ClinVar Miner

Submissions for variant NM_199461.4(NANOS1):c.231CTC[3] (p.Ser83del)

dbSNP: rs587777031
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002515744 SCV003251459 benign not provided 2023-12-14 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV002515744 SCV003916645 benign not provided 2023-12-01 criteria provided, single submitter clinical testing NANOS1: PM4:Supporting, BS1, BS2
OMIM RCV000055617 SCV000083842 pathogenic Spermatogenic failure 12 2013-03-01 no assertion criteria provided literature only
Reproductive Health Research and Development, BGI Genomics RCV000055617 SCV001142413 likely benign Spermatogenic failure 12 2020-01-06 no assertion criteria provided curation NM_199461.2:c.240_242delCTC in the NANOS1 gene has an allele frequency of 0.022 in European (Finnish) subpopulation in the gnomAD database. This in-frame deletion happens in a repetitive region without known function. Kusz-Zamelczyk et al. reported this variant as p.Pro77_Ser78delinsPro (PMID: 23315541). Using the quantitative yeast two-hybrid assay, the author tested both mutated NANOS1 alleles for interaction with GEMIN3, and found that the p.Pro34Thr, p.Pro77_Ser78delinsPro allele reduced interaction with GEMIN3 by 14% (PMID: 23315541). In one pedigree, the variant segregate with the phenotype. In contrary, in the second pedigree (patient 2), the father passed this variant to his son, indicating his father is fertile although he has this variant. Taken together, we interprete this variant as Benign/Likely benign variant (PMID: 23315541). ACMG/AMP criteria applied: BS1, BP3.
PreventionGenetics, part of Exact Sciences RCV003915019 SCV004740809 likely benign NANOS1-related disorder 2021-03-16 no assertion criteria provided clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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