NM_000834.5(GRIN2B):c.397A>G (p.Ile133Val) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 25, 2023
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:: RCV003813449.2

Allele description [Variation Report for NM_000834.5(GRIN2B):c.397A>G (p.Ile133Val)]

NM_000834.5(GRIN2B):c.397A>G (p.Ile133Val)

Gene:

GRIN2B:glutamate ionotropic receptor NMDA type subunit 2B [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12p13.1

Genomic location:

Preferred name:

NM_000834.5(GRIN2B):c.397A>G (p.Ile133Val)

HGVS:

NC_000012.12:g.13865812T>C
NG_031854.2:g.121201A>G
NM_000834.5:c.397A>GMANE SELECT
NM_001413992.1:c.397A>G
NM_001413993.1:c.397A>G
NM_001413994.1:c.397A>G
NM_001413995.1:c.397A>G
NP_000825.2:p.Ile133Val
NP_001400921.1:p.Ile133Val
NP_001400922.1:p.Ile133Val
NP_001400923.1:p.Ile133Val
NP_001400924.1:p.Ile133Val
NC_000012.11:g.14018746T>C

Protein change:

I133V

Molecular consequence:

NM_000834.5:c.397A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001413992.1:c.397A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001413993.1:c.397A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001413994.1:c.397A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001413995.1:c.397A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Intellectual disability, autosomal dominant 6 (MRD6)
Synonyms:: INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL DOMINANT 6, WITH OR WITHOUT SEIZURES
Identifiers:: MONDO: MONDO:0013509; MedGen: C3151411; OMIM: 613970

Name:: Developmental and epileptic encephalopathy, 27 (DEE27)
Synonyms:: Epileptic encephalopathy, early infantile, 27
Identifiers:: MONDO: MONDO:0014505; MedGen: C4015316; Orphanet: 3451; OMIM: 616139

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Homo sapiens general transcription factor IIH, polypeptide 4, 52kDa (GTF2H4), mR...
Homo sapiens general transcription factor IIH, polypeptide 4, 52kDa (GTF2H4), mRNA
gi|34222289|ref|NM_001517.3|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004610154	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 25, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004610154

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 25, 2023)

germline

clinical testing

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

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004610154.1

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

Description

This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 133 of the GRIN2B protein (p.Ile133Val). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with GRIN2B-related conditions. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt GRIN2B protein function with a negative predictive value of 95%. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Sep 29, 2024

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