CHRNA10

protein-coding

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

Gene summary

Contributes to acetylcholine-gated monoatomic cation-selective channel activity. Involved in acetylcholine receptor signaling pathway and membrane depolarization. Acts upstream of or within positive regulation of cytosolic calcium ion concentration. Part of acetylcholine-gated channel complex. Is active in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_020402.4

Inheritance

—

ClinVar variants

U:89B:7

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.93

Max pathogenic AF

—

Genomic locus

chr11:3,665,587-3,671,384

External References & Databases

Ensembl (ENSG00000129749)

Transcript & Mutation Effects

hg38 • Region Span ~5.8 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 CHRNA10 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 94

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020402.4. 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	1 clinvar		2
missense			88 clinvar	6 clinvar		94
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	89	7	0	96

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020402.4	RefSeq	NP_065135.2	5	MANE Select
ENST00000250699.2	Ensembl	ENSP00000250699.2	5	MANE Select
NM_001303034.2	RefSeq	NP_001289963.1	2	Standard
NM_001303035.2	RefSeq	NP_001289964.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Neuroactive ligand-receptor interaction - Homo sapiens (human)

Biological Process

signal transduction
positive regulation of cytosolic calcium ion concentration
chemical synaptic transmission
synaptic transmission, cholinergic
ion transmembrane transport

Molecular Function

transmembrane signaling receptor activity
signaling receptor binding
extracellular ligand-gated ion channel activity
calcium channel activity
acetylcholine-gated cation-selective channel activity

Cellular Component

integral component of plasma membrane
membrane
cell junction
axon
neuron projection

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000250699
Coding exons: 5
Length: 5798
Individuals with no LoFs: 125633
Homozygous LoFs: 1
Heterozygous LoFs: 114
Defined: 125748
p: 0.000457

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.140	317	310	1.02	0.0000225	2825
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00047	0.00046	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0022	0.0022	notable
Finnish	0.00022	0.00014	rare
European (Non-Finnish)	0.00034	0.00031	rare
South Asian	0.00056	0.00056	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.156

Intolerance Scores

LoFtool: 0.278
RVIS EVS: 0.84
RVIS percentile EVS: 88.38

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.204

Gene Damage Prediction

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