In our study, we used whole‐exome sequencing, family segregation and bioinformatics to identify a homozygous 3 bp duplication in the GPI remodelling gene PGAP1 (c.1226_1229dup p.(Val411Argfs*3) [NM_024989.4]) in a female patient with a neurodevelopmental disorder, encephalopathy and nonspecific autosomal recessive forms of intellectual disability (ARID). The gene discussed is PGAP1; the disease is Encephalopathy.