CHRNA9

cholinergic receptor nicotinic alpha 9 subunit, the group of Cholinergic receptors nicotinic subunits

Basic information

Region (hg38): 4:40335332-40355217

Links

ENSG00000174343 ∙ NCBI:55584 ∙ OMIM:605116 ∙ HGNC:14079 ∙ Uniprot:Q9UGM1 ∙ 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 CHRNA9 gene.

• Inborn genetic diseases (22 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHRNA9 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				2		2
missense			23	2		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	4	0

Variants in CHRNA9

This is a list of pathogenic ClinVar variants found in the CHRNA9 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-40335490-T-C		not specified	Uncertain significance (Dec 27, 2023)
4-40335523-G-C		not specified	Uncertain significance (Jan 02, 2024)
4-40335861-G-C			Likely benign (Mar 29, 2018)
4-40335929-T-C		not specified	Uncertain significance (Jul 26, 2021)
4-40335950-C-T		not specified	Uncertain significance (Nov 17, 2022)
4-40337233-T-C			Likely benign (Mar 01, 2023)
4-40337297-G-C		not specified	Uncertain significance (Jan 09, 2024)
4-40337300-G-A		not specified	Uncertain significance (Jan 19, 2024)
4-40337319-T-A		not specified	Uncertain significance (May 11, 2022)
4-40337325-G-C		not specified	Uncertain significance (Apr 13, 2023)
4-40337333-G-T		not specified	Uncertain significance (Dec 08, 2023)
4-40348890-A-T		not specified	Uncertain significance (Nov 05, 2021)
4-40348928-C-T		not specified	Uncertain significance (Nov 07, 2022)
4-40348929-G-A			Uncertain significance (Sep 23, 2019)
4-40348938-G-A		not specified	Uncertain significance (May 09, 2022)
4-40348982-G-T		not specified	Uncertain significance (Feb 22, 2023)
4-40349021-T-C		not specified	Uncertain significance (Aug 16, 2021)
4-40349059-T-G		not specified	Uncertain significance (Oct 29, 2021)
4-40349090-G-A		not specified	Uncertain significance (Dec 14, 2021)
4-40349191-G-A			Likely benign (Mar 01, 2023)
4-40349244-A-T		not specified	Uncertain significance (Dec 09, 2023)
4-40353993-G-A		not specified	Uncertain significance (Jun 29, 2022)
4-40354017-T-C		not specified	Uncertain significance (Feb 10, 2022)
4-40354036-T-C		not specified	Uncertain significance (Aug 30, 2021)
4-40354065-G-A		not specified	Uncertain significance (May 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHRNA9	protein_coding	protein_coding	ENST00000310169	5	19889

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000704	0.911	125642	0	105	125747	0.000418

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.102	276	271	1.02	0.0000154	3180
Missense in Polyphen		143	133.87	1.0682		1602
Synonymous	-0.379	117	112	1.05	0.00000720	916
Loss of Function	1.63	11	18.6	0.592	9.66e-7	215

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000557	0.000557
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000333	0.000326
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000519	0.000519
Middle Eastern	0.000333	0.000326
South Asian	0.000523	0.000523
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ionotropic receptor with a probable role in the modulation of auditory stimuli. Agonist binding induces a conformation change that leads to the opening of an ion-conducting channel across the plasma membrane (PubMed:11752216, PubMed:25282151). 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 (PubMed:11752216, PubMed:25282151). 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. May also regulate keratinocyte adhesion (PubMed:11021840). {ECO:0000269|PubMed:11021840, ECO:0000269|PubMed:11752216, ECO:0000269|PubMed:25282151, ECO:0000305}.
• Pathway: Neuroactive ligand-receptor interaction - Homo sapiens (human);Neuronal System;Neurotransmitter receptors and postsynaptic signal transmission;Transmission across Chemical Synapses;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: 0.167

Intolerance Scores

• loftool: 0.300
• rvis_EVS: 0.42
• rvis_percentile_EVS: 77.23

Haploinsufficiency Scores

• pHI: 0.150
• hipred: N
• hipred_score: 0.350

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.103

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chrna9
• 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); hearing/vestibular/ear phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: signal transduction;positive regulation of cytosolic calcium ion concentration;chemical synaptic transmission;ion transmembrane transport;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: plasma membrane;integral component of plasma membrane;acetylcholine-gated channel complex;cell junction;neuron projection;synapse;cholinergic synapse;integral component of postsynaptic specialization membrane
• Molecular function: transmembrane signaling receptor activity;extracellular ligand-gated ion channel activity;calcium channel activity;protein binding;acetylcholine-gated cation-selective channel activity