CHRNB3

cholinergic receptor nicotinic beta 3 subunit, the group of Cholinergic receptors nicotinic subunits

Basic information

Region (hg38): 8:42697366-42737407

Links

ENSG00000147432 ∙ NCBI:1142 ∙ OMIM:118508 ∙ HGNC:1963 ∙ Uniprot:Q05901 ∙ 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 CHRNB3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHRNB3 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					1	1
missense			24	1	1	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	1	2

Variants in CHRNB3

This is a list of pathogenic ClinVar variants found in the CHRNB3 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-42708717-C-T		not specified	Uncertain significance (Dec 03, 2021)
8-42708739-C-T			Benign (Apr 04, 2018)
8-42708756-C-A		not specified	Uncertain significance (Jul 12, 2022)
8-42708798-G-T		not specified	Uncertain significance (Jun 21, 2023)
8-42708833-T-C		not specified	Uncertain significance (Apr 14, 2022)
8-42708866-G-A		not specified	Uncertain significance (Jan 30, 2024)
8-42730657-G-A		not specified	Uncertain significance (Apr 08, 2022)
8-42731697-G-A		not specified	Uncertain significance (Nov 18, 2022)
8-42731705-T-A		not specified	Uncertain significance (May 01, 2024)
8-42731723-G-A		not specified	Uncertain significance (Dec 12, 2023)
8-42731729-T-C		not specified	Uncertain significance (Jan 05, 2022)
8-42731776-G-A		not specified	Uncertain significance (May 29, 2024)
8-42731784-T-G			Uncertain significance (Jun 01, 2023)
8-42731806-T-C		not specified	Uncertain significance (Apr 06, 2024)
8-42731923-G-A		not specified	Uncertain significance (Oct 17, 2023)
8-42731944-A-G		not specified	Uncertain significance (Sep 07, 2022)
8-42731962-T-C		not specified	Uncertain significance (Jun 27, 2023)
8-42731962-T-G		not specified	Uncertain significance (Feb 13, 2024)
8-42731981-A-G		not specified	Uncertain significance (Jun 16, 2024)
8-42732009-A-C		not specified	Uncertain significance (Oct 21, 2021)
8-42732041-T-C		not specified	Uncertain significance (Oct 30, 2023)
8-42732074-A-C		not specified	Uncertain significance (Apr 12, 2022)
8-42732118-G-A		not specified	Uncertain significance (Jan 16, 2024)
8-42732214-A-G		not specified	Uncertain significance (Oct 29, 2021)
8-42732379-T-C		not specified	Uncertain significance (Nov 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHRNB3	protein_coding	protein_coding	ENST00000289957	6	40032

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000859	0.930	125572	1	174	125747	0.000696

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.841	220	258	0.853	0.0000142	2994
Missense in Polyphen		110	132.63	0.82939		1536
Synonymous	0.839	96	107	0.897	0.00000683	900
Loss of Function	1.71	11	19.1	0.577	9.76e-7	228

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000789	0.000787
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00578	0.00578
Finnish	0.00	0.00
European (Non-Finnish)	0.000336	0.000334
Middle Eastern	0.00578	0.00578
South Asian	0.000240	0.000229
Other	0.000489	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: After binding acetylcholine, the AChR responds by an extensive change in conformation that affects all subunits and leads to opening of an ion-conducting channel across the plasma membrane.
• Pathway: Neuroactive ligand-receptor interaction - Homo sapiens (human);Neuronal System;Neurotransmitter receptors and postsynaptic signal transmission;Transmission across Chemical Synapses;Highly calcium permeable nicotinic acetylcholine receptors;Presynaptic nicotinic acetylcholine receptors;Highly calcium permeable postsynaptic nicotinic acetylcholine receptors;Postsynaptic nicotinic acetylcholine receptors;Activation of Nicotinic Acetylcholine Receptors;Acetylcholine binding and downstream events (Consensus)

Recessive Scores

• pRec: 0.175

Intolerance Scores

• loftool: 0.490
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.56

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.251
• ghis: 0.423

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.210

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Chrnb3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: signal transduction;chemical synaptic transmission;synaptic transmission, cholinergic;neuromuscular synaptic transmission;ion transmembrane transport;response to nicotine;regulation of membrane potential;nervous system process;excitatory postsynaptic potential;regulation of synaptic vesicle exocytosis
• Cellular component: plasma membrane;integral component of plasma membrane;acetylcholine-gated channel complex;integral component of membrane;cell junction;neuron projection;synapse;postsynaptic membrane;dopaminergic synapse
• Molecular function: extracellular ligand-gated ion channel activity;channel activity;acetylcholine receptor activity;acetylcholine-gated cation-selective channel activity;acetylcholine binding