Table 3

Identified mutations and other potentially pathogenic variants in the 38 patients with previously unknown genotype. A) Patients with two clearly pathogenic variants in one gene; B) Patients with a single or no clear pathogenic variant in one gene. Mutations are described according to the latest nomenclature conventions described in HGVS

Patient#	Principal mutations (p.)	Principal mutations (c.)	Sanger validation/segregation	Mutation, as predicted by (among SIFT, PPhen2 & Mutation T@ster)	Additional potentially pathogenic variants	Frequency of additional variants in EVSdb	Geographic origin	Inbred	BBS inclusion criteria
A)
*BBS1*
ALO47	p.[R160Q]; [R160Q]	c.[479G→A]; [479G→A]	SV	PP, MT	–		Turkey	Yes (BBS1, BBS4)	No
P1	p.? ; ?	c.[1473+4A→G]; [1473+4A→G]	SV + S	MT (Ex14 splice site altered]	–		Tunisia	Yes^*	Yes
P9	p.? ; ?	c.[1110G→A]; [1110G→A]	SV + S	MT (Ex11 splice site altered]	AHI1/JBTS3: p.[R830W]; [=]	2.83%	Tunisia	Yes^*	No
AMK19	p.? ; [M390R]	c.[951+1G→A]; [1169T→G]	SV + S	MT (Ex10 splice site altered]; S	TTC21B/NPHP12: p.[R713I]; (=), BBS7: p.[D412G]; [=]	NF, 0.23%	NA	NA	No
P12	p.[A14Lfs^28] ; [A14Lfs^28]	c.[39del]; [39del]	SV + S	MT	–		Tunisia	Yes^*	Yes
P11	p.[R146^*]; [R146^*]	c.[436C→T]; [436C→T]	SV + S	MT	CCDC28B: Ex2 splice site altered (F110F]; [=]	2.07%	Tunisia	Yes^*	Yes
AIO57	p.[E224K]; [E224K]	c.[670G→A]; [670G→A]	SV	S, PP	NPHP3: p.[R1074H]; (=), ALMS1: p.[S2102L]; [=]	0.01%, 3.07%	Morocco	Yes (BBS1, BBS3, NPHP5, JBTS2)	No
*BBS2*
P2	p.? ; ?	c.[345+5G→A]; [345+5G→A]	SV + S	(Ex2 splice site altered]	–		Tunisia	Yes^*	Yes
AGL23	p.[H665Tfs^11]; [H665Tfs^11]	c.[1992del]; [1992del]	SV + S	MT	TTC21B/NPHP12: p.[R616C]; [=]	0.31%	India	Yes (ALMS1, NPHP1, NPHP3, NPHP6, NPHP8]	No
P7	p.[R189^*]; [R189^*]	c.[565C→T]; [565C→T]	SV + S	MT	NPHP4: p.[R674H]; [R674H]	NF	Tunisia	Yes^*	Yes
AKX44	p.[R272^*]; [R272^*]	c.[814C→T]; [814C→T]	SV	MT	SDCCAG8/BBS16: p.[Q505E]; [=]	NF	Algeria	Yes (BBS7, BBS12, NPHP8)	Yes
ALG76	p.[L209P]; [L209P]	c.[626T→C]; [626T→C]	SV + S	S, PP, MT	–		Turkey	Yes (BBS2, NPHP8)	Yes
*BBS3/ARL6*
ALG42	p.[del Ex1-3]; [del Ex1-3]	c.[(?_−30)_(123+?))del; [(?_−30)_(123+?)]del	SV + S	–	–		Turkey	Yes (ALMS1, BBS3, BBS4, BBS9, BBS14, NPHP2, NPHP3)	Yes
*BBS4*
P3	p.[del Ex4-5-6] ; [del Ex4-5-6]	c.[(157−?)_(405+?)del]; [(157−?)_(405+?)del] (g.[24029..24285]_(33661..34498))del];g.[24029..24285]_(33661..34498))del]	SV + S	–	BBS5: p.[N184S]; [=]	0.57%	Tunisia	Yes^*	Yes
*BBS5*
P13	p.[L50R]; [L50R]	c.[149T→G]; [149T→G]	SV + S	S, PP, MT	–		Tunisia	Yes^*	Yes
ALG5	p.[R138H]; [R138H]	c.[413G→A]; [413G→A]	SV + S	S, PP, MT	–		France	No	No
*BBS6/MKKS*
P10	p.? ; ?	c.[1272+1G→A]; [1272+1G→A]	SV + S	MT (Ex5 splice site altered)	NPHP4: p.[R959Q]; [=]	NF	Tunisia	Yes^*	Yes
*BBS8/TTC8*
P14	p.? ; ?	c.[329+1G→A]; [329+1G→A]	SV + S	MT (Ex4 splice site altered]	AHI1/JBTS3: p.[R830W]; [=]	2.83%	Tunisia	Yes^*	Yes
*BBS10*
P8	p.[S396Lfs^6]; [S396Lfs^6]	c.[1171_1181dupGCATTTATACC]; [1171–1181dupGCATTTATACC]	SV + S	MT			Tunisia	Yes^*	Yes
JSL	p.[V707^*]; [R95S]	c.[2119–2120delGT]; [285A→T]	SV + S	MT; S, PP, MT			NA	NA	NA
BBH64	p.[T483Nfs^*8]; [?]	c.[1448–1452delCTCAA]; [?]	S	MT	CCDC28B: Ex2 splice site altered (F110F) ; (=]	2.07%	NA	No	No
AMR64	p.[L414S]; [L414S]	c.[1241T→C]; [1241T→C]	SV	S, PP	CCDC28B: Ex2 splice site altered (F110F) ; (=]	2.07%	NA	NA	Yes
AKR68	p.[L414S]; [L414S]	c.[1241T→C]; [1241T→C]	SV	S, PP	CEP290/BBS14: p.[K1870Nfs^*4]; [=]	NF	NA	Yes (BBS10, JBTS3)	No
*ALMS1*
AIA84	p.[E1114Rfs^9); (E1114Rfs^9]	c.[3340del]; [3340del]	SV	MT			Turkey	Yes (ALMS1, BBS14)	Yes
AKO26	p.[R3629^*]; [R3629^*]	c.[10885C→T]; [10885C→T]	SV + S	MT	WDPCP/BBS15: p.[V329M]; (=), AHI1/JBTS3: p.[R548H]; [=]	0.13%, 1.65%	France	Yes (ALMS1, BBS12)	Yes
ALB64	p.[S577^]; [S577^]	c.[1730C→G]; [1730C→G]	SV + S	MT	IQCB1/NPHP5: p.[E481K]; [=]	0.17%	Portugal	Yes (BBS7, BBS12, BBS14, ALMS1)	No

