CHRNA6

cholinergic receptor nicotinic alpha 6 subunit, the group of Cholinergic receptors nicotinic subunits

Basic information

Region (hg38): 8:42752619-42796392

Links

ENSG00000147434 ∙ NCBI:8973 ∙ OMIM:606888 ∙ HGNC:15963 ∙ Uniprot:Q15825 ∙ 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 CHRNA6 gene.

• Inborn genetic diseases (11 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHRNA6 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					3	3
missense			10	1	1	12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	4

Variants in CHRNA6

This is a list of pathogenic ClinVar variants found in the CHRNA6 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-42753296-C-A		not specified	Uncertain significance (Feb 22, 2023)
8-42755922-G-C		not specified	Uncertain significance (Dec 20, 2021)
8-42755955-G-A		not specified	Uncertain significance (Feb 01, 2023)
8-42756174-T-C		not specified	Uncertain significance (Dec 05, 2022)
8-42756193-T-C		not specified	Uncertain significance (Aug 04, 2023)
8-42756202-T-C		not specified	Likely benign (Apr 25, 2022)
8-42756207-G-A		not specified	Uncertain significance (Jun 28, 2022)
8-42756210-C-T		not specified	Uncertain significance (Oct 12, 2022)
8-42756276-A-T		not specified	Uncertain significance (Feb 05, 2024)
8-42756312-G-A		not specified	Uncertain significance (Mar 16, 2022)
8-42756315-G-A		not specified	Uncertain significance (Dec 16, 2023)
8-42756380-C-T			Benign (Feb 26, 2018)
8-42756401-C-T			Benign (Mar 29, 2018)
8-42756467-C-T			Benign (Feb 08, 2018)
8-42757016-G-A		not specified	Uncertain significance (Jan 03, 2024)
8-42765156-G-A		not specified	Uncertain significance (May 23, 2023)
8-42765177-C-G			Benign (Jan 17, 2018)
8-42768382-A-G		not specified	Uncertain significance (Jan 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHRNA6	protein_coding	protein_coding	ENST00000276410	6	43773

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.57e-8	0.559	125553	1	192	125746	0.000768

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.125	262	268	0.979	0.0000136	3275
Missense in Polyphen		125	136.52	0.91559		1754
Synonymous	0.565	97	104	0.930	0.00000586	954
Loss of Function	1.06	14	19.0	0.737	9.06e-7	229

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000750	0.000750
Ashkenazi Jewish	0.00	0.00
East Asian	0.000653	0.000653
Finnish	0.000926	0.000924
European (Non-Finnish)	0.00117	0.00116
Middle Eastern	0.000653	0.000653
South Asian	0.000163	0.000163
Other	0.000979	0.000978

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: Nicotine addiction - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Cholinergic synapse - Homo sapiens (human);Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics;Nicotine Activity on Dopaminergic Neurons;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: 0.148

Intolerance Scores

• loftool: 0.353
• rvis_EVS: -0.78
• rvis_percentile_EVS: 12.97

Haploinsufficiency Scores

• pHI: 0.0566
• hipred: N
• hipred_score: 0.197
• ghis: 0.436

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.178

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chrna6
• 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: signal transduction;chemical synaptic transmission;synaptic transmission, cholinergic;neuromuscular synaptic transmission;regulation of dopamine secretion;ion transmembrane transport;response to nicotine;regulation of membrane potential;nervous system process;membrane depolarization;excitatory postsynaptic potential;regulation of synaptic vesicle exocytosis
• Cellular component: plasma membrane;integral component of plasma membrane;acetylcholine-gated channel complex;cell junction;neuron projection;synapse;dopaminergic synapse;integral component of postsynaptic membrane;integral component of presynaptic membrane
• Molecular function: extracellular ligand-gated ion channel activity;protein binding;acetylcholine receptor activity;acetylcholine-gated cation-selective channel activity;acetylcholine binding