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NM_004959.5(NR5A1):c.274C>T (p.Arg92Trp) AND 46,XX sex reversal 4

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Mar 23, 2016
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:
RCV000490553.7

Allele description [Variation Report for NM_004959.5(NR5A1):c.274C>T (p.Arg92Trp)]

NM_004959.5(NR5A1):c.274C>T (p.Arg92Trp)

Gene:
NR5A1:nuclear receptor subfamily 5 group A member 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9q33.3
Genomic location:
Preferred name:
NM_004959.5(NR5A1):c.274C>T (p.Arg92Trp)
HGVS:
  • NC_000009.12:g.124500686G>A
  • NG_008176.1:g.11735C>T
  • NM_004959.5:c.274C>TMANE SELECT
  • NP_004950.2:p.Arg92Trp
  • NC_000009.11:g.127262965G>A
  • NM_004959.4:c.274C>T
  • p.R92W
Protein change:
R92W; ARG92TRP
Links:
OMIM: 184757.0019; dbSNP: rs886039769
NCBI 1000 Genomes Browser:
rs886039769
Molecular consequence:
  • NM_004959.5:c.274C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
46,XX sex reversal 4 (SRXX4)
Synonyms:
46,XX SEX REVERSAL, SRY-NEGATIVE; 46, XX sex reversal 4
Identifiers:
MONDO: MONDO:0060489; MedGen: C4479552; OMIM: 617480

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000579208OMIM
no assertion criteria provided
Pathogenic
(Apr 23, 2021)
germlineliterature only

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

SCV000622150Undiagnosed Diseases Network, NIH
criteria provided, single submitter

(Bashamboo A et al. (Hum Mol Genet 2016))
Uncertain significance
(Mar 23, 2016)
de novoclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
African Americande novoyes1not providednot providednot providednoclinical testing

Citations

PubMed

NR5A1 is a novel disease gene for 46,XX testicular and ovotesticular disorders of sex development.

Baetens D, Stoop H, Peelman F, Todeschini AL, Rosseel T, Coppieters F, Veitia RA, Looijenga LH, De Baere E, Cools M.

Genet Med. 2017 Apr;19(4):367-376. doi: 10.1038/gim.2016.118. Epub 2016 Aug 4.

PubMed [citation]
PMID:
27490115
PMCID:
PMC5392598

Identical NR5A1 Missense Mutations in Two Unrelated 46,XX Individuals with Testicular Tissues.

Igarashi M, Takasawa K, Hakoda A, Kanno J, Takada S, Miyado M, Baba T, Morohashi KI, Tajima T, Hata K, Nakabayashi K, Matsubara Y, Sekido R, Ogata T, Kashimada K, Fukami M.

Hum Mutat. 2017 Jan;38(1):39-42. doi: 10.1002/humu.23116. Epub 2016 Sep 21.

PubMed [citation]
PMID:
27610946
See all PubMed Citations (3)

Details of each submission

From OMIM, SCV000579208.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (3)

Description

In 5 patients from 4 unrelated families with 46,XX sex reversal (SRXX4; 617480), Bashamboo et al. (2016) identified a c.274C-T transition in the NR5A1 gene that resulted in an arg-to-trp substitution at codon 92 (R92W). In 1 of these families, a sister had 46,XY sex reversal (SRXY3; 612965) due to the same variant. In 2 families, the variant was maternally inherited, in 1 it occurred as a de novo event, and in 1 family the mutation was not present in the father, but the mother was deceased and no DNA was available. The variant was absent from the dbSNP (build 138), ExAC, and 1000 Genomes Project databases, and from an internal database containing exomes of 400 individuals as well as more than 1,000 fertile controls Sanger sequenced for NR5A1. The arg92 residue in NR5A1 is evolutionarily conserved to zebrafish.

In 3 unrelated probands with 46,XX (ovo)testicular disorder of sexual development (DSD), Baetens et al. (2017) found a c.274C-T transition in exon 4 of the NR5A1 gene (c.274C-T, NM_004959.4) that resulted in an R92W substitution in the protein. Several unaffected female first-degree relatives of the probands from each of the families also carried this mutation, suggesting that this variant is weakly penetrant. A potential founder effect was suggested by haplotype analysis. The arg92 residue is highly evolutionarily conserved to zebrafish and located in the Ftz-F1 region, probably involved with DNA-binding specificity and stability. The R92W mutation was absent from the Exome Sequencing Project (ESP), ExAC, Genome of the Netherlands (GoNL), and 1000 Genomes Project databases and from an in-house exome database.

Igarashi et al. (2017) identified the R92W mutation (c.274C-T, NM_004959.4) in 2 unrelated Japanese patients with 46,XX testicular/ovotesticular DSD. The mutation was absent from the clinically normal mothers and from 200 Japanese controls. One of the fathers, who was unaffected, carried the mutation; the other father was not available for analysis. In vitro assays showed that the mutant protein was less sensitive than wildtype to NR0B1 (300473)-induced suppression on the SOX9 (608160) enhancer element.

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

From Undiagnosed Diseases Network, NIH, SCV000622150.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1African American1not providednoclinical testing PubMed (1)

Description

Likely pathogenicity based on finding it once in our study inferred de novo in a 31-year-old 46,XX male with hypogonadism, decreased testicular size, and primary testicular failure. This patient has been reported in PMID 27378692.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Oct 8, 2024