Patient#	Gene	Potential mutations (p.)	Potential mutations (c.)	Frequency in EVSdb	Mutation, as predicted by (among SIFT, PPhen2 & mutation T@ster)	Geographic origin	Consanguinity	BBS inclusion criteria
B)
AHR2	*BBS3/ARL6*	p.[D179N]; [=]	c.[535G→A]; [=]	NF	MT (Ex8 splice site altered]	Reunion	Yes. BBS3, JBTS3	No
AIY87	*BBS9*	p.[P641S]; [=]	c.[1921C→T]; [=]	NF	S, PP, MT	NA	Yes: BBS5, ALMS1, NPHP12, NPHP5, BBS14	No
AKE98	*ALMS1*	p.[P2679L]; [P2679L]	c.[8036C→T]; [8036C→T]	NF	S, P	Melanesia	Yes: BBS12, BBS9, CEP290, NPHP1, MKS1	Yes
	*NPHP4*	p.[V1228G]; [=]	c.[3683T→G]; [=]	0.10%	S, P
	*NPHP3*	p.[A519G]; [=]	c.[1556C→G]; [=]	NF	P, MT
	*INVS/NPHP2*	p.[N1061Kfs^20]; [N1061Kfs^20]	c.[3176_3177insA]; [3176_3177insA]	NF	–
AIX45	*TMEM67/ NPHP11*	p.[Y486C]; [=]	c.[1457A→G]; [=]	0.01%	P, MT	NA	Yes	Yes
AMA28	*MKKS/BBS6*	p.[A242S]; [=]	c.[724G→T]; [=]	0.58%	S, P	France	No	Yes
	*NPHP1*	p.[E569G]; [=]	c.[1706A→G]; [=]	NF	S, P, MT
AMO77	*TTC21B/ NPHP12*	p.[R863W]; [=]	c.[2587C→T]; [=]	0.23%	S, P, MT	NA	NA	Yes
AHL86	*AHI1/JBTS3*	p.[R830W]; [=]	c.[2488C→T]; [=]	2.83%	S, P, MT	NA	NA	No
	*INVS/NPHP2*	p.[T122P]; [=]	c.[364A→C]; [=]	NF	S, P, MT
ALA60						Caucasian	No	Yes
AKT96						France	No	No
AMT10						France	No	Yes
AIF95						NA	No	No
AKK32						France	No	No

↵* Patients from consanguineous families, but not genotyped on affymetrix SNP arrays. In bold: previously reported mutations in other studies. Mutation prediction software equivalents: possibly/probably damaging (polyphen2), damaging (SIFT), disease causing (mutation taster). Ex, exon; S, SIFT; PP, PolyPhen2; MT, mutation T@ster.
(?): The exact nature of the second heterogeneous mutation could not be identified by high-throughput sequencing. An abnormal loss of coverage is observed at the very end of BBS10. The exact nature of this apparently complex mutation is still under investigation by direct sequencing, but appears to involve an alu insertion coupled with a duplication/inversion. Amino acid conservation of non-reported missense mutations is shown in supplementary figure S4. SV: Sanger validation; S: segregation validated.
Consanguinity was documented by clinicians, and in most cases, BBS patients from consanguineous families were genotyped on Affymetrix 250k SNP arrays. When so, BBS and other targeted genes located within homozygous regions are thus indicated in ( ).