A genetic survey on three autochthonous goat breeds reared in Italy was carried out by a proteomic approach. This methodology, further to providing the phenotypic frequency of identified as1 genetic variants, allowed to determine (i) the additional constitutive presence of a non-allelic as1-casein (CN) F like protein in goat strong as1 variants; (ii) an as1-CN B2 like protein, expressed at very low quantitative level, in goat weak as1-CN variants, and, as main focus; (iii) the occurrence of a new as1-CN D1 variant characterised by the lack of as1 (f59-69) sequence otherwise encoded by exon 9 in goat as1 B2 reference. The same exon skipping event had been identified since 1990, as responsible of the weak quantitative class of as1-CN D variant (0.6 g/L), while the new as1-CN D1, has been quantitatively classified as an intermediate variant, since 1.8 g/L per allele was assessed in the milk.