GRIN3A

glutamate ionotropic receptor NMDA type subunit 3A, the group of Glutamate ionotropic receptor NMDA type subunits

Basic information

Region (hg38): 9:101569352-101738647

Links

ENSG00000198785 ∙ NCBI:116443 ∙ OMIM:606650 ∙ HGNC:16767 ∙ Uniprot:Q8TCU5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GRIN3A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GRIN3A gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			59	3	1	63
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			11			11
Total	0	0	70	3	1

Variants in GRIN3A

This is a list of pathogenic ClinVar variants found in the GRIN3A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-101573220-G-A		not specified	Uncertain significance (Nov 06, 2023)
9-101573307-C-T		not specified	Uncertain significance (Nov 03, 2023)
9-101573314-C-T		not specified	Uncertain significance (Jun 10, 2022)
9-101573337-T-C			Benign (Aug 10, 2018)
9-101573346-C-T		not specified	Uncertain significance (Dec 03, 2021)
9-101573401-G-A		not specified	Uncertain significance (May 31, 2023)
9-101573421-C-A		not specified	Uncertain significance (Apr 25, 2023)
9-101573422-C-T		not specified	Uncertain significance (Apr 06, 2024)
9-101573437-A-G			Likely benign (Aug 15, 2018)
9-101573454-T-A		not specified	Uncertain significance (Dec 28, 2023)
9-101573485-C-T		not specified	Uncertain significance (Sep 17, 2021)
9-101573494-G-T		not specified	Uncertain significance (Jun 11, 2024)
9-101579261-A-G		not specified	Uncertain significance (Dec 15, 2022)
9-101579352-T-A		not specified	Uncertain significance (Jan 05, 2022)
9-101594414-C-T		not specified	Uncertain significance (Dec 01, 2022)
9-101594473-A-G		not specified	Uncertain significance (Feb 17, 2023)
9-101594522-C-A		not specified	Uncertain significance (Jan 04, 2022)
9-101594675-T-A		not specified	Uncertain significance (Oct 24, 2023)
9-101594726-C-T		not specified	Uncertain significance (Aug 17, 2022)
9-101594735-C-T		not specified	Uncertain significance (Aug 16, 2021)
9-101594767-T-G		not specified	Uncertain significance (Oct 12, 2022)
9-101594773-C-A		not specified	Uncertain significance (Apr 20, 2024)
9-101594777-G-C		not specified	Uncertain significance (Oct 12, 2021)
9-101594782-G-C		not specified	Uncertain significance (Jun 11, 2021)
9-101594836-T-C		not specified	Uncertain significance (Oct 29, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GRIN3A	protein_coding	protein_coding	ENST00000361820	9	169228

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.453	0.547	125709	0	39	125748	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.743	547	598	0.915	0.0000323	7298
Missense in Polyphen		179	234.01	0.76491		2973
Synonymous	-0.357	247	240	1.03	0.0000132	2232
Loss of Function	4.61	9	40.7	0.221	0.00000213	460

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000485	0.000362
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000185	0.000185
Middle Eastern	0.000381	0.000381
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: NMDA receptor subtype of glutamate-gated ion channels with reduced single-channel conductance, low calcium permeability and low voltage-dependent sensitivity to magnesium. Mediated by glycine. May play a role in the development of dendritic spines. May play a role in PPP2CB-NMDAR mediated signaling mechanism (By similarity). {ECO:0000250}.
• Pathway: Glutamatergic synapse - Homo sapiens (human);Nicotine addiction - Homo sapiens (human);cAMP signaling pathway - Homo sapiens (human);Amphetamine addiction - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Alcoholism - Homo sapiens (human);Cocaine addiction - Homo sapiens (human);Levomethadyl Acetate Action Action Pathway;Fluoxetine Action Pathway;Citalopram Action Pathway;Escitalopram Action Pathway;Imipramine Action Pathway;Desipramine Action Pathway;Levallorphan Action Pathway;Dimethylthiambutene Action Pathway;Ethylmorphine Action Pathway;Pentazocine Action Pathway;Naltrexone Action Pathway;Buprenorphine Action Pathway;Alvimopan Action Pathway;Naloxone Action Pathway;Dihydromorphine Action Pathway;Methadone Metabolism Pathway;Nicotine Action Pathway;Nalbuphine Action Pathway;Ketobemidone Action Pathway;Lidocaine (Local Anaesthetic) Action Pathway;Mepivacaine Action Pathway;Chloroprocaine Action Pathway;Cocaine Action Pathway;Dibucaine Action Pathway;Levobupivacaine Action Pathway;Benzocaine Action Pathway;Bupivacaine Action Pathway;Levorphanol Action Pathway;Propoxyphene Action Pathway;Tramadol Action Action Pathway;Diphenoxylate Action Pathway;Anileridine Action Pathway;Methadone Action Pathway;Oxycodone Action Pathway;Oxybuprocaine Action Pathway;Prilocaine Action Pathway;Procaine Action Pathway;Proparacaine Action Pathway;Ropivacaine Action Pathway;Codeine Action Pathway;Morphine Action Pathway;Heroin Action Pathway;Alfentanil Action Pathway;Oxymorphone Action Pathway;Hydrocodone Action Pathway;Hydromorphone Action Pathway;Sufentanil Action Pathway;Remifentanil Action Pathway;Fentanyl Action Pathway;Carfentanil Action Pathway;3-Methylthiofentanyl Action Pathway;Methadyl Acetate Action Pathway;Dezocine Action Pathway (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.232
• rvis_EVS: 0.21
• rvis_percentile_EVS: 67.53

Haploinsufficiency Scores

• pHI: 0.430
• hipred: Y
• hipred_score: 0.753
• ghis: 0.538

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.673

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Grin3a
• Phenotype: normal phenotype; vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: calcium ion transport;dendrite development;ionotropic glutamate receptor signaling pathway;response to ethanol;regulation of postsynaptic membrane potential;prepulse inhibition;calcium ion transmembrane transport;regulation of synaptic vesicle exocytosis
• Cellular component: plasma membrane;postsynaptic density;membrane;integral component of membrane;NMDA selective glutamate receptor complex;cell junction;neuron projection;neuronal cell body;synapse;postsynaptic membrane;glutamatergic synapse
• Molecular function: NMDA glutamate receptor activity;calcium channel activity;protein binding;glycine binding;identical protein binding;protein phosphatase 2A binding;transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential