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NM_000475.5(NR0B1):c.376G>A (p.Val126Met)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(3);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Sep 21, 2021)
Last evaluated:
Dec 31, 2019
Accession:
VCV000225425.6
Variation ID:
225425
Description:
single nucleotide variant
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NM_000475.5(NR0B1):c.376G>A (p.Val126Met)

Allele ID
227422
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
Xp21.2
Genomic location
X: 30308988 (GRCh38) GRCh38 UCSC
X: 30327105 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_858:g.5391G>A
LRG_858t1:c.376G>A LRG_858p1:p.Val126Met
NC_000023.10:g.30327105C>T
... more HGVS
Protein change
V126M
Other names
-
Canonical SPDI
NC_000023.11:30308987:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00583 (T)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00279
Exome Aggregation Consortium (ExAC) 0.00279
The Genome Aggregation Database (gnomAD) 0.00153
1000 Genomes Project 0.00583
Links
ClinGen: CA10376402
dbSNP: rs193205940
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 2 criteria provided, single submitter Mar 1, 2017 RCV000614813.2
Benign 1 criteria provided, single submitter Dec 31, 2019 RCV000864291.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations May 28, 2019 RCV000490511.2
Likely benign 1 no assertion criteria provided - RCV001574018.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
NR0B1 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
121 286

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Mar 18, 2016)
criteria provided, single submitter
Method: reference population
Congenital adrenal hypoplasia, X-linked
Allele origin: germline
Soonchunhyang University Bucheon Hospital,Soonchunhyang University Medical Center
Accession: SCV000267426.1
Submitted: (Apr 14, 2016)
Evidence details
Publications
PubMed (2)
Benign
(Mar 01, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000730536.1
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Congenital adrenal hypoplasia, X-linked
Allele origin: unknown
Mendelics
Accession: SCV001141569.1
Submitted: (Oct 22, 2019)
Evidence details
Benign
(Dec 31, 2019)
criteria provided, single submitter
Method: clinical testing
Congenital adrenal hypoplasia, X-linked
46,XY sex reversal, type 2
Allele origin: germline
Invitae
Accession: SCV001005073.2
Submitted: (Jan 29, 2020)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Study: VKGL Data-share Consensus
Accession: SCV001800706.1
Submitted: (Aug 19, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001971719.1
Submitted: (Sep 21, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Novel mutations in DAX1 of X-linked adrenal hypoplasia congenita over several generations in one family. Xu XQ Endocrine practice : official journal of the American College of Endocrinology and the American Association of Clinical Endocrinologists 2013 PMID: 23512386
DAX-1 gene mutations and deletions in Japanese patients with adrenal hypoplasia congenita and hypogonadotropic hypogonadism. Kinoshita E Hormone research 1997 PMID: 9195207

Text-mined citations for rs193205940...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 07, 2021