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NM_001134407.3(GRIN2A):c.547T>A (p.Phe183Ile)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(2);Uncertain significance(3)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Aug 31, 2021)
Last evaluated:
Jun 17, 2020
Accession:
VCV000129189.11
Variation ID:
129189
Description:
single nucleotide variant
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NM_001134407.3(GRIN2A):c.547T>A (p.Phe183Ile)

Allele ID
134635
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
16p13.2
Genomic location
16: 9938419 (GRCh38) GRCh38 UCSC
16: 10032276 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
Q12879:p.Phe183Ile
NC_000016.10:g.9938419A>T
NC_000016.9:g.10032276A>T
... more HGVS
Protein change
F183I
Other names
-
Canonical SPDI
NC_000016.10:9938418:A:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00004
Trans-Omics for Precision Medicine (TOPMed) 0.00006
Trans-Omics for Precision Medicine (TOPMed) 0.00010
The Genome Aggregation Database (gnomAD) 0.00004
Exome Aggregation Consortium (ExAC) 0.00004
Links
ClinGen: CA153033
UniProtKB: Q12879#VAR_067726
dbSNP: rs587780353
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Jun 17, 2020 RCV000711852.6
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts May 22, 2020 RCV000989528.3
Likely benign 1 criteria provided, single submitter May 14, 2013 RCV000117178.2
Uncertain significance 1 criteria provided, single submitter Oct 27, 2017 RCV000716783.1
Pathogenic 1 no assertion criteria provided Jan 1, 2017 RCV000656052.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
GRIN2A Little evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
1221 1267

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(May 14, 2013)
criteria provided, single submitter
Method: clinical testing
AllHighlyPenetrant
(Autosomal dominant inheritance)
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV000151342.1
Submitted: (Apr 30, 2014)
Evidence details
Uncertain significance
(Sep 18, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000842258.1
Submitted: (Aug 31, 2018)
Evidence details
Publications
PubMed (5)
Benign
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Epilepsy, focal, with speech disorder and with or without mental retardation
Allele origin: unknown
Mendelics
Accession: SCV001139948.1
Submitted: (Oct 22, 2019)
Evidence details
Uncertain significance
(Oct 27, 2017)
criteria provided, single submitter
Method: clinical testing
History of neurodevelopmental disorder
Allele origin: germline
Ambry Genetics
Accession: SCV000847626.3
Submitted: (Nov 30, 2020)
Evidence details
Publications
PubMed (1)
Comment:
The p.F183I variant (also known as c.547T>A), located in coding exon 2 of the GRIN2A gene, results from a T to A substitution at nucleotide … (more)
Likely benign
(May 22, 2020)
criteria provided, single submitter
Method: clinical testing
Epilepsy, focal, with speech disorder and with or without mental retardation
Allele origin: germline
Invitae
Accession: SCV001011206.3
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Jun 17, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001815411.1
Submitted: (Aug 31, 2021)
Evidence details
Comment:
Reported previously in an individual with benign epilepsy with centrotemporal spikes (rolandic epilepsy) and mild developmental delay; however, the F183I variant was inherited from an … (more)
Pathogenic
(Jan 01, 2017)
no assertion criteria provided
Method: case-control
Rolandic epilepsy
Allele origin: germline
Bioinformatics Core,Luxembourg Center for Systems Biomedicine
Study: EUROEPINOMICS COGIE
Accession: SCV000588328.1
Submitted: (Aug 09, 2017)
Evidence details
Publications
PubMed (1)
Comment:
CAADphred>15

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Exome-wide analysis of mutational burden in patients with typical and atypical Rolandic epilepsy. Bobbili DR European journal of human genetics : EJHG 2018 PMID: 29358611
Altered zinc sensitivity of NMDA receptors harboring clinically-relevant mutations. Serraz B Neuropharmacology 2016 PMID: 27288002
Experience with targeted next generation sequencing for the care of lung cancer: insights into promises and limitations of genomic oncology in day-to-day practice. Rangachari D Cancer treatment communications 2015 PMID: 26601054
Ionotropic GABA and Glutamate Receptor Mutations and Human Neurologic Diseases. Yuan H Molecular pharmacology 2015 PMID: 25904555
Rare variants in γ-aminobutyric acid type A receptor genes in rolandic epilepsy and related syndromes. Reinthaler EM Annals of neurology 2015 PMID: 25726841
Mutations in GRIN2A cause idiopathic focal epilepsy with rolandic spikes. Lemke JR Nature genetics 2013 PMID: 23933819

Text-mined citations for rs587780353...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021