CHRM5

cholinergic receptor muscarinic 5, the group of Cholinergic receptors muscarinic

Basic information

Region (hg38): 15:33968497-34067458

Links

ENSG00000184984 ∙ NCBI:1133 ∙ OMIM:118496 ∙ HGNC:1954 ∙ Uniprot:P08912 ∙ 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 CHRM5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHRM5 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			19	1	1	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			14			14
Total	0	0	33	1	2

Variants in CHRM5

This is a list of pathogenic ClinVar variants found in the CHRM5 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-34003116-A-G		not specified	Uncertain significance (Sep 17, 2021)
15-34003123-C-A		not specified	Uncertain significance (Aug 16, 2021)
15-34003130-G-C		not specified	Uncertain significance (Nov 08, 2022)
15-34038827-C-T		not specified	Uncertain significance (Jul 25, 2023)
15-34038851-G-C		not specified	Uncertain significance (Mar 07, 2023)
15-34038856-C-T		not specified	Uncertain significance (May 15, 2023)
15-34038881-C-T		not specified	Uncertain significance (Jun 18, 2021)
15-34038884-G-A		not specified	Uncertain significance (Jan 17, 2023)
15-34038904-C-T		not specified	Uncertain significance (Apr 20, 2023)
15-34038907-C-G		not specified	Uncertain significance (Aug 22, 2023)
15-34038911-C-A		not specified	Uncertain significance (Jan 19, 2022)
15-34038917-C-G		not specified	Uncertain significance (Mar 25, 2024)
15-34038935-C-T		not specified	Uncertain significance (May 13, 2024)
15-34038977-G-A		not specified	Uncertain significance (Apr 15, 2024)
15-34039021-C-T		not specified	Uncertain significance (Sep 17, 2021)
15-34039024-C-G		not specified	Uncertain significance (Aug 11, 2022)
15-34039032-T-G		not specified	Likely benign (Mar 25, 2024)
15-34039033-C-A		not specified	Uncertain significance (Dec 13, 2022)
15-34062743-C-G		not specified	Uncertain significance (Jun 19, 2024)
15-34062745-A-G		not specified	Uncertain significance (Feb 10, 2022)
15-34062787-C-T		not specified	Uncertain significance (Dec 28, 2023)
15-34062867-G-C		not specified	Uncertain significance (Apr 29, 2024)
15-34062994-A-G		not specified	Uncertain significance (Aug 28, 2023)
15-34063141-C-T		not specified	Uncertain significance (Feb 17, 2024)
15-34063142-G-A		not specified	Uncertain significance (Aug 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHRM5	protein_coding	protein_coding	ENST00000383263	1	96371

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00403	0.989	125715	0	32	125747	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.20	235	293	0.802	0.0000158	3475
Missense in Polyphen		83	134.93	0.61513		1651
Synonymous	-0.125	114	112	1.01	0.00000571	1088
Loss of Function	2.36	7	17.7	0.395	0.00000118	188

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000262	0.000262
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000938	0.0000924
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.0000544	0.0000544
South Asian	0.000196	0.000196
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The muscarinic acetylcholine receptor mediates various cellular responses, including inhibition of adenylate cyclase, breakdown of phosphoinositides and modulation of potassium channels through the action of G proteins. Primary transducing effect is Pi turnover.
• Pathway: Regulation of actin cytoskeleton - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Cholinergic synapse - Homo sapiens (human);GPCRs, Class A Rhodopsin-like;Regulation of Actin Cytoskeleton;Calcium Regulation in the Cardiac Cell;Monoamine GPCRs;Signaling by GPCR;Signal Transduction;Muscarinic acetylcholine receptors;Amine ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (q) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.0829

Intolerance Scores

• loftool: 0.586
• rvis_EVS: 0.38
• rvis_percentile_EVS: 75.51

Haploinsufficiency Scores

• pHI: 0.286
• hipred: N
• hipred_score: 0.289

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.185

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chrm5
• 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); digestive/alimentary phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; muscle phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: gastric acid secretion;G protein-coupled receptor signaling pathway;G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger;adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway;G protein-coupled acetylcholine receptor signaling pathway;chemical synaptic transmission;cell population proliferation;dopamine transport;transmission of nerve impulse;regulation of phosphatidylinositol dephosphorylation;G protein-coupled serotonin receptor signaling pathway
• Cellular component: plasma membrane;integral component of plasma membrane;cell junction;dendrite;postsynaptic membrane
• Molecular function: phosphatidylinositol phospholipase C activity;G protein-coupled receptor activity;G protein-coupled serotonin receptor activity;G protein-coupled acetylcholine receptor activity;neurotransmitter receptor activity