Table 2 Parkinson’s disease causal proteins from CSF.

From: A proteogenomic view of Parkinson’s disease causality and heterogeneity

Gene Symbol	SomaScan ID	Protein ID	Gene ID	Nr of IVs	Method	β	FDR	Colocalization PP.H4.abf	Horizontal Pleiotropy (P value)	Olink
GPNMB^a	5080_131	Q14956	10457	11	IVW	0.14	1.17 × 10⁻¹⁷	0.94	0.65	OID05139 r² = 0.762 p = 4.09 × 10⁻¹⁷
FCGR2B	3310_62	P31994	2213	17	IVW	0.07	5.11 × 10⁻¹⁴	0.96	0.49	OID00442 r² = 0.837 p = 4.23 × 10⁻²³
FCGR2A	3309_2	P12318	2212	18	IVW	0.07	2.70 × 10⁻¹²	0.95	0.26	OID01244 r² = 0.392 p = 3.73 × 10−⁴
CTSB	8007_19	P07858	1508	12	IVW	−0.11	2.63 × 10⁻¹⁰	0.22	0.47	–
HLA-DQA2^b	7757_5	P01906	3118	33	IVW	−0.14	1.43 × 10⁻⁹	0.03	0.00	–
CD38	11505_1	P28907	952	1	Wald ratio	−0.53	2.45 × 10⁻⁹	0.45	NA	OID00308 r² = 0.003 p = 0.986
HP	3054_3	P00738	3240	19	IVW	0.06	2.01 × 10⁻⁶	0.01	0.60	–
LTF	2780_35	P02788	4057	23	IVW	0.05	2.16 × 10⁻⁶	0.04	0.65	–
HAVCR2	5134_52	Q8TDQ0	84868	13	IVW	−0.10	2.87 × 10⁻⁵	0.30	0.67	OID01410 r² = 0.797 p = 1.52 × 10⁻¹⁹
BST1^b	4535_50	Q10588	683	10	IVW	0.12	4.00 × 10⁻⁵	0.24	0.00	OID01436 r² = 0.639 p = 7.99 × 10⁻¹¹
CLEC3B	5701_81	P05452	7123	4	IVW	−0.16	1.02 × 10⁻⁴	0.29	0.97	–
HAPLN1	3196_6	P10915	1404	15	IVW	0.06	3.21 × 10⁻⁴	0.05	0.79	–
MANEA	8014_359	Q5SRI9	79694	17	IVW	0.05	3.21 × 10⁻⁴	0.10	0.94	–
NQO2	9754_33	P16083	4835	11	IVW	0.05	3.21 × 10⁻⁴	0.05	0.98	OID01173 r² = 0.276 p = 0.018
ARSA^a	3583_54	P15289	410	5	IVW	0.13	6.82 × 10⁻⁴	0.58	0.62	OID01479 r² = 0.383 p = 5.41 × 10⁻⁴
LGALS3	3066_12	P17931	3958	8	IVW	0.07	7.11 × 10⁻⁴	0.02	0.50	OID00578 r² = 0.584 p = 7.96 × 10⁻⁹
IL1RL1	4234_8	Q01638	9173	26	IVW	0.03	9.63 × 10⁻⁴	0.01	0.90	OID00634 r² = 0.879 p = 4.45 × 10⁻²⁸
PAM	5620_13	P19021	5066	12	IVW	0.09	9.63 × 10⁻⁴	0.08	0.47	OID01256 r² = 0.496 p = 2.54 × 10⁻⁶
TPSAB1	9409_11	Q15661	64499 7177	8	IVW	−0.06	0.0011	0.15	0.80	OID00941 r² = 0.803 p = 5.24 × 10⁻²⁰
HSP90B1	6393_63	P14625	7184	22	IVW	0.04	0.0011	0.03	0.19	OID05159 r² = 0.045 p = 0.772
GLCE	7808_5	O94923	26035	14	IVW	0.05	0.0015	0.10	0.96	–
MANSC4	9578_263	A6NHS7	100287284	18	IVW	0.05	0.0016	0.02	0.85	–
RABEPK	13599_15	Q7Z6M1	10244	10	IVW	−0.05	0.0021	0.10	0.86	–
ICAM1	4342_10	P05362	3383	8	IVW	−0.07	0.0021	0.32	0.74	OID01230 r² = 0.099 p = 0.473
C4B^b,c	2182_54	P0C0L4 P0C0L5	720 721	101	IVW	0.02	0.0021	0.00	0.00	–
LCT^b	9017_58	P09848	3938	25	IVW	0.04	0.0021	0.00	0.00	–
SIRPB1	6247_9	O00241	10326	25	IVW	−0.03	0.0023	0.01	0.60	OID01430 r² = 0.348 p = 0.002
C4A^b,c	2182_54	P0C0L4 P0C0L5	720 721	101	IVW	0.02	0.0023	0.00	0.00	–
PCSK7	4459_68	Q16549	9159	18	IVW	−0.04	0.0028	0.02	0.98	–
IL9	5834_18	P15248	3578	12	IVW	0.06	0.0028	0.05	0.96	–
CLN5^a	8874_53	O75503	1203	2	IVW	−0.15	0.0028	0.38	NA	–
AGT	3484_60	P01019	183	4	IVW	0.12	0.0039	0.06	0.97	–
CD274	5060_62	Q9NZQ7	29126	16	IVW	0.08	0.0042	0.02	0.46	OID00518 r² = 0.120 p = 0.373
RBP7	14208_3	Q96R05	116362	3	IVW	0.20	0.0047	0.09	NA	–
