GRIN3B

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

Basic information

Region (hg38): 19:1000419-1009732

Links

ENSG00000116032 ∙ NCBI:116444 ∙ OMIM:606651 ∙ HGNC:16768 ∙ Uniprot:O60391 ∙ 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 GRIN3B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GRIN3B 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				2	2	4
missense			106	3	4	113
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	106	5	7

Variants in GRIN3B

This is a list of pathogenic ClinVar variants found in the GRIN3B region.

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

Position	Type	Phenotype	Significance	ClinVar
19-1000421-A-G			Benign (Oct 09, 2018)
19-1000525-C-G		not specified	Uncertain significance (Sep 27, 2021)
19-1000567-C-T		not specified	Uncertain significance (Oct 13, 2021)
19-1000585-C-T		not specified	Uncertain significance (Jun 16, 2022)
19-1000601-C-T		not specified	Uncertain significance (Sep 07, 2022)
19-1000613-G-A		not specified	Uncertain significance (Jul 12, 2023)
19-1000645-C-G		not specified	Uncertain significance (Mar 16, 2024)
19-1000649-G-T		not specified	Uncertain significance (Dec 18, 2023)
19-1000677-C-A			Likely benign (Mar 01, 2022)
19-1000682-G-A		not specified	Uncertain significance (Oct 05, 2021)
19-1000690-G-A		not specified	Uncertain significance (Jan 23, 2023)
19-1000702-C-G		not specified	Uncertain significance (Mar 15, 2024)
19-1000778-T-C		not specified	Uncertain significance (Nov 28, 2023)
19-1000786-C-T			Benign (Mar 25, 2019)
19-1000787-A-T		not specified	Uncertain significance (Feb 28, 2023)
19-1000804-A-G		not specified	Uncertain significance (Nov 22, 2021)
19-1000859-C-T		not specified	Uncertain significance (Jun 16, 2024)
19-1003142-C-G		not specified	Uncertain significance (Jan 02, 2024)
19-1003179-T-C		not specified	Uncertain significance (Apr 17, 2024)
19-1003223-G-C		not specified	Uncertain significance (Feb 06, 2023)
19-1003322-C-T		not specified	Uncertain significance (Feb 10, 2022)
19-1003325-C-T		not specified	Uncertain significance (Feb 10, 2022)
19-1003350-G-A		not specified	Likely benign (Aug 08, 2022)
19-1003365-C-T		not specified	Uncertain significance (Jan 19, 2024)
19-1003371-C-T		not specified	Uncertain significance (Jan 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GRIN3B	protein_coding	protein_coding	ENST00000234389	9	9314

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.02e-7	0.887	72506	8221	44938	125665	0.240

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.03	632	563	1.12	0.0000432	6347
Missense in Polyphen		228	195.72	1.1649		2043
Synonymous	-1.69	307	271	1.13	0.0000223	2347
Loss of Function	1.64	14	22.4	0.625	0.00000109	258

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.439	0.433
Ashkenazi Jewish	0.295	0.288
East Asian	0.0669	0.0643
Finnish	0.310	0.297
European (Non-Finnish)	0.301	0.287
Middle Eastern	0.0669	0.0643
South Asian	0.196	0.192
Other	0.266	0.255

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.
• 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) (Consensus)

Haploinsufficiency Scores

• pHI: 0.0563
• hipred: N
• hipred_score: 0.472

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.833

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Grin3b
• Phenotype: growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: ionotropic glutamate receptor signaling pathway;protein insertion into membrane;regulation of calcium ion transport;calcium ion transmembrane transport
• Cellular component: plasma membrane;NMDA selective glutamate receptor complex;cell junction;neuronal cell body;postsynaptic membrane
• Molecular function: ionotropic glutamate receptor activity;cation channel activity;calcium channel activity;glycine binding;neurotransmitter receptor activity;neurotransmitter binding