Germline mutations in the major melanoma susceptibility gene
CDKN2A
explain genetic predisposition in only 10–40% of melanoma‐prone families. In our study we comprehensively characterized 488 melanoma cases from 451 non‐
CDKN2A/CDK4
families for mutations in 30 established and candidate melanoma susceptibility genes using a custom‐designed targeted gene panel approach. We identified (likely) pathogenic variants in established melanoma susceptibility genes in 18 families (
n
= 3
BAP1
,
n
= 15
MITF
p.E318K; diagnostic yield 4.0%). Among the three identified
BAP1
‐families, there were no reported diagnoses of uveal melanoma or malignant mesothelioma. We additionally identified two potentially deleterious missense variants in the telomere maintenance genes
ACD
and
TERF2IP
, but none in the
POT1
gene.
MC1R
risk variants were strongly enriched in our familial melanoma cohort compared to healthy controls (R variants: OR 3.67, 95% CI 2.88–4.68,
p
<0.001). Several variants of interest were also identified in candidate melanoma susceptibility genes, in particular rare (pathogenic) variants in the albinism gene
OCA2
were repeatedly found. We conclude that multigene panel testing for familial melanoma is appropriate considering the additional 4% diagnostic yield in non‐
CDKN2A/CDK4
families. Our study shows that
BAP1
and
MITF
are important genes to be included in such a diagnostic test.