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NM_000834.5(GRIN2B):c.1745C>T (p.Pro582Leu) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 20, 2021
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:
RCV001908529.6

Allele description [Variation Report for NM_000834.5(GRIN2B):c.1745C>T (p.Pro582Leu)]

NM_000834.5(GRIN2B):c.1745C>T (p.Pro582Leu)

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.1745C>T (p.Pro582Leu)
HGVS:
  • NC_000012.12:g.13611760G>A
  • NG_031854.2:g.375253C>T
  • NM_000834.5:c.1745C>TMANE SELECT
  • NP_000825.2:p.Pro582Leu
  • NC_000012.11:g.13764694G>A
Protein change:
P582L
Links:
dbSNP: rs796052581
NCBI 1000 Genomes Browser:
rs796052581
Molecular consequence:
  • NM_000834.5:c.1745C>T - 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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002167447Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Apr 20, 2021) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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, SCV002167447.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant is not present in population databases (ExAC no frequency). This sequence change replaces proline with leucine at codon 582 of the GRIN2B protein (p.Pro582Leu). The proline residue is highly conserved and there is a moderate physicochemical difference between proline and leucine. This variant has not been reported in the literature in individuals with GRIN2B-related conditions. 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. 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 expected to disrupt GRIN2B protein function.

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

Last Updated: Sep 29, 2024