The histone variant that replaces H3 at centromeres is CENP-A.
Histones package DNA into nucleosomes, but centromeric nucleosomes use CENP-A in place of canonical histone H3. In humans, CENP-A is encoded by the CENPA gene and is concentrated at centromeric chromatin, where it helps define the location of the kinetochore.
This matters because kinetochores provide the attachment site for spindle microtubules during cell division. By helping recruit proteins such as CENP-C, CENP-A supports accurate chromosome segregation. Its position can be inherited epigenetically, meaning centromere identity is not determined solely by a unique DNA sequence.
A common mix-up is H3.1 or H3.3: these are canonical H3 variants with other roles, while CENP-A is the specialized centromeric H3 variant. CENP-A is also called cenH3 in many organisms, although names differ across species. Human cells load new CENP-A nucleosomes mainly during G1 phase, after DNA replication has finished.