Table 3 Population-Specific Low-Frequency (PSLF) Potentially Pathogenic Variants or Potentially Oncogenic Variants (PPV/POVs, n = 17) identified in 217 African ancestral prostate cancer (PCa) patients from the SAPCS (n = 186) and PPCG (n = 31) study cohorts and impacting 12 DNA Damage Repair (DDR) or PCa-associated genes, either known or unknown as PCa germline testing (GT) gene candidates

From: Pathogenic variants reveal candidate genes for prostate cancer germline testing for men of African ancestry

Gene	PPV/ POV	Chr position: nt change	rsID	AA Change	SAPCS (n)	PPCG (n)	MAF (this study)	MAF ALL gnomAD	MAF AFR gnomAD	MAF SAC (n = 49)	MAF EAC (n = 40)	PC	VAF
ATM ^a	POV	chr11:108227834:A/G	rs150143957	D44G	6	0	0.0161 (SAPCS)	0.0002	0.0007	0.0204	0.025	No	NA
PMS2 ^a	POV	chr7:5978683:TGA/T	rs587779335	L729fs	2	2	0.0092 (ALL) 0.0054 (SAPCS) 0.0323 (PPCG)	0.0077	0.0304	0.0306	0.025	No	NA
PREX2	POV	chr8:68093713:A/G	rs138027402	K787E	6	0	0.0161 (SAPCS)	0.0004	0.0014	0	0	YES	All(6) > 0.46
PREX2	POV	chr8:68099845:T/C	rs150773140	Splice	5	0	0.0134 (SAPCS)	0.0006	0.0021	0	0	YES	All(5) > 0.3
PREX2	POV	chr8:68121013:C/T	rs143386950	R1230W	5	0	0.0134 (SAPCS)	0.0000	0.0002	0	0	YES	All(5) > 0.36
POLG	PPV	chr15:89323423:A/G	rs202037973	F749S	5	0	0.0134 (SAPCS)	0.0002	0.0009	0	0	YES	All(5) > 0.42
POLQ	POV	chr3:121537146:G/T	rs141125457	L232I	9	1	0.0230 (ALL) 0.0242 (SAPCS) 0.0161 (PPCG)	0.0031	0.0107	0	0	YES	All(10) > 0.39
CREBBP ^b	POV	chr16:3728437:G/GC	rs754959530	Q2204fs	4	0	0.0108 (SAPCS)	0.0008	0.0028	0	0	YES	All(4) > 0.46
CREBBP ^b	POV	chr16:3729070: CTCCCCGGGG/C	rs777318563	TPG1990-1992del	4	0	0.0108 (SAPCS)	0.0000	0.0003	0.0204	0	No	NA
FAT1	POV	chr4:186603302:C/A	rs199719692	D3742Y	7	0	0.0188 (SAPCS)	0.0002	0.0007	0.0204	0	No	NA
FAT1	POV	chr4:186663530:C/T	rs149295542	V117M	5	1	0.0138 (ALL) 0.0134 (SAPCS) 0.0161 (PPCG)	0.0018	0.0067	0.0204	0.025	No	NA
ROS1	POV	chr6:117352995:A/G	rs17079086	F1439S	14	0	0.0403 (SAPCS)^c	0.0033	0.0133	0.0816	0.025	No	NA
ROS1	POV	chr6:117360384:C/T	rs151330473	G1135R	15	0	0.0403 (SAPCS)	0.0001	0.0008	0.0102	0.0125	No	NA
ASPM	POV	chr1:197100727:G/A	rs112946633	R2842W	23	0	0.0618 (SAPCS)	0.0001	0.0004	0.0306	0	No	NA
HERC2	POV	chr15:28238605: AGAATACTATTTC/A	rs774838885	GNSIL1245-1249V	4	0	0.0108 (SAPCS)	0.0000	0.0003	0.0204	0.0125	No	NA
PSM1	POV	chr2:189791888:G/C	rs5742973	E27Q	4	0	0.0108 (SAPCS)	0.0005	0.0014	0	0.0125	No	NA
TET2	POV	chr4:105233964:C/G	rs147112198	H8D	5	0	0.0134 (SAPCS)	0.0006	0.0023	0.0	0	No	NA

AA amino acid, AFR African, ALL all populations, chr chromosome, EAC east African Controls, nt nucleotide, MAF minor allele frequency, PC potential candidates, PPCG Pan Prostate Cancer Group, SAC southern African Controls, SAPCS Southern African Prostate Cancer Study, unk unknown.
^aKnown PCa germline testing panel gene.
^bAn additional GT gene candidate not identified within the rare variant analyses (Table 1 and Table 2).
^cA single patient presented as homozygous.

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