PCDH11XY (protocadherin 11 X Y linked)

Certainty Style Key

Certainty styling is being phased out topic by topic.

Hover over keys for definitions:
True   Likely   Speculative
Human Uniqueness Compared to "Great Apes": 
Absolute Difference
MOCA Domain: 

Protocadherin11X with its homologue Protocadherin11Y is of particular interest because it is located in a region of homology between the X and Y chromosomes generated by a duplication now dated at 6MYA (million years ago). The interest of this gene pair is increased by the case (see topic  Sex Chromosome Aneuploidies) that a gene for asymmetry, the putative defining feature of the human brain, is located in a region of XY homology. Such regions have been identified across mammalian evolution and dated. The Xq21.3/Yp region stands out as hominin specific,, and within this region the Protocadherin 11 XY gene pair remains expressed from both chromosomes and has been subject to accelerated evolution (16 amino-acid substitutions in the Y, and 5 in the X sequence), and according to a recent analysis positive selection on the Y.


Timing of appearance of the difference in the Hominin Lineage as a defined date or a lineage separation event. The point in time associated with lineage separation events may change in the future as the scientific community agrees upon better time estimates. Lineage separation events are defined in 2017 as:

  • the Last Common Ancestor (LCA) of humans and old world monkeys was 25,000 - 30,000 thousand (25 - 30 million) years ago
  • the Last Common Ancestor (LCA) of humans and chimpanzees was 6,000 - 8,000 thousand (6 - 8 million) years ago
  • the emergence of the genus Homo was 2,000 thousand (2 million) years ago
  • the Last Common Ancestor (LCA) of humans and neanderthals was 500 thousand years ago
  • the common ancestor of modern humans was 100 - 300 thousand years ago

Possible Appearance: 
6,000 thousand years ago
Probable Appearance: 
6,000 thousand years ago
Definite Appearance: 
160 thousand years ago
Background Information: 

The class of XY homologous genes is distinct from both those that are X linked and those that are Y linked. Whereas father to son transmission is absent in the former and characteristic of the latter, XY transmission resembles autosomal transmission in including both father to son and father to daughter transmission. The most distinctive characteristic is same-sex concordance, the tendency for a characteristic to be transmitted from a father to children of the same sex.


The class includes genes that are pseudo-autosomal, that is within the region at the telomeres of the short arms of the X and Y within which there is obligatory recombination in male meiosis. Gene sequences here are identical on the X and Y. Pseudo-autosomal region one (PAR1) includes 16 genes, and a much smaller region (PAR2) at the telomeres of the long arms of the X and Y chromosomes includes three genes and recombines much less frequently.


Within both PAR1 and PAR2 there is strict sequence homology between genes on the X and genes on the Y. But a further class of sequences exists within the non-recombining portion of the Y chromosome and this includes XY homologous genes that are not identical in sequence.This class is of particular interest because it includes genes that are homologous but not identical on the X and Y chromosome. Such genes can account for a sexual dimorphism i.e. the target of sexual selection. According to some authors sexual selection and speciation are related. A sexual dimorphism that stands out in Homo sapiens is that concerning verbal and spatial ability.

Implications for Understanding Modern Humans: 

The Protocadherin11XY gene pair has the potential for explaining cerebral development in the hominin lineage. Dating of the original duplication to approximately 6,000,000 years ago suggests that this was related, and may have been causal in, the  separation of the hominin and chimpanzee lineages. If the Xq21.3/Yp11.2 duplication generated the ' hominid stratum ' on the Y chromosome then change within this region must be assumed relate to each of the successive changes in this lineage. Since the other two genes within the region have been eliminated the burden of explanation falls on Protocadherin11Y  and on the chromosomal rearrangements affecting this gene as well as the sequence changes within it.

Occurrence in Other Animals: 

Protocadherin11X is present throughout the mammalian order, and is described as under purifying selection. It is expressed predominantly in the nervous system and during development, and presumably codes for a cell-surface adhesion molecule that specifies a certain set of pathways including cortical connections. Protocadherin11Y is present only in Homo sapiens.

Genetics Topic Attributes
Gene symbols follow the HUGO Gene Nomenclature Committee standard.
Gene Symbol Type of Human-Specific Changes
PCDH11X;PCDH11Y Copy Number Changes, Expression Pattern Change


  1. Accelerated evolution of Protocadherin11X/Y: a candidate gene-pair for cerebral asymmetry and language., Williams, N. A., Close J. P., Giouzeli M., and Crow T. J. , Am J Med Genet B Neuropsychiatr Genet, 09/2006, Volume 141B, Issue 6, p.623-33, (2006)
  2. The Speciation of Modern Homo Sapiens, Crow, T. , Proceedings of the British Academy, Volume 106, (2002)