CHRNA10

cholinergic receptor nicotinic alpha 10 subunit, the group of Cholinergic receptors nicotinic subunits

Basic information

Region (hg38): 11:3665587-3671384

Links

ENSG00000129749 ∙ NCBI:57053 ∙ OMIM:606372 ∙ HGNC:13800 ∙ Uniprot:Q9GZZ6 ∙ 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 CHRNA10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHRNA10 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			34	1		35
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			2			2
Total	0	0	37	1	0

Variants in CHRNA10

This is a list of pathogenic ClinVar variants found in the CHRNA10 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-3666177-C-T		not specified	Uncertain significance (Nov 15, 2023)
11-3666179-G-T		not specified	Uncertain significance (Aug 14, 2024)
11-3666220-G-A		not specified	Uncertain significance (Jan 09, 2024)
11-3666231-C-T		not specified	Uncertain significance (Jul 20, 2021)
11-3666240-C-T		not specified	Likely benign (Nov 10, 2022)
11-3666250-T-G		not specified	Uncertain significance (Jun 02, 2024)
11-3666288-C-T		not specified	Likely benign (Apr 15, 2024)
11-3666321-G-A		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
11-3666331-C-T		not specified	Uncertain significance (Jul 12, 2022)
11-3666381-G-A		not specified	Uncertain significance (Oct 01, 2024)
11-3666424-G-A		not specified	Uncertain significance (Oct 26, 2022)
11-3666430-G-C		not specified	Uncertain significance (Jul 27, 2022)
11-3666450-C-T		not specified	Uncertain significance (Dec 27, 2023)
11-3666525-G-A		not specified	Uncertain significance (Nov 03, 2023)
11-3666534-A-C		not specified	Uncertain significance (Jul 25, 2023)
11-3666546-G-C		not specified	Uncertain significance (Jan 30, 2024)
11-3666549-G-A		not specified	Uncertain significance (Aug 10, 2021)
11-3667240-G-A		not specified	Uncertain significance (Jun 14, 2023)
11-3667243-A-G		not specified	Uncertain significance (Sep 16, 2021)
11-3667351-T-A		not specified	Uncertain significance (Apr 08, 2022)
11-3667366-G-A		not specified	Uncertain significance (Oct 05, 2023)
11-3667391-G-A		not specified	Uncertain significance (Jul 02, 2024)
11-3667423-C-A		not specified	Uncertain significance (Jan 10, 2023)
11-3667424-G-A		not specified	Uncertain significance (Apr 18, 2024)
11-3667429-C-T		not specified	Likely benign (May 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHRNA10	protein_coding	protein_coding	ENST00000250699	5	5798

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.79e-10	0.113	125633	1	114	125748	0.000457

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.140	317	310	1.02	0.0000225	2825
Missense in Polyphen		109	100.48	1.0848		1021
Synonymous	-0.122	141	139	1.01	0.0000105	1013
Loss of Function	0.263	15	16.1	0.929	9.75e-7	150

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000592	0.000591
Ashkenazi Jewish	0.00	0.00
East Asian	0.00218	0.00218
Finnish	0.000216	0.000139
European (Non-Finnish)	0.000337	0.000308
Middle Eastern	0.00218	0.00218
South Asian	0.000557	0.000555
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ionotropic receptor with a probable role in the modulation of auditory stimuli. Agonist binding may induce an extensive change in conformation that affects all subunits and leads to opening of an ion-conducting channel across the plasma membrane. The channel is permeable to a range of divalent cations including calcium, the influx of which may activate a potassium current which hyperpolarizes the cell membrane. In the ear, this may lead to a reduction in basilar membrane motion, altering the activity of auditory nerve fibers and reducing the range of dynamic hearing. This may protect against acoustic trauma. {ECO:0000269|PubMed:11752216}.
• Pathway: Neuroactive ligand-receptor interaction - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.156

Intolerance Scores

• loftool: 0.278
• rvis_EVS: 0.84
• rvis_percentile_EVS: 88.38

Haploinsufficiency Scores

• pHI: 0.0349
• hipred: N
• hipred_score: 0.170
• ghis: 0.462

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.204

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chrna10
• Phenotype: hearing/vestibular/ear 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;positive regulation of cytosolic calcium ion concentration;chemical synaptic transmission;synaptic transmission, cholinergic;ion transmembrane transport;regulation of cell population proliferation;regulation of membrane potential;inner ear morphogenesis;nervous system process;detection of mechanical stimulus involved in sensory perception of sound;excitatory postsynaptic potential;negative regulation of ERK1 and ERK2 cascade;calcium ion transmembrane transport
• Cellular component: integral component of plasma membrane;membrane;cell junction;axon;neuron projection;perikaryon;synapse;cholinergic synapse;integral component of postsynaptic specialization membrane
• Molecular function: transmembrane signaling receptor activity;signaling receptor binding;extracellular ligand-gated ion channel activity;calcium channel activity;acetylcholine-gated cation-selective channel activity