CHRM1

cholinergic receptor muscarinic 1, the group of Cholinergic receptors muscarinic

Basic information

Region (hg38): 11:62908679-62921807

Links

ENSG00000168539 ∙ NCBI:1128 ∙ OMIM:118510 ∙ HGNC:1950 ∙ Uniprot:P11229 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CHRM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHRM1 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	3	2	6
missense		1	22			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	23	3	2

Variants in CHRM1

This is a list of pathogenic ClinVar variants found in the CHRM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-62909734-G-A		not specified	Uncertain significance (May 09, 2023)
11-62909747-C-T		not specified	Uncertain significance (Aug 30, 2021)
11-62909758-C-T		not specified	Uncertain significance (Mar 15, 2024)
11-62909794-C-T		not specified	Uncertain significance (Aug 27, 2024)
11-62909824-C-T		not specified	Uncertain significance (Dec 01, 2022)
11-62909827-A-G		See cases • CHRM1-related neurodevelopmental disorder	Likely pathogenic (Jul 30, 2024)
11-62909964-T-G			Benign (Apr 24, 2018)
11-62909990-G-A		not specified	Uncertain significance (Feb 12, 2024)
11-62910089-C-T		not specified	Uncertain significance (Jul 02, 2024)
11-62910100-C-T		not specified	Uncertain significance (Jun 03, 2022)
11-62910110-T-G		not specified	Uncertain significance (Oct 12, 2024)
11-62910115-G-A		not specified	Uncertain significance (Jun 21, 2021)
11-62910253-C-A		not specified	Uncertain significance (Oct 13, 2023)
11-62910258-G-A			Benign (Dec 31, 2019)
11-62910325-C-A		not specified	Uncertain significance (Dec 15, 2023)
11-62910364-G-C		not specified	Uncertain significance (Aug 12, 2021)
11-62910369-A-T			Likely benign (Jun 05, 2018)
11-62910410-G-A		not specified	Uncertain significance (May 08, 2024)
11-62910411-C-T			Likely benign (May 24, 2018)
11-62910437-G-C		not specified	Uncertain significance (Aug 16, 2021)
11-62910463-C-T		not specified	Uncertain significance (Dec 06, 2023)
11-62910483-C-T			Uncertain significance (Mar 01, 2017)
11-62910662-C-T		not specified	Uncertain significance (Aug 22, 2023)
11-62910692-G-A		not specified	Uncertain significance (Sep 01, 2021)
11-62910863-T-G			Uncertain significance (Mar 23, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHRM1	protein_coding	protein_coding	ENST00000306960	1	13129

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.991	0.00941	121991	0	1	121992	0.00000410

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.76	160	293	0.546	0.0000191	2935
Missense in Polyphen		21	78.339	0.26807		864
Synonymous	0.285	116	120	0.967	0.00000725	1017
Loss of Function	3.47	0	14.0	0.00	7.56e-7	142

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000901	0.00000901
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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: PI3K-Akt signaling pathway - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);cAMP signaling pathway - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Cholinergic synapse - Homo sapiens (human);Secretion of Hydrochloric Acid in Parietal Cells;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;GPCRs, Class A Rhodopsin-like;Regulation of Actin Cytoskeleton;Calcium Regulation in the Cardiac Cell;Monoamine GPCRs;Signaling by GPCR;Signal Transduction;ion channels and their functional role in vascular endothelium;activation of csk by camp-dependent protein kinase inhibits signaling through the t cell receptor;chrebp regulation by carbohydrates and camp;role of -arrestins in the activation and targeting of map kinases;activation of camp-dependent protein kinase pka;Muscarinic acetylcholine receptors;Amine ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);roles of arrestin dependent recruitment of src kinases in gpcr signaling;actions of nitric oxide in the heart;GPCR ligand binding;agrin in postsynaptic differentiation;-arrestins in gpcr desensitization;G alpha (q) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.531

Intolerance Scores

• rvis_EVS: -0.69
• rvis_percentile_EVS: 14.97

Haploinsufficiency Scores

• pHI: 0.258
• hipred: Y
• hipred_score: 0.707
• ghis: 0.618

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.395

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chrm1
• Phenotype: endocrine/exocrine gland phenotype; immune system phenotype; homeostasis/metabolism phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system 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

Gene ontology

• Biological process: cellular protein modification process;signal transduction;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;protein kinase C-activating G protein-coupled receptor signaling pathway;phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway;G protein-coupled acetylcholine receptor signaling pathway;chemical synaptic transmission;neuromuscular synaptic transmission;nervous system development;cell population proliferation;positive regulation of cell population proliferation;regulation of locomotion;positive regulation of ion transport;saliva secretion;cognition;regulation of postsynaptic membrane potential;positive regulation of intracellular protein transport;G protein-coupled serotonin receptor signaling pathway
• Cellular component: plasma membrane;integral component of plasma membrane;membrane;cell junction;dendrite;axon terminus;Schaffer collateral - CA1 synapse;glutamatergic synapse;cholinergic synapse;integral component of presynaptic membrane;integral component of postsynaptic density membrane
• Molecular function: phosphatidylinositol phospholipase C activity;G protein-coupled receptor activity;G protein-coupled serotonin receptor activity;drug binding;G protein-coupled acetylcholine receptor activity;neurotransmitter receptor activity;neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential