Hemizygous Variants

Definition [ref]

  • Variants falling within regions without allelic counterparts.
  • Pertaining to a diploid cell with only one copy of a gene instead of the usual two copies.

Hemizygous variants are those that are X-linked and are not in the pseudoautosomal regions [ref]:

  • The pseudoautosomal regions get their name because any genes within them (so far at least 29 have been found) [ref] are inherited just like any autosomal genes. PAR1 comprises 2.6 Mbp of the short-arm tips of both X and Y chromosomes in humans and great apes (X and Y are 155 Mbp and 59 Mbp in total). PAR2 is at the tips of the long arms, spanning 320 kbp [ref].

VarSome Clinical callers

Example of X-linked variant within pseudoautosomal region:

VarSome Clinical would call the variant above as heterozygous. In this case, VarSome Clinical's Sentieon/GATK variant caller does not distinguish between heterozygous and hemizygous terms. However, since the difference between the terms hemizygous and heterozygous is largely semantic, we feel the variant is still called correctly.