Table 3 Putatively causal rare (PIP > 0.05 and non-Finnish EUR MAF < 0.01) variants significantly associated at the study-wide level (P < 1 × 10−8) with the risk of prostate cancer

From: Assessing the contribution of rare protein-coding germline variants to prostate cancer risk and severity in 37,184 cases

Gene

Protein Change

Variant (Chr:Pos:ref:alt, HGVS)

P

OR [95% CI]

MAF (non-Finnish EUR)

MAF (Finnish Eur)

PIP

HOXB13

ENST00000290295:p.Gly84Glu

17:48728343:C:T, NC_000017.11:g.48728343C>T

1.95 × 10−181

4.69 [4.22–5.21]

0.00244

0.00786

1

ANO7

ENST00000274979:p.Glu226Lys

2:241200185:G:A, NC_000002.12:g.241200185G>C

4.57 × 10−26

0.699 [0.659–0.741]

0.00793

0.0619

0.985

CHEK2

ENST00000328354:p.Thr367fs

22:28695868:AG:A, NC_000022.11:g.28695869del

1.17 × 10−20

1.67 [1.46–1.91]

0.00255

0.00861

0.078

SPDL1

ENST00000265295:p.Arg20Gln

5:169588475:G:A, NC_000005.10:g.169588475G>A

3.06 × 10−13

0.718 [0.663–0.777]

0.00679

0.0346

0.996

AR

ENST00000374690:p.Glu654Lys

X:67711476:G:A, NC_000023.11:g.67711476G>A

1.28 × 10−11

0.706 [0.655–0.761]

6.90 × 10−4

0.0194

0.604

BIK

ENST00000216115:p.Ala139_ Leu148del

22:43129228: GTGCTGCTGGCGCTGCTGCTGCTGCTGGCGC:G, NC_000022.11:g. 43129228del

2.04 × 10−11

2.08 [1.68–2.57]

1.94 × 10−4

0.00331

0.3

TERT

ENST00000310581:p.Asp684Gly

5:1279370:T:C, NC_000005.10:g.1279370T>C

4.67 × 10−10

0.134 [0.071–0.252]

1.5 × 10−5

0.00151

0.985

  1. The P-value reported is from the Stouffer’s meta-analysis and as this does not generate an effect-size we report here the effect estimate (OR) from the FinnGen cohort as calculated with REGENIE using Firth’s logistic regression. Minor allele frequencies (MAF) from gnomAD non-Finnish European and Finnish-European populations.
  2. Chr:Pos:ref:alt chromosome, genomics position (GRCh38), reference allele, alternate allele, HGVS human genome variation society nomenclature, OR odds ratio, 95% CI 95% confidence interval, PIP posterior inclusion probability as calculated by SuSiE in FinnGen.
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