Through exome sequencing, we identified an entire list of migraine-associated (p-value < 0.00001) variants and prioritised 17 as the most significant (9.091 × 10−05) functional variants distributed among 12 genes (RETNLB, SCAI, ADH4, ESPL1, CPT2, FLG, PPP4R1, SERPINB5, ZNF66, ETAA1, EXO1 and CPA6) in the Saudi females suffering from migraine. The gene discussed is CPA6; the disease is migraine disorder.