Table 1 Candidate potentially pathogenic (PP) SVs identified in 170 PCa patients

From: Rare pathogenic structural variants show potential to enhance prostate cancer germline testing for African men

Genes	Gene impact type¹	1stChr	pos1	2ndChr	pos2	SV type	ClinVar / dbVar concordance	MAF African (this study)	MAF African (control)²	MAF European (this study)	MAF African (dbVar)³	MAF European (dbVar)³
Potentially Pathogenic SV (PP-SV)
SLC3A1	IED	chr2	44281377	chr2	44281612	DUP	L-pathogenic	0.01 ⁴	0	0	0.0075	1.3e-04
OCA2	pLoF	chr15	28017719	chr15	28020677	DEL	L-pathogenic	0.004	0.02	0	0.0015	0.001
PIGN	pLoF	chr18	62152637	chr18	62157701	DEL	Pathogenic	0.004	0	0	0.0013	1.3e-04
SLC7A2	pLoF	chr8	17418976	chr8	17544122	DEL	In dbVar	0.009	0	0	0.003	0
DNAJC15	pLoF	chr13	43078470	chr13	43079390	DEL	In dbVar	0	0	0.009	0	1.0e-04
BCL2L11	pLoF	chr2	111122626	chr2	111125901	DEL	This study	0.005	0	0	NA	NA
BARD1	pLoF	chr2	214768022	chr2	214772899	DEL	This study	0.005	0	0	NA	NA
COL4A2/ COL4A1	CG	chr13	110294204	chr13	110633815	DUP	In dbVar	0.005	0	0	1.3e-04	6.3e-06
SLC2A5	IED	chr1	9045605	chr1	9049441	DUP	In dbVar	0	0	0.009	7.3e-04	0.002
FOXP1	pLoF	chr3	71097066	chr3	74525618	INV	This study	0.009	0	0	NA	NA
WASF1	pLoF	chr6	108167886	chr6	110172775	INV	In dbVar	0.004	0	0	9.6e-05	0
MLH1	pLoF	chr3	37000362	chr3	39352689	INV	In dbVar	0.004	0	0	4e-04	6.4e-06
RB1	pLoF	chr13	48466588	chr13	48473911	INV	In dbVar	0.004	0	0	1.8e-04	1.3e-05
CTNNA1	pLoF	chr5	138903881	chr19	21614900	TRA	This study	0	0	0.009	NA	NA
AK8-DST	pLoF	chr9	132876361	chr6	56896165	TRA	This study	0	0	0.009	NA	NA
PP-SV candidates classified as ‘cautionary’
LTBP1/BIRC6	CG	chr2	32403832	chr2	33107415	DUP	In dbVar	0	0	0.009	1.0e-04	0.0018
PHC3-PRKACA	pLoF	chr3	170090742	chr19	14110142	TRA	This study	0.004	0	0	NA	NA
KCTD3-DST	pLoF	chr1	215567414	chr6	56652607	TRA	This study	0.009	0	0	NA	NA
PKHD1	pLoF	chr6	51981375	chr15	30874073	TRA	This study	0.009	0	0	NA	NA

CG copy gain, chr chromosome, DEL deletion, DUP duplication, IED intragenic exon duplication, INV inversion, L-pathogenic Likely pathogenic, MAF minor allele frequency, pLoF potentially loss-of-function, pos position, TRA translocation. Note, all gene names are in italics.
¹Gene impact type based on gene annotation.
²Population-matched Southern African non-cancer control cohort (n = 49).
³The ancestry-related MAF in dbVar were based on gnomAD³² or TOPMed⁴² SV study. The details of all dbVar studies (dbVar study name and ID) and reported allele frequencies were shown in Supplementary Data 1.
⁴Presenting at low-frequency rather than rare variants within the ancestrally-defined patient cohort.

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Table 1 Candidate potentially pathogenic (PP) SVs identified in 170 PCa patients

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