Main candidate genes from DecodeME - 2025

[forestglip]

These are the main candidate genes suggested by the data from the DecodeME study based on different methods: Tier 1 and 2 genes as defined by the DecodeME paper, significant genes using MAGMA test, and the nearest genes to the top 25 most significant loci.

I posted the same information on the DecodeME thread, and @Kitty suggested making a dedicated thread with the same information to be used as an easy to access reference and which can be updated as needed. This will be a locked thread, just meant to refer to for quickly seeing which genes might be interesting based on DecodeME.

Gene	Method	Chromosome	Position (GRCh38)	Reference allele	Effect allele	P-value
LRRC7	MAGMA	1	69696474	A	G	2.06E-07
							xxxxx
NEGR1	Nearest (1 of 2)	1	73126414	C	CA	1.19E-07
LRRIQ3	Nearest (1 of 2)	1	73126414	C	CA	1.19E-07
							xxxxx
ZNF644	Nearest	1	91028158	C	T	1.89E-07
							xxxxx
RABGAP1L	Tier 1	1	173846152	T	C	2.56E-08
DARS2	Tier 1, MAGMA, Nearest	1	173846152	T	C	2.56E-08
RC3H1	Tier 1	1	173846152	T	C	2.56E-08
GPR52	Tier 1	1	173846152	T	C	2.56E-08
ZBTB37	Tier 1, MAGMA	1	173846152	T	C	2.56E-08
TNFSF4	Tier 1	1	173846152	T	C	2.56E-08
ANKRD45	Tier 1	1	173846152	T	C	2.56E-08
KLHL20	Tier 1	1	173846152	T	C	2.56E-08
PRDX6	Tier 1	1	173846152	T	C	2.56E-08
SERPINC1	Tier 1	1	173846152	T	C	2.56E-08
SLC9C2	Tier 1	1	173846152	T	C	2.56E-08
							xxxxx
CACNA1E	Nearest	1	181676091	G	A	8.85E-07
							xxxxx
VRK2	Nearest	2	57808420	G	A	9.49E-07
							xxxxx
PLCL1	Nearest	2	197882813	A	G	6.64E-07
							xxxxx
HTT	Nearest	4	3240118	C	T	8.03E-07
							xxxxx
ECI2	Nearest	6	4336259	T	C	2.90E-07
							xxxxx
BTN2A2	Tier 1	6	26239176	A	G	4.11E-09
TRIM38	Tier 1	6	26239176	A	G	4.11E-09
ZNF322	Tier 1	6	26239176	A	G	4.11E-09
ABT1	Tier 1	6	26239176	A	G	4.11E-09
HFE	Tier 1	6	26239176	A	G	4.11E-09
BTN3A3	Tier 1	6	26239176	A	G	4.11E-09
HMGN4	Tier 1	6	26239176	A	G	4.11E-09
H4C8	MAGMA, Nearest	6	26239176	A	G	4.11E-09
							xxxxx
ZNF311	MAGMA	6	29016371	G	A	2.25E-06
							xxxxx
FBXL4	Tier 2	6	97984426	C	CA	4.85E-08
POU3F2	Nearest (1 of 2)	6	97984426	C	CA	4.85E-08
MMS22L	Nearest (1 of 2)	6	97984426	C	CA	4.85E-08
							xxxxx
MLLT10	Nearest (1 of 2)	10	21748880	A	G	6.34E-07
DNAJC1	Nearest (1 of 2)	10	21748880	A	G	6.34E-07
							xxxxx
SOX6	Nearest	11	16217844	C	G	1.08E-07
							xxxxx
SLC2A14	Nearest	12	7860921	T	A	5.79E-07
							xxxxx
SUDS3	Tier 1, MAGMA	12	118202773	CTTTTTTTTTTTTT	C	1.64E-07
PEBP1	Tier 1	12	118202773	CTTTTTTTTTTTTT	C	1.64E-07
VSIG10	Tier 1	12	118202773	CTTTTTTTTTTTTT	C	1.64E-07
TAOK3	Nearest, MAGMA	12	118202773	CTTTTTTTTTTTTT	C	1.64E-07
							xxxxx
DNAH10	MAGMA	12	123924955	G	A	2.43E-07
ZNF664	MAGMA	12	123924955	G	A	2.43E-07
CCDC92	MAGMA	12	123924955	G	A	2.43E-07
							xxxxx
OLFM4	Nearest, Tier 2	13	53194927	GT	G	1.16E-07
							xxxxx
PCDH17	Nearest	13	58456743	T	C	9.42E-07
							xxxxx
CCPG1	Tier 2	15	54866724	A	G	7.62E-09
UNC13C	Nearest (1 of 2)	15	54866724	A	G	7.62E-09
							xxxxx
SHISA6	Nearest	17	11325637	G	C	8.26E-08
							xxxxx
CA10	Tier 1, Nearest	17	52183006	C	T	2.11E-09
							xxxxx
DCC	Nearest	18	53232948	C	T	2.48E-07
							xxxxx
CDK5RAP1	Nearest	20	33363039	G	A	5.41E-07
							xxxxx
CSE1L	Tier 1, MAGMA	20	48914387	T	TA	9.51E-12
ARFGEF2	Tier 1, MAGMA, Nearest	20	48914387	T	TA	9.51E-12
DDX27	Tier 1	20	48914387	T	TA	9.51E-12
STAU1	Tier 1, MAGMA	20	48914387	T	TA	9.51E-12
ZNFX1	Tier 1	20	48914387	T	TA	9.51E-12
B4GALT5	Tier 1	20	48914387	T	TA	9.51E-12
PTGIS	Tier 1	20	48914387	T	TA	9.51E-12
							xxxxx
MRPL39	Nearest	21	25487862	A	AG	5.10E-07

Sources:
Tier 1 and 2 genes: Candidate genes document
MAGMA genes: Supplementary table 4
Top 25 loci: Supplementary table 3, with nearest gene to each lead variant found with LocusZoom.

Spoiler: List of only genes for easy copying

LRRC7
NEGR1
LRRIQ3
ZNF644
RABGAP1L
DARS2
RC3H1
GPR52
ZBTB37
TNFSF4
ANKRD45
KLHL20
PRDX6
SERPINC1
SLC9C2
CACNA1E
VRK2
PLCL1
HTT
ECI2
BTN2A2
TRIM38
ZNF322
ABT1
HFE
BTN3A3
HMGN4
H4C8
ZNF311
FBXL4
POU3F2
MMS22L
MLLT10
DNAJC1
SOX6
SLC2A14
SUDS3
PEBP1
VSIG10
TAOK3
DNAH10
ZNF664
CCDC92
OLFM4
PCDH17
CCPG1
UNC13C
SHISA6
CA10
DCC
CDK5RAP1
CSE1L
ARFGEF2
DDX27
STAU1
ZNFX1
B4GALT5
PTGIS
MRPL39