Table 1. P and PL variants in WM... | American Society of Hematology

Table 1.

P and PL variants in WM families

Patient ID	Chr	Position	Variant ID	Ref	Var	Gene symbol	Mode of inheritance	Variant pathogenicity	ClinVariant ID	AF_popmax	MetaSVM	REVEL	CADD phred	spliceAI	Tier
Fam20_Pt4	17	7577568	rs730882005	C	A	*TP53*	AD	P	376574	.	Damaging	0.958	31	Tolerated	1
Fam26_Pt2	2	25469529	rs1234388246	G	GC	*DNMT3A*	AD	P	985294	.	.	.	.	Tolerated	1
Fam41_Pt1	9	139412682	rs1290954710	C	T	*NOTCH1*	AD	LP	445806	.	Damaging	0.439	28.9	Tolerated	1
Fam41_Pt2	9	139412682	rs1290954710	C	T	*NOTCH1*	AD	LP	445806	.	Damaging	0.439	28.9	Tolerated	1
Fam54_Pt2	17	7577120	rs28934576	C	T	*TP53*	AD	P	12366	.	Damaging	0.868	23.9	Tolerated	1
Fam55_Pt1	17	48703927	rs767121010	G	A	*CACNA1G*	AD	LP	426883	.	Tolerated	0.075	23.5	Tolerated	1
Fam60_Pt1	12	112888193	rs397516801	A	G	*PTPN11*	AD	P	44603	.	Damaging	0.668	25.9	Tolerated	1
Fam37_Pt1	20	35555631	rs515726146	A	AC	*SAMHD1*	AD, AR	P	126413	.	.	.	.	Tolerated	1
Fam37_Pt2	20	35555631	rs515726146	A	AC	*SAMHD1*	AD, AR	P	126413	.	.	.	.	Tolerated	1
Fam37_Pt3	9	111662096	rs111033171	A	G	*ELP1*	AD, AR	P	6085	0.00006479	.	.	.	Tolerated	1
Fam37_Pt4	9	111662096	rs111033171	A	G	*ELP1*	AD, AR	P	6085	0.00006479	.	.	.	Tolerated	1
Fam2_Pt1	9	111662096	rs111033171	A	G	*ELP1*	AD, AR	P	6085	0.00006479	.	.	.	Tolerated	1
Fam2_Pt2	9	111662096	rs111033171	A	G	*ELP1*	AD, AR	P	6085	0.00006479	.	.	.	Tolerated	1
Fam2_Pt4	9	111662096	rs111033171	A	G	*ELP1*	AD, AR	P	6085	0.00006479	.	.	.	Tolerated	1
Fam3_Pt1	3	48508395	rs72556554	G	A	*TREX1*	AD, AR	P	.	0.0003	Damaging	0.828	31	Tolerated	1
Fam3_Pt2	3	48508395	rs72556554	G	A	*TREX1*	AD, AR	P	4179	0.0003	Damaging	0.828	31	Tolerated	1
Fam3_Pt3	3	48508395	rs72556554	G	A	*TREX1*	AD, AR	P	4179	0.0003	Damaging	0.828	31	Tolerated	1
Fam24_Pt1	17	40693092	rs104894592	C	T	*NAGLU*	AD, AR	P	1562	0.0001	.	.	35	Tolerated	1
Fam32_Pt3	7	6029587	rs587780064	C	A	*PMS2*	AD, AR	P	127802	.	.	.	35	Damaging	1
Fam44_Pt3	1	169500043	rs118203907	T	C	F5	AD, AR	P	649	.	Damaging	0.972	31	Tolerated	1
Fam45_Pt1	8	55537568	rs760689800	C	T	*RP1*	AD, AR	P	1065648	.	.	.	25.2	Tolerated	1
Fam45_Pt2	8	55537568	rs760689800	C	T	*RP1*	AD, AR	P	1065648	.	.	.	25.2	Tolerated	1
Fam48_Pt1	7	124481134	.	G	T	*POT1*	AD, AR	P	1042147	.	.	.	38	Tolerated	1
