Severe type I Plasminogen (PLG) deficiency was clinically diagnosed after hyaline-positive periodic acid Schiff material was detected in the histologic study of superior tarsal conjunctiva and vulvar pseudomembrane of the patient. Direct immunofluorescence also confirmed multiple deposits of fibrinogen in the dermis. Plasma plasminogen activity was calculated in a <5% value (reference values, 75% to 150%) and sequencing of the PLG gene evidenced the homozygous mutation in c.2377T/A (p.Tyr793Asn), confirming the molecular diagnosis of congenital deficiency of plasminogen type 1. Genotype-Phenotype correlation among family members evidenced the recessive hereditary pattern of clinical manifestations of chronic inflammatory disease of the mucous membranes due to PLG deficiency, but co-dominance effect to present a decreased plasma plasminogen activity (46%) among heterozygous asymptomatic individuals. SNPs/CNVs whole genome array hybridization analysis in the patient, detected long Loss of Heterozygosity regions (LOH) and demonstrated the consanguinity in the family. Proteomic analysis identified impaired secretion of mutant PLG tissue specific proteins, as definitive molecular etiopathogenesis of the type I PLG deficiency in the patient.