Novel clinical, molecular and bioinformatics insights into the genetic background of autism

Talli, Ioanna; Dovrolis, Nikolas; Oulas, Anastasis; Stavrakaki, Stavroula; Makedou, Kali; Spyrou, George M.; Maroulakou, Ioanna

doi:10.1186/s40246-022-00415-x

Human Genomics

Table 4 Total of 84 unique top variants for severe vs non-severe molecular classification selected from LOOCV

From: Novel clinical, molecular and bioinformatics insights into the genetic background of autism

rs_ids	gene	chrom	start	end	aa_change	impact	aaf_1kg_all
rs76264143	AGRN	chr1	982843	982844		intron variant	0.04
rs2748972	C1orf222	chr1	1891476	1891477	S/P	missense variant	0.13
rs1763347	COL11A1	chr1	103354427	103354428	G	synonymous variant	0.62
rs12119908	LRRC71	chr1	156902221	156902222	R/H	missense variant	0.20
rs822431	LRRC71	chr1	156902280	156902281	S/A	missense variant	0.28
rs4570419	ARHGEF11	chr1	156907030	156907031		intron variant	0.22
rs2275199	ARHGEF11	chr1	156909694	156909695	N	synonymous variant	0.19
rs2275206	ARHGEF11	chr1	156939066	156939067		splice region variant	0.18
rs12063382	ACTN2	chr1	236925843	236925844	S	synonymous variant	0.20
rs1061157	BMPR2	chr2	203421198	203421199	R	synonymous variant	0.12
rs2921705	NGEF	chr2	233792564	233792565		intron variant	0.17
rs34116584	AGXT	chr2	241808313	241808314	P/L	missense variant	0.08
rs66494441	AGXT	chr2	241808462	241808463		intron variant	-1.00
rs34726174	AC104809.3	chr2	241871846	241871847	G/R	missense variant	0.13
rs4683158	FYCO1	chr3	46010076	46010077	R/Q	missense variant	0.93
rs4682801	FYCO1	chr3	46021217	46021218	R	synonymous variant	0.76
rs12492868	PRSS50	chr3	46755936	46755937	T	synonymous variant	0.38
rs34788938	PRSS50	chr3	46759009	46759010	Q/P	missense variant	0.31
rs56260729	TNK2	chr3	195594949	195594950	P/L	missense variant	0.12
rs2070018	FGA	chr4	155508626	155508627		intron variant	0.89
rs2271704	MROH2B	chr5	41008779	41008780	L/P	missense variant	0.78
rs316408	ZNF131	chr5	43066773	43066774		upstream gene variant	0.67
rs3749787	NMUR2	chr5	151784182	151784183	L	synonymous variant	0.23
rs7965	MRPL22	chr5	154346324	154346325	K	synonymous variant	0.06
rs2251702	C6orf229	chr6	24797646	24797647	H	synonymous variant	0.52
rs62000984	HIST1H1A	chr6	26017674	26017675	L	synonymous variant	0.09
rs2969042	IQCE	chr7	2612293	2612294		intron variant	0.26
rs2969043	IQCE	chr7	2612294	2612295		intron variant	0.26
rs10264715	NPC1L1	chr7	44555405	44555406	Y	synonymous variant	0.08
rs34947817	OR2A12	chr7	143792990	143792991	S/N	missense variant	0.11
rs10230228	OR2A2	chr7	143806687	143806688	Q/K	missense variant	0.16
rs10252253	OR2A2	chr7	143807303	143807304	L/P	missense variant	0.16
rs7791767	SSPO	chr7	149513151	149513152		non coding transcript exon variant	0.21
rs10250401	SSPO	chr7	149515102	149515103		non coding transcript exon variant	0.20
rs622106	KIAA1456	chr8	12878676	12878677	A	synonymous variant	0.71
rs3739310	KIAA1456	chr8	12878806	12878807	C/G	missense variant	0.65
rs503550	KIAA1456	chr8	12879061	12879062	L	synonymous variant	0.71
rs608909	KIAA1456	chr8	12879333	12879334	V	synonymous variant	0.71