Fam53_Pt1	X	153363118	rs179363901	G	A	*MECP2*	XL	P	11845	.	Tolerated	0.229	22.4	Tolerated	1
Fam2_Pt1	12	49312533	rs1272967209	GTA	G	CCDC65	AR	P	88685	.	.	.	.	Tolerated	2
Fam7_Pt2	1	63868019	rs199682486	G	A	ALG6	AR	P	95529	0.0008	.	.	.	Damaging	2
Fam3_Pt3	2	31596738	rs148412639	C	G	XDH	AR	LP	505602	0.0008	.	.	34	Damaging	2
Fam4_Pt2	1	17313566	rs765632065	AG	A	ATP13A2	AR	P	465253	0.0012	.	.	.	Tolerated	2
Fam6_Pt2	15	56736015	rs185005213	G	A	MNS1	AR	P	973691	0.0001	.	.	37	Tolerated	2
Fam6_Pt3	15	56736015	rs185005213	G	A	MNS1	AR	P	973691	0.0001	.	.	37	Tolerated	2
Fam10_Pt1	8	67986544	rs766020802	CAA	C	CSPP1	AR	P	575640	0.0001	.	.	.	Tolerated	2
Fam10_Pt3	8	67986544	rs766020802	CAA	C	CSPP1	AR	P	575640	0.0001	.	.	.	Tolerated	2
Fam11_Pt1	1	43221287	rs118203996	G	A	P3H1	AR	P	1258	.	.	.	36	Tolerated	2
Fam11_Pt2	1	43221287	rs118203996	G	A	P3H1	AR	P	1258	.	.	.	36	Tolerated	2
Fam14_Pt2	1	27121547	rs139073416	C	A	PIGV	AR	P	1284	0.0001	Damaging	0.83	25.1	Tolerated	2
Fam14_Pt3	6	135754219	rs372659908	G	A	AHI1	AR	P	217525	0.00006483	.	.	36	Tolerated	2
Fam14_Pt6	11	88070745	rs587777533	A	C	CTSC	AR	P	139655	0.0001	.	.	36	Tolerated	2
Fam19_Pt1	2	26644264	rs142371860	C	T	DRC1	AR	P	55840	0.0006	.	.	36	Tolerated	2
Fam19_Pt2	2	26644264	rs142371860	C	T	DRC1	AR	P	55840	0.0006	.	.	36	Tolerated	2
Fam20_Pt1	11	68548130	rs80356779	G	A	CPT1A	AR	P	65644	0.0012	Damaging	0.785	24.8	Tolerated	2
Fam22_Pt1	10	104590667	rs777638364	C	T	CYP17A1	AR	P	1338524	.	Damaging	0.908	31	Tolerated	2
Fam24_Pt1	19	44012925	rs761661864	A	C	ETHE1	AR	LP	577939	.	.	.	35	Damaging	2
Fam24_Pt2	19	44012925	rs761661864	A	C	ETHE1	AR	LP	577939	.	.	.	35	Damaging	2
Fam27_Pt1	8	68030481	rs766633448	A	C	CSPP1	AR	LP	1464866	.	.	.	32	Damaging	2
Fam27_Pt1	6	74348214	rs727504156	TG	T	SLC17A5	AR	P	167693	0.0001	.	.	.	Tolerated	2
Fam27_Pt2	17	18058028	rs184435771	G	A	MYO15A	AR	P	228276	0.0002	Damaging	0.89	32	Tolerated	2
Fam27_Pt2	6	74348214	rs727504156	TG	T	SLC17A5	AR	P	167693	0.0001	.	.	.	Tolerated	2
Fam29_Pt1	16	88876475	rs745594160	T	TA	APRT	AR	P	203396	0.0001	.	.	.	Tolerated	2
Fam34_Pt2	17	8076835	rs201558321	T	C	SNORD118	AR	P	929280	.	.	.	.	Tolerated	2
Fam35_Pt1	3	52409343	rs762545991	T	TG	DNAH1	AR	P	478376	.	.	.	.	Tolerated	2
Fam35_Pt1	1	12026314	.	AAGG	A	PLOD1	AR	LP	14367	.	.	.	.	Tolerated	2
Fam38_Pt1	8	145740366	rs386833845	CA	C	RECQL4	AR	P	6066	0.0012	.	.	.	Tolerated	2
