We have identified and characterized a 55 kDa nuclear protein (referred to as nmt55) from human breast tumors and MCF-7, human adenocarcinoma breast cell line, using site-directed monoclonal antibodies. Measurements of estrogen receptors (ER) and progesterone receptors (PR), by ligand binding assays, in cytosols of 63 human breast tumors permitted classifications of these tumors into four phenotypes (ER+/PR+, ER+/ PR-, ER-/PR-, ER-/PR+). Nuclear protein (nmt55) expression in these tumors, as determined from Western blot analyses, showed a statistically significant association (p = 0.001) with tumor hormonal phenotype. Review of the pathologic characteristics of tumors analyzed suggested that lack of nmt55 expression was significantly associated with mean tumor size (p < 0.03), mean ER (p = 0.001) and mean PR (p < 0.002), but was not associated with tumor stage, grade, or type. To further study this protein, we cloned and sequenced a 2.5 kb cDNA using a monoclonal antibody to nmt55. The complete predicted open reading frame encodes a protein with 471 amino acids and a calculated molecular mass of 54,169 Da. The deduced amino acid sequence exhibited unique regions rich in glutamine, histidine, arginine, and glutamic acid. Northern blot analysis of RNA from MCF-7 cells and ER+/PR+ human breast tumors showed a 2.6 kb mRNA. Southern blot analysis suggested the presence of a single copy of this gene. Chromosomal mapping, using fluorescent in situ hybridization (FISH), located nmt55 gene to the X chromosome, region q13. The extensive homology between nmt55 and RNA binding proteins suggested that nmt55 may be involved in hnRNA splicing. The strong association observed between expression of nmt55, tumor hormonal phenotype, mean tumor size, mean ER, and mean PR content suggests that loss of nmt55 expression may be related to events involved in hormone insensitivity, tumor differentiation, and unregulated tumor cell growth and metastases.