NM_000901.5(NR3C2):c.2903dup (p.Pro969fs) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jul 12, 2018
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:: RCV001008236.1

Allele description [Variation Report for NM_000901.5(NR3C2):c.2903dup (p.Pro969fs)]

NM_000901.5(NR3C2):c.2903dup (p.Pro969fs)

Gene:

NR3C2:nuclear receptor subfamily 3 group C member 2 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

4q31.23

Genomic location:

Preferred name:

NM_000901.5(NR3C2):c.2903dup (p.Pro969fs)

HGVS:

NC_000004.12:g.148081396dup
NG_013350.1:g.366126dup
NM_000901.5:c.2903dupMANE SELECT
NM_001166104.2:c.2552dup
NM_001354819.1:c.2552dup
NP_000892.2:p.Pro969fs
NP_001159576.1:p.Pro852fs
NP_001341748.1:p.Pro852fs
NC_000004.11:g.149002547dup
NM_000901.4:c.2903dupT
NR_148974.2:n.2664dup

Protein change:

P852fs

Links:

dbSNP: rs1578859390

NCBI 1000 Genomes Browser:

rs1578859390

Molecular consequence:

NM_000901.5:c.2903dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001166104.2:c.2552dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354819.1:c.2552dup - frameshift variant - [Sequence Ontology: SO:0001589]
NR_148974.2:n.2664dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001168002	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely pathogenic (Jul 12, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001168002

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely pathogenic
(Jul 12, 2018)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV001168002.1

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

Description

The c.2903dupT variant in the NR3C2 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This frameshift variant replaces the typical last 16 amino acid residues in the NR3C2 protein with 44 different amino acid residues. This alteration may interfere with the proper formation and/or function of the NR3C2 protein. The c.2903dupT variant is not observed in large population cohorts (Lek et al., 2016). We interpret c.2903dupT as a likely pathogenic variant.

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

Last Updated: Apr 23, 2022

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