Fam38_Pt2	8	145740366	rs386833845	CA	C	RECQL4	AR	P	6066	0.0012	.	.	.	Tolerated	2
Fam40_Pt2	11	66637890	rs200030109	C	A	PC	AR	LP	203916	0.0012	Damaging	0.79	25.5	Tolerated	2
Fam42_Pt1	2	69627594	rs374514431	C	A	NFU1	AR	P	30700	0.0012	Damaging	0.972	29.5	Tolerated	2
Fam43_Pt1	9	133946976	.	AG	A	LAMC3	AR	LP	504359	.	.	.	.	Tolerated	2
Fam43_Pt2	7	50544323	rs201951824	C	T	DDC	AR	P	202181	0.0012	Tolerated	0.381	31	Tolerated	2
Fam43_Pt2	3	46747402	rs375470385	G	A	TMIE	AR	LP	504683	0.00006479	.	.	.	Damaging	2
Fam43_Pt3	3	46747402	rs375470385	G	A	TMIE	AR	LP	504683	0.00006479	.	.	.	Damaging	2
Fam43_Pt3	6	151751289	rs144972972	T	C	RMND1	AR	P	225255	0.0002	Tolerated	0.803	25.2	Tolerated	2
Fam57_Pt2	2	211460259	.	G	C	CPS1	AR	LP	449391	.	Damaging	0.959	27.4	Tolerated	2
Fam60_Pt1	14	76201609	rs541400148	C	T	TTLL5	AR	P	1072044	0.0012	.	.	33	Tolerated	2
Fam60_Pt2	14	76201609	rs541400148	C	T	TTLL5	AR	P	1072044	0.0012	.	.	33	Tolerated	2
Fam61_Pt1	3	49137706	rs751537797; rs149346696	G	A	QARS1	AR	P	941594	.	.	.	34	Tolerated	2

Patient ID	Chr	Position	Variant ID	Ref	Var	Gene symbol	Mode of inheritance	Variant pathogenicity	ClinVariant ID	AF_popmax	MetaSVM	REVEL	CADD phred	spliceAI	Tier
Fam20_Pt4	17	7577568	rs730882005	C	A	*TP53*	AD	P	376574	.	Damaging	0.958	31	Tolerated	1
Fam26_Pt2	2	25469529	rs1234388246	G	GC	*DNMT3A*	AD	P	985294	.	.	.	.	Tolerated	1
Fam41_Pt1	9	139412682	rs1290954710	C	T	*NOTCH1*	AD	LP	445806	.	Damaging	0.439	28.9	Tolerated	1
Fam41_Pt2	9	139412682	rs1290954710	C	T	*NOTCH1*	AD	LP	445806	.	Damaging	0.439	28.9	Tolerated	1
Fam54_Pt2	17	7577120	rs28934576	C	T	*TP53*	AD	P	12366	.	Damaging	0.868	23.9	Tolerated	1
Fam55_Pt1	17	48703927	rs767121010	G	A	*CACNA1G*	AD	LP	426883	.	Tolerated	0.075	23.5	Tolerated	1
Fam60_Pt1	12	112888193	rs397516801	A	G	*PTPN11*	AD	P	44603	.	Damaging	0.668	25.9	Tolerated	1
Fam37_Pt1	20	35555631	rs515726146	A	AC	*SAMHD1*	AD, AR	P	126413	.	.	.	.	Tolerated	1
Fam37_Pt2	20	35555631	rs515726146	A	AC	*SAMHD1*	AD, AR	P	126413	.	.	.	.	Tolerated	1
Fam37_Pt3	9	111662096	rs111033171	A	G	*ELP1*	AD, AR	P	6085	0.00006479	.	.	.	Tolerated	1
Fam37_Pt4	9	111662096	rs111033171	A	G	*ELP1*	AD, AR	P	6085	0.00006479	.	.	.	Tolerated	1
Fam2_Pt1	9	111662096	rs111033171	A	G	*ELP1*	AD, AR	P	6085	0.00006479	.	.	.	Tolerated	1
Fam2_Pt2	9	111662096	rs111033171	A	G	*ELP1*	AD, AR	P	6085	0.00006479	.	.	.	Tolerated	1
