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NM_001282717.2(STAG3):c.1936dup (p.Ala646fs) AND Spermatogenic failure 61

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 20, 2021
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:
RCV001797555.1

Allele description [Variation Report for NM_001282717.2(STAG3):c.1936dup (p.Ala646fs)]

NM_001282717.2(STAG3):c.1936dup (p.Ala646fs)

Gene:
STAG3:STAG3 cohesin complex component [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
7q22.1
Genomic location:
Preferred name:
NM_001282717.2(STAG3):c.1936dup (p.Ala646fs)
HGVS:
  • NC_000007.14:g.100200844dup
  • NG_034114.1:g.28121dup
  • NM_001282716.1:c.1936dup
  • NM_001282717.2:c.1936dupMANE SELECT
  • NM_001282718.2:c.1762dup
  • NM_001375438.1:c.1936dup
  • NM_012447.4:c.1936dup
  • NP_001269645.1:p.Ala646fs
  • NP_001269646.1:p.Ala646fs
  • NP_001269647.1:p.Ala588fs
  • NP_001362367.1:p.Ala646fs
  • NP_036579.2:p.Ala646fs
  • NC_000007.13:g.99798467dup
  • NM_001282718.2:c.1762dupG
  • NR_028039.1:n.3364dup
  • NR_028040.1:n.2676dup
  • NR_166147.1:n.2525dup
Nucleotide change:
1-BP DUP, 1762G
Protein change:
A588fs
Links:
OMIM: 608489.0006; dbSNP: rs1251996684
NCBI 1000 Genomes Browser:
rs1251996684
Molecular consequence:
  • NM_001282716.1:c.1936dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001282717.2:c.1936dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001282718.2:c.1762dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001375438.1:c.1936dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_012447.4:c.1936dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_028039.1:n.3364dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_028040.1:n.2676dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_166147.1:n.2525dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Spermatogenic failure 61 (SPGF61)
Identifiers:
MONDO: MONDO:0030507; MedGen: C5562048; OMIM: 619672

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002039147OMIM
no assertion criteria provided
Pathogenic
(Dec 20, 2021) 		germlineliterature only

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

Help

Summary from all submissions

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

Citations

PubMed

Sequencing of a 'mouse azoospermia' gene panel in azoospermic men: identification of RNF212 and STAG3 mutations as novel genetic causes of meiotic arrest.

Riera-Escamilla A, Enguita-Marruedo A, Moreno-Mendoza D, Chianese C, Sleddens-Linkels E, Contini E, Benelli M, Natali A, Colpi GM, Ruiz-Castañé E, Maggi M, Baarends WM, Krausz C.

Hum Reprod. 2019 Jun 4;34(6):978-988. doi: 10.1093/humrep/dez042. Erratum in: Hum Reprod. 2020 Aug 1;35(8):1945-1946. doi: 10.1093/humrep/deaa179.

PubMed [citation]
PMID:
31125047

Details of each submission

From OMIM, SCV002039147.1

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

Description

In an infertile Spanish man (07-002) with complete meiotic arrest (SPGF61; 619672), Riera-Escamilla et al. (2019) identified compound heterozygosity for mutations in the STAG3 gene: a 1-bp duplication (c.1762dupG, NM_001282718.2), causing a frameshift predicted to result in a premature termination codon (Ala588GlyfsTer9) and thus a protein lacking the entire armadillo-type domain; and a splice site mutation in intron 23 of STAG3 (c.2394+1G-A; 608489.0007). The 1-bp duplication was found in the gnomAD database with a minor allele frequency of 0.000004073, whereas the splicing mutation was not present in gnomAD. Sanger sequencing showed that the proband's fertile brother was a heterozygous carrier of the 1-bp duplication.

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

Last Updated: Dec 24, 2023