Rare and common coding variants in lipid metabolism-related genes and their association with coronary artery disease

Li, Wei; Wang, Yongyi; Huang, Ritai; Lian, Feng; Xu, Genxing; Wang, Weijun; Xue, Song

doi:10.1186/s12872-024-03759-5

Table 4 Rare nonsynonymous variants identified in this study

From: Rare and common coding variants in lipid metabolism-related genes and their association with coronary artery disease

Gene	chr	pos	Ref/Alt	DNA	AA	novel	Effect	dbSNP ID	MAF (gnomAD)	Number of variants		SIFT	sift_class	PolyPhen	polyphen_class	ACMG
Gene	chr	pos	Ref/Alt	DNA	AA	novel	Effect	dbSNP ID	MAF (gnomAD)	case	control	SIFT	sift_class	PolyPhen	polyphen_class	ACMG
ANGPTL3	1	62,598,787	T/C	c.587T > C	p.Ile196Thr		missense variant	rs201826477	0.00001974	0	1	0.01	deleterious	0.998	probably damaging	VUS
ANGPTL3	1	62,598,796	T/C	c.596T > C	p.Ile199Thr		missense variant	rs112068132	0.00004609	1	1	0	deleterious	0.197	benign	VUS
ANGPTL4	19	8,364,461	G/A	c.140G > A	p.Gly47Glu	yes	missense variant		/	1	0	0.003	deleterious	1	probably damaging	VUS
ANGPTL4	19	8,371,453	G/A	c.970G > A	p.Val324Ile		missense variant	rs200918932	0.00006572	1	0	0.1	tolerated	0.023	benign	VUS
ANGPTL4	19	8,373,780	A/G	c.1115 A > G	p.Gln372Arg		missense variant	rs756440132	0.0001248	0	1	0.3	tolerated	0.003	benign	VUS
APOA1	11	116,837,116	G/C	c.85 C > G	p.Gln29Glu		missense variant	rs1254205437(G/T)	/	1	0	0.11	tolerated	0.005	benign	VUS
APOA1	11	116,837,080	C/A	c.121G > T	p.Val41Leu		missense variant	rs201148448	0.000006569	1	1	0.07	tolerated	0.001	benign	VUS
APOA1	11	116,837,053	C/T	c.148G > A	p.Gly50Ser		missense variant	rs28931574	0.00000657	0	1	0.08	tolerated	0.998	probably damaging	VUS
APOA1	11	116,836,173	G/T	c.439 C > A	p.Arg147Ser		missense variant	rs1591330063(G/C)	/	1	0	0.649	tolerated	0.101	benign	VUS
APOA5	11	116,791,670	C/A	c.77G > T	p.Gly26Val		missense variant	rs548745995	/	1	0	0.19	tolerated	0.642	possibly damaging	VUS
APOA5	11	116,790,166	G/C	c.1063 C > G	p.Leu355Val		missense variant	rs556600766(G/A)	/	1	0	0.005	deleterious	0.124	benign	VUS
APOC1	19	44,916,230	T/TCTTGGAT	c.99_105dup	p.Lys36LeufsTer3		frameshift variant	rs767630355	0.00001978	0	1	-	-	-	-	VUS
APOC1	19	44,916,292	G/A	c.161G > A	p.Arg54His		missense variant	rs369438021	0.00003289	1	0	0.6	tolerated	0	benign	VUS
CETP	16	56,962,013	C/G	c.34 C > G	p.Leu12Val		missense variant	rs1460617147(C/T)	/	0	1	0.294	tolerated	0.772	possibly damaging	VUS
CETP	16	56,969,935	G/A	c.461G > A	p.Arg154Gln		missense variant	rs184615182	0.00001971	1	0	0.37	tolerated	0.003	benign	VUS
LDLR	19	11,105,250	G/A	c.344G > A	p.Arg115His		missense variant	rs201102461	0.00008546	0	1	0.04	deleterious	0.102	benign	VUS
LDLR	19	11,105,408	G/A	c.502G > A	p.Asp168Asn		missense variant	rs200727689^a	0.000006569	1	0	0.03	deleterious	1	probably damaging	LP
