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NM_007327.4(GRIN1):c.957G>A (p.Pro319=) AND Intellectual disability, autosomal dominant 8

Germline classification:
Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:
Mar 27, 2022
Review status:
criteria provided, conflicting classifications
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:
RCV000767988.4

Allele description [Variation Report for NM_007327.4(GRIN1):c.957G>A (p.Pro319=)]

NM_007327.4(GRIN1):c.957G>A (p.Pro319=)

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.957G>A (p.Pro319=)
HGVS:
  • NC_000009.12:g.137157026G>A
  • NG_011507.1:g.22870G>A
  • NM_000832.7:c.957G>A
  • NM_001185090.2:c.1020G>A
  • NM_001185091.2:c.1020G>A
  • NM_007327.4:c.957G>AMANE SELECT
  • NM_021569.4:c.957G>A
  • NP_000823.4:p.Pro319=
  • NP_001172019.1:p.Pro340=
  • NP_001172020.1:p.Pro340=
  • NP_015566.1:p.Pro319=
  • NP_067544.1:p.Pro319=
  • NC_000009.11:g.140051478G>A
Links:
dbSNP: rs766888803
NCBI 1000 Genomes Browser:
rs766888803
Molecular consequence:
  • NM_000832.7:c.957G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001185090.2:c.1020G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001185091.2:c.1020G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_007327.4:c.957G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_021569.4:c.957G>A - synonymous variant - [Sequence Ontology: SO:0001819]

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
SCV000898731Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Oct 24, 2018)
germlineclinical testing

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

SCV003299345Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely benign
(Mar 27, 2022)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot 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

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 Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago, SCV000898731.1

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

Description

GRIN1 NM_007327.3 exon 6 p.Pro319= (c.957G>A): This variant has not been reported in the literature and is present in 0.03% (6/19618) of East Asian alleles in the Genome Aggregation Database (http://gnomad.broadinstitute.org/variant/9-140051478-G-A). Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. Of note, this variant is a silent variant and does not change the amino acid, reducing the probability that this variant is disease causing. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.

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

From Invitae, SCV003299345.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 14, 2024