TABLE 3.

Recessive variants in ASD patients detected in genes with substantial evidence of involvement in ASD.

Patient ID	Protein	Gene	CADD score	dbSNP ID*	gnomAD frequency **%	gnomAD homozygous count	QCI computed pathogenicity$	SFARI genes score	ASD Evidence∀
1	p.R2814Q	VPS13B NM_017890.5	32	148333124	0.0002	0	VUS	1	Yu et al. (2013)
1	p.E122Q	PIGN NM_012327.6	26.7	200756305	0.07	1	VUS	NA	Maydan et al. (2011)
55	p.R2814Q	VPS13B NM_017890.5	32	148333124	0.0002	0	VUS	1
55	p.E122Q	PIGN NM_012327.6	26.7	200756305	0.07	1	VUS	NA
56	p.R2814Q	VPS13B NM_017890.5	32	148333124	0.0002	0	VUS	1
56	p.E122Q	PIGN NM_012327.6	26.7	200756305	0.07	1	VUS	NA
5	p.V1594F	RYR2 NM_001035.3	24.3	NA	NA	NA	VUS	NA	Hamdan et al. (2014)
6	p.V3189fs*7	DNAH3 NM_017539.2	<10	NA	NA	NA	VUS	2	Guo et al. (2017)
6	p.Q556H	TSPYL2 NM_022117.4	17.95	NA	NA	NA	VUS	NA	Moey et al. (2016)
57	p.Q556H	TSPYL2 NM_022117.4	17.95	NA	NA	NA	VUS	NA
11	p.T2359N	SYNE NM_182961.41	22.8	142747430	0.014	0	VUS	2	Jiang et al. (2013)
11	p.Q107L	TGIF1 NM_174886.3	23.1	28939693	0.031	0	Likely Benign	NA	Latypova et al. (2021)
13	p.D267G	CADPS2 NM_139175.2	24.9	773840565	NA	NA	VUS	2	Okamoto et al. (2011), Grabowski et al. (2017)
15	p.F82L	UPF3B NM_080632.3	23.6	NA	NA	NA	VUS	1	Tejada et al. (2019)
17	p.R332W	CHRNG NM_005199.5	25.7	567899708	0.066	4	VUS	NA	Kalınlı et al. (2019)
18	p.V212A	AMT NM_001164712.2	27.1	201141125	0.0003	0	VUS	2	Yu et al. (2013)
21	p.A241fs	KDM5C NM_001353981.2	NA	NA	NA	NA	VUS	1	Moey et al. (2016)
22	p.A194T	FH NM_000143.4	29.9	587782215	0.006	0	VUS	NA	Luo et al. (2020)
30	p.R1060H	ASTN1 NM_207108.3	26	201593312	0.007	0	VUS	NA	Lionel et al. (2014)
31	p.N2868Y	LYST NM_000081.4	25.9	NA	NA	NA	VUS	NA	Manoli et al. (2010)
32	p.P537S	EPHA6 NM_001080448.3	26.8	1463599601	0.001	0	VUS	NA	Schneider et al. (2015)
32	p.R474C	TECTA NM_005422.4	27.6	756326790	0.002	0	VUS	2	Toma et al. (2014)
32	p.P1087S	ROBO2 NM_002942.5	21.6	0.00006409	0.00007	NA	VUS	2	Connolly et al. (2017)
47	p.G355E	TRAF3IP1 NM_015650.4	29.60	560016209	0.012	0	VUS	NA	Bizet et al. (2015)
49	p.M1V	C12orf57 NM_001301834.1	21.9	587776954	0.003	0	VUS	S	Akizu et al. (2013)
50	p.M1V	C12orf57 NM_001301834.1	21.9	587776954	0.003	0	VUS	S
50	p.E79G	WNK3 NM_020922.5	22.9	NA	NA	NA	VUS	2	Qiao et al. (2008)

Summary of 21 recessive variants detected in 19 patients with ASD., Identified variant(s) per family separated by borderline. Reported genes as the Reference Sequence (RefSeq) name and accession numbers.NA, indicates novel variants not previously reported in the gnomAD or SFARI, databases. ** Reported gnomAD, frequency was observed out of 141,456 individuals. ^*** SFARI, Gene Score is a ranking system that estimates the strength of evidence of the reported ASD, gene in the SFARI, database, with S = ASD, syndromic category and scores ranging from 1 to 3, with 1 being the higher score indicating the stronger association evidence with ASD. ^$ The imputed ACMG, classification criteria used in QCI, Interpret; VUS, is a variant of uncertain significance. ∀ Genes have been previously associated with or reported in patients with ASD, or neurodevelopmental disorders.