rs608052	KIAA1456	chr8	12879538	12879539	R/G	missense variant	0.70
rs7826836	KIAA1456	chr8	12888907	12888908	S/A	missense variant	0.67
rs1799931	NAT2	chr8	18258369	18258370	G/E	missense variant	0.08
rs16892543	MMP16	chr8	89340161	89340162	P	synonymous variant	0.21
rs1328285	CCDC171	chr9	15922136	15922137		intron variant	0.88
rs62559879	ANKRD18B	chr9	33566233	33566234	A	synonymous variant	0.16
rs11791445	C9orf84	chr9	114476747	114476748	M/L	missense variant	0.14
rs12352352	C9orf84	chr9	114484782	114484783	P	synonymous variant	0.14
rs10512411	C9orf84	chr9	114490228	114490229	A	synonymous variant	0.14
rs73563696	NDOR1	chr9	140108856	140108857	S	synonymous variant	0.14
rs76301014	OR6M1	chr11	123676387	123676388	R/C	missense variant	0.12
rs1298463	ZFC3H1	chr12	72013831	72013832	A	synonymous variant	0.51
rs6538681	CCDC38	chr12	96284649	96284650	A	synonymous variant	0.75
rs2985989	COG3	chr13	46108853	46108854	L	synonymous variant	0.81
rs12586727	TTC6	chr14	38218342	38218343	I/V	missense variant	0.21
rs2229518	TJP1	chr15	30008888	30008889	A	synonymous variant	0.79
rs12904906	ANXA2	chr15	60689994	60689995		intron variant	0.11
rs714181	SLX4	chr16	3640273	3640274	P/L	missense variant	0.24
rs3743690	ACSM1	chr16	20635417	20635418	K	splice region variant	0.18
rs2301672	ACSM1	chr16	20636813	20636814	S	synonymous variant	0.18
rs12922670	CDH15	chr16	89234947	89234948		upstream gene variant	0.06
rs9890913	ASIC2	chr17	31618550	31618551	L	synonymous variant	0.13
rs77247739	TSEN54	chr17	73518327	73518328	Q/P	missense variant	0.07
rs3744183	ENGASE	chr17	77075666	77075667	I	synonymous variant	0.42
rs3744184	ENGASE	chr17	77075669	77075670	P	synonymous variant	0.41
rs3744185	ENGASE	chr17	77075672	77075673	P	synonymous variant	0.42
rs3744186	ENGASE	chr17	77076439	77076440	S	synonymous variant	0.39
rs3752042	CCDC40	chr17	78010412	78010413		upstream gene variant	0.12
rs11082414	SETBP1	chr18	42529995	42529996	V/L	missense variant	0.16
rs78047294	MED16	chr19	871986	871987	T	synonymous variant	0.17
rs17445374	ZNF431	chr19	21326357	21326358	D/G	missense variant	0.14
rs2280746	USF2	chr19	35770055	35770056	V/I	missense variant	0.20
rs12104393	CCDC114	chr19	48801217	48801218		intron variant	0.15
rs2242463	CCDC114	chr19	48806976	48806977	D	synonymous variant	0.15
rs28582401	CCDC114	chr19	48807366	48807367	L	synonymous variant	0.15
rs2617667	ZNF813	chr19	53993669	53993670	A/T	missense variant	0.30
rs17373408	BPIFB6	chr20	31624299	31624300	S	synonymous variant	0.07
rs2070326	BPIFB4	chr20	31678533	31678534	L	synonymous variant	0.22
rs3787220	NCOA6	chr20	33337750	33337751	P	synonymous variant	0.80
rs6060043	NCOA6	chr20	33364583	33364584		intron variant	0.81
rs4811888	ZBP1	chr20	56182182	56182183	Q/E	missense variant	0.13
rs5939319	XG	chrX	2700156	2700157	D/N	missense variant	0.04
rs7049300	NLGN4X	chrX	5821785	5821786	T	synonymous variant	0.12
rs6150	NR0B1	chrX	30327366	30327367	C	synonymous variant	0.10
rs5952285	KDM6A	chrX	44913051	44913052		intron variant	0.24
rs5952682	KDM6A	chrX	44966794	44966795		intron variant	0.24

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