Fam2_Pt4	9	111662096	rs111033171	A	G	*ELP1*	AD, AR	P	6085	0.00006479	.	.	.	Tolerated	1
Fam3_Pt1	3	48508395	rs72556554	G	A	*TREX1*	AD, AR	P	.	0.0003	Damaging	0.828	31	Tolerated	1
Fam3_Pt2	3	48508395	rs72556554	G	A	*TREX1*	AD, AR	P	4179	0.0003	Damaging	0.828	31	Tolerated	1
Fam3_Pt3	3	48508395	rs72556554	G	A	*TREX1*	AD, AR	P	4179	0.0003	Damaging	0.828	31	Tolerated	1
Fam24_Pt1	17	40693092	rs104894592	C	T	*NAGLU*	AD, AR	P	1562	0.0001	.	.	35	Tolerated	1
Fam32_Pt3	7	6029587	rs587780064	C	A	*PMS2*	AD, AR	P	127802	.	.	.	35	Damaging	1
Fam44_Pt3	1	169500043	rs118203907	T	C	F5	AD, AR	P	649	.	Damaging	0.972	31	Tolerated	1
Fam45_Pt1	8	55537568	rs760689800	C	T	*RP1*	AD, AR	P	1065648	.	.	.	25.2	Tolerated	1
Fam45_Pt2	8	55537568	rs760689800	C	T	*RP1*	AD, AR	P	1065648	.	.	.	25.2	Tolerated	1
Fam48_Pt1	7	124481134	.	G	T	*POT1*	AD, AR	P	1042147	.	.	.	38	Tolerated	1
Fam53_Pt1	X	153363118	rs179363901	G	A	*MECP2*	XL	P	11845	.	Tolerated	0.229	22.4	Tolerated	1
Fam2_Pt1	12	49312533	rs1272967209	GTA	G	CCDC65	AR	P	88685	.	.	.	.	Tolerated	2
Fam7_Pt2	1	63868019	rs199682486	G	A	ALG6	AR	P	95529	0.0008	.	.	.	Damaging	2
Fam3_Pt3	2	31596738	rs148412639	C	G	XDH	AR	LP	505602	0.0008	.	.	34	Damaging	2
Fam4_Pt2	1	17313566	rs765632065	AG	A	ATP13A2	AR	P	465253	0.0012	.	.	.	Tolerated	2
Fam6_Pt2	15	56736015	rs185005213	G	A	MNS1	AR	P	973691	0.0001	.	.	37	Tolerated	2
Fam6_Pt3	15	56736015	rs185005213	G	A	MNS1	AR	P	973691	0.0001	.	.	37	Tolerated	2
Fam10_Pt1	8	67986544	rs766020802	CAA	C	CSPP1	AR	P	575640	0.0001	.	.	.	Tolerated	2
Fam10_Pt3	8	67986544	rs766020802	CAA	C	CSPP1	AR	P	575640	0.0001	.	.	.	Tolerated	2
Fam11_Pt1	1	43221287	rs118203996	G	A	P3H1	AR	P	1258	.	.	.	36	Tolerated	2
Fam11_Pt2	1	43221287	rs118203996	G	A	P3H1	AR	P	1258	.	.	.	36	Tolerated	2
Fam14_Pt2	1	27121547	rs139073416	C	A	PIGV	AR	P	1284	0.0001	Damaging	0.83	25.1	Tolerated	2
Fam14_Pt3	6	135754219	rs372659908	G	A	AHI1	AR	P	217525	0.00006483	.	.	36	Tolerated	2
Fam14_Pt6	11	88070745	rs587777533	A	C	CTSC	AR	P	139655	0.0001	.	.	36	Tolerated	2
Fam19_Pt1	2	26644264	rs142371860	C	T	DRC1	AR	P	55840	0.0006	.	.	36	Tolerated	2
Fam19_Pt2	2	26644264	rs142371860	C	T	DRC1	AR	P	55840	0.0006	.	.	36	Tolerated	2
Fam20_Pt1	11	68548130	rs80356779	G	A	CPT1A	AR	P	65644	0.0012	Damaging	0.785	24.8	Tolerated	2
Fam22_Pt1	10	104590667	rs777638364	C	T	CYP17A1	AR	P	1338524	.	Damaging	0.908	31	Tolerated	2
