NM_001134407.3(GRIN2A):c.82_84del (p.Glu28del) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 17, 2017
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:: RCV000484425.1

Allele description [Variation Report for NM_001134407.3(GRIN2A):c.82_84del (p.Glu28del)]

NM_001134407.3(GRIN2A):c.82_84del (p.Glu28del)

Gene:

GRIN2A:glutamate ionotropic receptor NMDA type subunit 2A [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16p13.2

Genomic location:

Preferred name:

NM_001134407.3(GRIN2A):c.82_84del (p.Glu28del)

HGVS:

NC_000016.10:g.10180329_10180331del
NG_011812.2:g.7425_7427del
NM_000833.5:c.82_84del
NM_001134407.3:c.82_84delMANE SELECT
NM_001134408.2:c.82_84del
NP_000824.1:p.Glu28del
NP_001127879.1:p.Glu28del
NP_001127880.1:p.Glu28del
NC_000016.9:g.10274185_10274187del
NC_000016.9:g.10274186_10274188del
NG_011812.1:g.7425_7427del
NM_000833.3:c.82_84delGAG

Protein change:

E28del

Links:

dbSNP: rs767188122

NCBI 1000 Genomes Browser:

rs767188122

Molecular consequence:

NM_000833.5:c.82_84del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001134407.3:c.82_84del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001134408.2:c.82_84del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000573409	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Uncertain significance (Feb 17, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000573409

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Uncertain significance
(Feb 17, 2017)

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, SCV000573409.4

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

Description

The c.82_84delGAG variant in the GRIN2A gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The c.82_84delGAG variant results in the in-frame deletion of three base pairs, which is predicted to cause loss of the Glutamic Acid residue at position 28 in the protein, denoted p.Glu28del. The deleted residue is conserved through mammals. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. The c.82_84delGAG variant is not observed with any significant frequency in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). We interpret c.82_84delGAG as a variant of uncertain significance.

#	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: Sep 29, 2024

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