nstd180 (Levchenko et al. 2020)
- Organism:
- Human
- Study Type:
- Case-Control
- Submitter:
- Anastasia Levchenko
- Description:
- In the present study NRG1, PIP4K2A, HTR2C, GSK3B, BDNF, and NGF were analyzed by sequencing a cohort of 19 patients with bipolar affective disorder, 41 patients with recurrent depressive disorder, 55 patients with depressive episode, and 34 healthy controls. Sequencing analysis resulted in 149 VCFs with 49 different variants, of which eight are novel, i.e. not listed in any of the three databases – dbSNP, ExAC, or gnomAD. Among the novel variants, four are 2- to 81-bp deletions, one is a 1-bp duplication, and three are 1-bp substitutions. The novel variants (all in a heterozygous state, except for the 81-bp deletion present on the X chromosome in a male) were each present in one to three patients with depression, indicating minor allele frequency from 0.7% to 2% in the population under study. The 81-bp deletion in the last exon of all HTR2C’s transcripts, NC_000023.11:g.114906768_114906848del, creates an inframe deletion of 27 amino acids (ENST00000276198.5 and ENST00000371951.5) or frameshift deletion of 27 amino acids, resulting in 1 aa inserted (ENST00000371950.3). The variant is deleterious for ENST00000276198.5 and ENST00000371951.5 according to PROVEAN (Choi and Chan, 2015). Moreover, it may affect splicing of the last intron of all HTR2C's transcripts, by erasing multiple exonic splicing enhancer motifs, as deemed by HumanSplicingFinder (Desmet et al., 2009). This deletion was present on both chromosomal copies in one patient with recurrent depressive disorder of moderate severity. No association with clinical subphenotypes was established for that variant. See Variant Summary counts for nstd180 in dbVar Variant Summary.
- Publication(s):
- Levchenko et al. 2020