. 2018 Oct 9;13(10):e0205422. doi: 10.1371/journal.pone.0205422

Table 3. Spectrum of detected genetic variants in Serbian patients with PCD.

GENE	dbSNP ID	Genomic coordinates	Genetic variants		Allele freq Eur (%)^a	ACMG classification^b	DANN^c	SIFT/Provean^d	Patient ID	Reference from HGMD/ClinVar
GENE	dbSNP ID	Genomic coordinates	Nucleotide change	Amino acid change	Allele freq Eur (%)^a	ACMG classification^b	DANN^c	SIFT/Provean^d	Patient ID	Reference from HGMD/ClinVar
*CCDC40*	rs397515393	chr17-78013765	c. 248delC	p.Ala83ValfsTer84	0	Pathogenic (PVS1, PS3)	NA	Not applicable	P5	[25]
*CCDC40*	rs747233125	chr17-78060006	c. 2440C>T	p.Arg814Ter	0	Pathogenic (PVS1, PM2, PM4, PP2)	0.9899	Damaging	P13, P14	[26]
*DNAI1*	-	chr9-34500765	c. 947_948insG	p.Thr318TyrfsTer11	unknown	NA^e	NA	Not applicable	P9, P10	novel
	rs867262419	chr9-34512140	c.1345_1349delCTTAA	p.Asn450LeufsTer6	0	NA^e	NA	Not applicable	P21	novel
	-	chr9-34514506	c.1684G>A	p.Asp562Asn	0	Uncertain Significance (PM2, PP3)	0.9993	Damaging	P21	novel
*DNAH5*	-	chr5-13864748	c. 4356-2A>G	-	0	Pathogenic (PVS1, PM2, PP3)	0.9949	Not applicable	P4	novel
	-	chr5-13809281	c.7624T>C	p.Trp2542Arg	0	Uncertain Significance (PM2, PP3)	0.9919	Damaging	P4	novel
	rs137949961	chr5-13777417	c.8999G>A	p.Arg3000Gln	0.26	Uncertain Significance (PP3)	0.9989	Damaging	P6	ClinVar 219734
	rs140782270	chr5-13914743	c.1206T>A	p.Asn402Lys	0.13	Uncertain Significance (PM2, PP3)	0.9979	Damaging	P20	ClinVar 188080
	-	chr 5–13718980	c.8012A>G	p.Gln2701Arg	0	NA^e	NA	Damaging	P20	novel
*DNAL1*	rs751754576	chr14-74154044	c.347A>T	p.Lys116IIe	0	Uncertain Significance (PM2, PP3)	0.9926	Damaging	P1	novel
	rs535885451	chr14-74154047	c.350T>G	p.Leu117Trp	0	Uncertain Significance (PM1, PM2, PP3)	NA	Damaging	P1	novel
	-	chr14-74156171	c.485G>A	p.Trp162Ter	0	Uncertain Significance (PM2, PM4, PP3)	0.9946	Damaging	P1	novel
*LRRC6*	rs200906172	chr8-133673857	c.27T>G	p.Ile9Met	0	Uncertain Significance (PM2, BS4)	0.9907	Damaging	P2	ClinVar 473106
*DNAH11*	-	chr7- 21788220	c.8533C>G	p. Arg2845Gly	0.13	Likely benign (PM1, PM2, PP5, BP1, BP4, BP6)	0.9813	Damaging	P3	ClinVar 359658
*SPAG16*	rs61752199	chr2-214354811	c.1067G>A	p.Ser356Asn	2	Uncertain Significance (PM1, BS1)	0.9964	Damaging	P8	novel
*SPAG16*	-	chr2-214174834	c. 331G>A	p.Asp111Asn	0	Uncertain Significance (PP3)	0.9993	Damaging	P11	novel
*SPAG17*	rs17185492	chr1-118644524	c. 473A>T	p.Glu158Val	17	Benign (PP2, BS1, BA1,)	0.9927	Damaging	P8, P11	novel

All identified genetic variants were numbered based on cDNA reference sequences and as recommended by the Human Genome Variation Society (http://www.hgvs.org/mutnomen). RefSeq accession numbers for the sequences used in the analyses were as follows: NM_017950.3 (CCDC40), NM_012144.2 (DNAI1), NM_001369.2 (DNAH5), NM_031427.3 (DNAL1), NM_001277115.1 (DNAH11), NM_012472.3 (LRRC6), NM_024532.4 (SPAG16), and NM_206996.2 (SPAG17).

^a According to VarSome (1000 Genome Project, ExaC)

^b ACMG: American College of Medical Genetics and Genomics.

^c Deleterious annotation of genetic variants using neural networks (DANN). The value range is from 0 to 1, with 1 given to the variants predicted to be the most damaging.

^d SIFT (sorts intolerant from tolerant) is an in silico prediction tool based on sequence homology derived from closely related sequences collected through PSI-BLAST. Provean (Protein Variation Effect Analyzer) is an in silico tool that predicts how nonsynonymous or in-frame indel variant will affect a protein's biological function.

^e This variant does not have automated ACMG/AMP 2015 interpretation