CHRM4

cholinergic receptor muscarinic 4, the group of Cholinergic receptors muscarinic

Basic information

Region (hg38): 11:46383788-46391776

Links

ENSG00000180720 ∙ NCBI:1132 ∙ OMIM:118495 ∙ HGNC:1953 ∙ Uniprot:P08173 ∙ 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 CHRM4 gene.

• Inborn genetic diseases (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHRM4 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in CHRM4

This is a list of pathogenic ClinVar variants found in the CHRM4 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-46385275-C-T		not specified	Uncertain significance (Sep 06, 2022)
11-46385306-C-T		not specified	Uncertain significance (Aug 09, 2021)
11-46385418-G-C		not specified	Uncertain significance (Oct 14, 2023)
11-46385467-G-T		not specified	Uncertain significance (Feb 27, 2023)
11-46385470-G-A		not specified	Uncertain significance (Nov 30, 2021)
11-46385492-C-T		not specified	Uncertain significance (Sep 06, 2022)
11-46385509-C-T		not specified	Uncertain significance (Dec 27, 2022)
11-46385512-G-C		not specified	Uncertain significance (Jun 23, 2023)
11-46385705-G-A		not specified	Uncertain significance (Jan 09, 2024)
11-46385740-T-G		not specified	Uncertain significance (Jul 19, 2023)
11-46385765-C-T		not specified	Uncertain significance (Aug 02, 2021)
11-46385836-G-A		not specified	Uncertain significance (Oct 26, 2022)
11-46385864-C-T		not specified	Uncertain significance (Apr 07, 2023)
11-46386022-G-A		not specified	Uncertain significance (Aug 13, 2021)
11-46386034-A-G		not specified	Uncertain significance (Jul 17, 2023)
11-46386251-C-T		not specified	Uncertain significance (Jan 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHRM4	protein_coding	protein_coding	ENST00000433765	1	1468

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.974	0.0256	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.73	179	316	0.567	0.0000220	3081
Missense in Polyphen		41	133.13	0.30796		1421
Synonymous	-0.577	149	140	1.06	0.0000105	1051
Loss of Function	3.11	0	11.3	0.00	5.87e-7	120

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)	0.00	0.00
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 inhibition of adenylate cyclase.
• Pathway: Regulation of actin cytoskeleton - 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 (i) signalling events;GPCR downstream signalling (Consensus)

Intolerance Scores

• loftool: 0.102
• rvis_EVS: -0.96
• rvis_percentile_EVS: 9.09

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.786
• ghis: 0.588

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.194

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chrm4
• 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; growth/size/body region 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); muscle phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: signal transduction;cell surface receptor signaling pathway;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;regulation of locomotion;G protein-coupled serotonin receptor signaling pathway
• Cellular component: plasma membrane;integral component of plasma membrane;cell junction;dendrite;postsynaptic membrane
• Molecular function: G protein-coupled receptor activity;G protein-coupled serotonin receptor activity;G protein-coupled acetylcholine receptor activity;neurotransmitter receptor activity