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NM_199461.4(NANOS1):c.231CTC[3] (p.Ser83del) AND Spermatogenic failure 12

Germline classification:
Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:
Jan 6, 2020
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000055617.6

Allele description [Variation Report for NM_199461.4(NANOS1):c.231CTC[3] (p.Ser83del)]

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

Genes:
LOC130004821:ATAC-STARR-seq lymphoblastoid silent region 2865 [Gene]
NANOS1:nanos C2HC-type zinc finger 1 [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
10q26.11
Genomic location:
Preferred name:
NM_199461.4(NANOS1):c.231CTC[3] (p.Ser83del)
Other names:
S78del
HGVS:
  • NC_000010.11:g.119030032CTC[3]
  • NG_050764.1:g.5317CTC[3]
  • NM_199461.3:c.240_242delCTC
  • NM_199461.4:c.231CTC[3]MANE SELECT
  • NP_955631.1:p.Ser83del
  • NC_000010.10:g.120789543_120789545del
  • NC_000010.10:g.120789544CTC[3]
  • NM_199461.2:c.240_242delCTC
Protein change:
S83del; SER78DEL
Links:
OMIM: 608226.0001; dbSNP: rs587777031
NCBI 1000 Genomes Browser:
rs587777031
Molecular consequence:
  • NM_199461.4:c.231CTC[3] - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:
Spermatogenic failure 12 (SPGF12)
Identifiers:
MONDO: MONDO:0014172; MedGen: C3809427; OMIM: 615413

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000083842OMIM
no assertion criteria provided
Pathogenic
(Mar 1, 2013)
germlineliterature only

PubMed (1)
[See all records that cite this PMID]

SCV001142413Reproductive Health Research and Development, BGI Genomics
no assertion criteria provided
Likely benign
(Jan 6, 2020)
germlinecuration

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Citations

PubMed

Mutations of NANOS1, a human homologue of the Drosophila morphogen, are associated with a lack of germ cells in testes or severe oligo-astheno-teratozoospermia.

Kusz-Zamelczyk K, Sajek M, Spik A, Glazar R, Jędrzejczak P, Latos-Bieleńska A, Kotecki M, Pawelczyk L, Jaruzelska J.

J Med Genet. 2013 Mar;50(3):187-93. doi: 10.1136/jmedgenet-2012-101230. Epub 2013 Jan 12.

PubMed [citation]
PMID:
23315541

Details of each submission

From OMIM, SCV000083842.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In 2 infertile Polish men with azoospermia (SPGF12; 615413), Kusz-Zamelczyk et al. (2013) identified heterozygosity for deletion of a single serine residue (Pro77_Ser78delinsPro) from a stretch of 6 serine residues in the NANOS1 gene. The deletion was not found in 400 fertile Polish men who had at least 2 children, or in the 1000 Genomes Project database. The first patient inherited the deletion from his mother, and an infertile maternal uncle also carried the deletion; the second patient inherited the deletion from his father, indicating incomplete penetrance. In a yeast 2-hybrid assay, the mutant allele caused an approximately 14% decrease in NANOS1 interaction with GEMIN3 (DDX20; 606168). In both patients, a P34T variant in NANOS1 was also present on the mutant allele; however, P34T was present among fertile and infertile men at the same allele frequency (approximately 4.9%) and, when tested alone, did not alter NANOS1-GEMIN3 binding in the yeast 2-hybrid assay. Kusz-Zamelczyk et al. (2013) also noted that the only P34T homozygotes identified in the study were the second infertile man and his deletion-carrying father. Seminiferous tubule histology was available for the first patient and showed a Sertoli cell-only phenotype, with complete lack of germ cells.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Reproductive Health Research and Development, BGI Genomics, SCV001142413.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 20, 2024