics England; GI, gastrointestinal; GMC, Genomic Medicine Centres; HPO, Human Phenotype Ontology; Isol, isolated; JBTS, Joubert syndrome; MKS, Meckel Gruber syndrome; MS, multisystemic; PKD, polycystic kidney disease; Poss, possible; Prob, probable; RD, retinal dystrophy; RMCD, rare multisystem ciliopathy disorders; RP, retinitis pigmentosa; Sol, solved; Syn, syndrome; Unr, unreported; Uns, unsolved.