PLA2G7	5015_15	Q13093	7941	14	IVW	0.04	0.0061	0.05	0.57	OID01283 r² = 0.478 p = 6.71 × 10⁻⁶
EGF	5509_7	P01133	1950	3	IVW	−0.13	0.010	0.11	NA	OID00662 r² = 0.762 p = 3.93 × 10⁻¹⁷
ASIP	5676_54	P42127	434	3	IVW	−0.13	0.010	0.17	NA	–
TPSB2	3403_1	P20231	64499	10	IVW	−0.05	0.011	0.15	0.27	–
ACP1	3858_5	P24666	52	15	IVW	0.04	0.011	0.04	0.88	–
RNASE3	5741_55	P12724	6037	6	IVW	0.09	0.011	0.01	0.26	OID01211 r² = 0.920 p = 5.14 × 10⁻³⁵
A4GALT	8759_29	Q9NPC4	53947	2	IVW	−0.21	0.012	0.11	NA	–
DSCAM	9175_48	O60469	1826	3	IVW	−0.30	0.015	0.19	NA	–
COLEC11	4430_44	Q9BWP8	78989	8	IVW	−0.05	0.016	0.03	0.61	–
SPOCK2	5491_12	Q92563	9806	8	IVW	0.08	0.017	0.03	0.98	–
VWA2	7128_9	Q5GFL6	340706	5	IVW	−0.11	0.018	0.04	0.76	–
RPN1	10490_3	P04843	6184	10	IVW	0.08	0.020	0.02	0.57	–
ADAMTS4	2809_25	O75173	9507	8	IVW	−0.06	0.020	0.19	0.36	–
PDCD1LG2	3004_67	Q9BQ51	80380	12	IVW	−0.09	0.020	0.04	0.07	OID00458 r² = 0.740 p = 9.00 × 10⁻¹⁶
PRTN3	3514_49	P24158	5657	2	IVW	0.17	0.020	0.06	NA	OID00618 r² = 0.779 p = 2.99 × 10⁻¹⁸
ADGRE2	4546_27	Q9UHX3	30817	10	IVW	−0.05	0.020	0.01	0.87	–
RNASE2	8394_56	P10153	6036	10	IVW	0.06	0.020	0.02	0.61	–
MPIG6B	7065_1	O95866	80739	18	IVW	−0.05	0.020	0.00	0.18	–
SIGLEC9	3007_7	Q9Y336	27180	19	IVW	0.03	0.020	0.02	0.99	OID00294 r² = 0.311 p = 0.007
TAPBPL	6364_7	Q9BX59	55080	10	IVW	−0.03	0.020	0.03	0.50	–
LRP12^a	7744_10	Q9Y561	29967	1	Wald ratio	0.73	0.023	0.66	NA	–
DNAJC30	7866_11	Q96LL9	84277	3	IVW	−0.09	0.024	0.03	NA	–
CCL15	3509_1	Q16663	6359	3	IVW	−0.08	0.024	0.12	NA	OID00629 r² = 0.836 p = 6.47 × 10⁻²³
VTN	13125_45	P04004	7448	22	IVW	−0.03	0.028	0.01	0.75	–
NUCB1	10451_11	Q02818	4924	3	IVW	−0.12	0.029	0.05	NA	–
TRH	5659_11	P20396	7200	4	IVW	−0.08	0.029	0.07	0.75	–
POSTN	6645_53	Q15063	10631	8	IVW	−0.07	0.034	0.02	0.76	–
PLXNB2^a	10855_55	O15031	23654	36	IVW	−0.02	0.034	0.08	0.09	OID01218 rho = 0283 p = 0.015
IL18R1	14079_14	Q13478	8809	23	IVW	0.03	0.034	0.01	0.79	OID00517 r² = 0.806 p = 2.64 × 10⁻²⁰
IDUA	3169_70	P35475	3425	3	IVW	0.10	0.038	0.00	NA	OID00393 r² = 0.743 p = 6.12 × 10⁻¹⁶
CFD	13678_169	P00746	1675	10	IVW	−0.05	0.039	0.01	0.58	–
GGH^a	9370_69	Q92820	8836	4	IVW	0.08	0.040	0.02	0.49	–
FGFRL1	6237_11	Q8N441	53834	5	IVW	0.13	0.046	0.00	0.07	–
LMAN2L	8013_9	Q9H0V9	81562	3	IVW	−0.15	0.049	0.03	NA	–

Horizontal pleiotropy p value calculated with MRPRESSO.
By definition, all SOMAmers in Table 2 have a significant CSF cis pQTL according to Supplementary Table 5.
The “Olink” column represents the corresponding Olink ID, followed by the reversed Pearson’s correlation coefficient (r²) and the p value for the correlation.
^aPD protein marker in Supplementary Table 3.
^bCorrected by removing outliers by MRPRESSO.
^cHas homolog detected by the same SOMAmer

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Table 2 Parkinson’s disease causal proteins from CSF.

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