LDLR	19	11,105,492	C/G	c.586 C > G	p.Pro196Ala		missense variant	rs1013147010	/	0	1	0.194	tolerated	0.988	probably damaging	VUS
LDLR	19	11,105,505	T/G	c.599T > G	p.Phe200Cys		missense variant	rs879254586	/	1	0	0.18	tolerated	0.779	possibly damaging	VUS
LDLR	19	11,116,900	C/T	c.1747 C > T	p.His583Tyr		missense variant	rs730882109^b	0.00003286	1	0	0	deleterious	1	probably damaging	VUS
LIPC	15	58,563,522	G/A	c.1187G > A	p.Ser396Asn		missense variant	rs1015457944	0.00000657	0	1	0.26	tolerated	0.725	possibly damaging	VUS
LIPC	15	58,563,665	C/T	c.1330 C > T	p.Arg444Cys		missense variant	rs573340043	0.00004599	1	0	0.06	tolerated	0.809	possibly damaging	VUS
LPL	8	19,951,811	G/A	c.292G > A	p.Ala98Thr		missense variant	rs145657341	0.00006574	1	0	0.04	deleterious	1	probably damaging	VUS
LPL	8	19,954,327	G/A	c.749G > A	p.Arg250His		missense variant	rs750750025	0.00001314	0	1	0.15	tolerated	0.767	possibly damaging	VUS
LPL	8	19,955,927	G/A	c.862G > A	p.Ala288Thr		missense variant	rs1800011	0.00001314	1	0	0	deleterious	0.933	probably damaging	VUS
PCSK9	1	55,046,626	C/T	c.503 C > T	p.Ala168Val		missense variant	rs770592607	0.00001973	0	1	0.33	tolerated	0.003	benign	VUS
PCSK9	1	55,052,650	G/A	c.658G > A	p.Ala220Thr		missense variant splice region variant	rs768795323	0.00001314	1	0	0.03	deleterious	0.313	benign	VUS
PCSK9	1	55,052,698	G/A	c.706G > A	p.Gly236Ser		missense variant	rs149489325	0.00003284	0	1	0.04	deleterious	0.957	probably damaging	VUS
PCSK9	1	55,052,739	C/A	c.747 C > A	p.Ser249Arg		missense variant	rs768846693	0.00001314	1	0	0.01	deleterious	0.996	probably damaging	VUS
PCSK9	1	55,061,420	C/T	c.1727 C > T	p.Pro576Leu		missense variant	rs72646525	0.00005255	1	0	0.19	tolerated	0.011	benign	VUS
SCARB1	12	124,863,717	C/T	c.4G > A	p.Gly2Ser		missense variant	rs4238001	0.08561	0	1	0.1	tolerated	0.994	probably damaging	B
SCARB1	12	124,811,911	T/C	c.685 A > G	p.Ser229Gly		missense variant	rs10396213	0.0001184	1	1	0.09	tolerated	0.41	benign	VUS
SCARB1	12	124,811,899	C/T	c.697G > A	p.Leu233Phe	yes	missense variant		/	1	0	0.147	tolerated	0.903	possibly damaging	VUS

chr, chromosome; pos, genomic position based on GRCh38.p13; Ref/Alt, reference allele/alternative allele; MAF, minor allele frequency in the Genome Aggregation Database; ACMG, variant classification: pathogenic (P), likely pathogenic (LP), variant of uncertain significance (VUS), likely benign (LB) and benign (B)
^aAnnotated as Pathogenic/Likely pathogenic in the ClinVar database (ncbi.nlm.nih.gov/clinvar/variation/183,136/)
^bAnnotated as Conflicting interpretations of pathogenicity in the ClinVar database (ncbi.nlm.nih.gov/clinvar/variation/200,921/)

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ISSN: 1471-2261

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