Exome sequencing reveals SYCE1 mutation associated with autosomal recessive azoospermia in an Iranian family; the second report in the worldwide

Background: 30-55% of couples’ infertility is due to male infertility. Azoospermia which is characterized by absence of sperm in the ejaculate, accounts for 10-15% of infertility in the males and generally affects 1% of this population. Azoospermia is confirmed using endocrine tests and urologic and genetic analyses. Currently the most common genetic causes of azoospermia are; mutations in CFTR gene, chromosomal abnormalities and microdeletions of chromosome Y.Objective: Identification of disease-causing gene in a large Iranian pedigree affected to azoospermia.Materials and Methods: Consent form was signed. DNA was isolated from peripheral blood leukocytes of proband and family members of a consanguineous Iranian family affected to azoospermia. Whole exome sequencing (WES) was done on proband. Preliminary filtering of sequence variations was done to identify all nonsynonymous, stop-gain, stop-loss, deletion, insertion, and splice sites homozygous variants present in the proband. Subsequently, variations with a MAF > 0.01 in public databases (1000Genomes, ExAc, ESP, GnomAD, Iranome, HEX, SISu and GME-Variome) were removed to find the probable disease-causing variations. Candidate variants were PCR-amplified and sequenced by Sanger method subsequently checked in family members in order to co-segregation analysis.Results: This approach led us to identify a novel splice site variation c.375-2A> G in SYCE1 in the proband and this variant co-segregated with the disease status in the family and was not found in 200 ethnically matched controls or in 100 in-house control exomes and Iranome database.Conclusion: Our study resulted in the second report of azoospermia with mutation in SYCE1 gene in worldwide. Mutation in this gene has been previously reported only two times: in two sisters from a consanguineous Arab family from Israel with primary ovarian failure (2014) and in two affected brothers from a consanguineous Jewish family with azoospermia (2015). SYCE1 encodes Synaptonemal complex (SC) central element 1 protein which plays an essential role during meiosis and its significance was previously demonstrated in a mutant mouse model so that male and female Syce1 null mice were infertile. Our variation resulted in RNA mis-splicing of SYCE1, and a premature stop codon. So, this variation can be resulted in inhibiting of synapsis initiation and consequently, completion of meiosis. Our results emphasize the importance of SC proteins in spermatogenenesis and suggests that a low percentage of infertility cases may be due to mutations in SC genes. The characterization of these mutations, together with available functional studies, will enable a deeper understanding of the underlying molecular bases for some of the infertile cases.

Keywords:

Azoospermia , Splice site variation , SYCE1 , Synaptonemal complex , Whole exome sequencing