A Biallelic Frameshift Indel in PPP1R35 as a Cause of Primary Microcephaly

Authors

Moez Dawood
Gulsen Akay
Tadahiro Mitani
Dana Marafi
Jawid M Fatih
Alper Gezdirici
Hossein Najmabadi
Kimia Kahrizi
Jaya Punetha
Christopher M Grochowski
Haowei Du
Angad Jolly
He Li
Zeynep Coban-Akdemir
Fritz J Sedlazeck
Jill V Hunter
Shalini N Jhangiani
Donna Muzny
Davut Pehlivan
Jennifer E Posey
Claudia M B Carvalho
Richard A Gibbs
James R Lupski

Publication Date

3-1-2023

Journal

American Journal of Medical Genetics

Abstract

Protein phosphatase 1 regulatory subunit 35 (PPP1R35) encodes a centrosomal protein required for recruiting microtubule-binding elongation machinery. Several proteins in this centriole biogenesis pathway correspond to established primary microcephaly (MCPH) genes, and multiple model organism studies hypothesize PPP1R35 as a candidate MCPH gene. Here, using exome sequencing (ES) and family-based rare variant analyses, we report a homozygous, frameshifting indel deleting the canonical stop codon in the last exon of PPP1R35 [Chr7: c.753_*3delGGAAGCGTAGACCinsCG (p.Trp251Cysfs*22)]; the variant allele maps in a 3.7 Mb block of absence of heterozygosity (AOH) in a proband with severe MCPH (-4.3 SD at birth, -6.1 SD by 42 months), pachygyria, and global developmental delay from a consanguineous Turkish kindred. Droplet digital PCR (ddPCR) confirmed mutant mRNA expression in fibroblasts. In silico prediction of the translation of mutant PPP1R35 is expected to be elongated by 18 amino acids before encountering a downstream stop codon. This complex indel allele is absent in public databases (ClinVar, gnomAD, ARIC, 1000 genomes) and our in-house database of 14,000+ exomes including 1800+ Turkish exomes supporting predicted pathogenicity. Comprehensive literature searches for PPP1R35 variants yielded two probands affected with severe microcephaly (-15 SD and -12 SD) with the same homozygous indel from a single, consanguineous, Iranian family from a cohort of 404 predominantly Iranian families. The lack of heterozygous cases in two large cohorts representative of the genetic background of these two families decreased our suspicion of a founder allele and supports the contention of a recurrent mutation. We propose two potential secondary structure mutagenesis models for the origin of this variant allele mediated by hairpin formation between complementary GC rich segments flanking the stop codon via secondary structure mutagenesis.

Keywords

PPP1R35, microcephaly, primary microcephaly, MCPH, centrosome, centriole, complex indel

Comments

Supplementary Materials

PMID: 36598158