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NM_007327.4(GRIN1):c.1447A>C (p.Lys483Gln) AND Intellectual disability, autosomal dominant 8

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Nov 10, 2022
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:
RCV002463982.1

Allele description [Variation Report for NM_007327.4(GRIN1):c.1447A>C (p.Lys483Gln)]

NM_007327.4(GRIN1):c.1447A>C (p.Lys483Gln)

Gene:
GRIN1:glutamate ionotropic receptor NMDA type subunit 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9q34.3
Genomic location:
Preferred name:
NM_007327.4(GRIN1):c.1447A>C (p.Lys483Gln)
HGVS:
  • NC_000009.12:g.137161396A>C
  • NG_011507.1:g.27240A>C
  • NM_000832.7:c.1447A>C
  • NM_001185090.2:c.1510A>C
  • NM_001185091.2:c.1510A>C
  • NM_007327.4:c.1447A>CMANE SELECT
  • NM_021569.4:c.1447A>C
  • NP_000823.4:p.Lys483Gln
  • NP_001172019.1:p.Lys504Gln
  • NP_001172020.1:p.Lys504Gln
  • NP_015566.1:p.Lys483Gln
  • NP_067544.1:p.Lys483Gln
  • NC_000009.11:g.140055848A>C
Protein change:
K483Q
Molecular consequence:
  • NM_000832.7:c.1447A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001185090.2:c.1510A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001185091.2:c.1510A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_007327.4:c.1447A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_021569.4:c.1447A>C - missense variant - [Sequence Ontology: SO:0001583]
Functional consequence:
unknown functional consequence
Observations:
1

Condition(s)

Name:
Intellectual disability, autosomal dominant 8 (NDHMSD)
Synonyms:
Mental retardation, autosomal dominant 8; Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant
Identifiers:
MONDO: MONDO:0013655; MedGen: C3280282; OMIM: 614254

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002754577Servicio Canario de Salud, Hospital Universitario Nuestra Sra. de Candelaria
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Nov 10, 2022)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
caucasiangermlineyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Servicio Canario de Salud, Hospital Universitario Nuestra Sra. de Candelaria, SCV002754577.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1caucasian1not providednot providedclinical testing PubMed (1)

Description

The c.1447A>C (p.Lys483Gln) variant has been identified in our laboratory in a 10-year-old female with delayed psychomotor development, pharmacoresistant epilepsy and focal cortical dysplasia type 1. It was identified as de novo (maternity and paternity confirmed) in the patient. This variant was absent from large population databases, including the Genome Aggregation Database (http://gnomad.broadinstitute.org/). Has not been previously published as pathogenic or benign to our knowledge. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function (MutationTaster, SIFT, PolyPhen, CADD). Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Aug 5, 2023