NM_004959.5(NR5A1):c.895_897del (p.Gln299del) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 27, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV001983449.4

Allele description [Variation Report for NM_004959.5(NR5A1):c.895_897del (p.Gln299del)]

NM_004959.5(NR5A1):c.895_897del (p.Gln299del)

Gene:

NR5A1:nuclear receptor subfamily 5 group A member 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

9q33.3

Genomic location:

Preferred name:

NM_004959.5(NR5A1):c.895_897del (p.Gln299del)

HGVS:

NC_000009.12:g.124493124_124493126del
NG_008176.1:g.19296_19298del
NM_004959.5:c.895_897delMANE SELECT
NP_004950.2:p.Gln299del
NC_000009.11:g.127255402_127255404del
NC_000009.11:g.127255403_127255405del

Protein change:

Q299del

Links:

dbSNP: rs2131279929

NCBI 1000 Genomes Browser:

rs2131279929

Molecular consequence:

NM_004959.5:c.895_897del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:: Oligosynaptic infertility (SPGF1)
Synonyms:: SPERMATOGENIC FAILURE 1; OLIGOCHIASMATIC INFERTILITY
Identifiers:: MONDO: MONDO:0009776; MedGen: C0403810; OMIM: 258150

Name:: 46,XY disorder of sex development
Synonyms:: 46, XY disorder of sex development (DSD)
Identifiers:: MONDO: MONDO:0020040; MedGen: C2751824

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002271967	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 27, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002271967

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 27, 2023)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002271967.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This variant, c.895_897del, results in the deletion of 1 amino acid(s) of the NR5A1 protein (p.Gln299del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with NR5A1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1489814). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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