Table 1 Gene-level associations with glucose and HbA1c levels.

From: Gene-level analysis of rare variants in 379,066 whole exome sequences identifies an association of GIGYF1 loss of function with type 2 diabetes

Gene	Variant set	Title	p-value	Effect (SD)	Effect (IFCC units)	95% CI− (IFCC units)	95% CI+ (IFCC units)	IFCC units	n carrier measured
GCK	pLOF	Glucose	1.56 × 10^–9	1.00	1.24	0.84	1.65	mmol/L	35
GIGYF1	pLOF	Glucose	4.42 × 10^–12	0.62	0.77	0.55	0.98	mmol/L	121
GCK	missense	Glucose	6.15 × 10^–11	0.49	0.61	0.42	0.79	mmol/L	173
G6PC2	missense	Glucose	4.62 × 10^–83	− 0.27	− 0.33	− 0.36	− 0.3	mmol/L	5128
GCK	pLOF	HbA1c	2.64 × 10^–17	1.29	8.75	6.73	10.78	mmol/mol	38
GIGYF1	pLOF	HbA1c	1.28 × 10^–14	0.64	4.33	3.23	5.43	mmol/mol	129
HNF1A	pLOF	HbA1c	2.14 × 10^–7	0.59	4.01	2.50	5.53	mmol/mol	68
TNRC6B	pLOF	HbA1c	2.36 × 10^–7	0.58	3.94	2.45	5.43	mmol/mol	70
RHAG	pLOF	HbA1c	3.31 × 10^–34	− 0.86	− 5.81	− 6.75	− 4.88	mmol/mol	179
EPB41	pLOF	HbA1c	3.14 × 10^–17	− 0.53	− 3.58	− 4.41	− 2.75	mmol/mol	226
PTPRH	pLOF	HbA1c	4.39 × 10^–10	0.11	0.74	0.51	0.97	mmol/mol	2924
APOB	pLOF	HbA1c	6.94 × 10^–8	0.23	1.57	1.00	2.15	mmol/mol	478
PLD1	pLOF	HbA1c	2.99 × 10^–7	0.23	1.56	0.96	2.16	mmol/mol	438
EPB42	pLOF	HbA1c	6.11 × 10^–7	− 0.31	− 2.08	− 2.90	− 1.26	mmol/mol	234
GCK	missense	HbA1c	1.86 × 10^–17	0.56	3.83	2.94	4.71	mmol/mol	201
G6PC2	missense	HbA1c	6.71 × 10^–45	− 0.18	− 1.21	− 1.38	− 1.04	mmol/mol	5574
PFAS	missense	HbA1c	2.09 × 10^–8	− 0.05	− 0.32	− 0.44	− 0.21	mmol/mol	12,621
PDX1	missense	HbA1c	2.54 × 10^–7	0.06	0.41	0.25	0.56	mmol/mol	6694
PIEZO1	missense	HbA1c	1.0 × 10^–132	− 0.15	− 1.00	− 1.07	− 0.92	mmol/mol	26,726
AMPD3	missense	HbA1c	7.28 × 10^–34	0.13	0.86	0.72	1.00	mmol/mol	8258
PFKM	missense	HbA1c	2.16 × 10^–28	− 0.28	− 1.92	− 2.26	− 1.58	mmol/mol	1353
ANK1	missense	HbA1c	3.12 × 10^–19	− 0.13	− 0.87	− 1.06	− 0.68	mmol/mol	4342
PFKL	missense	HbA1c	2.69 × 10^–14	0.10	0.68	0.50	0.85	mmol/mol	5245
AXL	missense	HbA1c	4.11 × 10^–12	− 0.08	− 0.54	− 0.69	− 0.39	mmol/mol	6827
LCAT	missense	HbA1c	1.29 × 10^–11	− 0.27	− 1.82	− 2.34	− 1.29	mmol/mol	565
PLA2G12A	missense	HbA1c	5.74 × 10^–11	− 0.08	− 0.51	− 0.67	− 0.36	mmol/mol	6761
PLD1	missense	HbA1c	1.51 × 10^–10	0.08	0.57	0.40	0.75	mmol/mol	5180
APEH	missense	HbA1c	1.86 × 10^–10	0.29	1.96	1.36	2.57	mmol/mol	429
TNFRSF13B	missense	HbA1c	4.63 × 10^–9	− 0.08	− 0.51	− 0.68	− 0.34	mmol/mol	5470
BLVRB	missense	HbA1c	2.53 × 10^–8	− 0.07	− 0.48	− 0.65	− 0.31	mmol/mol	5533
TMC8	missense	HbA1c	3.01 × 10^–8	0.11	0.77	0.50	1.05	mmol/mol	2095
HK1	missense	HbA1c	1.08 × 10^–7	− 0.16	− 1.08	− 1.48	− 0.68	mmol/mol	988
SLC4A1	missense	HbA1c	1.76 × 10^–7	− 0.15	− 1.04	− 1.43	− 0.65	mmol/mol	1025
TFR2	missense	HbA1c	4.24 × 10^–7	− 0.12	− 0.84	− 1.16	− 0.51	mmol/mol	1491
CARHSP1	missense	HbA1c	6.78 × 10^–7	− 0.13	− 0.86	− 1.20	− 0.52	mmol/mol	1360

pLOF or damaging missense variants (CADD score ≥ 25) were aggregated per gene. The effect is shown in standard deviations (SD) of transformed values as well as in International Federation of Clinical Chemistry (IFCC) units.
CI confidence interval.

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Table 1 Gene-level associations with glucose and HbA1c levels.

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