Fam24_Pt1	19	44012925	rs761661864	A	C	ETHE1	AR	LP	577939	.	.	.	35	Damaging	2
Fam24_Pt2	19	44012925	rs761661864	A	C	ETHE1	AR	LP	577939	.	.	.	35	Damaging	2
Fam27_Pt1	8	68030481	rs766633448	A	C	CSPP1	AR	LP	1464866	.	.	.	32	Damaging	2
Fam27_Pt1	6	74348214	rs727504156	TG	T	SLC17A5	AR	P	167693	0.0001	.	.	.	Tolerated	2
Fam27_Pt2	17	18058028	rs184435771	G	A	MYO15A	AR	P	228276	0.0002	Damaging	0.89	32	Tolerated	2
Fam27_Pt2	6	74348214	rs727504156	TG	T	SLC17A5	AR	P	167693	0.0001	.	.	.	Tolerated	2
Fam29_Pt1	16	88876475	rs745594160	T	TA	APRT	AR	P	203396	0.0001	.	.	.	Tolerated	2
Fam34_Pt2	17	8076835	rs201558321	T	C	SNORD118	AR	P	929280	.	.	.	.	Tolerated	2
Fam35_Pt1	3	52409343	rs762545991	T	TG	DNAH1	AR	P	478376	.	.	.	.	Tolerated	2
Fam35_Pt1	1	12026314	.	AAGG	A	PLOD1	AR	LP	14367	.	.	.	.	Tolerated	2
Fam38_Pt1	8	145740366	rs386833845	CA	C	RECQL4	AR	P	6066	0.0012	.	.	.	Tolerated	2
Fam38_Pt2	8	145740366	rs386833845	CA	C	RECQL4	AR	P	6066	0.0012	.	.	.	Tolerated	2
Fam40_Pt2	11	66637890	rs200030109	C	A	PC	AR	LP	203916	0.0012	Damaging	0.79	25.5	Tolerated	2
Fam42_Pt1	2	69627594	rs374514431	C	A	NFU1	AR	P	30700	0.0012	Damaging	0.972	29.5	Tolerated	2
Fam43_Pt1	9	133946976	.	AG	A	LAMC3	AR	LP	504359	.	.	.	.	Tolerated	2
Fam43_Pt2	7	50544323	rs201951824	C	T	DDC	AR	P	202181	0.0012	Tolerated	0.381	31	Tolerated	2
Fam43_Pt2	3	46747402	rs375470385	G	A	TMIE	AR	LP	504683	0.00006479	.	.	.	Damaging	2
Fam43_Pt3	3	46747402	rs375470385	G	A	TMIE	AR	LP	504683	0.00006479	.	.	.	Damaging	2
Fam43_Pt3	6	151751289	rs144972972	T	C	RMND1	AR	P	225255	0.0002	Tolerated	0.803	25.2	Tolerated	2
Fam57_Pt2	2	211460259	.	G	C	CPS1	AR	LP	449391	.	Damaging	0.959	27.4	Tolerated	2
Fam60_Pt1	14	76201609	rs541400148	C	T	TTLL5	AR	P	1072044	0.0012	.	.	33	Tolerated	2
Fam60_Pt2	14	76201609	rs541400148	C	T	TTLL5	AR	P	1072044	0.0012	.	.	33	Tolerated	2
Fam61_Pt1	3	49137706	rs751537797; rs149346696	G	A	QARS1	AR	P	941594	.	.	.	34	Tolerated	2

Variants are shown in GRCh37 genomic coordinates. AF_popmax - highest population allele frequency in gnomAD version 3. Tier 1 variants include variants in the genes associated with either AD or AD, AR, or XL mode of inheritance (highlighted in bold face); tier 2 variants include variants found in AR genes.

Chr, chromosome; Fam, family; ID, identification; Pt, patient; Ref, reference.

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