A Homozygous AKNA Frameshift Variant Is Associated with Microcephaly in a Pakistani Family

Genes (Basel). 2021 Sep 24;12(10):1494. doi: 10.3390/genes12101494.


Primary microcephaly (MCPH) is a prenatal condition of small brain size with a varying degree of intellectual disability. It is a heterogeneous genetic disorder with 28 associated genes reported so far. Most of these genes encode centrosomal proteins. Recently, AKNA was recognized as a novel centrosomal protein that regulates neurogenesis via microtubule organization, making AKNA a likely candidate gene for MCPH. Using linkage analysis and whole-exome sequencing, we found a frameshift variant in exon 12 of AKNA (NM_030767.4: c.2737delG) that cosegregates with microcephaly, mild intellectual disability and speech impairment in a consanguineous family from Pakistan. This variant is predicted to result in a protein with a truncated C-terminus (p.(Glu913Argfs*42)), which has been shown to be indispensable to AKNA's localization to the centrosome and a normal brain development. Moreover, the amino acid sequence is altered from the beginning of the second of the two PEST domains, which are rich in proline (P), glutamic acid (E), serine (S), and threonine (T) and common to rapidly degraded proteins. An impaired function of the PEST domains may affect the intracellular half-life of the protein. Our genetic findings compellingly substantiate the predicted candidacy, based on its newly ascribed functional features, of the multifaceted protein AKNA for association with MCPH.

Keywords: AKNA; autosomal recessive primary microcephaly (MCPH); cerebral cortex; linkage/haplotype analysis; whole-exome sequencing (WES).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Centrosome / metabolism
  • Cerebral Cortex / diagnostic imaging
  • Cerebral Cortex / pathology
  • Child
  • DNA-Binding Proteins / genetics*
  • Exome Sequencing
  • Female
  • Frameshift Mutation / genetics
  • Genetic Linkage / genetics
  • Genetic Predisposition to Disease*
  • Haplotypes / genetics
  • Homozygote
  • Humans
  • Intellectual Disability / epidemiology
  • Intellectual Disability / genetics*
  • Intellectual Disability / pathology
  • Male
  • Microcephaly / epidemiology
  • Microcephaly / genetics*
  • Microcephaly / pathology
  • Nuclear Proteins / genetics*
  • Pakistan / epidemiology
  • Pedigree
  • Transcription Factors / genetics*


  • AKNA protein, human
  • DNA-Binding Proteins
  • Nuclear Proteins
  • Transcription Factors