GRIN3B

protein-coding

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

Gene summary

The protein encoded by this gene is a subunit of an N-methyl-D-aspartate (NMDA) receptor. The encoded protein is found primarily in motor neurons, where it forms a heterotetramer with GRIN1 to create an excitatory glycine receptor. Variations in this gene have been proposed to be linked to schizophrenia. [provided by RefSeq, Nov 2015]

MANE transcript

NM_138690.3

Inheritance

—

ClinVar variants

U:252B:14

Top phenotype

Neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.63

Max pathogenic AF

—

Genomic locus

chr19:1,000,419-1,009,732

External References & Databases

Ensembl (ENSG00000116032)

Transcript & Mutation Effects

hg38 • Region Span ~9.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GRIN3B variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 252

not providedTotal: 9

Neurodevelopmental disorderTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_138690.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	4 clinvar	2 clinvar	7
missense			250 clinvar	7 clinvar	1 clinvar	258
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	252	11	3	266

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_138690.3	RefSeq	NP_619635.1	9	MANE Select
ENST00000234389.3	Ensembl	ENSP00000234389.3	9	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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)

Biological Process

ionotropic glutamate receptor signaling pathway
protein insertion into membrane
regulation of calcium ion transport
calcium ion transmembrane transport

Molecular Function

ionotropic glutamate receptor activity
cation channel activity
calcium channel activity
glycine binding
neurotransmitter receptor activity

Cellular Component

plasma membrane
NMDA selective glutamate receptor complex
cell junction
neuronal cell body
postsynaptic membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000234389
Coding exons: 9
Length: 9314
Individuals with no LoFs: 72506
Homozygous LoFs: 8221
Heterozygous LoFs: 44938
Defined: 125665
p: 0.240

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.03	632	563	1.12	0.0000432	6347
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.12	0.11	notable
Latino/Admixed American	0.32	0.26	notable
Ashkenazi Jewish	0.30	0.29	notable
East Asian	0.067	0.064	notable
Finnish	0.31	0.30	notable
European (Non-Finnish)	0.30	0.29	notable
South Asian	0.20	0.19	notable
Other	0.27	0.26	notable

dbNSFP Gene Annotations

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.;

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.833

Gene Damage Prediction

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