NM_004959.5(NR5A1):c.129CAA[1] (p.Asn44del) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 21, 2019
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:: RCV001056064.6

Allele description [Variation Report for NM_004959.5(NR5A1):c.129CAA[1] (p.Asn44del)]

NM_004959.5(NR5A1):c.129CAA[1] (p.Asn44del)

Gene:

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

Variant type:

Microsatellite

Cytogenetic location:

9q33.3

Genomic location:

Preferred name:

NM_004959.5(NR5A1):c.129CAA[1] (p.Asn44del)

HGVS:

NC_000009.12:g.124503191GTT[1]
NC_000009.12:g.124503191_124503193GTT[1]
NG_008176.1:g.9227CAA[1]
NM_004959.5:c.129CAA[1]MANE SELECT
NP_004950.2:p.Asn44del
NC_000009.11:g.127265468_127265470del
NC_000009.11:g.127265470GTT[1]
NM_004959.4:c.132_134del
NM_004959.5:c.132_134delMANE SELECT

Protein change:

N44del

Links:

dbSNP: rs1832494273

NCBI 1000 Genomes Browser:

rs1832494273

Molecular consequence:

NM_004959.5:c.129CAA[1] - 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
SCV001220483	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 21, 2019)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 29582157, 30103258, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001220483

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 21, 2019)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

Next-generation sequencing reveals genetic landscape in 46, XY disorders of sexual development patients with variable phenotypes.

Wang H, Zhang L, Wang N, Zhu H, Han B, Sun F, Yao H, Zhang Q, Zhu W, Cheng T, Cheng K, Liu Y, Zhao S, Song H, Qiao J.

Hum Genet. 2018 Mar;137(3):265-277. doi: 10.1007/s00439-018-1879-y. Epub 2018 Mar 26.

PubMed [citation]

PMID:: 29582157

Novel NR5A1 mutations found in Chinese patients with 46, XY disorders of sex development.

Yu B, Liu Z, Gao Y, Mao J, Wang X, Hao M, Ma W, Huang Q, Zhang R, Nie M, Wu X.

Clin Endocrinol (Oxf). 2018 Nov;89(5):613-620. doi: 10.1111/cen.13831. Epub 2018 Sep 19.

PubMed [citation]

PMID:: 30103258

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV001220483.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This variant has been reported to affect NR5A1 protein function (PMID: 29582157, 30103258). For these reasons, this variant has been classified as Pathogenic. This variant has been observed in individuals with clinical features of 46 XY disorders of sex development (PMID: 29582157, 30103258, Invitae). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (ExAC no frequency). This variant, c.132_134del, results in the deletion of 1 amino acid(s) of the NR5A1 protein (p.Asn44del), but otherwise preserves the integrity of the reading frame.

#	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: Mar 5, 2024

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